PolIVb influences RNA-directed DNA-methylation independently of its role in siRNA biogenesis

被引:212
作者
Mosher, Rebecca A. [1 ]
Schwach, Frank [1 ]
Studhollme, David [1 ]
Baulcombe, David C. [1 ]
机构
[1] Sainsbury Lab, Norwich NR4 7UH, Norfolk, England
关键词
RNA polymerase IV; RNA silencing; demethylation;
D O I
10.1073/pnas.0709632105
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
DNA-dependent RNA polymerase (Pol)IV in Arabidopsis exists in two isoforms (PolIVa and PolIVb), with NRPD1a and NRPD1b as their respective largest subunits, Both isoforms are implicated in production and activity of siRNAs and in RNA-directed DNA methylation (RdDM). Deep sequence analysis of siRNAs in WT Arabidopsis flowers and in nrpd1a and nrpd1b mutants identified >4,200 loci producing siRNAs in a PolIV-dependent manner, with PolIVb reinforcing siRNA production by PolIVa. Transposable element identity and pericentromeric localization are both features that predispose a locus for siRNA production via PolIV proteins and determine the extent to which siRNA production relies on PolIVb. Detailed analysis of DNA methylation at PolIV-dependent loci revealed unexpected deviations from the previously noted association of PolIVb-dependent siRNA production and RdDM. Notably, PolIVb functions independently in DNA methylation and siRNA generation. Additionally, we have uncovered siRNA-directed loss of DNA methylation, a process requiring both PolIV isoforms. From these findings, we infer that the role of PolIVb in siRNA production is secondary to a role in chromatin modification and is influenced by chromatin context.
引用
收藏
页码:3145 / 3150
页数:6
相关论文
共 33 条
[1]   Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis [J].
Borsani, O ;
Zhu, JH ;
Verslues, PE ;
Sunkar, R ;
Zhu, JK .
CELL, 2005, 123 (07) :1279-1291
[2]   Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes [J].
Cao, XF ;
Jacobsen, SE .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 :16491-16498
[3]   Two-step recruitment of RNA-directed DNA methylation to tandem repeats [J].
Chan, Simon W. -L. ;
Zhang, Xiaoyu ;
Bernatavichute, Yana V. ;
Jacobsen, Steven E. .
PLOS BIOLOGY, 2006, 4 (11) :1923-1933
[4]  
CHAN SW, 2006, PLOS GENET, V2
[5]   RNA Pol II subunit Rpb7 promotes centromeric transcription and RNAi-directed chromatin silencing [J].
Djupedal, I ;
Portoso, M ;
Spåhr, H ;
Bonilla, C ;
Gustafsson, CM ;
Allshire, RC ;
Ekwall, K .
GENES & DEVELOPMENT, 2005, 19 (19) :2301-2306
[6]   Establishment and maintenance of a heterochromatin domain [J].
Hall, IM ;
Shankaranarayana, GD ;
Noma, KI ;
Ayoub, N ;
Cohen, A ;
Grewal, SIS .
SCIENCE, 2002, 297 (5590) :2232-2237
[7]   Pathways through the small RNA world of plants [J].
Herr, AJ .
FEBS LETTERS, 2005, 579 (26) :5879-5888
[8]   RNA polymerase IV directs silencing of endogenous DNA [J].
Herr, AJ ;
Jensen, MB ;
Dalmay, T ;
Baulcombe, DC .
SCIENCE, 2005, 308 (5718) :118-120
[9]   Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis [J].
Huettel, Bruno ;
Kanno, Tatsuo ;
Daxinger, Lucia ;
Aufsatz, Werner ;
Matzke, Antonius J. M. ;
Matzke, Marjori .
EMBO JOURNAL, 2006, 25 (12) :2828-2836
[10]   Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase [J].
Jackson, JP ;
Lindroth, AM ;
Cao, XF ;
Jacobsen, SE .
NATURE, 2002, 416 (6880) :556-560