Journal
GENOME RESEARCH
Volume 20, Issue 7, Pages 899-907Publisher
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.103473.109
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Funding
- Swedish Medical Research Council (VR-M)
- Swedish Cancer Research Foundation (Cancerfonden)
- Swedish Childhood Cancer Society (Barncancerfonden)
- Department of Genetics & Pathology, Rudbeck Laboratory
- Uppsala University Medical Faculty, Uppsala University
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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.
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