Split (1)

train · 816k rows

paragraph_index int64	sec string	p_has_citation int64	cites string	citeids list	pmid int64	cited_id string	sentences string	all_sent_cites list	sent_len int64	sentence_batch_index int64	sent_has_citation float64	qc_fail bool	cited_sentence string	cites_in_sentence list	cln_sentence string	is_cap bool	is_alpha bool	ends_wp bool	cit_qc bool	lgtm bool	__index_level_0__ int64
1	INTRODUCTION	1	9	[ "b9", "b10", "b11", "b12", "b12", "b11" ]	16,820,531	pmid-9849937\|pmid-8865343\|pmid-7937706\|pmid-10465734\|pmid-10465734\|pmid-7937706\|pmid-15981252	Only a few methods allowed for flexibility of the DNA and protein side chains during the docking.	[ "9", "10", "11", "12", "12", "11" ]	97	7,100	0	false	Only a few methods allowed for flexibility of the DNA and protein side chains during the docking.	[]	Only a few methods allowed for flexibility of the DNA and protein side chains during the docking.	true	true	true	true	true	1,151
1	INTRODUCTION	1	11	[ "b9", "b10", "b11", "b12", "b12", "b11" ]	16,820,531	pmid-9849937\|pmid-8865343\|pmid-7937706\|pmid-10465734\|pmid-10465734\|pmid-7937706\|pmid-15981252	They, however, required extensive knowledge to position the two components relative to each other (12) and problems were encountered in the absence of such information (11).	[ "9", "10", "11", "12", "12", "11" ]	173	7,101	1	false	They, however, required extensive knowledge to position the two components relative to each other and problems were encountered in the absence of such information.	[ "12", "11" ]	They, however, required extensive knowledge to position the two components relative to each other and problems were encountered in the absence of such information.	true	true	true	true	true	1,151
2	INTRODUCTION	1	13	[ "b13", "b14", "b15", "b18", "b13", "b19", "b20", "b21" ]	16,820,531	NA\|pmid-15981252\|pmid-15256668\|pmid-15751947\|NA\|pmid-2038059\|pmid-10647179\|pmid-8107872	Here we demonstrate that both global and local DNA flexibility can successfully be accounted for in protein−DNA modelling using HADDOCK (High Ambiguity Driven DOCKing) (13), a computational docking approach developed in our group.	[ "13", "14", "15", "18", "13", "19", "20", "21" ]	230	7,102	1	false	Here we demonstrate that both global and local DNA flexibility can successfully be accounted for in protein−DNA modelling using HADDOCK (High Ambiguity Driven DOCKing), a computational docking approach developed in our group.	[ "13" ]	Here we demonstrate that both global and local DNA flexibility can successfully be accounted for in protein−DNA modelling using HADDOCK (High Ambiguity Driven DOCKing), a computational docking approach developed in our group.	true	true	true	true	true	1,152
2	INTRODUCTION	1	14	[ "b13", "b14", "b15", "b18", "b13", "b19", "b20", "b21" ]	16,820,531	NA\|pmid-15981252\|pmid-15256668\|pmid-15751947\|NA\|pmid-2038059\|pmid-10647179\|pmid-8107872	HADDOCK makes use of available experimental and bioinformatics data to drive the docking process (14).	[ "13", "14", "15", "18", "13", "19", "20", "21" ]	102	7,103	1	false	HADDOCK makes use of available experimental and bioinformatics data to drive the docking process.	[ "14" ]	HADDOCK makes use of available experimental and bioinformatics data to drive the docking process.	true	true	true	true	true	1,152
2	INTRODUCTION	1	13	[ "b13", "b14", "b15", "b18", "b13", "b19", "b20", "b21" ]	16,820,531	NA\|pmid-15981252\|pmid-15256668\|pmid-15751947\|NA\|pmid-2038059\|pmid-10647179\|pmid-8107872	Its successful use in NMR-based structure calculations of protein–DNA and protein–RNA complexes has been shown previously (15–18).	[ "13", "14", "15", "18", "13", "19", "20", "21" ]	130	7,104	0	false	Its successful use in NMR-based structure calculations of protein–DNA and protein–RNA complexes has been shown previously.	[ "15–18" ]	Its successful use in NMR-based structure calculations of protein–DNA and protein–RNA complexes has been shown previously.	true	true	true	true	true	1,152
2	INTRODUCTION	1	13	[ "b13", "b14", "b15", "b18", "b13", "b19", "b20", "b21" ]	16,820,531	NA\|pmid-15981252\|pmid-15256668\|pmid-15751947\|NA\|pmid-2038059\|pmid-10647179\|pmid-8107872	Global and local DNA flexibility is introduced in the docking by allowing the DNA sugar-phosphate backbone and DNA base pairs to sample conformations during a semi-flexible refinement stage and by starting the docking from a library of pre-generated DNA structures representing various degrees of conformational flexibil...	[ "13", "14", "15", "18", "13", "19", "20", "21" ]	324	7,105	0	false	Global and local DNA flexibility is introduced in the docking by allowing the DNA sugar-phosphate backbone and DNA base pairs to sample conformations during a semi-flexible refinement stage and by starting the docking from a library of pre-generated DNA structures representing various degrees of conformational flexibil...	[]	Global and local DNA flexibility is introduced in the docking by allowing the DNA sugar-phosphate backbone and DNA base pairs to sample conformations during a semi-flexible refinement stage and by starting the docking from a library of pre-generated DNA structures representing various degrees of conformational flexibil...	true	true	true	true	true	1,152
2	INTRODUCTION	1	13	[ "b13", "b14", "b15", "b18", "b13", "b19", "b20", "b21" ]	16,820,531	NA\|pmid-15981252\|pmid-15256668\|pmid-15751947\|NA\|pmid-2038059\|pmid-10647179\|pmid-8107872	The latter allows for the sampling of a larger conformational space.	[ "13", "14", "15", "18", "13", "19", "20", "21" ]	68	7,106	0	false	The latter allows for the sampling of a larger conformational space.	[]	The latter allows for the sampling of a larger conformational space.	true	true	true	true	true	1,152
2	INTRODUCTION	1	13	[ "b13", "b14", "b15", "b18", "b13", "b19", "b20", "b21" ]	16,820,531	NA\|pmid-15981252\|pmid-15256668\|pmid-15751947\|NA\|pmid-2038059\|pmid-10647179\|pmid-8107872	Flexibility in the protein is introduced as described previously (13), first along the side chains at the interface and then for both backbone and side chains.	[ "13", "14", "15", "18", "13", "19", "20", "21" ]	159	7,107	1	false	Flexibility in the protein is introduced as described previously, first along the side chains at the interface and then for both backbone and side chains.	[ "13" ]	Flexibility in the protein is introduced as described previously, first along the side chains at the interface and then for both backbone and side chains.	true	true	true	true	true	1,152
2	INTRODUCTION	1	19	[ "b13", "b14", "b15", "b18", "b13", "b19", "b20", "b21" ]	16,820,531	NA\|pmid-15981252\|pmid-15256668\|pmid-15751947\|NA\|pmid-2038059\|pmid-10647179\|pmid-8107872	We demonstrate here the feasibility of this approach for three repressor complexes in their monomeric form: Cro from bacteriophage 434 (19), the Lac headpiece of Escherichia coli (20) and Arc from bacteriophage P22 (21).	[ "13", "14", "15", "18", "13", "19", "20", "21" ]	220	7,108	1	false	We demonstrate here the feasibility of this approach for three repressor complexes in their monomeric form: Cro from bacteriophage 434, the Lac headpiece of Escherichia coli and Arc from bacteriophage P22.	[ "19", "20", "21" ]	We demonstrate here the feasibility of this approach for three repressor complexes in their monomeric form: Cro from bacteriophage 434, the Lac headpiece of Escherichia coli and Arc from bacteriophage P22.	true	true	true	true	true	1,152
