A SWI/SNF Chromatin-Remodeling Complex Acts in Noncoding RNA-Mediated Transcriptional Silencing

Zhu, Yanjing; Rowley, M. Jordan; Böhmdorfer, Gudrun; Wierzbicki, Andrzej

doi:10.1016/j.molcel.2012.11.011

Cited by 178 publications

(194 citation statements)

References 56 publications

(114 reference statements)

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“…Studies of Arabidopsis suggested a model in which lncRNAs recruit Swi/Snf ATP-dependent chromatin-remodeling complex to genomic sites to position nucleosomes and silence gene expression 36 ( Fig. 1B).…”

Section: Lncrnas As Partners Of Atpdependent Chromatin-remodeling Facmentioning

confidence: 99%

“…37 The Pol V-transcribed lncRNAs can bind to IDN2 (an RNA-binding protein essential for transcription silencing), 38,39 which then binds to the SWI3B subunit of Swi/ Snf complex to recruit the remodeling complex to the sites of lncRNA transcription to establish repressive chromatin environment. 36 Therefore, lncRNAs can indirectly recruit chromatin-remodeling complex to local genomic sites to reposition nucleosomes for gene repression.…”

Section: Lncrnas As Partners Of Atpdependent Chromatin-remodeling Facmentioning

confidence: 99%

“…(B), Pol V-transcribed lncRNA tethers SWI3B-containing SWI/SNF chromatin-remodeling complex to genomic loci to repress gene expression in Arabidopsis. 36 Such action is accomplished through a RNA-binding protein IDN2, which binds both lncRNA and SWI3B.…”

Section: Lncrna Transcription Can Be Controlled By Atp-dependent Chromentioning

confidence: 99%

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Long non-coding RNA and chromatin remodeling

2015

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Section: Lncrnas As Partners Of Atpdependent Chromatin-remodeling Facmentioning

confidence: 99%

Section: Lncrnas As Partners Of Atpdependent Chromatin-remodeling Facmentioning

confidence: 99%

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Long non-coding RNA and chromatin remodeling

2015

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“…Mapping nucleosome positioning was performed with 2-g samples of 14-d-old wild-type, swp73a-1, and swp73b-1 seedlings according to Saleh et al (2008) and Zhu et al (2013) with minor modifications (i.e., the buffer contained 1% proteinase inhibitor cocktail [Sigma-Aldrich] instead of pepstatin A and aprotinin). Two hundred Kunitz units of micrococcal nuclease (NEB) were used for digestion of each sample.…”

Section: Mnase Mapping Of Nucleosome Positioningmentioning

confidence: 99%

SWP73 Subunits of Arabidopsis SWI/SNF Chromatin Remodeling Complexes Play Distinct Roles in Leaf and Flower Development

et al. 2015

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(T.J.S.)Arabidopsis thaliana SWP73A and SWP73B are homologs of mammalian BRAHMA-associated factors (BAF60s) that tether SWITCH/SUCROSE NONFERMENTING chromatin remodeling complexes to transcription factors of genes regulating various cell differentiation pathways. Here, we show that Arabidopsis thaliana SWP73s modulate several important developmental pathways. While undergoing normal vegetative development, swp73a mutants display reduced expression of FLOWERING LOCUS C and early flowering in short days. By contrast, swp73b mutants are characterized by retarded growth, severe defects in leaf and flower development, delayed flowering, and male sterility. MNase-Seq, transcript profiling, and ChIP-Seq studies demonstrate that SWP73B binds the promoters of ASYMMETRIC LEAVES1 and 2, KANADI1 and 3, and YABBY2, 3, and 5 genes, which regulate leaf development and show coordinately altered transcription in swp73b plants. Lack of SWP73B alters the expression patterns of APETALA1, APETALA3, and the MADS box gene AGL24, whereas other floral organ identity genes show reduced expression correlating with defects in flower development. Consistently, SWP73B binds to the promoter regions of APETALA1 and 3, SEPALLATA3, LEAFY, UNUSUAL FLORAL ORGANS, TERMINAL FLOWER1, AGAMOUS-LIKE24, and SUPPRESSOR OF CONSTANS OVEREXPRESSION1 genes, and the swp73b mutation alters nucleosome occupancy on most of these loci. In conclusion, SWP73B acts as important modulator of major developmental pathways, while SWP73A functions in flowering time control.

