Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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 Community
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2
INTRODUCTION
1
8
[ "b8", "b3", "b4", "b9", "b7", "b10", "b13", "b2", "b14", "b15", "b16", "b17" ]
17,090,584
pmid-16473542|pmid-16567016|pmid-16600909|pmid-15469823|pmid-16081530|pmid-15851028|pmid-16131612|pmid-15630419|pmid-15692015|pmid-16839878|pmid-15242620|pmid-16839879|pmid-15924141|pmid-16473542|pmid-16839878|pmid-15924141|pmid-16741077|pmid-12650452|pmid-15024409
DCL4 and DCL3 process such dsRNA substrates to produce the predominant siRNA size classes, 21 and 24 nt, respectively (3,4).
[ "8", "3", "4", "9", "7", "10", "13", "2", "14", "15", "16", "17" ]
124
9,500
0
false
DCL4 and DCL3 process such dsRNA substrates to produce the predominant siRNA size classes, 21 and 24 nt, respectively.
[ "3,4" ]
DCL4 and DCL3 process such dsRNA substrates to produce the predominant siRNA size classes, 21 and 24 nt, respectively.
true
true
true
true
true
1,509
2
INTRODUCTION
1
9
[ "b8", "b3", "b4", "b9", "b7", "b10", "b13", "b2", "b14", "b15", "b16", "b17" ]
17,090,584
pmid-16473542|pmid-16567016|pmid-16600909|pmid-15469823|pmid-16081530|pmid-15851028|pmid-16131612|pmid-15630419|pmid-15692015|pmid-16839878|pmid-15242620|pmid-16839879|pmid-15924141|pmid-16473542|pmid-16839878|pmid-15924141|pmid-16741077|pmid-12650452|pmid-15024409
Like miRNAs, certain DCL4-dependent endogenous 21 nt siRNAs silence their target genes in trans (9).
[ "8", "3", "4", "9", "7", "10", "13", "2", "14", "15", "16", "17" ]
100
9,501
1
false
Like miRNAs, certain DCL4-dependent endogenous 21 nt siRNAs silence their target genes in trans.
[ "9" ]
Like miRNAs, certain DCL4-dependent endogenous 21 nt siRNAs silence their target genes in trans.
true
true
true
true
true
1,509
2
INTRODUCTION
1
7
[ "b8", "b3", "b4", "b9", "b7", "b10", "b13", "b2", "b14", "b15", "b16", "b17" ]
17,090,584
pmid-16473542|pmid-16567016|pmid-16600909|pmid-15469823|pmid-16081530|pmid-15851028|pmid-16131612|pmid-15630419|pmid-15692015|pmid-16839878|pmid-15242620|pmid-16839879|pmid-15924141|pmid-16473542|pmid-16839878|pmid-15924141|pmid-16741077|pmid-12650452|pmid-15024409
These trans-acting siRNAs (ta-siRNAs) associate with AGO-RISC (7) and target complementary mRNAs for cleavage and degradation.
[ "8", "3", "4", "9", "7", "10", "13", "2", "14", "15", "16", "17" ]
126
9,502
1
false
These trans-acting siRNAs (ta-siRNAs) associate with AGO-RISC and target complementary mRNAs for cleavage and degradation.
[ "7" ]
These trans-acting siRNAs (ta-siRNAs) associate with AGO-RISC and target complementary mRNAs for cleavage and degradation.
true
true
true
true
true
1,509
2
INTRODUCTION
1
8
[ "b8", "b3", "b4", "b9", "b7", "b10", "b13", "b2", "b14", "b15", "b16", "b17" ]
17,090,584
pmid-16473542|pmid-16567016|pmid-16600909|pmid-15469823|pmid-16081530|pmid-15851028|pmid-16131612|pmid-15630419|pmid-15692015|pmid-16839878|pmid-15242620|pmid-16839879|pmid-15924141|pmid-16473542|pmid-16839878|pmid-15924141|pmid-16741077|pmid-12650452|pmid-15024409
The biogenesis of ta-siRNAs depends on miRNA-directed cleavage of non-coding TAS transcripts to generate products that are converted by RDR6 into dsRNA substrates for DCL4 (10–13).
[ "8", "3", "4", "9", "7", "10", "13", "2", "14", "15", "16", "17" ]
180
9,503
0
false
The biogenesis of ta-siRNAs depends on miRNA-directed cleavage of non-coding TAS transcripts to generate products that are converted by RDR6 into dsRNA substrates for DCL4.
[ "10–13" ]
The biogenesis of ta-siRNAs depends on miRNA-directed cleavage of non-coding TAS transcripts to generate products that are converted by RDR6 into dsRNA substrates for DCL4.
true
true
true
true
true
1,509
2
INTRODUCTION
1
2
[ "b8", "b3", "b4", "b9", "b7", "b10", "b13", "b2", "b14", "b15", "b16", "b17" ]
17,090,584
pmid-16473542|pmid-16567016|pmid-16600909|pmid-15469823|pmid-16081530|pmid-15851028|pmid-16131612|pmid-15630419|pmid-15692015|pmid-16839878|pmid-15242620|pmid-16839879|pmid-15924141|pmid-16473542|pmid-16839878|pmid-15924141|pmid-16741077|pmid-12650452|pmid-15024409
The DCL3-dependent 24 nt siRNAs, mostly derived from repetitive DNA loci (repeat-associated siRNAs; ra-siRNA), likely mediate the establishment and maintenance of chromatin states through RNA-dependent DNA methylation and histone modification (2).
[ "8", "3", "4", "9", "7", "10", "13", "2", "14", "15", "16", "17" ]
247
9,504
1
false
The DCL3-dependent 24 nt siRNAs, mostly derived from repetitive DNA loci (repeat-associated siRNAs; ra-siRNA), likely mediate the establishment and maintenance of chromatin states through RNA-dependent DNA methylation and histone modification.
[ "2" ]
The DCL3-dependent 24 nt siRNAs, mostly derived from repetitive DNA loci (repeat-associated siRNAs; ra-siRNA), likely mediate the establishment and maintenance of chromatin states through RNA-dependent DNA methylation and histone modification.
true
true
true
true
true
1,509
2
INTRODUCTION
1
8
[ "b8", "b3", "b4", "b9", "b7", "b10", "b13", "b2", "b14", "b15", "b16", "b17" ]
17,090,584
pmid-16473542|pmid-16567016|pmid-16600909|pmid-15469823|pmid-16081530|pmid-15851028|pmid-16131612|pmid-15630419|pmid-15692015|pmid-16839878|pmid-15242620|pmid-16839879|pmid-15924141|pmid-16473542|pmid-16839878|pmid-15924141|pmid-16741077|pmid-12650452|pmid-15024409
The biogenesis of ra-siRNAs requires the RNA polymerases POL IVa and RDR2 (14,15).
[ "8", "3", "4", "9", "7", "10", "13", "2", "14", "15", "16", "17" ]
82
9,505
0
false
The biogenesis of ra-siRNAs requires the RNA polymerases POL IVa and RDR2.
[ "14,15" ]
The biogenesis of ra-siRNAs requires the RNA polymerases POL IVa and RDR2.
true
true
true
true
true
1,509
2
INTRODUCTION
1
8
[ "b8", "b3", "b4", "b9", "b7", "b10", "b13", "b2", "b14", "b15", "b16", "b17" ]
17,090,584
pmid-16473542|pmid-16567016|pmid-16600909|pmid-15469823|pmid-16081530|pmid-15851028|pmid-16131612|pmid-15630419|pmid-15692015|pmid-16839878|pmid-15242620|pmid-16839879|pmid-15924141|pmid-16473542|pmid-16839878|pmid-15924141|pmid-16741077|pmid-12650452|pmid-15024409
Another argonaute protein, AGO4, is involved in the ra-siRNA pathway, probably as the effector component of the putative RNA-induced transcriptional silencing complex (16,17).
[ "8", "3", "4", "9", "7", "10", "13", "2", "14", "15", "16", "17" ]
175
9,506
0
false
Another argonaute protein, AGO4, is involved in the ra-siRNA pathway, probably as the effector component of the putative RNA-induced transcriptional silencing complex.
[ "16,17" ]
Another argonaute protein, AGO4, is involved in the ra-siRNA pathway, probably as the effector component of the putative RNA-induced transcriptional silencing complex.
true
true
true
true
true
1,509
3
INTRODUCTION
1
21
[ "b18", "b20", "b21" ]
17,090,584
pmid-15705854|pmid-16449203|pmid-16111943|pmid-9557705|pmid-15118162|pmid-15931223
A subsequent step in the biogenesis of all plant sRNAs is methylation of their 3′-terminal nucleotide at the 2′-hydroxyl group by the methyltransferase HEN1 (18–20), which protects them from degradation and oligouridylation (21).
