In contrast, antisense cheRNA, which originates from the complementary strand of the protein-coding gene, may interact with diverse chromatin modulators to repress local transcription. We found that intergenic cheRNA, including intergenic cheRNA with high levels of H3K9me3 (a mark associated with closed/repressed chromatin), may act as a transcriptional activator. The computational framework presented here provides a reliable approach to identifying cheRNA, and for studying cell-type specific gene regulation. CheRNA provides a powerful way to profile the nuclear transcriptional landscape, especially to profile the noncoding transcriptome. A possible new role of H3K9me3 modification coincident with icheRNA may be associated with active enhancer derived from ancient mobile elements, while a potential cis-repressive function of antisense cheRNA ( as-cheRNA) is likely to be involved in transiently modulating cell type-specific cis-regulation.Īuthor Summary Chromatin-enriched nuclear RNA (cheRNA) is a class of gene regulatory non-coding RNAs. We also explore two novel genomic associations, suggesting cheRNA may have diverse functions. Moreover, we quantify the transcriptional correlation of icheRNA and adjacent genes, and suggest that icheRNA may be the cis-acting transcriptional regulator that is more positively associated with neighboring gene expression than eRNA predicted by state-of-art method or CAGE signal. We have used Tuxedo to analyze gold-standard K562 cell datasets and further characterize the genomic features of intergenic cheRNA ( icheRNA) and their similarity to those of enhancer RNA ( eRNA). Tuxedo not only assembles a more complete transcriptome, but also identifies cheRNA with higher accuracy. In this study, we survey four computational strategies for nuclear RNA-seq data analysis and show that a new pipeline, Tuxedo, outperforms other approaches. Until now, a rigorous analytic pipeline for nuclear RNA-seq has been lacking. RNA sequencing of two biochemical fractions of nuclei reveals a unique class of lncRNAs, termed chromatin-enriched nuclear RNAs ( cheRNAs) that are tightly bound to chromatin and putatively function to cis-activate gene expression. ![]() Long noncoding RNAs ( lncRNAs) localize in the cell nucleus and influence gene expression through a variety of molecular mechanisms.
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