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“…CLSY1 and DRD1 interact with Pol IV and Pol V, respectively, and might be required to provide a chromatin environment favorable for recruitment or transcriptional activity of these heterochromatic RNA polymerases. Recently, SWI3B, a component of the ATP-dependent chromatin remodeling complex SWI/SNF, was described as an IDN2 interactor that is guided by lncRNAs to position nucleosomes at RdDM target sites (15). The 24-nt siRNA profile of frg1 frg2 double-mutants did not show any changes at siRNA clusters that depend on Pol IV but not on genes downstream of siRNA production, which argues against an involvement of FRG1 and FRG2 in Pol IV transcription.…”

Section: Discussionmentioning

confidence: 98%

SNF2 chromatin remodeler-family proteins FRG1 and -2 are required for RNA-directed DNA methylation

Groth

Stroud

Feng

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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DNA methylation in Arabidopsis thaliana is maintained by at least four different enzymes: DNA METHYLTRANSFERASE1 (MET1), CHROMO-METHYLASE3 (CMT3), DOMAINS REARRANGED METHYLTRANSFER-ASE2 (DRM2), and CHROMOMETHYLASE2 (CMT2). However, DNA methylation is established exclusively by the enzyme DRM2, which acts in the RNA-directed DNA methylation (RdDM) pathway. Some RdDM components belong to gene families and have partially redundant functions, such as the endoribonucleases DICER-LIKE 2, 3, and 4, and INVOLVED IN DE NOVO2 (IDN2) interactors IDN2-LIKE 1 and 2. Traditional mutagenesis screens usually fail to detect genes if they are redundant, as the loss of one gene can be compensated by a related gene. In an effort to circumvent this issue, we used coexpression data to identify closely related genes that are coregulated with genes in the RdDM pathway. Here we report the discovery of two redundant proteins, SNF2-RING-HELICASE-LIKE1 and -2 (FRG1 and -2) that are putative chromatin modifiers belonging to the SNF2 family of helicase-like proteins. Analysis of genome-wide bisulfite sequencing shows that simultaneous mutations of FRG1 and -2 cause defects in methylation at specific RdDM targeted loci. We also show that FRG1 physically associates with Su(var)3-9-related SUVR2, a known RdDM component, in vivo. Combined, our results identify FRG1 and FRG2 as previously unidentified components of the RdDM machinery.epigenetic | plant C ytosine methylation is an epigenetic mark present in many eukaryotes and is involved in silencing of transposable elements and other repetitive sequences that impose threats to genome integrity. Moreover, DNA methylation in regulatory regions suppresses the expression of genes and disturbances in methylation patterns can lead to developmental defects (1).In the model plant Arabidopsis, DNA methylation occurs at CG, CHG, and CHH sequences (H = A, T, or C) and is maintained through DNA replication by different mechanisms, depending on the sequence context: symmetric CG and CHG methylation are maintained primarily by MET1 and CMT3, respectively, whereas the asymmetric CHH methylation is maintained by either CMT2 or DRM2 (2, 3). Initial DNA methylation establishment-or de novo methylation-in any sequence context is carried out by DRM2 (4, 5). DRM2 is guided to its target loci via a complex pathway known as RNA-directed DNA methylation (RdDM). RdDM depends on the production of both small interfering RNA (siRNA), and overlapping long-noncoding transcripts. According to current knowledge, chromatin-associated proteins, including SAWADEE HOMEODOMAIN HOMOLOG1 (SHH1)/DTF1 and CLASSY1 (CLSY1), recruit and assist RNA POLYMERASE IV (Pol IV), which produces transcripts that are converted to double-stranded RNA by RNA-DEPENDENT RNA POLY-MERASE2 (RDR2) and subsequently cleaved into 24-nt siRNAs by DICER-LIKE3 (DCL3). ARGONAUTE4 (AGO4) binds siRNAs and is recruited to the RNA POLYMERASE V (Pol V) complex, as well as to long noncoding transcripts (lncRNA) produced by Pol V. AGO4 ultimately interacts with DRM2, whi...

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A SWI/SNF Chromatin-Remodeling Complex Acts in Noncoding RNA-Mediated Transcriptional Silencing

Cited by 178 publications

References 56 publications

Long non-coding RNA and chromatin remodeling

Long non-coding RNA and chromatin remodeling

SWP73 Subunits of Arabidopsis SWI/SNF Chromatin Remodeling Complexes Play Distinct Roles in Leaf and Flower Development

SNF2 chromatin remodeler-family proteins FRG1 and -2 are required for RNA-directed DNA methylation

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