[ "18", "20", "21" ]
229
9,507
1
false
A subsequent step in the biogenesis of all plant sRNAs is methylation of their 3′-terminal nucleotide at the 2′-hydroxyl group by the methyltransferase HEN1, which protects them from degradation and oligouridylation.
[ "18–20", "21" ]
A subsequent step in the biogenesis of all plant sRNAs is methylation of their 3′-terminal nucleotide at the 2′-hydroxyl group by the methyltransferase HEN1, which protects them from degradation and oligouridylation.
true
true
true
true
true
1,510
4
INTRODUCTION
1
22
[ "b22", "b23", "b24", "b25", "b25", "b26", "b26" ]
17,090,584
pmid-9303318|pmid-9335491|pmid-16273107|pmid-12941703|pmid-12941703|pmid-16040651|pmid-16040651
RNA silencing that affects transgene expression can spread locally cell-to-cell and systemically via vascular tissues throughout the plant (22,23).
[ "22", "23", "24", "25", "25", "26", "26" ]
147
9,508
0
false
RNA silencing that affects transgene expression can spread locally cell-to-cell and systemically via vascular tissues throughout the plant.
[ "22,23" ]
RNA silencing that affects transgene expression can spread locally cell-to-cell and systemically via vascular tissues throughout the plant.
true
true
true
true
true
1,511
4
INTRODUCTION
1
24
[ "b22", "b23", "b24", "b25", "b25", "b26", "b26" ]
17,090,584
pmid-9303318|pmid-9335491|pmid-16273107|pmid-12941703|pmid-12941703|pmid-16040651|pmid-16040651
Although the nature of the sequence-specific silencing signal is unknown, cell-to-cell spread of transgene silencing is correlated with DCL4-generated 21 nt siRNAs (24).
[ "22", "23", "24", "25", "25", "26", "26" ]
169
9,509
1
false
Although the nature of the sequence-specific silencing signal is unknown, cell-to-cell spread of transgene silencing is correlated with DCL4-generated 21 nt siRNAs.
[ "24" ]
Although the nature of the sequence-specific silencing signal is unknown, cell-to-cell spread of transgene silencing is correlated with DCL4-generated 21 nt siRNAs.
true
true
true
true
true
1,511
4
INTRODUCTION
1
25
[ "b22", "b23", "b24", "b25", "b25", "b26", "b26" ]
17,090,584
pmid-9303318|pmid-9335491|pmid-16273107|pmid-12941703|pmid-12941703|pmid-16040651|pmid-16040651
Interestingly, longer-range cell-to-cell movement of transgene silencing requires RDR6 (25), which is normally coupled to DCL4 for the biogenesis of 21 nt ta-siRNAs.
[ "22", "23", "24", "25", "25", "26", "26" ]
165
9,510
1
false
Interestingly, longer-range cell-to-cell movement of transgene silencing requires RDR6, which is normally coupled to DCL4 for the biogenesis of 21 nt ta-siRNAs.
[ "25" ]
Interestingly, longer-range cell-to-cell movement of transgene silencing requires RDR6, which is normally coupled to DCL4 for the biogenesis of 21 nt ta-siRNAs.
true
true
true
true
true
1,511
4
INTRODUCTION
1
25
[ "b22", "b23", "b24", "b25", "b25", "b26", "b26" ]
17,090,584
pmid-9303318|pmid-9335491|pmid-16273107|pmid-12941703|pmid-12941703|pmid-16040651|pmid-16040651
It is speculated that RDR6 is involved in a relay amplification of the silencing signal (25).
[ "22", "23", "24", "25", "25", "26", "26" ]
93
9,511
1
false
It is speculated that RDR6 is involved in a relay amplification of the silencing signal.
[ "25" ]
It is speculated that RDR6 is involved in a relay amplification of the silencing signal.
true
true
true
true
true
1,511
4
INTRODUCTION
1
26
[ "b22", "b23", "b24", "b25", "b25", "b26", "b26" ]
17,090,584
pmid-9303318|pmid-9335491|pmid-16273107|pmid-12941703|pmid-12941703|pmid-16040651|pmid-16040651
RDR6 was also implicated in systemic transgene silencing (26).
[ "22", "23", "24", "25", "25", "26", "26" ]
62
9,512
1
false
RDR6 was also implicated in systemic transgene silencing.
[ "26" ]
RDR6 was also implicated in systemic transgene silencing.
true
true
true
true
true
1,511
4
INTRODUCTION
1
26
[ "b22", "b23", "b24", "b25", "b25", "b26", "b26" ]
17,090,584
pmid-9303318|pmid-9335491|pmid-16273107|pmid-12941703|pmid-12941703|pmid-16040651|pmid-16040651
The spread of the silencing signal is a potential component of plant defense against ongoing virus infections, especially for protection of the shoot apical meristem (26).
[ "22", "23", "24", "25", "25", "26", "26" ]
171
9,513
1
false
The spread of the silencing signal is a potential component of plant defense against ongoing virus infections, especially for protection of the shoot apical meristem.
[ "26" ]
The spread of the silencing signal is a potential component of plant defense against ongoing virus infections, especially for protection of the shoot apical meristem.
true
true
true
true
true
1,511
5
INTRODUCTION
1
27
[ "b27", "b28", "b31", "b19", "b32", "b29", "b31", "b19" ]
17,090,584
pmid-15703763|pmid-10542148|pmid-16810317|pmid-16421273|pmid-15220420|pmid-15024409|pmid-16810317|pmid-16421273|pmid-16377568|pmid-16699516
More generally, RNA silencing may represent an adaptive immune response of plants against viruses (27).
[ "27", "28", "31", "19", "32", "29", "31", "19" ]
103
9,514
1
false
More generally, RNA silencing may represent an adaptive immune response of plants against viruses.
[ "27" ]
More generally, RNA silencing may represent an adaptive immune response of plants against viruses.
true
true
true
true
true
1,512
5
INTRODUCTION
1
27
[ "b27", "b28", "b31", "b19", "b32", "b29", "b31", "b19" ]
17,090,584
pmid-15703763|pmid-10542148|pmid-16810317|pmid-16421273|pmid-15220420|pmid-15024409|pmid-16810317|pmid-16421273|pmid-16377568|pmid-16699516
sRNAs of distinct size-classes have been detected in plants infected with RNA viruses of different families (28–31) and DNA geminiviruses (19,32).
[ "27", "28", "31", "19", "32", "29", "31", "19" ]
146
9,515
0
false
sRNAs of distinct size-classes have been detected in plants infected with RNA viruses of different families and DNA geminiviruses.
[ "28–31", "19,32" ]
sRNAs of distinct size-classes have been detected in plants infected with RNA viruses of different families and DNA geminiviruses.
false
true
true
true
false
1,512
5
INTRODUCTION
1
27
[ "b27", "b28", "b31", "b19", "b32", "b29", "b31", "b19" ]
17,090,584
pmid-15703763|pmid-10542148|pmid-16810317|pmid-16421273|pmid-15220420|pmid-15024409|pmid-16810317|pmid-16421273|pmid-16377568|pmid-16699516
RNA viruses are mainly targeted by DCL4 and DCL2, which produce 21 and 22 nt viral siRNAs (29–31).
[ "27", "28", "31", "19", "32", "29", "31", "19" ]
98
9,516
0
false
RNA viruses are mainly targeted by DCL4 and DCL2, which produce 21 and 22 nt viral siRNAs.
[ "29–31" ]
RNA viruses are mainly targeted by DCL4 and DCL2, which produce 21 and 22 nt viral siRNAs.
true
true
true
true
true
1,512
5
INTRODUCTION
1
19
[ "b27", "b28", "b31", "b19", "b32", "b29", "b31", "b19" ]
17,090,584
pmid-15703763|pmid-10542148|pmid-16810317|pmid-16421273|pmid-15220420|pmid-15024409|pmid-16810317|pmid-16421273|pmid-16377568|pmid-16699516
Our previous work implicated DCL2 and DCL3 in production of 22 and 24 nt geminiviral siRNAs, respectively, and an additional DCL activity producing 21 nt geminiviral siRNAs (19).
[ "27", "28", "31", "19", "32", "29", "31", "19" ]
178
9,517
1
false
Our previous work implicated DCL2 and DCL3 in production of 22 and 24 nt geminiviral siRNAs, respectively, and an additional DCL activity producing 21 nt geminiviral siRNAs.