2	INTRODUCTION	1	13	[ "b13", "b14", "b15", "b18", "b13", "b19", "b20", "b21" ]	16,820,531	NA\|pmid-15981252\|pmid-15256668\|pmid-15751947\|NA\|pmid-2038059\|pmid-10647179\|pmid-8107872	The first two recognize the DNA major groove via an α-helix/turn/α-helix motif and the last one via a two-stranded antiparallel β-sheet motif.	[ "13", "14", "15", "18", "13", "19", "20", "21" ]	142	7,109	0	false	The first two recognize the DNA major groove via an α-helix/turn/α-helix motif and the last one via a two-stranded antiparallel β-sheet motif.	[]	The first two recognize the DNA major groove via an α-helix/turn/α-helix motif and the last one via a two-stranded antiparallel β-sheet motif.	true	true	true	true	true	1,152
2	INTRODUCTION	1	13	[ "b13", "b14", "b15", "b18", "b13", "b19", "b20", "b21" ]	16,820,531	NA\|pmid-15981252\|pmid-15256668\|pmid-15751947\|NA\|pmid-2038059\|pmid-10647179\|pmid-8107872	To drive the docking we make use of mutation data, sequence/structure conservation, DNA footprinting and ethylation interference data.	[ "13", "14", "15", "18", "13", "19", "20", "21" ]	134	7,110	0	false	To drive the docking we make use of mutation data, sequence/structure conservation, DNA footprinting and ethylation interference data.	[]	To drive the docking we make use of mutation data, sequence/structure conservation, DNA footprinting and ethylation interference data.	true	true	true	true	true	1,152
2	INTRODUCTION	1	13	[ "b13", "b14", "b15", "b18", "b13", "b19", "b20", "b21" ]	16,820,531	NA\|pmid-15981252\|pmid-15256668\|pmid-15751947\|NA\|pmid-2038059\|pmid-10647179\|pmid-8107872	We show that our approach is successful in predicting protein–DNA complexes from unbound constituents by accounting for both global and local DNA flexibility during the docking.	[ "13", "14", "15", "18", "13", "19", "20", "21" ]	177	7,111	0	false	We show that our approach is successful in predicting protein–DNA complexes from unbound constituents by accounting for both global and local DNA flexibility during the docking.	[]	We show that our approach is successful in predicting protein–DNA complexes from unbound constituents by accounting for both global and local DNA flexibility during the docking.	true	true	true	true	true	1,152
0	DISCUSSION	0	null	null	16,820,531	pmid-12001221\|pmid-14754428\|pmid-12784359\|pmid-12784368\|pmid-8735272\|NA\|pmid-10966773\|NA	Our modelling of protein−DNA complexes is based on AIRs to drive the docking process.	null	85	7,112	0	false	null	null	Our modelling of protein−DNA complexes is based on AIRs to drive the docking process.	true	true	true	true	true	1,153
0	DISCUSSION	0	null	null	16,820,531	pmid-12001221\|pmid-14754428\|pmid-12784359\|pmid-12784368\|pmid-8735272\|NA\|pmid-10966773\|NA	These are essential in successfully positioning the protein at the interface of the DNA and, together with flexibility, influence DNA bending in the semi-flexible refinement stage.	null	180	7,113	0	false	null	null	These are essential in successfully positioning the protein at the interface of the DNA and, together with flexibility, influence DNA bending in the semi-flexible refinement stage.	true	true	true	true	true	1,153
0	DISCUSSION	0	null	null	16,820,531	pmid-12001221\|pmid-14754428\|pmid-12784359\|pmid-12784368\|pmid-8735272\|NA\|pmid-10966773\|NA	We used a limited number of easily obtainable experimental data to define the restraints.	null	89	7,114	0	false	null	null	We used a limited number of easily obtainable experimental data to define the restraints.	true	true	true	true	true	1,153
0	DISCUSSION	0	null	null	16,820,531	pmid-12001221\|pmid-14754428\|pmid-12784359\|pmid-12784368\|pmid-8735272\|NA\|pmid-10966773\|NA	These were nevertheless sufficient to accurately predict the conformation of the DNA in the complex when starting from canonical B-DNA.	null	135	7,115	0	false	null	null	These were nevertheless sufficient to accurately predict the conformation of the DNA in the complex when starting from canonical B-DNA.	true	true	true	true	true	1,153
0	DISCUSSION	0	null	null	16,820,531	pmid-12001221\|pmid-14754428\|pmid-12784359\|pmid-12784368\|pmid-8735272\|NA\|pmid-10966773\|NA	This information subsequently allowed us to refine our models by performing docking from a custom-built DNA library instead of canonical B-DNA.	null	143	7,116	0	false	null	null	This information subsequently allowed us to refine our models by performing docking from a custom-built DNA library instead of canonical B-DNA.	true	true	true	true	true	1,153
0	DISCUSSION	0	null	null	16,820,531	pmid-12001221\|pmid-14754428\|pmid-12784359\|pmid-12784368\|pmid-8735272\|NA\|pmid-10966773\|NA	This two-stage docking approach significantly improves the conformation of the DNA in the resulting complexes; the protein, however, is less affected and its conformation remains close to the conformation of the respective starting unbound structures.	null	251	7,117	0	false	null	null	This two-stage docking approach significantly improves the conformation of the DNA in the resulting complexes; the protein, however, is less affected and its conformation remains close to the conformation of the respective starting unbound structures.	true	true	true	true	true	1,153
1	DISCUSSION	1	14	[ "b14" ]	16,820,531	pmid-9849937\|pmid-8865343\|pmid-7937706\|pmid-10465734\|pmid-10465734\|pmid-7937706\|pmid-15981252	In this study we did not investigate the effects of a variable number or type of restraints on the docking results.	[ "14" ]	115	7,118	0	false	In this study we did not investigate the effects of a variable number or type of restraints on the docking results.	[]	In this study we did not investigate the effects of a variable number or type of restraints on the docking results.	true	true	true	true	true	1,154
1	DISCUSSION	1	14	[ "b14" ]	16,820,531	pmid-9849937\|pmid-8865343\|pmid-7937706\|pmid-10465734\|pmid-10465734\|pmid-7937706\|pmid-15981252	From analogous protein−protein docking studies it is known that the amount of or the ambiguity in the data can influence the reproducibility of the docking.	[ "14" ]	156	7,119	0	false	From analogous protein−protein docking studies it is known that the amount of or the ambiguity in the data can influence the reproducibility of the docking.	[]	From analogous protein−protein docking studies it is known that the amount of or the ambiguity in the data can influence the reproducibility of the docking.	true	true	true	true	true	1,154
1	DISCUSSION	1	14	[ "b14" ]	16,820,531	pmid-9849937\|pmid-8865343\|pmid-7937706\|pmid-10465734\|pmid-10465734\|pmid-7937706\|pmid-15981252	HADDOCK allows the random deletion of a fraction of the restraints for each docking trial to account for errors in their definition, an approach that has proved successful in the past (14).	[ "14" ]	189	7,120	1	false	HADDOCK allows the random deletion of a fraction of the restraints for each docking trial to account for errors in their definition, an approach that has proved successful in the past.	[ "14" ]	HADDOCK allows the random deletion of a fraction of the restraints for each docking trial to account for errors in their definition, an approach that has proved successful in the past.	true	true	true	true	true	1,154
1	DISCUSSION	1	14	[ "b14" ]	16,820,531	pmid-9849937\|pmid-8865343\|pmid-7937706\|pmid-10465734\|pmid-10465734\|pmid-7937706\|pmid-15981252	This option was not used in this study.	[ "14" ]	39	7,121	0	false	This option was not used in this study.	[]	This option was not used in this study.	true	true	true	true	true	1,154
