Abstract
Non-coding RNAs (ncRNAs) are powerful regulators of gene expression but medium-sized (50-300 nts in length) ncRNAs (msRNAs) are barely picked-up precisely by RNA-sequencing. Here we describe msRNA-sequencing (msRNAseq), a modified protocol that associated with a computational analyses pipeline identified about ~1800 msRNA loci, including over 300 putatively novel msRNAs, in human and murine cells. We focused on the identification and initial characterization of three POLIII-derived transcripts. The validation of these uncharacterized msRNAs identified an ncRNA in antisense orientation from the POLR3E locus transcribed by POLIII. This msRNA, termed POLAR (POLR3E Antisense RNA), has a strikingly short half-life, localizes to paraspeckles (PSPs) and associates with PSP-associated proteins indicating that msRNAseq identifies functional msRNAs. Thus, our analyses will pave the way for analysing the roles of msRNAs in cells, development and diseases.
Keywords:
Msrna; ncRNA; polar; poliii; polr3e.
Publication types
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Research Support, Non-U.S. Gov't
MeSH terms
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Humans
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Paraspeckles / genetics
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Paraspeckles / metabolism*
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RNA Polymerase III / genetics
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RNA Polymerase III / metabolism*
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RNA, Antisense / genetics*
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RNA, Messenger / analysis
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RNA, Messenger / genetics*
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RNA, Untranslated / genetics*
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Sequence Analysis, RNA / methods*
Substances
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RNA, Antisense
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RNA, Messenger
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RNA, Untranslated
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POLR3E protein, human
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RNA Polymerase III
Grants and funding
This work was supported by the DFG [391498659].