[ "19" ]
Our previous work implicated DCL2 and DCL3 in production of 22 and 24 nt geminiviral siRNAs, respectively, and an additional DCL activity producing 21 nt geminiviral siRNAs.
true
true
true
true
true
1,512
5
INTRODUCTION
1
27
[ "b27", "b28", "b31", "b19", "b32", "b29", "b31", "b19" ]
17,090,584
pmid-15703763|pmid-10542148|pmid-16810317|pmid-16421273|pmid-15220420|pmid-15024409|pmid-16810317|pmid-16421273|pmid-16377568|pmid-16699516
Neither the function of these geminivirus-derived siRNAs, nor siRNA biogenesis for other DNA viruses has been examined using the genetic resources acquired from the study of endogenous sRNA species.
[ "27", "28", "31", "19", "32", "29", "31", "19" ]
198
9,518
0
false
Neither the function of these geminivirus-derived siRNAs, nor siRNA biogenesis for other DNA viruses has been examined using the genetic resources acquired from the study of endogenous sRNA species.
[]
Neither the function of these geminivirus-derived siRNAs, nor siRNA biogenesis for other DNA viruses has been examined using the genetic resources acquired from the study of endogenous sRNA species.
true
true
true
true
true
1,512
6
INTRODUCTION
1
27
[ "b27", "b27", "b33", "b30", "b27", "b34" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
Viruses modified to carry a sequence homologous to a host-encoded gene are informative tools for studying siRNA-dependent silencing.
[ "27", "27", "33", "30", "27", "34" ]
132
9,519
0
false
Viruses modified to carry a sequence homologous to a host-encoded gene are informative tools for studying siRNA-dependent silencing.
[]
Viruses modified to carry a sequence homologous to a host-encoded gene are informative tools for studying siRNA-dependent silencing.
true
true
true
true
true
1,513
6
INTRODUCTION
1
27
[ "b27", "b27", "b33", "b30", "b27", "b34" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
Such constructs can trigger silencing of the homologous gene at both post-transcriptional and transcriptional levels (27).
[ "27", "27", "33", "30", "27", "34" ]
122
9,520
1
false
Such constructs can trigger silencing of the homologous gene at both post-transcriptional and transcriptional levels.
[ "27" ]
Such constructs can trigger silencing of the homologous gene at both post-transcriptional and transcriptional levels.
true
true
true
true
true
1,513
6
INTRODUCTION
1
27
[ "b27", "b27", "b33", "b30", "b27", "b34" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
This phenomenon is called virus induced gene silencing (VIGS).
[ "27", "27", "33", "30", "27", "34" ]
62
9,521
0
false
This phenomenon is called virus induced gene silencing (VIGS).
[]
This phenomenon is called virus induced gene silencing (VIGS).
true
true
true
true
true
1,513
6
INTRODUCTION
1
27
[ "b27", "b27", "b33", "b30", "b27", "b34" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
RDR6 and its cofactor SGS3 are important for VIGS triggered by both RNA virus (RNA-VIGS) (27) and DNA geminivirus vectors (DNA-VIGS) (33).
[ "27", "27", "33", "30", "27", "34" ]
138
9,522
1
false
RDR6 and its cofactor SGS3 are important for VIGS triggered by both RNA virus (RNA-VIGS) and DNA geminivirus vectors (DNA-VIGS).
[ "27", "33" ]
RDR6 and its cofactor SGS3 are important for VIGS triggered by both RNA virus (RNA-VIGS) and DNA geminivirus vectors (DNA-VIGS).
true
true
true
true
true
1,513
6
INTRODUCTION
1
30
[ "b27", "b27", "b33", "b30", "b27", "b34" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
Recently, DCL4- and DCL2-dependent viral siRNAs have been implicated in RNA-VIGS (30).
[ "27", "27", "33", "30", "27", "34" ]
86
9,523
1
false
Recently, DCL4- and DCL2-dependent viral siRNAs have been implicated in RNA-VIGS.
[ "30" ]
Recently, DCL4- and DCL2-dependent viral siRNAs have been implicated in RNA-VIGS.
true
true
true
true
true
1,513
6
INTRODUCTION
1
27
[ "b27", "b27", "b33", "b30", "b27", "b34" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
Similar to transgene-induced silencing, VIGS can spread cell-to-cell and systemically (27).
[ "27", "27", "33", "30", "27", "34" ]
91
9,524
1
false
Similar to transgene-induced silencing, VIGS can spread cell-to-cell and systemically.
[ "27" ]
Similar to transgene-induced silencing, VIGS can spread cell-to-cell and systemically.
true
true
true
true
true
1,513
6
INTRODUCTION
1
27
[ "b27", "b27", "b33", "b30", "b27", "b34" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
Peele et al.
[ "27", "27", "33", "30", "27", "34" ]
12
9,525
0
false
Peele et al.
[]
Peele et al.
true
true
true
true
true
1,513
6
INTRODUCTION
1
34
[ "b27", "b27", "b33", "b30", "b27", "b34" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
(34) revealed virus-independent spreading of DNA-VIGS from geminivirus-infected tissues to the shoot apical meristem, from which viruses are normally excluded.
[ "27", "27", "33", "30", "27", "34" ]
159
9,526
1
false
revealed virus-independent spreading of DNA-VIGS from geminivirus-infected tissues to the shoot apical meristem, from which viruses are normally excluded.
[ "34" ]
revealed virus-independent spreading of DNA-VIGS from geminivirus-infected tissues to the shoot apical meristem, from which viruses are normally excluded.
false
true
true
true
false
1,513
6
INTRODUCTION
1
27
[ "b27", "b27", "b33", "b30", "b27", "b34" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
The pathways mediating DNA-VIGS have not been thoroughly dissected; given the cytoplasmic and nuclear steps in replication of DNA viruses, they are ideal for studying virus-induced RNA silencing in its entirety.
[ "27", "27", "33", "30", "27", "34" ]
211
9,527
0
false
The pathways mediating DNA-VIGS have not been thoroughly dissected; given the cytoplasmic and nuclear steps in replication of DNA viruses, they are ideal for studying virus-induced RNA silencing in its entirety.
[]
The pathways mediating DNA-VIGS have not been thoroughly dissected; given the cytoplasmic and nuclear steps in replication of DNA viruses, they are ideal for studying virus-induced RNA silencing in its entirety.
true
true
true
true
true
1,513
6
INTRODUCTION
1
27
[ "b27", "b27", "b33", "b30", "b27", "b34" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
Furthermore, DNA viruses do not code for their own RDRs and are therefore useful for examining the role of host RDRs in different silencing processes.
[ "27", "27", "33", "30", "27", "34" ]
150
9,528
0
false
Furthermore, DNA viruses do not code for their own RDRs and are therefore useful for examining the role of host RDRs in different silencing processes.
[]
Furthermore, DNA viruses do not code for their own RDRs and are therefore useful for examining the role of host RDRs in different silencing processes.
true
true
true
true
true
1,513
7
INTRODUCTION
1
35
[ "b35", "b36", "b37", "b38" ]
17,090,584
pmid-16724105|pmid-16731914|pmid-14976549|pmid-15131083|pmid-15661355
Despite silencing-based responses to viral infection, plant viruses can still establish robust infection in susceptible hosts, in part by suppressing RNA silencing.
[ "35", "36", "37", "38" ]
164
9,529
0
false
Despite silencing-based responses to viral infection, plant viruses can still establish robust infection in susceptible hosts, in part by suppressing RNA silencing.
[]
Despite silencing-based responses to viral infection, plant viruses can still establish robust infection in susceptible hosts, in part by suppressing RNA silencing.
true
true
true
true
true
1,514
7
INTRODUCTION
1
35
[ "b35", "b36", "b37", "b38" ]
17,090,584
pmid-16724105|pmid-16731914|pmid-14976549|pmid-15131083|pmid-15661355
Plant viruses encode various suppressor proteins that do not share common features, although many of them bind short or long dsRNA (35,36).
[ "35", "36", "37", "38" ]
139
9,530
0
false
Plant viruses encode various suppressor proteins that do not share common features, although many of them bind short or long dsRNA.
[ "35,36" ]
Plant viruses encode various suppressor proteins that do not share common features, although many of them bind short or long dsRNA.
true
true
true
true
true
1,514
7
INTRODUCTION
1
37
[ "b35", "b36", "b37", "b38" ]
17,090,584
pmid-16724105|pmid-16731914|pmid-14976549|pmid-15131083|pmid-15661355
For example, the RNA tombusvirus-encoded suppressor P19 binds siRNA duplexes selectively, which might sequester them from the silencing process (37).