1	DISCUSSION	1	14	[ "b14" ]	16,820,531	pmid-9849937\|pmid-8865343\|pmid-7937706\|pmid-10465734\|pmid-10465734\|pmid-7937706\|pmid-15981252	The AIRs were defined with an upper distance limit of 2.0 Å that can affect the packing of the docking solutions.	[ "14" ]	113	7,122	0	false	The AIRs were defined with an upper distance limit of 2.0 Å that can affect the packing of the docking solutions.	[]	The AIRs were defined with an upper distance limit of 2.0 Å that can affect the packing of the docking solutions.	true	true	true	true	true	1,154
1	DISCUSSION	1	14	[ "b14" ]	16,820,531	pmid-9849937\|pmid-8865343\|pmid-7937706\|pmid-10465734\|pmid-10465734\|pmid-7937706\|pmid-15981252	For the Lac/O1 and Arc/operator complexes the BSA was comparable to that of the reference (1496 ± 103 Å versus 1560 Å and 1990 ± 155 Å versus 2072 Å, respectively).	[ "14" ]	164	7,123	0	false	For the Lac/O1 and Arc/operator complexes the BSA was comparable to that of the reference.	[ "1496 ± 103 Å versus 1560 Å and 1990 ± 155 Å versus 2072 Å, respectively" ]	For the Lac/O1 and Arc/operator complexes the BSA was comparable to that of the reference.	true	true	true	true	true	1,154
1	DISCUSSION	1	14	[ "b14" ]	16,820,531	pmid-9849937\|pmid-8865343\|pmid-7937706\|pmid-10465734\|pmid-10465734\|pmid-7937706\|pmid-15981252	For the Cro/O1R complex the BSA of the top ranking solutions was larger than that of the reference (1694 ± 52 Å versus 1453 Å).	[ "14" ]	127	7,124	0	false	For the Cro/O1R complex the BSA of the top ranking solutions was larger than that of the reference.	[ "1694 ± 52 Å versus 1453 Å" ]	For the Cro/O1R complex the BSA of the top ranking solutions was larger than that of the reference.	true	true	true	true	true	1,154
1	DISCUSSION	1	14	[ "b14" ]	16,820,531	pmid-9849937\|pmid-8865343\|pmid-7937706\|pmid-10465734\|pmid-10465734\|pmid-7937706\|pmid-15981252	The tighter packing might contribute to the significant increase in the fraction of native contacts (Table 3) for the Cro/O1R complex, with respect to the other two test systems.	[ "14" ]	178	7,125	0	false	The tighter packing might contribute to the significant increase in the fraction of native contacts (Table 3) for the Cro/O1R complex, with respect to the other two test systems.	[]	The tighter packing might contribute to the significant increase in the fraction of native contacts (Table 3) for the Cro/O1R complex, with respect to the other two test systems.	true	true	true	true	true	1,154
2	DISCUSSION	0	null	null	16,820,531	NA\|pmid-15981252\|pmid-15256668\|pmid-15751947\|NA\|pmid-2038059\|pmid-10647179\|pmid-8107872	We have demonstrated that the use of readily available non-structural experimental data and the incorporation of DNA flexibility during the docking significantly improve repressor−DNA complex prediction in comparison to rigid-body docking.	null	239	7,126	0	false	null	null	We have demonstrated that the use of readily available non-structural experimental data and the incorporation of DNA flexibility during the docking significantly improve repressor−DNA complex prediction in comparison to rigid-body docking.	true	true	true	true	true	1,155
2	DISCUSSION	0	null	null	16,820,531	NA\|pmid-15981252\|pmid-15256668\|pmid-15751947\|NA\|pmid-2038059\|pmid-10647179\|pmid-8107872	The method successfully predicted global conformational changes taking place in the DNA upon complexation.	null	106	7,127	0	false	null	null	The method successfully predicted global conformational changes taking place in the DNA upon complexation.	true	true	true	true	true	1,155
2	DISCUSSION	0	null	null	16,820,531	NA\|pmid-15981252\|pmid-15256668\|pmid-15751947\|NA\|pmid-2038059\|pmid-10647179\|pmid-8107872	The information extracted from these results is sufficient to refine the models by starting a second docking round from custom-built DNA libraries of pre-bent and twisted structures.	null	182	7,128	0	false	null	null	The information extracted from these results is sufficient to refine the models by starting a second docking round from custom-built DNA libraries of pre-bent and twisted structures.	true	true	true	true	true	1,155
3	DISCUSSION	0	null	null	16,820,531	null	The flexible protein−DNA docking approach described in this paper has biological implications since it can benefit studies of protein–DNA interactions at several levels.	null	169	7,129	0	false	null	null	The flexible protein−DNA docking approach described in this paper has biological implications since it can benefit studies of protein–DNA interactions at several levels.	true	true	true	true	true	1,156
3	DISCUSSION	0	null	null	16,820,531	null	It can be used to generate models of protein–DNA complexes when the structure of the unbound protein is known and suitable experimental data are available.	null	155	7,130	0	false	null	null	It can be used to generate models of protein–DNA complexes when the structure of the unbound protein is known and suitable experimental data are available.	true	true	true	true	true	1,156
3	DISCUSSION	0	null	null	16,820,531	null	It is also applicable to study the effects of mutations or different operator sequences on complex formation.	null	109	7,131	0	false	null	null	It is also applicable to study the effects of mutations or different operator sequences on complex formation.	true	true	true	true	true	1,156
3	DISCUSSION	0	null	null	16,820,531	null	In addition, it can assist in experimental structural studies: it can, for example, speed up structure determination of protein–DNA complexes by NMR by providing initial models to guide the tedious NMR analysis and assignment process.	null	234	7,132	0	false	null	null	In addition, it can assist in experimental structural studies: it can, for example, speed up structure determination of protein–DNA complexes by NMR by providing initial models to guide the tedious NMR analysis and assignment process.	true	true	true	true	true	1,156
3	DISCUSSION	0	null	null	16,820,531	null	In summary, by allowing the inclusion of a large variety of experimental and/or bioinformatics data, together with a flexible description of the DNA, the proposed docking approach should be a useful tool in structural studies of protein–DNA and even protein–RNA interactions provided suitable RNA models are available fo...	null	333	7,133	0	false	null	null	In summary, by allowing the inclusion of a large variety of experimental and/or bioinformatics data, together with a flexible description of the DNA, the proposed docking approach should be a useful tool in structural studies of protein–DNA and even protein–RNA interactions provided suitable RNA models are available fo...	true	true	true	true	true	1,156
0	INTRODUCTION	1	1	[ "b1", "b2", "b3" ]	16,855,292	pmid-9305837\|pmid-11988475\|pmid-16079127	A nucleosome comprises ∼200 bp of DNA, an octameric core of two copies each of histones H2A, H2B, H3 and H4, and the linker histone H1.	[ "1", "2", "3" ]	135	7,134	0	false	A nucleosome comprises ∼200 bp of DNA, an octameric core of two copies each of histones H2A, H2B, H3 and H4, and the linker histone H1.	[]	A nucleosome comprises ∼200 bp of DNA, an octameric core of two copies each of histones H2A, H2B, H3 and H4, and the linker histone H1.	true	true	true	true	true	1,157
0	INTRODUCTION	1	1	[ "b1", "b2", "b3" ]	16,855,292	pmid-9305837\|pmid-11988475\|pmid-16079127	The core histone proteins contain histone-fold domains and histone-fold extensions responsible for histone–histone and histone–DNA interactions, and N-terminal tail domains.	[ "1", "2", "3" ]	173	7,135	0	false	The core histone proteins contain histone-fold domains and histone-fold extensions responsible for histone–histone and histone–DNA interactions, and N-terminal tail domains.	[]	The core histone proteins contain histone-fold domains and histone-fold extensions responsible for histone–histone and histone–DNA interactions, and N-terminal tail domains.	true	true	true	true	true	1,157
