DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV

Zhang, Heng; Yang, Zihui; Zeng, Liang; Tanaka, Kaori; Zhang, Cui Jun; Ma, Jun; Bai, Ge; Wang, Pengcheng; Zhang, Su Wei; Liu, Zhang Wei; Cai, Tao; Tang, Kai; Liu, Renyi; Shi, Xiaobing; He, Xin; Zhu, Jian Kang

doi:10.1073/pnas.1300585110

Cited by 164 publications

(196 citation statements)

References 37 publications

Supporting

Mentioning

179

Contrasting

Unclassified

Order By: Relevance

“…In many cases, siRNA accumulation at endogenous genomic loci is not sufficient to induce DNA methylation, as in the epiallele fwa-d in Arabidopsis [54] or the B-I paramutable allele of maize [55]. In other cases, a significantly decreased abundance of siRNAs does not reduce DNA methylation levels [22].…”

Section: Discussionmentioning

confidence: 99%

“…Since the Pol IV-interacting protein DTF1/SHH1 binds to H3K9me2 and helps recruit Pol IV to a subset of RdDM loci [21,22], we tested the possibility that DTF1/ SHH1 preferentially targets ID and/or PD loci. However, we found that the ID loci are less enriched for DTF1-dependent DMRs (Supplementary information, Figure S5), suggesting that multiple factors are involved in recruiting Pol IV to different types of RdDM target loci.…”

Section: Dicer-independent Dna Methylation At Rddm Target Locimentioning

confidence: 99%

“…Clean reads were generated by trimming off adaptor and low-quality sequences (q < 20) and then were mapped to the Arabidopsis genome (TAIR 10) using BSMAP (Bisulfite Sequence Mapping Program) allowing two mismatches [22]. DMRs were identified using a published method with slight modifications [22].…”

Section: Whole-genome Bisulfite Sequencing and Data Analysismentioning

confidence: 99%

“…It has been shown that an H3K9me2-binding protein, DTF1/SHH1, is required for Pol IV recruitment to a subset of RdDM target loci [21,22], whereas two SRA-domain-containing proteins SUVH2/9, which bind to methylated DNA, are required for Pol V occupancy at RdDM loci [23,24]. Both DTF1/ SHH1 and SUVH2/9 interact with putative ATP-dependent chromatin remodeling factors, including CLSY1 and DRD1, which are presumed to facilitate transcription by RNA Pol IV and Pol V, respectively [22,24].…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Dicer-independent RNA-directed DNA methylation in Arabidopsis

et al. 2015

Self Cite

View full text Add to dashboard Cite

RNA-directed DNA methylation (RdDM) is an important de novo DNA methylation pathway in plants. Small interfering RNAs (siRNAs) generated by Dicers from RNA polymerase IV (Pol IV) transcripts are thought to guide sequence-specific DNA methylation. To gain insight into the mechanism of RdDM, we performed whole-genome bisulfite sequencing of a collection of Arabidopsis mutants, including plants deficient in Pol IV (nrpd1) or Dicer (dcl1/2/3/4) activity. Unexpectedly, of the RdDM target loci that required Pol IV and/or Pol V, only 16% were fully dependent on Dicer activity. DNA methylation was partly or completely independent of Dicer activity at the remaining Pol IV-and/ or Pol V-dependent loci, despite the loss of 24-nt siRNAs. Instead, DNA methylation levels correlated with the accumulation of Pol IV-dependent 25-50 nt RNAs at most loci in Dicer mutant plants. Our results suggest that RdDM in plants is largely guided by a previously unappreciated class of Dicer-independent non-coding RNAs, and that siRNAs are required to maintain DNA methylation at only a subset of loci.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Dicer-independent Dna Methylation At Rddm Target Locimentioning

confidence: 99%

Section: Whole-genome Bisulfite Sequencing and Data Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Dicer-independent RNA-directed DNA methylation in Arabidopsis

et al. 2015

Self Cite

View full text Add to dashboard Cite

show abstract

“…In RdDM pathways acting at predominantly transposable elements (TEs), SAWADEE HOMEODOMAIN HOMOLOG (SHH)1 binds and recruits RNA Polymerase IV (PolIV) to transcribe methylated DNA (3,4). The PolIV transcripts are then made double-stranded by RNA-dependent RNA polymerase (RDR)2 and cleaved by Dicer-like 3 (DCL3) into 24-nt sRNAs that are loaded into and guide AGONAUTE (AGO)4 to complementary scaffold RNAs transcribed from the same locus by RNA polymerase V (PolV).…”

mentioning

confidence: 99%

Epigenetic transitions leading to heritable, RNA-mediated de novo silencing in Arabidopsis thaliana

