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Front. Genet. | doi: 10.3389/fgene.2018.00154

Correlation analyses reveal a limited role of transcription in genome-wide differential microRNA expression in mammals

Xiaoxiao Zhang1, Siling Hu1, Jia Su1, Zixuan Xie1, Wenjing Li1 and  Yan Zeng1*
  • 1Nanjing Agricultural University, China

Transcription initiates the cascade of gene expression and is often assumed to play a predominant role in determining how much gene products are ultimately expressed. The relationship between mRNA levels and protein levels has been studied extensively to reveal the degrees of transcriptional and post-transcriptional regulation of protein expression. The extent to which transcription globally controls the differential expression of non-coding RNAs, however, is poorly defined. microRNAs (miRNAs) are a class of small, non-coding RNAs whose biogenesis involves transcription followed by extensive processing. Here, using hundreds of datasets produced from the ENCODE (Encyclopedia of DNA Elements) project we calculated the correlations between transcriptional activity and mature miRNA expression in diverse human cells, human tissues, and mouse tissues. While correlations vary among samples, most correlation coefficients are small. Interestingly, excluding miRNAs that were discovered later or weighting miRNA expression improves the correlations. Our results suggest that transcription contributes only modestly to differential miRNA expression at the genome-wide scale in mammals.

Keywords: miRNA, tran, pri-miRNA, MiRNA processing, Correlation analysis, ENCODE datasets

Received: 19 Dec 2017; Accepted: 13 Apr 2018.

Edited by:

Stefano Volinia, University of Ferrara, Italy

Reviewed by:

Walter J. Lukiw, LSU Health Sciences Center New Orleans, United States
Zofia Szweykowska-Kulinska, Adam Mickiewicz University in Poznań, Poland  

Copyright: © 2018 Zhang, Hu, Su, Xie, Li and Zeng. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Yan Zeng, Nanjing Agricultural University, Nanjing, China, zengyan@njau.edu.cn