title: DNA methylation signature of intergenic region involves in nucleosome remodeler DDM1-mediated repression of aberrant gene transcriptional read-through.
abstract: The strict and efficient transcription termination is required to prevent production of aberrant read-through transcripts that may cause transcriptional interference at neighboring genes. However, the exact regulatory mechanism remains poorly understood. Through a genetic screening of a LUCIFERASE (LUC) reporter system, we found that Arabidopsis nucleosome remodeler DECREASE IN DNA METHYLATION1 (DDM1) is a key component of this regulatory machinery and plays an important role in transcription termination, thus limiting transcriptional read-through (TRT). By whole-genome strand-specific RNA sequencing, we identified and confirmed 43 endogenous TRTs between genes, transposable elements (TEs), or genes and TEs in the ddm1-10 mutant, which mainly occurred at heterochromatin regions. The DNA methylation analysis of these TRT regions revealed that TRT occurred frequently at the intergenic regions with a higher methylation level in wild type comparing to the regions where TRT did not occur. Our results suggest that the level of intergenic DNA methylation may involve in preventing aberrant gene TRT or producing new gene during evolution.
authors: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
authors: Xiaojing
authors: X
authors: Yan
authors: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
authors: Xiaomei
authors: X
authors: Dong
authors: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
authors: Lei
authors: L
authors: Liu
authors: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
authors: Yongqing
authors: Y
authors: Yang
authors: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
authors: Jinsheng
authors: J
authors: Lai
authors: State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China. Electronic address: guoyan@cau.edu.cn.
authors: Yan
authors: Y
authors: Guo
mesh_terms: D017360:Arabidopsis / Q000166:cytology / Q000235:genetics / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D042002:Chromatin Assembly and Disassembly; D019175:DNA Methylation; D021901:DNA, Intergenic / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D009154:Mutation; D009707:Nucleosomes / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; C118957:DDM1 protein, Arabidopsis; D021901:DNA, Intergenic; D004268:DNA-Binding Proteins; D009707:Nucleosomes; D014157:Transcription Factors
keywords: Arabidopsis; DDM1; DNA methylation; Intergenic region; Transcriptional read-through