Bond

Baulcombe

2015

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

117

124

View full text Add to dashboard Cite

In plants, RNA-directed DNA methylation (RdDM), a mechanism where epigenetic modifiers are guided to target loci by small RNAs, plays a major role in silencing of transposable elements (TEs) to maintain genome integrity. So far, two RdDM pathways have been identified: RNA Polymerase IV (PolIV)-RdDM and RNA-dependent RNA Polymerase 6 (RDR6)-RdDM. PolIV-RdDM involves a selfreinforcing feedback mechanism that maintains TE silencing, but cannot explain how epigenetic silencing is first initiated. A function of RDR6-RdDM is to reestablish epigenetic silencing of active TEs, but it is unknown if this pathway can induce DNA methylation at naïve, non-TE loci. To investigate de novo establishment of RdDM, we have used virus-induced gene silencing (VIGS) of an active FLOWERING WAGENINGEN epiallele. Using genetic mutants we show that unlike PolIV-RdDM, but like RDR6-RdDM, establishment of VIGS-mediated RdDM requires PolV and DRM2 but not Dicer like-3 and other PolIV pathway components. DNA methylation in VIGS is likely initiated by a process guided by virus-derived small (s) RNAs that are 21/22-nt in length and reinforced or maintained by 24-nt sRNAs. We demonstrate that VIGS-RdDM as a tool for gene silencing can be enhanced by use of mutant plants with increased production of 24-nt sRNAs to reinforce the level of RdDM.RNA-directed DNA methylation | virus-induced gene silencing | epigenetics | Arabidopsis thaliana M ethylation of cytosine (C) residues of DNA is a stable and heritable modification that mediates epigenetic control in eukaryotic genomes. In plants this modification occurs at CG, CHG, and CHH sequences (where H can be C, A, or T) and involves RNA-directed DNA methylation (RdDM) pathways. The DNA methyltransferases in these pathways are guided to target loci by ribonucleoproteins in which a small (s)RNA is the specificity determinant (1, 2).There are two mechanisms to maintain DNA methylation. In RdDM pathways acting at predominantly transposable elements (TEs), SAWADEE HOMEODOMAIN HOMOLOG (SHH)1 binds and recruits RNA Polymerase IV (PolIV) to transcribe methylated DNA (3, 4). The PolIV transcripts are then made double-stranded by RNA-dependent RNA polymerase (RDR)2 and cleaved by Dicer-like 3 (DCL3) into 24-nt sRNAs that are loaded into and guide AGONAUTE (AGO)4 to complementary scaffold RNAs transcribed from the same locus by RNA polymerase V (PolV). The sRNA-bound AGO and the PolV transcript interact and recruit the de novo methyltransferase DRM2 that modifies C residues of the DNA strand acting as the template for PolV (5).Maintenance of CG and CHG methylation during DNA replication occurs via MET1, the plant homolog of the mammalian DNA methyltransferase DNMT1, and the plant-specific CHROMOMETHYLASE 3 (CMT3) that works in concert with the SU(VAR)3-9 HOMOLOG (SUVH) SET domain histone methyltransferse KRYPTONITE. Both MET1 and CMT3 act independently of sRNAs but maintenance of CHH methylation within euchromatin is dependent on the continuous operation of the sRNA establishment mechanism, resulting in a self-...

show abstract

UAP56 associates with DRM2 and is localized to chromatin in Arabidopsis

et al. 2019

View full text Add to dashboard Cite

Repeated sequence expression and transposable element mobilization are tightly controlled by multilayer processes, which include DNA 5′‐cytosine methylation. The RNA‐directed DNA methylation (RdDM) pathway, which uses siRNAs to guide sequence‐specific directed DNA methylation, emerged specifically in plants. RdDM ensures DNA methylation maintenance on asymmetric CHH sites and specifically initiates de novo methylation in all cytosine sequence contexts through the action of DRM DNA methyltransferases, of which DRM2 is the most prominent. The RdDM pathway has been well described, but how DRM2 is recruited onto DNA targets and associates with other RdDM factors remains unknown. To address these questions, we developed biochemical approaches to allow the identification of factors that may escape genetic screens, such as proteins encoded by multigenic families. Through both conventional and affinity purification of DRM2, we identified DEAD box RNA helicases U2AF56 Associated Protein 56 (UAP56a/b), which are widespread among eukaryotes, as new DRM2 partners. We have shown that, similar to DRM2 and other RdDM actors, UAP56 has chromatin‐associated protein properties. We confirmed this association both in vitro and in vivo in reproductive tissues. In addition, our experiments also suggest that UAP56 may exhibit differential distribution in cells depending on plant organ. While originally identified for its role in splicing, our study suggests that UAP56 may also have other roles, and our findings allow us to initiate discussion about its potential role in the RdDM pathway.

show abstract

DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV

Cited by 164 publications

References 37 publications

Dicer-independent RNA-directed DNA methylation in Arabidopsis

Dicer-independent RNA-directed DNA methylation in Arabidopsis

Epigenetic transitions leading to heritable, RNA-mediated de novo silencing in Arabidopsis thaliana

UAP56 associates with DRM2 and is localized to chromatin in Arabidopsis

Contact Info

Product

Resources

About