0	INTRODUCTION	1	1	[ "b1", "b2", "b3" ]	16,855,292	pmid-9305837\|pmid-11988475\|pmid-16079127	The crystal structure of the nucleosome core particle revealed that the N-terminal tails are predominantly external to the particle and highly flexible, suggesting that they interact with DNA/histones, and also serve as targets for chromatin binding proteins and enzymatic functions (1).	[ "1", "2", "3" ]	287	7,136	1	false	The crystal structure of the nucleosome core particle revealed that the N-terminal tails are predominantly external to the particle and highly flexible, suggesting that they interact with DNA/histones, and also serve as targets for chromatin binding proteins and enzymatic functions.	[ "1" ]	The crystal structure of the nucleosome core particle revealed that the N-terminal tails are predominantly external to the particle and highly flexible, suggesting that they interact with DNA/histones, and also serve as targets for chromatin binding proteins and enzymatic functions.	true	true	true	true	true	1,157
0	INTRODUCTION	1	2	[ "b1", "b2", "b3" ]	16,855,292	pmid-9305837\|pmid-11988475\|pmid-16079127	Consistent with the idea that the histone-tails mediate the key nucleosome–nucleosome interactions that are essential for chromatin structures in vivo, the histone-tails were shown to be critical for both the intramolecular folding of nucleosomal arrays and the fiber–fiber interactions observed in vitro (2).	[ "1", "2", "3" ]	309	7,137	1	false	Consistent with the idea that the histone-tails mediate the key nucleosome–nucleosome interactions that are essential for chromatin structures in vivo, the histone-tails were shown to be critical for both the intramolecular folding of nucleosomal arrays and the fiber–fiber interactions observed in vitro.	[ "2" ]	Consistent with the idea that the histone-tails mediate the key nucleosome–nucleosome interactions that are essential for chromatin structures in vivo, the histone-tails were shown to be critical for both the intramolecular folding of nucleosomal arrays and the fiber–fiber interactions observed in vitro.	true	true	true	true	true	1,157
0	INTRODUCTION	1	3	[ "b1", "b2", "b3" ]	16,855,292	pmid-9305837\|pmid-11988475\|pmid-16079127	The locations and interactions of the H3 tail domain are dependent upon the degree of the condensation of a nucleosomal array, and alterations in the tail-interactions may elaborate different structural and functional states of chromatin (3).	[ "1", "2", "3" ]	242	7,138	1	false	The locations and interactions of the H3 tail domain are dependent upon the degree of the condensation of a nucleosomal array, and alterations in the tail-interactions may elaborate different structural and functional states of chromatin.	[ "3" ]	The locations and interactions of the H3 tail domain are dependent upon the degree of the condensation of a nucleosomal array, and alterations in the tail-interactions may elaborate different structural and functional states of chromatin.	true	true	true	true	true	1,157
0	INTRODUCTION	1	1	[ "b1", "b2", "b3" ]	16,855,292	pmid-9305837\|pmid-11988475\|pmid-16079127	Thus, the core histone tail domains are essential determinants of chromatin fiber dynamics.	[ "1", "2", "3" ]	91	7,139	0	false	Thus, the core histone tail domains are essential determinants of chromatin fiber dynamics.	[]	Thus, the core histone tail domains are essential determinants of chromatin fiber dynamics.	true	true	true	true	true	1,157
0	INTRODUCTION	1	1	[ "b1", "b2", "b3" ]	16,855,292	pmid-9305837\|pmid-11988475\|pmid-16079127	In the chromatin context in vivo, the tails electrostatically interact with DNA.	[ "1", "2", "3" ]	80	7,140	0	false	In the chromatin context in vivo, the tails electrostatically interact with DNA.	[]	In the chromatin context in vivo, the tails electrostatically interact with DNA.	true	true	true	true	true	1,157
0	INTRODUCTION	1	1	[ "b1", "b2", "b3" ]	16,855,292	pmid-9305837\|pmid-11988475\|pmid-16079127	In addition, histone tails also interact with other tails, other histone domains and non-histone proteins.	[ "1", "2", "3" ]	106	7,141	0	false	In addition, histone tails also interact with other tails, other histone domains and non-histone proteins.	[]	In addition, histone tails also interact with other tails, other histone domains and non-histone proteins.	true	true	true	true	true	1,157
1	INTRODUCTION	1	4	[ "b4", "b7", "b8", "b9", "b7", "b10", "b12" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	The histone-tail-binding proteins associate with specifically modified tails and induce various chromatin functions.	[ "4", "7", "8", "9", "7", "10", "12" ]	116	7,142	0	false	The histone-tail-binding proteins associate with specifically modified tails and induce various chromatin functions.	[]	The histone-tail-binding proteins associate with specifically modified tails and induce various chromatin functions.	true	true	true	true	true	1,158
1	INTRODUCTION	1	4	[ "b4", "b7", "b8", "b9", "b7", "b10", "b12" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	In yeast, repressor proteins, such as Sir3p, and transcriptional activators, such as the bromodomain-containing protein Bdf1p, interact with the histone H4 tail (4–7).	[ "4", "7", "8", "9", "7", "10", "12" ]	167	7,143	0	false	In yeast, repressor proteins, such as Sir3p, and transcriptional activators, such as the bromodomain-containing protein Bdf1p, interact with the histone H4 tail.	[ "4–7" ]	In yeast, repressor proteins, such as Sir3p, and transcriptional activators, such as the bromodomain-containing protein Bdf1p, interact with the histone H4 tail.	true	true	true	true	true	1,158
1	INTRODUCTION	1	4	[ "b4", "b7", "b8", "b9", "b7", "b10", "b12" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	The N-terminal tail of histone H4 has four acetylated lysines: K5, K8, K12 and K16.	[ "4", "7", "8", "9", "7", "10", "12" ]	83	7,144	0	false	The N-terminal tail of histone H4 has four acetylated lysines: K5, K8, K12 and K16.	[]	The N-terminal tail of histone H4 has four acetylated lysines: K5, K8, K12 and K16.	true	true	true	true	true	1,158
1	INTRODUCTION	1	4	[ "b4", "b7", "b8", "b9", "b7", "b10", "b12" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	Of these, only K16 is strongly correlated with a specific regulatory function in yeast, where its acetylation state regulates the extent of heterochromatin silencing.	[ "4", "7", "8", "9", "7", "10", "12" ]	166	7,145	0	false	Of these, only K16 is strongly correlated with a specific regulatory function in yeast, where its acetylation state regulates the extent of heterochromatin silencing.	[]	Of these, only K16 is strongly correlated with a specific regulatory function in yeast, where its acetylation state regulates the extent of heterochromatin silencing.	true	true	true	true	true	1,158
1	INTRODUCTION	1	4	[ "b4", "b7", "b8", "b9", "b7", "b10", "b12" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	K16 is acetylated by Sas2p and deacetylated by Sir2p, and the balance of these opposing activities determines the extent of silencing spreading from telomeres (8,9).	[ "4", "7", "8", "9", "7", "10", "12" ]	165	7,146	0	false	K16 is acetylated by Sas2p and deacetylated by Sir2p, and the balance of these opposing activities determines the extent of silencing spreading from telomeres.	[ "8,9" ]	K16 is acetylated by Sas2p and deacetylated by Sir2p, and the balance of these opposing activities determines the extent of silencing spreading from telomeres.	true	true	true	true	true	1,158