[ "35", "36", "37", "38" ]
149
9,531
1
false
For example, the RNA tombusvirus-encoded suppressor P19 binds siRNA duplexes selectively, which might sequester them from the silencing process.
[ "37" ]
For example, the RNA tombusvirus-encoded suppressor P19 binds siRNA duplexes selectively, which might sequester them from the silencing process.
true
true
true
true
true
1,514
7
INTRODUCTION
1
38
[ "b35", "b36", "b37", "b38" ]
17,090,584
pmid-16724105|pmid-16731914|pmid-14976549|pmid-15131083|pmid-15661355
Viral silencing suppressors can cause defects in endogenous silencing pathways when expressed from transgenes (38), possibly due to their dsRNA binding property.
[ "35", "36", "37", "38" ]
161
9,532
1
false
Viral silencing suppressors can cause defects in endogenous silencing pathways when expressed from transgenes, possibly due to their dsRNA binding property.
[ "38" ]
Viral silencing suppressors can cause defects in endogenous silencing pathways when expressed from transgenes, possibly due to their dsRNA binding property.
true
true
true
true
true
1,514
8
INTRODUCTION
1
39
[ "b39", "b40", "b41", "b42" ]
17,090,584
pmid-6628362|pmid-14512531|pmid-8616237|pmid-11967097
Here we describe genetic requirements for the biogenesis of 21, 22 and 24 nt siRNAs associated with DNA viruses of the geminivirus [Cabbage leaf curl virus (CaLCuV)] and the pararetrovirus
[ "39", "40", "41", "42" ]
188
9,533
0
false
Here we describe genetic requirements for the biogenesis of 21, 22 and 24 nt siRNAs associated with DNA viruses of the geminivirus [Cabbage leaf curl virus (CaLCuV)] and the pararetrovirus
[]
Here we describe genetic requirements for the biogenesis of 21, 22 and 24 nt siRNAs associated with DNA viruses of the geminivirus [Cabbage leaf curl virus (CaLCuV)] and the pararetrovirus
true
true
false
true
false
1,515
8
INTRODUCTION
1
39
[ "b39", "b40", "b41", "b42" ]
17,090,584
pmid-6628362|pmid-14512531|pmid-8616237|pmid-11967097
[Cauliflower mosaic virus (CaMV)] families, which form circular minichromosomes in the nucleus (39,40).
[ "39", "40", "41", "42" ]
103
9,534
0
false
[Cauliflower mosaic virus (CaMV)] families, which form circular minichromosomes in the nucleus.
[ "39,40" ]
[Cauliflower mosaic virus (CaMV)] families, which form circular minichromosomes in the nucleus.
false
false
true
true
false
1,515
8
INTRODUCTION
1
39
[ "b39", "b40", "b41", "b42" ]
17,090,584
pmid-6628362|pmid-14512531|pmid-8616237|pmid-11967097
We contrast this to the predominantly 21 nt siRNAs derived from a cytoplasmic RNA tobamovirus [Oilseed rape mosaic virus (ORMV)]
[ "39", "40", "41", "42" ]
128
9,535
0
false
We contrast this to the predominantly 21 nt siRNAs derived from a cytoplasmic RNA tobamovirus [Oilseed rape mosaic virus (ORMV)]
[]
We contrast this to the predominantly 21 nt siRNAs derived from a cytoplasmic RNA tobamovirus [Oilseed rape mosaic virus (ORMV)]
true
true
false
true
false
1,515
8
INTRODUCTION
1
39
[ "b39", "b40", "b41", "b42" ]
17,090,584
pmid-6628362|pmid-14512531|pmid-8616237|pmid-11967097
We show that the three viruses are differentially targeted by the four Arabidopsis DCLs producing specific size classes of viral siRNAs.
[ "39", "40", "41", "42" ]
136
9,536
0
false
We show that the three viruses are differentially targeted by the four Arabidopsis DCLs producing specific size classes of viral siRNAs.
[]
We show that the three viruses are differentially targeted by the four Arabidopsis DCLs producing specific size classes of viral siRNAs.
true
true
true
true
true
1,515
8
INTRODUCTION
1
42
[ "b39", "b40", "b41", "b42" ]
17,090,584
pmid-6628362|pmid-14512531|pmid-8616237|pmid-11967097
Using a geminivirus VIGS vector (42) and Arabidopsis silencing mutants we find the four DCLs to be partially redundant for DNA-VIGS targeting an endogenous mRNA.
[ "39", "40", "41", "42" ]
161
9,537
1
false
Using a geminivirus VIGS vector and Arabidopsis silencing mutants we find the four DCLs to be partially redundant for DNA-VIGS targeting an endogenous mRNA.
[ "42" ]
Using a geminivirus VIGS vector and Arabidopsis silencing mutants we find the four DCLs to be partially redundant for DNA-VIGS targeting an endogenous mRNA.
true
true
true
true
true
1,515
8
INTRODUCTION
1
39
[ "b39", "b40", "b41", "b42" ]
17,090,584
pmid-6628362|pmid-14512531|pmid-8616237|pmid-11967097
However, extensive VIGS in newly emerging tissues requires DCL4 in conjunction with RDR6 and HEN1.
[ "39", "40", "41", "42" ]
98
9,538
0
false
However, extensive VIGS in newly emerging tissues requires DCL4 in conjunction with RDR6 and HEN1.
[]
However, extensive VIGS in newly emerging tissues requires DCL4 in conjunction with RDR6 and HEN1.
true
true
true
true
true
1,515
8
INTRODUCTION
1
39
[ "b39", "b40", "b41", "b42" ]
17,090,584
pmid-6628362|pmid-14512531|pmid-8616237|pmid-11967097
As a derivative of this study with CaMV and ORMV, we also uncover two novel viral strategies of silencing suppression.
[ "39", "40", "41", "42" ]
118
9,539
0
false
As a derivative of this study with CaMV and ORMV, we also uncover two novel viral strategies of silencing suppression.
[]
As a derivative of this study with CaMV and ORMV, we also uncover two novel viral strategies of silencing suppression.
true
true
true
true
true
1,515
0
DISCUSSION
0
null
null
17,090,584
pmid-16212497|pmid-16600909
Our analysis of viral siRNAs in Arabidopsis RNA silencing mutants shows that both gemini- and pararetro-viruses—two families of nuclear DNA viruses—are targeted by all four DCL activities.
null
188
9,540
0
false
null
null
Our analysis of viral siRNAs in Arabidopsis RNA silencing mutants shows that both gemini- and pararetro-viruses—two families of nuclear DNA viruses—are targeted by all four DCL activities.
true
true
true
true
true
1,516
0
DISCUSSION
0
null
null
17,090,584
pmid-16212497|pmid-16600909
This process results in 21, 22 and 24 nt siRNA production from viral coding and non-coding regions, but the relative contributions of DCL4 and DCL1 differ between CaLCuV and CaMV.
null
179
9,541
0
false
null
null
This process results in 21, 22 and 24 nt siRNA production from viral coding and non-coding regions, but the relative contributions of DCL4 and DCL1 differ between CaLCuV and CaMV.
true
true
true
true
true
1,516
0
DISCUSSION
0
null
null
17,090,584
pmid-16212497|pmid-16600909
In contrast, the cytoplasmic tobamovirus ORMV is primarily targeted by DCL4, resulting in production of predominantly 21 nt viral siRNAs.
null
137
9,542
0
false
null
null
In contrast, the cytoplasmic tobamovirus ORMV is primarily targeted by DCL4, resulting in production of predominantly 21 nt viral siRNAs.
true
true
true
true
true
1,516
0
DISCUSSION
0
null
null
17,090,584
pmid-16212497|pmid-16600909
Thus, the three viruses are differentially targeted by subsets of the four plant DCLs.
null
86
9,543
0
false
null
null
Thus, the three viruses are differentially targeted by subsets of the four plant DCLs.
true
true
true
true
true
1,516
1
DISCUSSION
1
4
[ "b4", "b15", "b11", "b12" ]
17,090,584
pmid-15314213|pmid-16428603|pmid-16081530|pmid-16600909|pmid-16839878|pmid-16040244|pmid-16129836
We observed no significant contribution of the plant RNA polymerases RDR6, RDR2 or POL IVa to viral siRNA biogenesis.
[ "4", "15", "11", "12" ]
117
9,544
0
false
We observed no significant contribution of the plant RNA polymerases RDR6, RDR2 or POL IVa to viral siRNA biogenesis.
