Chromatin Remodeling around Nucleosome-Free Regions Leads to Repression of Noncoding RNA Transcription

Abstract

Eukaryotic cells compact their DNA into a nucleoprotein complex known as chromatin. The most basic repeating unit of chromatin is the nucleosome, consisting of ϳ147 bp of DNA wrapped around an octamer of histone proteins (38). Nucleosomes are one of the most stable protein-DNA complexes known (38) and can effectively inhibit all DNA-dependent processes, including transcription, replication, repair, and recombination, by limiting the access of proteins to DNA (17). As a result, the mechanisms by which chromatin structure and nucleosome positions are specified and maintained in vivo are critical for the regulation of all DNA-dependent processes.Genome-wide maps of nucleosome positions have recently been generated in a number of organisms, including Saccharomyces cerevisiae (1,7,19,30,33,36,37,41,50,56,63,68,69), Drosophila melanogaster (42), Caenorhabditis elegans (31, 60), Oryzias latipes (52), and humans (6, 54). Each of these organisms displays a characteristic chromatin structure spanning gene-coding regions and transcriptional regulatory regions. Gene-coding regions generally have high nucleosome occupancy with arrays of well-phased nucleosomes extending from the 5Ј end of a gene. In contrast, transcriptional regulatory regions, such as promoters, enhancers, and terminators, have low nucleosome occupancy and often contain a nucleosomefree region (NFR). NFRs, also known as nucleosome-depleted regions (NDRs), typically represent regions with an increased accessibility to micrococcal nuclease (MNase) digestion. Thus, the term NFR refers to a deficiency in experimentally determined canonical nucleosomes and does not necessarily imply a complete lack of histones.To date, predominately two major classes of NFRs, 5Ј-NFRs and 3Ј-NFRs, have been characterized. In S. cerevisiae, these NFRs are typically ϳ80 to 300 bp in length and are flanked by two well-positioned nucleosomes that often contain the histone variant Htz1 (1, 50). 5Ј-NFRs, associated with the promoters of many genes, are highly enriched for sequence-specific transcription factor binding sites (7,37,63,68) and demarcate the mRNA transcription start site (TSS) to their downstream edge (1,37,63). 3Ј-NFRs are located at the 3Ј ends of genes and are enriched for transcription termination sites (TTSs) (41).Recent genome-wide expression analyses have demonstrated that the majority of eukaryotic genomes are transcribed (11-13, 16, 26, 43-45, 49, 51, 55, 64, 66), resulting in the identification of numerous noncoding RNA (ncRNA) transcripts. In S. cerevisiae, many of these ncRNA transcripts were found to initiate at the upstream edge of 5Ј-NFRs between tandemly oriented genes or at 3Ј-NFRs (45, 66). However, whether these transcripts are subjected to active regulation is not known. The conserved locations of ncRNA TSSs around NFRs strongly suggest that NFRs are general locations of transcription initiation and that the mechanisms controlling NFR accessibility are critical to transcriptional regulation of ncRNA.Multiple factors, including the physical properties of...

Enhancer RNA profiling predicts transcription factor activity

“…2A). Similar to the average length of a nucleosome free region (Yadon et al 2010), we set the h-radius based on the average estimated distance between the forward and reverse strand transcript peaks at eRNA origins (h = 150 bp; Supplemental Fig. S7B) and the H-radius as the average length of chromatin marks associated with active regulatory loci (H = 1500 bp; Supplemental Fig.…”

Nucleosome Remodeling and Epigenetics

“…For example, the yeast ISWI-type remodeler isw2 can slide nucleosomes onto a promoter to repress its activity (Whitehouse and Tsukiyama 2006). Genome-wide chromatin remodeling by ISW2 near promoters and in coding regions increases nucleosome density and enforces the accuracy of transcription (Yadon et al 2010). More specifically, the isw2 and isw1 complexes contribute to the positioning of nucleosomes in intergenic regions or in the middle of genes, respectively, which suppresses cryptic, antisense transcription that would otherwise pose a risk of interfering with sense transcription (Whitehouse et al 2007;Tirosh et al 2010).…”

Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8–Tup1 corepressor

“…The ATP-dependent Isw2 remodeling complex can negatively regulate the size of the NFR, and hence accessibility of transcriptional activators, by sliding nucleosomes from the gene bodies and into the middle of the NFRs of many of its targets (Yadon et al 2010;Sadeh and Allis 2011).…”