1	INTRODUCTION	1	4	[ "b4", "b7", "b8", "b9", "b7", "b10", "b12" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	The spreading is in part owing to Sir3p's preferential association with the H4-tails that have been deacetylated at K16.	[ "4", "7", "8", "9", "7", "10", "12" ]	120	7,147	0	false	The spreading is in part owing to Sir3p's preferential association with the H4-tails that have been deacetylated at K16.	[]	The spreading is in part owing to Sir3p's preferential association with the H4-tails that have been deacetylated at K16.	true	true	true	true	true	1,158
1	INTRODUCTION	1	4	[ "b4", "b7", "b8", "b9", "b7", "b10", "b12" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	In contrast, Bdf1p preferentially associates with acetylated H4-tails.	[ "4", "7", "8", "9", "7", "10", "12" ]	70	7,148	0	false	In contrast, Bdf1p preferentially associates with acetylated H4-tails.	[]	In contrast, Bdf1p preferentially associates with acetylated H4-tails.	true	true	true	true	true	1,158
1	INTRODUCTION	1	7	[ "b4", "b7", "b8", "b9", "b7", "b10", "b12" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	Bdf1p competes with a Sir2p deacetylase for binding to the acetylated H4-tails (7).	[ "4", "7", "8", "9", "7", "10", "12" ]	83	7,149	1	false	Bdf1p competes with a Sir2p deacetylase for binding to the acetylated H4-tails.	[ "7" ]	Bdf1p competes with a Sir2p deacetylase for binding to the acetylated H4-tails.	true	true	true	true	true	1,158
1	INTRODUCTION	1	4	[ "b4", "b7", "b8", "b9", "b7", "b10", "b12" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	Besides acetylation, methylated H3-tails are recognized by repressor proteins, such as heterochromatin protein 1 (HP1) and Polycomb, in higher eukaryotes (10–12).	[ "4", "7", "8", "9", "7", "10", "12" ]	162	7,150	0	false	Besides acetylation, methylated H3-tails are recognized by repressor proteins, such as heterochromatin protein 1 (HP1) and Polycomb, in higher eukaryotes.	[ "10–12" ]	Besides acetylation, methylated H3-tails are recognized by repressor proteins, such as heterochromatin protein 1 (HP1) and Polycomb, in higher eukaryotes.	true	true	true	true	true	1,158
1	INTRODUCTION	1	4	[ "b4", "b7", "b8", "b9", "b7", "b10", "b12" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	The chromodomains of HP1 and Polycomb associate with H3-tails methylated at K9 and K27, respectively, leading to changes in DNA template accessibility and higher-order chromatin structures.	[ "4", "7", "8", "9", "7", "10", "12" ]	189	7,151	0	false	The chromodomains of HP1 and Polycomb associate with H3-tails methylated at K9 and K27, respectively, leading to changes in DNA template accessibility and higher-order chromatin structures.	[]	The chromodomains of HP1 and Polycomb associate with H3-tails methylated at K9 and K27, respectively, leading to changes in DNA template accessibility and higher-order chromatin structures.	true	true	true	true	true	1,158
2	INTRODUCTION	1	13	[ "b13", "b14", "b18" ]	16,855,292	pmid-11498575\|pmid-11850414\|pmid-16246723	The molecular interaction partners of the histone tails in different states of modification are being elucidated and have been shown to play key roles in the regulation of all nuclear processes, leading to an ‘epigenetic code' or ‘histone code' hypothesis (13).	[ "13", "14", "18" ]	261	7,152	1	false	The molecular interaction partners of the histone tails in different states of modification are being elucidated and have been shown to play key roles in the regulation of all nuclear processes, leading to an ‘epigenetic code' or ‘histone code' hypothesis.	[ "13" ]	The molecular interaction partners of the histone tails in different states of modification are being elucidated and have been shown to play key roles in the regulation of all nuclear processes, leading to an ‘epigenetic code' or ‘histone code' hypothesis.	true	true	true	true	true	1,159
2	INTRODUCTION	1	13	[ "b13", "b14", "b18" ]	16,855,292	pmid-11498575\|pmid-11850414\|pmid-16246723	Based on this hypothesis, histone-tail-binding proteins have been isolated by affinity columns using histone tail peptides with specific modifications.	[ "13", "14", "18" ]	151	7,153	0	false	Based on this hypothesis, histone-tail-binding proteins have been isolated by affinity columns using histone tail peptides with specific modifications.	[]	Based on this hypothesis, histone-tail-binding proteins have been isolated by affinity columns using histone tail peptides with specific modifications.	true	true	true	true	true	1,159
2	INTRODUCTION	1	13	[ "b13", "b14", "b18" ]	16,855,292	pmid-11498575\|pmid-11850414\|pmid-16246723	This approach identified various factors, such as a nucleosome remodeling and deacetylase (NuRD) complex, hSNF2H, an inhibitor of acetyltransferase (INHAT) complex, a WD40-repeat protein WDR5, and 14-3-3 isoforms of phosphospecific binding proteins as H3-tail-binding proteins (14–18).	[ "13", "14", "18" ]	285	7,154	0	false	This approach identified various factors, such as a nucleosome remodeling and deacetylase (NuRD) complex, hSNF2H, an inhibitor of acetyltransferase (INHAT) complex, a WD40-repeat protein WDR5, and 14-3-3 isoforms of phosphospecific binding proteins as H3-tail-binding proteins.	[ "14–18" ]	This approach identified various factors, such as a nucleosome remodeling and deacetylase (NuRD) complex, hSNF2H, an inhibitor of acetyltransferase (INHAT) complex, a WD40-repeat protein WDR5, and 14-3-3 isoforms of phosphospecific binding proteins as H3-tail-binding proteins.	true	true	true	true	true	1,159
2	INTRODUCTION	1	13	[ "b13", "b14", "b18" ]	16,855,292	pmid-11498575\|pmid-11850414\|pmid-16246723	These identifications indicated that the peptide columns are a powerful approach to screen for the tail-binding proteins.	[ "13", "14", "18" ]	121	7,155	0	false	These identifications indicated that the peptide columns are a powerful approach to screen for the tail-binding proteins.	[]	These identifications indicated that the peptide columns are a powerful approach to screen for the tail-binding proteins.	true	true	true	true	true	1,159
2	INTRODUCTION	1	13	[ "b13", "b14", "b18" ]	16,855,292	pmid-11498575\|pmid-11850414\|pmid-16246723	However, the screening is probably biased, since the binding to the peptides is performed in vitro.	[ "13", "14", "18" ]	99	7,156	0	false	However, the screening is probably biased, since the binding to the peptides is performed in vitro.	[]	However, the screening is probably biased, since the binding to the peptides is performed in vitro.	true	true	true	true	true	1,159
2	INTRODUCTION	1	13	[ "b13", "b14", "b18" ]	16,855,292	pmid-11498575\|pmid-11850414\|pmid-16246723	Thus, many tail-binding proteins may still be unidentified.	[ "13", "14", "18" ]	59	7,157	0	false	Thus, many tail-binding proteins may still be unidentified.	[]	Thus, many tail-binding proteins may still be unidentified.	true	true	true	true	true	1,159
2	INTRODUCTION	1	13	[ "b13", "b14", "b18" ]	16,855,292	pmid-11498575\|pmid-11850414\|pmid-16246723	Therefore, it is worthwhile to perform the screening for the tail-binding proteins by in vivo binding.	[ "13", "14", "18" ]	102	7,158	0	false	Therefore, it is worthwhile to perform the screening for the tail-binding proteins by in vivo binding.	[]	Therefore, it is worthwhile to perform the screening for the tail-binding proteins by in vivo binding.	true	true	true	true	true	1,159
3	INTRODUCTION	0	null	null	16,855,292	pmid-11809876	Here we screened for potential histone H4-tail associated proteins using a protein differential display approach by two-dimensional gel electrophoresis (2DGE) comparing H4 tail deleted chromatin with wild-type chromatin.	null	220	7,159	0	false	null	null	Here we screened for potential histone H4-tail associated proteins using a protein differential display approach by two-dimensional gel electrophoresis (2DGE) comparing H4 tail deleted chromatin with wild-type chromatin.	true	true	true	true	true	1,160
