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Methods. 2013 Sep 1;63(1):76-84. doi: 10.1016/j.ymeth.2013.05.001. Epub 2013 May 16.

Small RNAs derived from structural non-coding RNAs.

Author information

1
Institut Curie, 26 rue d'Ulm, F-75248 Paris, France; CNRS UMR3215, Paris, France; INSERM U934, Paris, France; INSERM U900, Paris, France; Mines ParisTech, Fontainebleau, France. Electronic address: chongjian.chen@curie.fr.

Abstract

It has been shown in small RNA sequencing-based studies that some small RNA fragments are specifically processed from known structural non-coding RNAs, either through Dicer-dependent or Dicer-independent pathways. Although these small RNAs are often less abundant compared to microRNAs in normal mammalian tissues, they are always present in all sequenced libraries. In this paper, we use the ncPRO-seq pipeline, to describe different profiles of these small RNA fragments, and to discuss their potential processing pathways and functions. To assess whether more small RNA fragments can be detected in small RNA sequencing datasets, we decided to focus on small nuclear RNAs, abbreviated as snRNAs, which are associated with Sm ribonucleoproteins to form functional RNA-protein complexes. Here, we describe a group of small RNA fragments derived from snRNAs, which are typically highly enriched in regions bound by Sm proteins. Based on this, we propose the existence of a potential novel small RNA family associated with Sm proteins.

KEYWORDS:

Non-coding RNA; Small RNA sequencing; ncPRO-seq; snRNA

PMID:
23684746
DOI:
10.1016/j.ymeth.2013.05.001
[Indexed for MEDLINE]
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