[]
We observed no significant contribution of the plant RNA polymerases RDR6, RDR2 or POL IVa to viral siRNA biogenesis.
true
true
true
true
true
1,517
1
DISCUSSION
1
4
[ "b4", "b15", "b11", "b12" ]
17,090,584
pmid-15314213|pmid-16428603|pmid-16081530|pmid-16600909|pmid-16839878|pmid-16040244|pmid-16129836
Endogenous 21 nt ta-siRNA biogenesis requires RDR6 to produce dsRNA for DCL4 and 24 nt ra-siRNA biogenesis requires POL IVa and RDR2 to produce dsRNA for DCL3 (4,15).
[ "4", "15", "11", "12" ]
166
9,545
0
false
Endogenous 21 nt ta-siRNA biogenesis requires RDR6 to produce dsRNA for DCL4 and 24 nt ra-siRNA biogenesis requires POL IVa and RDR2 to produce dsRNA for DCL3.
[ "4,15" ]
Endogenous 21 nt ta-siRNA biogenesis requires RDR6 to produce dsRNA for DCL4 and 24 nt ra-siRNA biogenesis requires POL IVa and RDR2 to produce dsRNA for DCL3.
true
true
true
true
true
1,517
1
DISCUSSION
1
4
[ "b4", "b15", "b11", "b12" ]
17,090,584
pmid-15314213|pmid-16428603|pmid-16081530|pmid-16600909|pmid-16839878|pmid-16040244|pmid-16129836
The equivalent size-classes of viral siRNAs accumulate in the same DCL-determined manner without utilizing the upstream part of the endogenous pathways.
[ "4", "15", "11", "12" ]
152
9,546
0
false
The equivalent size-classes of viral siRNAs accumulate in the same DCL-determined manner without utilizing the upstream part of the endogenous pathways.
[]
The equivalent size-classes of viral siRNAs accumulate in the same DCL-determined manner without utilizing the upstream part of the endogenous pathways.
true
true
true
true
true
1,517
1
DISCUSSION
1
4
[ "b4", "b15", "b11", "b12" ]
17,090,584
pmid-15314213|pmid-16428603|pmid-16081530|pmid-16600909|pmid-16839878|pmid-16040244|pmid-16129836
Taken together with the findings of Gasciolli et al.
[ "4", "15", "11", "12" ]
52
9,547
0
false
Taken together with the findings of Gasciolli et al.
[]
Taken together with the findings of Gasciolli et al.
true
true
true
true
true
1,517
1
DISCUSSION
1
4
[ "b4", "b15", "b11", "b12" ]
17,090,584
pmid-15314213|pmid-16428603|pmid-16081530|pmid-16600909|pmid-16839878|pmid-16040244|pmid-16129836
and Xie et al.
[ "4", "15", "11", "12" ]
14
9,548
0
false
and Xie et al.
[]
and Xie et al.
false
true
true
true
false
1,517
1
DISCUSSION
1
12
[ "b4", "b15", "b11", "b12" ]
17,090,584
pmid-15314213|pmid-16428603|pmid-16081530|pmid-16600909|pmid-16839878|pmid-16040244|pmid-16129836
(12), we conclude that Arabidopsis DCLs are versatile size-specific enzymes, acting on many different dsRNA substrates present in plant cells.
[ "4", "15", "11", "12" ]
142
9,549
1
false
, we conclude that Arabidopsis DCLs are versatile size-specific enzymes, acting on many different dsRNA substrates present in plant cells.
[ "12" ]
, we conclude that Arabidopsis DCLs are versatile size-specific enzymes, acting on many different dsRNA substrates present in plant cells.
false
false
true
true
false
1,517
2
DISCUSSION
1
47
[ "b47", "b8", "b15", "b47", "b30", "b48", "b29" ]
17,090,584
pmid-16473542|pmid-16567016|pmid-16600909|pmid-15469823|pmid-16081530|pmid-15851028|pmid-16131612|pmid-15630419|pmid-15692015|pmid-16839878|pmid-15242620|pmid-16839879|pmid-15924141|pmid-16473542|pmid-16839878|pmid-15924141|pmid-16741077|pmid-12650452|pmid-15024409
Our results do not exclude involvement of POL IVb (47), or RDRs 1, 3a, 3b and 3c (8) in viral siRNA production.
[ "47", "8", "15", "47", "30", "48", "29" ]
111
9,550
1
false
Our results do not exclude involvement of POL IVb, or RDRs 1, 3a, 3b and 3c in viral siRNA production.
[ "47", "8" ]
Our results do not exclude involvement of POL IVb, or RDRs 1, 3a, 3b and 3c in viral siRNA production.
true
true
true
true
true
1,518
2
DISCUSSION
1
47
[ "b47", "b8", "b15", "b47", "b30", "b48", "b29" ]
17,090,584
pmid-16473542|pmid-16567016|pmid-16600909|pmid-15469823|pmid-16081530|pmid-15851028|pmid-16131612|pmid-15630419|pmid-15692015|pmid-16839878|pmid-15242620|pmid-16839879|pmid-15924141|pmid-16473542|pmid-16839878|pmid-15924141|pmid-16741077|pmid-12650452|pmid-15024409
However, POL IVb appears to be involved in maintaining heterochromatin at certain genomic repeats rather than ra-siRNA biogenesis (15,47).
[ "47", "8", "15", "47", "30", "48", "29" ]
138
9,551
0
false
However, POL IVb appears to be involved in maintaining heterochromatin at certain genomic repeats rather than ra-siRNA biogenesis.
[ "15,47" ]
However, POL IVb appears to be involved in maintaining heterochromatin at certain genomic repeats rather than ra-siRNA biogenesis.
true
true
true
true
true
1,518
2
DISCUSSION
1
29
[ "b47", "b8", "b15", "b47", "b30", "b48", "b29" ]
17,090,584
pmid-16473542|pmid-16567016|pmid-16600909|pmid-15469823|pmid-16081530|pmid-15851028|pmid-16131612|pmid-15630419|pmid-15692015|pmid-16839878|pmid-15242620|pmid-16839879|pmid-15924141|pmid-16473542|pmid-16839878|pmid-15924141|pmid-16741077|pmid-12650452|pmid-15024409
RDR1, although inducible by RNA viruses, is not required for the biogenesis of siRNAs derived from RNA viruses (30,48), the two DNA viruses (our unpublished data) or any endogenous loci tested so far (29).
[ "47", "8", "15", "47", "30", "48", "29" ]
205
9,552
1
false
RDR1, although inducible by RNA viruses, is not required for the biogenesis of siRNAs derived from RNA viruses, the two DNA viruses (our unpublished data) or any endogenous loci tested so far.
[ "30,48", "29" ]
RDR1, although inducible by RNA viruses, is not required for the biogenesis of siRNAs derived from RNA viruses, the two DNA viruses (our unpublished data) or any endogenous loci tested so far.
true
true
true
true
true
1,518
2
DISCUSSION
1
47
[ "b47", "b8", "b15", "b47", "b30", "b48", "b29" ]
17,090,584
pmid-16473542|pmid-16567016|pmid-16600909|pmid-15469823|pmid-16081530|pmid-15851028|pmid-16131612|pmid-15630419|pmid-15692015|pmid-16839878|pmid-15242620|pmid-16839879|pmid-15924141|pmid-16473542|pmid-16839878|pmid-15924141|pmid-16741077|pmid-12650452|pmid-15024409
To date, there is no evidence that RDR3a/b/c have a function.
[ "47", "8", "15", "47", "30", "48", "29" ]
61
9,553
0
false
To date, there is no evidence that RDR3a/b/c have a function.
[]
To date, there is no evidence that RDR3a/b/c have a function.
true
true
true
true
true
1,518
3
DISCUSSION
1
46
[ "b46", "b49", "b50" ]
17,090,584
pmid-15705854|pmid-16449203|pmid-16111943|pmid-9557705|pmid-15118162|pmid-15931223
The three size-classes of DNA viral siRNAs detected here are probably produced from dsRNA rather than from hairpin precursors, since sense and antisense strands accumulate for each size class.
[ "46", "49", "50" ]
192
9,554
0
false
The three size-classes of DNA viral siRNAs detected here are probably produced from dsRNA rather than from hairpin precursors, since sense and antisense strands accumulate for each size class.
[]
The three size-classes of DNA viral siRNAs detected here are probably produced from dsRNA rather than from hairpin precursors, since sense and antisense strands accumulate for each size class.
true
true
true
true
true
1,519
3
DISCUSSION
1
46
[ "b46", "b49", "b50" ]
17,090,584
pmid-15705854|pmid-16449203|pmid-16111943|pmid-9557705|pmid-15118162|pmid-15931223
However, certain hairpin-like regions of viral transcripts might be recognized as quasi-miRNA precursors by DCL1.