3	INTRODUCTION	0	null	null	16,855,292	pmid-11809876	We have found that a WD40-repeat protein, Pwp1p, interacts with chromatin through the H4-tail, which confirms that our approach is effective for identifying histone-tail-associated proteins.	null	190	7,160	0	false	null	null	We have found that a WD40-repeat protein, Pwp1p, interacts with chromatin through the H4-tail, which confirms that our approach is effective for identifying histone-tail-associated proteins.	true	true	true	true	true	1,160
0	DISCUSSION	0	null	null	16,855,292	pmid-9305837\|pmid-11988475\|pmid-16079127	We performed the protein differential display approach in 2DGE with the H4-tail deleted mutant to identify the H4-tail-associated-proteins by MS and identified 22 candidate proteins, including the H4-tail binding proteins, Arp4p and Isw1p, and proteins with the SANT and WD40-repeat, which may be a histone tail-binding ...	null	327	7,161	0	false	null	null	We performed the protein differential display approach in 2DGE with the H4-tail deleted mutant to identify the H4-tail-associated-proteins by MS and identified 22 candidate proteins, including the H4-tail binding proteins, Arp4p and Isw1p, and proteins with the SANT and WD40-repeat, which may be a histone tail-binding ...	true	true	true	true	true	1,161
0	DISCUSSION	0	null	null	16,855,292	pmid-9305837\|pmid-11988475\|pmid-16079127	We also provided in vivo evidence that one candidate, Pwp1p, associates with the rDNA chromatin in an H4 tail-dependent manner.	null	127	7,162	0	false	null	null	We also provided in vivo evidence that one candidate, Pwp1p, associates with the rDNA chromatin in an H4 tail-dependent manner.	true	true	true	true	true	1,161
1	DISCUSSION	1	14	[ "b14", "b16", "b15", "b17", "b18", "b54", "b55", "b54" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	In previous reports, in order to identify protein complexes capable of binding specifically to histone H3 N-terminal tail, nuclear extracts were applied to affinity columns displaying either unmodified H3 tails or the same tails but differently methylated at specific residues.	[ "14", "16", "15", "17", "18", "54", "55", "54" ]	277	7,163	0	false	In previous reports, in order to identify protein complexes capable of binding specifically to histone H3 N-terminal tail, nuclear extracts were applied to affinity columns displaying either unmodified H3 tails or the same tails but differently methylated at specific residues.	[]	In previous reports, in order to identify protein complexes capable of binding specifically to histone H3 N-terminal tail, nuclear extracts were applied to affinity columns displaying either unmodified H3 tails or the same tails but differently methylated at specific residues.	true	true	true	true	true	1,162
1	DISCUSSION	1	14	[ "b14", "b16", "b15", "b17", "b18", "b54", "b55", "b54" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	The NuRD complex binds specifically to unmodified H3 tails but not to K4 methylated tails (14).	[ "14", "16", "15", "17", "18", "54", "55", "54" ]	95	7,164	1	false	The NuRD complex binds specifically to unmodified H3 tails but not to K4 methylated tails.	[ "14" ]	The NuRD complex binds specifically to unmodified H3 tails but not to K4 methylated tails.	true	true	true	true	true	1,162
1	DISCUSSION	1	16	[ "b14", "b16", "b15", "b17", "b18", "b54", "b55", "b54" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	Two proteins, INHAT complex subunits SET and pp32, bind specifically to unmodified H3 tails but not to phosphorylated tails at T3 (16).	[ "14", "16", "15", "17", "18", "54", "55", "54" ]	135	7,165	1	false	Two proteins, INHAT complex subunits SET and pp32, bind specifically to unmodified H3 tails but not to phosphorylated tails at T3.	[ "16" ]	Two proteins, INHAT complex subunits SET and pp32, bind specifically to unmodified H3 tails but not to phosphorylated tails at T3.	true	true	true	true	true	1,162
1	DISCUSSION	1	14	[ "b14", "b16", "b15", "b17", "b18", "b54", "b55", "b54" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	hSNF2H and WDR5 were identified as H3 tail-binding proteins that associate with the methylated tail at K4 (15,17).	[ "14", "16", "15", "17", "18", "54", "55", "54" ]	114	7,166	0	false	hSNF2H and WDR5 were identified as H3 tail-binding proteins that associate with the methylated tail at K4.	[ "15,17" ]	hSNF2H and WDR5 were identified as H3 tail-binding proteins that associate with the methylated tail at K4.	false	true	true	true	false	1,162
1	DISCUSSION	1	18	[ "b14", "b16", "b15", "b17", "b18", "b54", "b55", "b54" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	The 14-3-3 isoforms also bind to the phosphorylated H3-tail at S10 (18).	[ "14", "16", "15", "17", "18", "54", "55", "54" ]	72	7,167	1	false	The 14-3-3 isoforms also bind to the phosphorylated H3-tail at S10.	[ "18" ]	The 14-3-3 isoforms also bind to the phosphorylated H3-tail at S10.	true	true	true	true	true	1,162
1	DISCUSSION	1	14	[ "b14", "b16", "b15", "b17", "b18", "b54", "b55", "b54" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	These protein identifications proved that the peptide affinity column is a powerful method to identify the tail-binding proteins.	[ "14", "16", "15", "17", "18", "54", "55", "54" ]	129	7,168	0	false	These protein identifications proved that the peptide affinity column is a powerful method to identify the tail-binding proteins.	[]	These protein identifications proved that the peptide affinity column is a powerful method to identify the tail-binding proteins.	true	true	true	true	true	1,162
1	DISCUSSION	1	14	[ "b14", "b16", "b15", "b17", "b18", "b54", "b55", "b54" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	However, this approach is dependent on the preparation of a nuclear extract and the salt concentration of the binding buffer.	[ "14", "16", "15", "17", "18", "54", "55", "54" ]	125	7,169	0	false	However, this approach is dependent on the preparation of a nuclear extract and the salt concentration of the binding buffer.	[]	However, this approach is dependent on the preparation of a nuclear extract and the salt concentration of the binding buffer.	true	true	true	true	true	1,162
1	DISCUSSION	1	14	[ "b14", "b16", "b15", "b17", "b18", "b54", "b55", "b54" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	Most importantly, the peptide conformation could be different from that in the chromatin context in vivo.	[ "14", "16", "15", "17", "18", "54", "55", "54" ]	105	7,170	0	false	Most importantly, the peptide conformation could be different from that in the chromatin context in vivo.	[]	Most importantly, the peptide conformation could be different from that in the chromatin context in vivo.	true	true	true	true	true	1,162
1	DISCUSSION	1	14	[ "b14", "b16", "b15", "b17", "b18", "b54", "b55", "b54" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	Thus, the screening may be restricted, and some proteins would not be identified.	[ "14", "16", "15", "17", "18", "54", "55", "54" ]	81	7,171	0	false	Thus, the screening may be restricted, and some proteins would not be identified.	[]	Thus, the screening may be restricted, and some proteins would not be identified.	true	true	true	true	true	1,162
