Next Article in Journal / Special Issue
Computational Characterization of ncRNA Fragments in Various Tissues of the Brassica rapa Plant
Previous Article in Journal
Long Non-Coding RNAs Regulating Immunity in Insects
Previous Article in Special Issue
MicroRNA MultiTool: A Software for Identifying Modified and Unmodified Human microRNA Using Mass Spectrometry
Article Menu

Export Article

Open AccessReview
Non-Coding RNA 2017, 3(1), 15; doi:10.3390/ncrna3010015

Identification of RNA Polymerase III-Transcribed SINEs at Single-Locus Resolution from RNA Sequencing Data

Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
*
Author to whom correspondence should be addressed.
Academic Editors: Jian-Hua Yang and Liang-Hu Qu
Received: 23 December 2016 / Revised: 27 February 2017 / Accepted: 14 March 2017 / Published: 21 March 2017
(This article belongs to the Special Issue Bioinformatics Softwares and Databases for Non-Coding RNA Research)
View Full-Text   |   Download PDF [2123 KB, uploaded 22 March 2017]   |  

Abstract

Short Interspersed Element (SINE) retrotransposons are one of the most abundant DNA repeat elements in the human genome. They have been found to impact the expression of protein-coding genes, but the possible roles in cell physiology of their noncoding RNAs, generated by RNA polymerase (Pol) III, are just starting to be elucidated. For this reason, Short Interspersed Element (SINE) expression profiling is becoming mandatory to obtain a comprehensive picture of their regulatory roles. However, their repeated nature and frequent location within Pol II-transcribed genes represent a serious obstacle to the identification and quantification of genuine, Pol III-derived SINE transcripts at single-locus resolution on a genomic scale. Among the recent Next Generation Sequencing technologies, only RNA sequencing (RNA-Seq) holds the potential to solve these issues, even though both technical and biological matters need to be taken into account. A bioinformatic pipeline has been recently set up that, by exploiting RNA-seq features and knowledge of SINE transcription mechanisms, allows for easy identification and profiling of transcriptionally active genomic loci which are a source of genuine Pol III SINE transcripts. View Full-Text
Keywords: SINE; Alu; mammalian-wide interspersed repeats (MIR); RNA polymerase III; non-coding RNA; RNA-Seq; bioinformatics SINE; Alu; mammalian-wide interspersed repeats (MIR); RNA polymerase III; non-coding RNA; RNA-Seq; bioinformatics
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Carnevali, D.; Dieci, G. Identification of RNA Polymerase III-Transcribed SINEs at Single-Locus Resolution from RNA Sequencing Data. Non-Coding RNA 2017, 3, 15.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Non-Coding RNA EISSN 2311-553X Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top