Characterization of the RNA content of chromatin

Abstract

Noncoding RNA (ncRNA) constitutes a significant portion of the mammalian transcriptome. Emerging evidence suggests that it regulates gene expression in cis or trans by modulating the chromatin structure. To uncover the functional role of ncRNA in chromatin organization, we deep sequenced chromatin-associated RNAs (CARs) from human fibroblast (HF) cells. This resulted in the identification of 141 intronic regions and 74 intergenic regions harboring CARs. The intronic and intergenic CARs show significant conservation across 44 species of placental mammals. Functional characterization of one of the intergenic CARs, Intergenic10, revealed that it regulates gene expression of neighboring genes through modulating the chromatin structure in cis. Our data suggest that ncRNA is an integral component of chromatin and that it may regulate various biological functions through fine-tuning of the chromatin architecture.

Hidden treasures in unspliced EST data

“…Their coordinates were converted to hg19 using the UCSC liftover tools. Coordinates of chromatin-associated RNAs (CARs) were taken from the supplemental material of [24] and lifted over to hg19.…”

“…A particular class of most unspliced transcripts are the 215 chromatin associated RNAs (CARs) [24]. Of these, 145 (67%) overlap unspliced EST clusters, and 179 are located within the range of RefSeq genes ±5 …”

“…Recently, deep sequencing was used to characterize 141 intronic regions and 74 intergenic regions harboring CARs [24].…”

Interplay of chromatin modifications and non-coding RNAs in the heart

“…80 Alternatively, native RNA-ChIP using MNase digestion have also been successfully applied to the study of chromatin associated RNAs. 92 In striking contrast ASSAGe, asymmetric strand specific analysis of gene expression; GRO-Seq, global run-on sequencing; NeT-Seq, native elongating transcript sequencing; RACe, rapid amplification of cDNA ends; BRiC-Seq, 5'-bromo-uridine immunoprecipitation chase-deep sequencing; SAGe, serial analysis of gene expression; PTeS, post-transcriptional exon scrambling; CARs, chromatin associated RNAs; FiSH, fluorescent in situ Hybridization; ChiP, chromatin immunoprecipitation; ChiRP, chromatin isolation by RNA purification; CHART, capture hybridization analysis of RNA targets; HiTS-CLiP, high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation; PAR-CLiP, photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation.…”

Chromatin computation: Epigenetic inheritance as a pattern reconstruction problem

“…This may subsequently facilitate localized spreading in cis and the (re-)establishment of chromatin domains. Further contributing to the complexity of how an epigenetic memory, long non-coding RNAs seem to have crucial roles in regulating gene expression by guiding chromatin-modifying enzyme complexes to particular genomic loci (Magistri et al, 2012;Lee, 2012;Mondal et al, 2010;Khalil et al, 2009). An increasing number of other molecular pathways involving small noncoding RNAs or DNA methylation in concert with histone modifications have been described (Moazed, 2011) as well.…”