1	DISCUSSION	1	14	[ "b14", "b16", "b15", "b17", "b18", "b54", "b55", "b54" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	By a yeast two-hybrid screen employing yeast genomic libraries in combination with a bait plasmid expressing a fragment of histone H4 (amino acids 1–59), only two proteins, Bdf1p and Hif1p, were identified (54,55).	[ "14", "16", "15", "17", "18", "54", "55", "54" ]	214	7,172	0	false	By a yeast two-hybrid screen employing yeast genomic libraries in combination with a bait plasmid expressing a fragment of histone H4 (amino acids 1–59), only two proteins, Bdf1p and Hif1p, were identified.	[ "54,55" ]	By a yeast two-hybrid screen employing yeast genomic libraries in combination with a bait plasmid expressing a fragment of histone H4, only two proteins, Bdf1p and Hif1p, were identified.	true	true	true	true	true	1,162
1	DISCUSSION	1	14	[ "b14", "b16", "b15", "b17", "b18", "b54", "b55", "b54" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	This indicates that the two-hybrid screen also has limitations.	[ "14", "16", "15", "17", "18", "54", "55", "54" ]	63	7,173	0	false	This indicates that the two-hybrid screen also has limitations.	[]	This indicates that the two-hybrid screen also has limitations.	true	true	true	true	true	1,162
1	DISCUSSION	1	54	[ "b14", "b16", "b15", "b17", "b18", "b54", "b55", "b54" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	The authors suggested that a folding difference may exist between the full-length histone H4 and the portion of amino acids 1–59 (54).	[ "14", "16", "15", "17", "18", "54", "55", "54" ]	134	7,174	1	false	The authors suggested that a folding difference may exist between the full-length histone H4 and the portion of amino acids 1–59.	[ "54" ]	The authors suggested that a folding difference may exist between the full-length histone H4 and the portion of amino acids 1–59.	true	true	true	true	true	1,162
1	DISCUSSION	1	14	[ "b14", "b16", "b15", "b17", "b18", "b54", "b55", "b54" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	Again, the tail in this assay may have a different conformation as compared to that in the chromatin context.	[ "14", "16", "15", "17", "18", "54", "55", "54" ]	109	7,175	0	false	Again, the tail in this assay may have a different conformation as compared to that in the chromatin context.	[]	Again, the tail in this assay may have a different conformation as compared to that in the chromatin context.	true	true	true	true	true	1,162
1	DISCUSSION	1	14	[ "b14", "b16", "b15", "b17", "b18", "b54", "b55", "b54" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	In this regard, our approach seems to be more suitable than the others to identify tail-binding proteins.	[ "14", "16", "15", "17", "18", "54", "55", "54" ]	105	7,176	0	false	In this regard, our approach seems to be more suitable than the others to identify tail-binding proteins.	[]	In this regard, our approach seems to be more suitable than the others to identify tail-binding proteins.	true	true	true	true	true	1,162
1	DISCUSSION	1	14	[ "b14", "b16", "b15", "b17", "b18", "b54", "b55", "b54" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	The nucleosome ladder was detected by MNase digestion in our H4-tail mutant, showing the maintenance of the nucleosome structure in the absence of H4-tails (50 and data not shown).	[ "14", "16", "15", "17", "18", "54", "55", "54" ]	180	7,177	0	false	The nucleosome ladder was detected by MNase digestion in our H4-tail mutant, showing the maintenance of the nucleosome structure in the absence of H4-tails (50 and data not shown).	[]	The nucleosome ladder was detected by MNase digestion in our H4-tail mutant, showing the maintenance of the nucleosome structure in the absence of H4-tails (50 and data not shown).	true	true	true	true	true	1,162
1	DISCUSSION	1	14	[ "b14", "b16", "b15", "b17", "b18", "b54", "b55", "b54" ]	16,855,292	pmid-7867066\|pmid-12620225\|pmid-12410229\|pmid-12379856\|pmid-12620225\|pmid-11242053\|pmid-12351676\|pmid-11850414\|pmid-15100215\|pmid-14636589\|pmid-15960974\|pmid-16246723\|pmid-11343701\|NA\|pmid-11343701	Therefore, our screening reflects the H4-tail binding ability in vivo.	[ "14", "16", "15", "17", "18", "54", "55", "54" ]	70	7,178	0	false	Therefore, our screening reflects the H4-tail binding ability in vivo.	[]	Therefore, our screening reflects the H4-tail binding ability in vivo.	true	true	true	true	true	1,162
2	DISCUSSION	0	null	null	16,855,292	pmid-11498575\|pmid-11850414\|pmid-16246723	We enriched chromatin proteins by the Mg2+-dependent oligomerization for an efficient identification of a histone-tail binding protein (Figure 2).	null	146	7,179	0	false	null	null	We enriched chromatin proteins by the Mg2+-dependent oligomerization for an efficient identification of a histone-tail binding protein (Figure 2).	true	true	true	true	true	1,163
2	DISCUSSION	0	null	null	16,855,292	pmid-11498575\|pmid-11850414\|pmid-16246723	However, silver stained 2D gels were not sensitive enough to identify Sir3p, whose abundance was reduced in western blot (Figure 3B).	null	133	7,180	0	false	null	null	However, silver stained 2D gels were not sensitive enough to identify Sir3p, whose abundance was reduced in western blot (Figure 3B).	true	true	true	true	true	1,163
2	DISCUSSION	0	null	null	16,855,292	pmid-11498575\|pmid-11850414\|pmid-16246723	Total mixture mass spectrometry is more sensitive than the silver stain.	null	72	7,181	0	false	null	null	Total mixture mass spectrometry is more sensitive than the silver stain.	true	true	true	true	true	1,163
2	DISCUSSION	0	null	null	16,855,292	pmid-11498575\|pmid-11850414\|pmid-16246723	This method will help to identify less-abundant proteins.	null	57	7,182	0	false	null	null	This method will help to identify less-abundant proteins.	true	true	true	true	true	1,163
3	DISCUSSION	1	32	[ "b32" ]	16,855,292	pmid-11809876	Our screening is based on in vivo binding activity.	[ "32" ]	51	7,183	0	false	Our screening is based on in vivo binding activity.	[]	Our screening is based on in vivo binding activity.	true	true	true	true	true	1,164
3	DISCUSSION	1	32	[ "b32" ]	16,855,292	pmid-11809876	So a candidate protein may interact either directly or indirectly with an H4-tail.	[ "32" ]	82	7,184	0	false	So a candidate protein may interact either directly or indirectly with an H4-tail.	[]	So a candidate protein may interact either directly or indirectly with an H4-tail.	true	true	true	true	true	1,164
3	DISCUSSION	1	32	[ "b32" ]	16,855,292	pmid-11809876	We identified Isw1p, whose fly homolog, ISWI, probably recognizes a DNA-bound H4-tail.	[ "32" ]	86	7,185	0	false	We identified Isw1p, whose fly homolog, ISWI, probably recognizes a DNA-bound H4-tail.	[]	We identified Isw1p, whose fly homolog, ISWI, probably recognizes a DNA-bound H4-tail.	true	true	true	true	true	1,164
3	DISCUSSION	1	32	[ "b32" ]	16,855,292	pmid-11809876	ISWI does not interact stably with the GST–H4 tail fusion protein in the absence of DNA (32).	[ "32" ]	93	7,186	1	false	ISWI does not interact stably with the GST–H4 tail fusion protein in the absence of DNA.	[ "32" ]	ISWI does not interact stably with the GST–H4 tail fusion protein in the absence of DNA.	true	true	true	true	true	1,164
3	DISCUSSION	1	32	[ "b32" ]	16,855,292	pmid-11809876	This type of a binding protein cannot be identified by a widely used approach such as the peptide affinity column.	[ "32" ]	114	7,187	0	false	This type of a binding protein cannot be identified by a widely used approach such as the peptide affinity column.	[]	This type of a binding protein cannot be identified by a widely used approach such as the peptide affinity column.	true	true	true	true	true	1,164