[ "46", "49", "50" ]
113
9,555
0
false
However, certain hairpin-like regions of viral transcripts might be recognized as quasi-miRNA precursors by DCL1.
[]
However, certain hairpin-like regions of viral transcripts might be recognized as quasi-miRNA precursors by DCL1.
true
true
true
true
true
1,519
3
DISCUSSION
1
46
[ "b46", "b49", "b50" ]
17,090,584
pmid-15705854|pmid-16449203|pmid-16111943|pmid-9557705|pmid-15118162|pmid-15931223
Interestingly, two of the three CaMV regions we probed (L1 and L2) are part of a 450 nt long, branched stem–loop structure within the 35S RNA leader (46).
[ "46", "49", "50" ]
154
9,556
1
false
Interestingly, two of the three CaMV regions we probed (L1 and L2) are part of a 450 nt long, branched stem–loop structure within the 35S RNA leader.
[ "46" ]
Interestingly, two of the three CaMV regions we probed (L1 and L2) are part of a 450 nt long, branched stem–loop structure within the 35S RNA leader.
true
true
true
true
true
1,519
3
DISCUSSION
1
46
[ "b46", "b49", "b50" ]
17,090,584
pmid-15705854|pmid-16449203|pmid-16111943|pmid-9557705|pmid-15118162|pmid-15931223
Whether plant DNA viruses, like some of their animal counterparts (49,50), code for true miRNAs is still an open question.
[ "46", "49", "50" ]
122
9,557
0
false
Whether plant DNA viruses, like some of their animal counterparts, code for true miRNAs is still an open question.
[ "49,50" ]
Whether plant DNA viruses, like some of their animal counterparts, code for true miRNAs is still an open question.
true
true
true
true
true
1,519
4
DISCUSSION
0
null
null
17,090,584
pmid-9303318|pmid-9335491|pmid-16273107|pmid-12941703|pmid-12941703|pmid-16040651|pmid-16040651
Our results suggest that DCL1, thought to mainly process hairpins in the miRNA pathway, also processes long dsRNA.
null
114
9,558
0
false
null
null
Our results suggest that DCL1, thought to mainly process hairpins in the miRNA pathway, also processes long dsRNA.
true
true
true
true
true
1,520
4
DISCUSSION
0
null
null
17,090,584
pmid-9303318|pmid-9335491|pmid-16273107|pmid-12941703|pmid-12941703|pmid-16040651|pmid-16040651
We observed 21 nt siRNAs from CaLCuV in the triple mutant lacking DCL2, DCL3 and DCL4 (Figure 4C) and DCL1-dependent processing of certain CaMV dsRNAs to 21 nt siRNAs (Figure 3).
null
178
9,559
0
false
null
null
We observed 21 nt siRNAs from CaLCuV in the triple mutant lacking DCL2, DCL3 and DCL4 (Figure 4C) and DCL1-dependent processing of certain CaMV dsRNAs to 21 nt siRNAs (Figure 3).
true
true
true
true
true
1,520
4
DISCUSSION
0
null
null
17,090,584
pmid-9303318|pmid-9335491|pmid-16273107|pmid-12941703|pmid-12941703|pmid-16040651|pmid-16040651
For CaLCuV, DCL1-mediated processing of viral dsRNA is inefficient, because presumed intermediates accumulate in addition to 21 nt siRNAs in infected d2d3d4 plants.
null
164
9,560
0
false
null
null
For CaLCuV, DCL1-mediated processing of viral dsRNA is inefficient, because presumed intermediates accumulate in addition to 21 nt siRNAs in infected d2d3d4 plants.
true
true
true
true
true
1,520
4
DISCUSSION
0
null
null
17,090,584
pmid-9303318|pmid-9335491|pmid-16273107|pmid-12941703|pmid-12941703|pmid-16040651|pmid-16040651
We hypothesize that DCL1 evolved to excise miRNA/miRNA* duplexes from hairpins, and lacks the processivity required to efficiently digest long dsRNA.
null
149
9,561
0
false
null
null
We hypothesize that DCL1 evolved to excise miRNA/miRNA* duplexes from hairpins, and lacks the processivity required to efficiently digest long dsRNA.
true
true
true
true
true
1,520
4
DISCUSSION
0
null
null
17,090,584
pmid-9303318|pmid-9335491|pmid-16273107|pmid-12941703|pmid-12941703|pmid-16040651|pmid-16040651
Thus, one would expect DCL1 to be out-competed by DCL4 for siRNA production.
null
76
9,562
0
false
null
null
Thus, one would expect DCL1 to be out-competed by DCL4 for siRNA production.
true
true
true
true
true
1,520
5
DISCUSSION
1
51
[ "b51", "b52" ]
17,090,584
pmid-15703763|pmid-10542148|pmid-16810317|pmid-16421273|pmid-15220420|pmid-15024409|pmid-16810317|pmid-16421273|pmid-16377568|pmid-16699516
As mentioned above, DCL1-dependent viral siRNAs are not sufficient to mediate establishment of total DNA-VIGS in newly emerging leaves.
[ "51", "52" ]
135
9,563
0
false
As mentioned above, DCL1-dependent viral siRNAs are not sufficient to mediate establishment of total DNA-VIGS in newly emerging leaves.
[]
As mentioned above, DCL1-dependent viral siRNAs are not sufficient to mediate establishment of total DNA-VIGS in newly emerging leaves.
true
true
true
true
true
1,521
5
DISCUSSION
1
51
[ "b51", "b52" ]
17,090,584
pmid-15703763|pmid-10542148|pmid-16810317|pmid-16421273|pmid-15220420|pmid-15024409|pmid-16810317|pmid-16421273|pmid-16377568|pmid-16699516
This distinction from DCL4 products may be functionally important, because miRNAs produced by DCL1 are thought to act in a cell-autonomous manner to regulate plant development.
[ "51", "52" ]
176
9,564
0
false
This distinction from DCL4 products may be functionally important, because miRNAs produced by DCL1 are thought to act in a cell-autonomous manner to regulate plant development.
[]
This distinction from DCL4 products may be functionally important, because miRNAs produced by DCL1 are thought to act in a cell-autonomous manner to regulate plant development.
true
true
true
true
true
1,521
5
DISCUSSION
1
51
[ "b51", "b52" ]
17,090,584
pmid-15703763|pmid-10542148|pmid-16810317|pmid-16421273|pmid-15220420|pmid-15024409|pmid-16810317|pmid-16421273|pmid-16377568|pmid-16699516
Since involvement of DCL1 in endogenous siRNA production was recently reported (51,52), it would be interesting to test whether all such DCL1-dependent sRNAs act locally to the cells that produce them.
[ "51", "52" ]
201
9,565
0
false
Since involvement of DCL1 in endogenous siRNA production was recently reported, it would be interesting to test whether all such DCL1-dependent sRNAs act locally to the cells that produce them.
[ "51,52" ]
Since involvement of DCL1 in endogenous siRNA production was recently reported, it would be interesting to test whether all such DCL1-dependent sRNAs act locally to the cells that produce them.
true
true
true
true
true
1,521
6
DISCUSSION
1
53
[ "b53", "b54", "b54", "b55", "b56" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
While RNA viruses are obliged to produce sense and antisense copies of their genome to replicate, only sense transcripts are required for replication of DNA viruses.
[ "53", "54", "54", "55", "56" ]
165
9,566
0
false
While RNA viruses are obliged to produce sense and antisense copies of their genome to replicate, only sense transcripts are required for replication of DNA viruses.
[]
While RNA viruses are obliged to produce sense and antisense copies of their genome to replicate, only sense transcripts are required for replication of DNA viruses.
true
true
true
true
true
1,522
6
DISCUSSION
1
53
[ "b53", "b54", "b54", "b55", "b56" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
In contrast to RNA viruses, DNA viruses do not encode an RDR that could theoretically complement host deficiencies for silencing-related RDRs.
[ "53", "54", "54", "55", "56" ]
142
9,567
0
false
In contrast to RNA viruses, DNA viruses do not encode an RDR that could theoretically complement host deficiencies for silencing-related RDRs.
[]
In contrast to RNA viruses, DNA viruses do not encode an RDR that could theoretically complement host deficiencies for silencing-related RDRs.
true
true
true
true
true
1,522
6
DISCUSSION
1
53
[ "b53", "b54", "b54", "b55", "b56" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
We show that both gemini- and pararetrovirus infections give rise to sense and antisense transcripts, which might form dsRNA precursors for viral siRNAs.
