Inefficient splicing of long non-coding RNAs is associated with higher transcript complexity in human and mouse

RNA Biol. 2023 Jan;20(1):563-572. doi: 10.1080/15476286.2023.2242649.

Abstract

Recent reports show that long non-coding RNAs (lncRNAs) have inefficient splicing and fewer alternative splice variants than mRNAs. Here, we have explored the efficiency of lncRNAs and mRNAs in producing various splice variants, given the number of exons in humans and mice. Intriguingly, lncRNAs produce more splice variants per exon, referred to as Transcript Complexity, than mRNAs. Most lncRNA splice variants are the product of the alternative last exon and exon skipping. LncRNAs and mRNAs with higher transcript complexity have shorter intron lengths. Longer exon length and GC/AG at 5'/3' splice sites are associated with higher transcript complexity in lncRNAs. Lastly, our results indicate that inefficient splicing of lncRNAs may facilitate multiple introns splicing and, thus, more spliced products per exon.

Keywords: Long non-coding RNA; alternative splicing; messenger RNA; splice variant; transcript complexity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing*
  • Animals
  • Exons
  • Humans
  • Introns
  • Mice
  • RNA Splice Sites
  • RNA, Long Noncoding* / metabolism
  • RNA, Messenger* / metabolism
  • Transcriptome*

Substances

  • RNA, Long Noncoding
  • RNA, Messenger
  • RNA Splice Sites

Grants and funding

KB is a registered Integrated Systems Biology master’s student and AD is a registered PhD student at the University of Hyderabad. A part of the work is funded by a Start-up Research Grant (SRG/2020/002146) awarded to MK from the Science and Engineering Research Board, Department of Science and Technology (SERB, DST), Government of India. AD and MK also acknowledge funding support from UoH-IoE Grant (UoH-IoE-RC2-21-012).