4	DISCUSSION	1	2	[ "b2", "b50" ]	16,855,292	pmid-11988475\|pmid-3048701	Histone tails are involved in folding higher-order chromatin structures (2).	[ "2", "50" ]	76	7,188	1	false	Histone tails are involved in folding higher-order chromatin structures.	[ "2" ]	Histone tails are involved in folding higher-order chromatin structures.	true	true	true	true	true	1,165
4	DISCUSSION	1	2	[ "b2", "b50" ]	16,855,292	pmid-11988475\|pmid-3048701	In the tail mutant strain, the chromatin structures may be altered at the higher-order folding level.	[ "2", "50" ]	101	7,189	0	false	In the tail mutant strain, the chromatin structures may be altered at the higher-order folding level.	[]	In the tail mutant strain, the chromatin structures may be altered at the higher-order folding level.	true	true	true	true	true	1,165
4	DISCUSSION	1	50	[ "b2", "b50" ]	16,855,292	pmid-11988475\|pmid-3048701	The MNase digestion produced a nucleosomal ladder in the H4-tailΔ, and its MNase sensitivity was higher than that of the WT, suggesting a structural alteration beyond the nucleosomal level by the tail-deletion (50).	[ "2", "50" ]	215	7,190	1	false	The MNase digestion produced a nucleosomal ladder in the H4-tailΔ, and its MNase sensitivity was higher than that of the WT, suggesting a structural alteration beyond the nucleosomal level by the tail-deletion.	[ "50" ]	The MNase digestion produced a nucleosomal ladder in the H4-tailΔ, and its MNase sensitivity was higher than that of the WT, suggesting a structural alteration beyond the nucleosomal level by the tail-deletion.	true	true	true	true	true	1,165
4	DISCUSSION	1	2	[ "b2", "b50" ]	16,855,292	pmid-11988475\|pmid-3048701	If there is a protein that recognizes the higher-order chromatin structure, then the amount of this protein would also be decreased in our screening.	[ "2", "50" ]	149	7,191	0	false	If there is a protein that recognizes the higher-order chromatin structure, then the amount of this protein would also be decreased in our screening.	[]	If there is a protein that recognizes the higher-order chromatin structure, then the amount of this protein would also be decreased in our screening.	true	true	true	true	true	1,165
4	DISCUSSION	1	2	[ "b2", "b50" ]	16,855,292	pmid-11988475\|pmid-3048701	Such a protein may be included among our candidate proteins.	[ "2", "50" ]	60	7,192	0	false	Such a protein may be included among our candidate proteins.	[]	Such a protein may be included among our candidate proteins.	true	true	true	true	true	1,165
4	DISCUSSION	1	2	[ "b2", "b50" ]	16,855,292	pmid-11988475\|pmid-3048701	We cannot examine this possibility at present, as there is no biochemical method to assess the folding of higher-order chromatin in vivo.	[ "2", "50" ]	137	7,193	0	false	We cannot examine this possibility at present, as there is no biochemical method to assess the folding of higher-order chromatin in vivo.	[]	We cannot examine this possibility at present, as there is no biochemical method to assess the folding of higher-order chromatin in vivo.	true	true	true	true	true	1,165
5	DISCUSSION	1	56	[ "b56", "b57", "b59", "b17" ]	16,855,292	pmid-11206068\|pmid-8675011\|pmid-12628926\|pmid-15960974	The WD40-repeat is defined by a sequence repeat of ∼40 amino acids, typically beginning with a glycine–histidine pair and ending with a tryptophan–aspartic acid pair.	[ "56", "57", "59", "17" ]	166	7,194	0	false	The WD40-repeat is defined by a sequence repeat of ∼40 amino acids, typically beginning with a glycine–histidine pair and ending with a tryptophan–aspartic acid pair.	[]	The WD40-repeat is defined by a sequence repeat of ∼40 amino acids, typically beginning with a glycine–histidine pair and ending with a tryptophan–aspartic acid pair.	true	true	true	true	true	1,166
5	DISCUSSION	1	56	[ "b56", "b57", "b59", "b17" ]	16,855,292	pmid-11206068\|pmid-8675011\|pmid-12628926\|pmid-15960974	This motif is shared among over 30 functional families, which are involved in signal transduction, mRNA synthesis, RNA splicing, vascular trafficking, cytoskeletal assembly, control of transcription initiation complex assembly and a chromatin-regulated complex (56).	[ "56", "57", "59", "17" ]	266	7,195	1	false	This motif is shared among over 30 functional families, which are involved in signal transduction, mRNA synthesis, RNA splicing, vascular trafficking, cytoskeletal assembly, control of transcription initiation complex assembly and a chromatin-regulated complex.	[ "56" ]	This motif is shared among over 30 functional families, which are involved in signal transduction, mRNA synthesis, RNA splicing, vascular trafficking, cytoskeletal assembly, control of transcription initiation complex assembly and a chromatin-regulated complex.	true	true	true	true	true	1,166
5	DISCUSSION	1	56	[ "b56", "b57", "b59", "b17" ]	16,855,292	pmid-11206068\|pmid-8675011\|pmid-12628926\|pmid-15960974	Among the chromatin-regulated proteins, several WD40-repeat proteins are known as histone-tail binding proteins.	[ "56", "57", "59", "17" ]	112	7,196	0	false	Among the chromatin-regulated proteins, several WD40-repeat proteins are known as histone-tail binding proteins.	[]	Among the chromatin-regulated proteins, several WD40-repeat proteins are known as histone-tail binding proteins.	true	true	true	true	true	1,166
5	DISCUSSION	1	56	[ "b56", "b57", "b59", "b17" ]	16,855,292	pmid-11206068\|pmid-8675011\|pmid-12628926\|pmid-15960974	For example, the transcriptional repressor proteins Tup1p, Groucho and transducin beta-like protein (TBL1)/TBL1-related protein (TBLR1) associate with a histone-tail via a domain other than the WD40-repeat domain (57–59).	[ "56", "57", "59", "17" ]	221	7,197	0	false	For example, the transcriptional repressor proteins Tup1p, Groucho and transducin beta-like protein (TBL1)/TBL1-related protein (TBLR1) associate with a histone-tail via a domain other than the WD40-repeat domain.	[ "57–59" ]	For example, the transcriptional repressor proteins Tup1p, Groucho and transducin beta-like protein (TBL1)/TBL1-related protein (TBLR1) associate with a histone-tail via a domain other than the WD40-repeat domain.	true	true	true	true	true	1,166
5	DISCUSSION	1	17	[ "b56", "b57", "b59", "b17" ]	16,855,292	pmid-11206068\|pmid-8675011\|pmid-12628926\|pmid-15960974	WDR5, a common component of three H3 K4 methyltransferase complexes (the mixed-lineage leukemia gene (MLL)1, MLL2 and hSet1), directly associates with a histone H3-tail di- and trimethylated at K4 via the WD40-repeat domain itself (17).	[ "56", "57", "59", "17" ]	236	7,198	1	false	WDR5, a common component of three H3 K4 methyltransferase complexes (the mixed-lineage leukemia gene (MLL)1, MLL2 and hSet1), directly associates with a histone H3-tail di- and trimethylated at K4 via the WD40-repeat domain itself.	[ "17" ]	WDR5, a common component of three H3 K4 methyltransferase complexes (the mixed-lineage leukemia gene (MLL)1, MLL2 and hSet1), directly associates with a histone H3-tail di- and trimethylated at K4 via the WD40-repeat domain itself.	true	true	true	true	true	1,166
5	DISCUSSION	1	56	[ "b56", "b57", "b59", "b17" ]	16,855,292	pmid-11206068\|pmid-8675011\|pmid-12628926\|pmid-15960974	We plan to investigate whether the three candidates (Pwp1p, Tif34p, and YDL156Wp) interact with the H4-tail directly or indirectly.	[ "56", "57", "59", "17" ]	131	7,199	0	false	We plan to investigate whether the three candidates interact with the H4-tail directly or indirectly.	[ "Pwp1p, Tif34p, and YDL156Wp" ]	We plan to investigate whether the three candidates interact with the H4-tail directly or indirectly.	true	true	true	true	true	1,166

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