[ "53", "54", "54", "55", "56" ]
153
9,568
0
false
We show that both gemini- and pararetrovirus infections give rise to sense and antisense transcripts, which might form dsRNA precursors for viral siRNAs.
[]
We show that both gemini- and pararetrovirus infections give rise to sense and antisense transcripts, which might form dsRNA precursors for viral siRNAs.
true
true
true
true
true
1,522
6
DISCUSSION
1
53
[ "b53", "b54", "b54", "b55", "b56" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
To account for their production without POL IV and RDR activities we propose that POL II-driven transcription on circular viral genomes could produce overlapping sense/antisense transcripts.
[ "53", "54", "54", "55", "56" ]
190
9,569
0
false
To account for their production without POL IV and RDR activities we propose that POL II-driven transcription on circular viral genomes could produce overlapping sense/antisense transcripts.
[]
To account for their production without POL IV and RDR activities we propose that POL II-driven transcription on circular viral genomes could produce overlapping sense/antisense transcripts.
true
true
true
true
true
1,522
6
DISCUSSION
1
53
[ "b53", "b54", "b54", "b55", "b56" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
Indeed, bidirectional POL II promoters in geminiviruses normally generate converging left- and rightward transcripts (53,54).
[ "53", "54", "54", "55", "56" ]
125
9,570
0
false
Indeed, bidirectional POL II promoters in geminiviruses normally generate converging left- and rightward transcripts.
[ "53,54" ]
Indeed, bidirectional POL II promoters in geminiviruses normally generate converging left- and rightward transcripts.
true
true
true
true
true
1,522
6
DISCUSSION
1
53
[ "b53", "b54", "b54", "b55", "b56" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
Thus, viral transcripts could extend beyond their overlapping polyadenylation signals prior to cleavage and polyadenylation.
[ "53", "54", "54", "55", "56" ]
124
9,571
0
false
Thus, viral transcripts could extend beyond their overlapping polyadenylation signals prior to cleavage and polyadenylation.
[]
Thus, viral transcripts could extend beyond their overlapping polyadenylation signals prior to cleavage and polyadenylation.
true
true
true
true
true
1,522
6
DISCUSSION
1
54
[ "b53", "b54", "b54", "b55", "b56" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
Degradation products of read-through transcripts have been detected for the geminiviral promoter region (54).
[ "53", "54", "54", "55", "56" ]
109
9,572
1
false
Degradation products of read-through transcripts have been detected for the geminiviral promoter region.
[ "54" ]
Degradation products of read-through transcripts have been detected for the geminiviral promoter region.
true
true
true
true
true
1,522
6
DISCUSSION
1
55
[ "b53", "b54", "b54", "b55", "b56" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
No bi-directional transcription has been reported for pararetroviruses, but we speculate that the strong CaMV enhancer of the 35S and 19S RNA promoters (55) can also drive POL II transcription in the antisense direction.
[ "53", "54", "54", "55", "56" ]
220
9,573
1
false
No bi-directional transcription has been reported for pararetroviruses, but we speculate that the strong CaMV enhancer of the 35S and 19S RNA promoters can also drive POL II transcription in the antisense direction.
[ "55" ]
No bi-directional transcription has been reported for pararetroviruses, but we speculate that the strong CaMV enhancer of the 35S and 19S RNA promoters can also drive POL II transcription in the antisense direction.
true
true
true
true
true
1,522
6
DISCUSSION
1
56
[ "b53", "b54", "b54", "b55", "b56" ]
17,090,584
pmid-15703763|pmid-15703763|pmid-15165191|pmid-16741077|pmid-15703763|pmid-11532181|NA|pmid-15956560|pmid-15956560|pmid-8317097|pmid-11433282
Bidirectional transcription driven by the CaMV 35S core promoter was documented for a reporter system in Arabidopsis (56).
[ "53", "54", "54", "55", "56" ]
122
9,574
1
false
Bidirectional transcription driven by the CaMV 35S core promoter was documented for a reporter system in Arabidopsis.
[ "56" ]
Bidirectional transcription driven by the CaMV 35S core promoter was documented for a reporter system in Arabidopsis.
true
true
true
true
true
1,522
7
DISCUSSION
1
57
[ "b57" ]
17,090,584
pmid-16724105|pmid-16731914|pmid-14976549|pmid-15131083|pmid-15661355
Numerous recent reports indicate that large parts of animal and plant genomes are transcribed in both orientations (57).
[ "57" ]
120
9,575
1
false
Numerous recent reports indicate that large parts of animal and plant genomes are transcribed in both orientations.
[ "57" ]
Numerous recent reports indicate that large parts of animal and plant genomes are transcribed in both orientations.
true
true
true
true
true
1,523
7
DISCUSSION
1
57
[ "b57" ]
17,090,584
pmid-16724105|pmid-16731914|pmid-14976549|pmid-15131083|pmid-15661355
Although the biological significance of antisense transcription is still unclear, it could serve as a genome surveillance mechanism to silence endogenous DNA repeats and multiple circular minichromosomes generated by DNA virus infection.
[ "57" ]
237
9,576
0
false
Although the biological significance of antisense transcription is still unclear, it could serve as a genome surveillance mechanism to silence endogenous DNA repeats and multiple circular minichromosomes generated by DNA virus infection.
[]
Although the biological significance of antisense transcription is still unclear, it could serve as a genome surveillance mechanism to silence endogenous DNA repeats and multiple circular minichromosomes generated by DNA virus infection.
true
true
true
true
true
1,523
8
DISCUSSION
0
null
null
17,090,584
pmid-6628362|pmid-14512531|pmid-8616237|pmid-11967097
Using the CaLCuV::Chl vector, we demonstrate that establishment and/or maintenance of extensive VIGS in newly growing tissues requires DCL4, HEN1 and RDR6.
null
155
9,577
0
false
null
null
Using the CaLCuV::Chl vector, we demonstrate that establishment and/or maintenance of extensive VIGS in newly growing tissues requires DCL4, HEN1 and RDR6.
true
true
true
true
true
1,524
8
DISCUSSION
0
null
null
17,090,584
pmid-6628362|pmid-14512531|pmid-8616237|pmid-11967097
DCL1, DCL2 and DCL3 present in combinations or individually are sufficient to support VIGS-mediated knockdown of ChlI transcript in the absence of DCL4, but not sufficient to establish the indicative chlorata phenotype in newly emerging leaves.
null
244
9,578
0
false
null
null
DCL1, DCL2 and DCL3 present in combinations or individually are sufficient to support VIGS-mediated knockdown of ChlI transcript in the absence of DCL4, but not sufficient to establish the indicative chlorata phenotype in newly emerging leaves.
true
true
true
true
true
1,524
9
DISCUSSION
0
null
null
17,090,584
null
Our model to explain these observations (Figure 7) is that DCL4-dependent 21 nt ChlI siRNAs of viral origin spread into the shoot apical meristem, from which viruses are normally excluded, to trigger ChlI silencing in newly formed structures.
null
242
9,579
0
false
null
null
Our model to explain these observations (Figure 7) is that DCL4-dependent 21 nt ChlI siRNAs of viral origin spread into the shoot apical meristem, from which viruses are normally excluded, to trigger ChlI silencing in newly formed structures.
true
true
true
true
true
1,525
9
DISCUSSION
0
null
null
17,090,584
null
Although Chl-VIGS in leaves formed before inoculation is associated with accumulation of three size classes of viral siRNAs, individual size classes are sufficient for ChlI mRNA knock-down.
null
189
9,580
0
false
null
null
Although Chl-VIGS in leaves formed before inoculation is associated with accumulation of three size classes of viral siRNAs, individual size classes are sufficient for ChlI mRNA knock-down.
true
true
true
true
true
1,525
9
DISCUSSION
0
null
null
17,090,584
null
Indeed, strong accumulation of DCL2-dependent 22 nt siRNAs is correlated with reduced ChlI transcript levels in the d3d4 mutant.
null
128
9,581
0
false
null
null
Indeed, strong accumulation of DCL2-dependent 22 nt siRNAs is correlated with reduced ChlI transcript levels in the d3d4 mutant.
true
true
true
true
true
1,525
9
DISCUSSION
0
null
null
17,090,584
null
Similar results were obtained for DCL3-dependent 24 nt siRNA accumulation in d2d4, and for DCL1-dependent 21 nt siRNA accumulation in d2d3d4.
null
141
9,582
0
false
null
null
Similar results were obtained for DCL3-dependent 24 nt siRNA accumulation in d2d4, and for DCL1-dependent 21 nt siRNA accumulation in d2d3d4.
