Characterization of the RNA content of chromatin
- Tanmoy Mondal1,
- Markus Rasmussen2,
- Gaurav Kumar Pandey1,
- Anders Isaksson2,3 and
- Chandrasekhar Kanduri1,3
- 1 Department of Genetics and Pathology, Uppsala University, Uppsala S-75185, Sweden;
- 2 Department of Medical Sciences, Cancer Pharmacology and Informatics, Uppsala University, Uppsala S-75185, Sweden
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.
Footnotes
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↵3 Corresponding authors.
E-mail kanduri.chandrasekhar{at}genpat.uu.se.
E-mail anders.isaksson{at}medsci.uu.se.
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[Supplemental material is available online at http://www.genome.org. The sequencing data from this study have been submitted to the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) under accession no. GSE21227.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.103473.109.
- Received November 23, 2009.
- Accepted April 12, 2010.
- Copyright © 2010 by Cold Spring Harbor Laboratory Press
Freely available online through the Genome Research Open Access option.