true
true
true
true
true
1,525
9
DISCUSSION
0
null
null
17,090,584
null
Nonetheless, extensive VIGS did not occur in emerging leaves of these mutant plants deficient in DCL4 activity.
null
111
9,583
0
false
null
null
Nonetheless, extensive VIGS did not occur in emerging leaves of these mutant plants deficient in DCL4 activity.
true
true
true
true
true
1,525
9
DISCUSSION
0
null
null
17,090,584
null
Therefore, we suggest that DCL4-dependent 21 nt siRNAs are transported to the shoot apical meristem where they act as primers for RDR6 coupled to DCL4 in a signal amplification loop (Figure 7) and guide RISC-mediated degradation of target mRNAs.
null
245
9,584
0
false
null
null
Therefore, we suggest that DCL4-dependent 21 nt siRNAs are transported to the shoot apical meristem where they act as primers for RDR6 coupled to DCL4 in a signal amplification loop (Figure 7) and guide RISC-mediated degradation of target mRNAs.
true
true
true
true
true
1,525
9
DISCUSSION
0
null
null
17,090,584
null
Both processes would require methylation of the 21 nt siRNAs mediated by HEN1.
null
78
9,585
0
false
null
null
Both processes would require methylation of the 21 nt siRNAs mediated by HEN1.
true
true
true
true
true
1,525
9
DISCUSSION
0
null
null
17,090,584
null
Alternatively, DCL4 and RDR6 might act only in the meristem to receive and amplify a silencing signal.
null
102
9,586
0
false
null
null
Alternatively, DCL4 and RDR6 might act only in the meristem to receive and amplify a silencing signal.
true
true
true
true
true
1,525
10
DISCUSSION
1
24
[ "b24", "b26" ]
17,090,584
pmid-16273107|pmid-16040651
Dunoyer et al.
[ "24", "26" ]
14
9,587
0
false
Dunoyer et al.
[]
Dunoyer et al.
true
true
true
true
true
1,526
10
DISCUSSION
1
24
[ "b24", "b26" ]
17,090,584
pmid-16273107|pmid-16040651
(24) concluded that cell-to-cell spread of silencing triggered by inverted-repeat transgenes requires DCL4 and is correlated with the accumulation of 21 nt but not 24 nt siRNAs.
[ "24", "26" ]
177
9,588
1
false
concluded that cell-to-cell spread of silencing triggered by inverted-repeat transgenes requires DCL4 and is correlated with the accumulation of 21 nt but not 24 nt siRNAs.
[ "24" ]
concluded that cell-to-cell spread of silencing triggered by inverted-repeat transgenes requires DCL4 and is correlated with the accumulation of 21 nt but not 24 nt siRNAs.
false
true
true
true
false
1,526
10
DISCUSSION
1
24
[ "b24", "b26" ]
17,090,584
pmid-16273107|pmid-16040651
They proposed that primary 21 nt siRNAs are short-range silencing signals and that long-range silencing signals are secondary 21 nt siRNAs generated by RDR6-mediated amplification.
[ "24", "26" ]
180
9,589
0
false
They proposed that primary 21 nt siRNAs are short-range silencing signals and that long-range silencing signals are secondary 21 nt siRNAs generated by RDR6-mediated amplification.
[]
They proposed that primary 21 nt siRNAs are short-range silencing signals and that long-range silencing signals are secondary 21 nt siRNAs generated by RDR6-mediated amplification.
true
true
true
true
true
1,526
10
DISCUSSION
1
24
[ "b24", "b26" ]
17,090,584
pmid-16273107|pmid-16040651
Our findings support this hypothesis, extending it to the spread of VIGS.
[ "24", "26" ]
73
9,590
0
false
Our findings support this hypothesis, extending it to the spread of VIGS.
[]
Our findings support this hypothesis, extending it to the spread of VIGS.
true
true
true
true
true
1,526
10
DISCUSSION
1
24
[ "b24", "b26" ]
17,090,584
pmid-16273107|pmid-16040651
This would suggest a mechanism for the exclusion of RNA viruses from the shoot apical meristem.
[ "24", "26" ]
95
9,591
0
false
This would suggest a mechanism for the exclusion of RNA viruses from the shoot apical meristem.
[]
This would suggest a mechanism for the exclusion of RNA viruses from the shoot apical meristem.
true
true
true
true
true
1,526
10
DISCUSSION
1
26
[ "b24", "b26" ]
17,090,584
pmid-16273107|pmid-16040651
Earlier work established a role for RDR6 in this exclusion (26).
[ "24", "26" ]
64
9,592
1
false
Earlier work established a role for RDR6 in this exclusion.
[ "26" ]
Earlier work established a role for RDR6 in this exclusion.
true
true
true
true
true
1,526
11
DISCUSSION
1
24
[ "b24", "b31" ]
17,090,584
pmid-16273107|pmid-16810317
The most abundant class of siRNAs derived from CaLCuV and CaMV is 24 nt long.
[ "24", "31" ]
77
9,593
0
false
The most abundant class of siRNAs derived from CaLCuV and CaMV is 24 nt long.
[]
The most abundant class of siRNAs derived from CaLCuV and CaMV is 24 nt long.
true
true
true
true
true
1,527
11
DISCUSSION
1
24
[ "b24", "b31" ]
17,090,584
pmid-16273107|pmid-16810317
Knocking out DCL3 eliminated 24 nt viral siRNAs without affecting viral DNA levels or VIGS.
[ "24", "31" ]
91
9,594
0
false
Knocking out DCL3 eliminated 24 nt viral siRNAs without affecting viral DNA levels or VIGS.
[]
Knocking out DCL3 eliminated 24 nt viral siRNAs without affecting viral DNA levels or VIGS.
true
true
true
true
true
1,527
11
DISCUSSION
1
24
[ "b24", "b31" ]
17,090,584
pmid-16273107|pmid-16810317
This is probably because DCL4 and DCL2 products (21 and 22 nt siRNAs) can mediate RNAi-like silencing in Arabidopsis (24,31).
[ "24", "31" ]
125
9,595
0
false
This is probably because DCL4 and DCL2 products (21 and 22 nt siRNAs) can mediate RNAi-like silencing in Arabidopsis.
[ "24,31" ]
This is probably because DCL4 and DCL2 products can mediate RNAi-like silencing in Arabidopsis.
true
true
true
true
true
1,527
11
DISCUSSION
1
24
[ "b24", "b31" ]
17,090,584
pmid-16273107|pmid-16810317
However, CaLCuV::Chl infection of the double mutant d2d4 still resulted in ChlI transcript knock-down, although mainly 24 nt viral ChlI siRNAs remained.
[ "24", "31" ]
152
9,596
0
false
However, CaLCuV::Chl infection of the double mutant d2d4 still resulted in ChlI transcript knock-down, although mainly 24 nt viral ChlI siRNAs remained.
[]
However, CaLCuV::Chl infection of the double mutant d2d4 still resulted in ChlI transcript knock-down, although mainly 24 nt viral ChlI siRNAs remained.
true
true
true
true
true
1,527
11
DISCUSSION
1
24
[ "b24", "b31" ]
17,090,584
pmid-16273107|pmid-16810317
Potentially, DCL3-dependent siRNAs are sufficient to target transcripts for degradation.
[ "24", "31" ]
88
9,597
0
false
Potentially, DCL3-dependent siRNAs are sufficient to target transcripts for degradation.
[]
Potentially, DCL3-dependent siRNAs are sufficient to target transcripts for degradation.
true
true
true
true
true
1,527
11
DISCUSSION
1
24
[ "b24", "b31" ]
17,090,584
pmid-16273107|pmid-16810317
This idea is reinforced by the higher accumulation of ORMV genomic RNA in d2d3d4 than in d2d4.
[ "24", "31" ]
94
9,598
0
false
This idea is reinforced by the higher accumulation of ORMV genomic RNA in d2d3d4 than in d2d4.
[]
This idea is reinforced by the higher accumulation of ORMV genomic RNA in d2d3d4 than in d2d4.
true
true
true
true
true
1,527
11
DISCUSSION
1
24
[ "b24", "b31" ]
17,090,584
pmid-16273107|pmid-16810317
Additionally, the 24 nt species might target the ChlI genomic DNA coding region, resulting in transcriptional silencing.
[ "24", "31" ]
120
9,599
0
false
Additionally, the 24 nt species might target the ChlI genomic DNA coding region, resulting in transcriptional silencing.
[]
Additionally, the 24 nt species might target the ChlI genomic DNA coding region, resulting in transcriptional silencing.
true
true
true
true
true
1,527