Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs

Mol Cell. 2017 Jan 5;65(1):25-38. doi: 10.1016/j.molcel.2016.11.029. Epub 2016 Dec 22.


Numerous long intervening noncoding RNAs (lincRNAs) are generated from the mammalian genome by RNA polymerase II (Pol II) transcription. Although multiple functions have been ascribed to lincRNAs, their synthesis and turnover remain poorly characterized. Here, we define systematic differences in transcription and RNA processing between protein-coding and lincRNA genes in human HeLa cells. This is based on a range of nascent transcriptomic approaches applied to different nuclear fractions, including mammalian native elongating transcript sequencing (mNET-seq). Notably, mNET-seq patterns specific for different Pol II CTD phosphorylation states reveal weak co-transcriptional splicing and poly(A) signal-independent Pol II termination of lincRNAs as compared to pre-mRNAs. In addition, lincRNAs are mostly restricted to chromatin, since they are rapidly degraded by the RNA exosome. We also show that a lincRNA-specific co-transcriptional RNA cleavage mechanism acts to induce premature termination. In effect, functional lincRNAs must escape from this targeted nuclear surveillance process.

Keywords: CPSF73; empigen; exosome; lincRNA; mNET-seq; phosphor CTD marks; polyadenylation; splicing; transcription termination.

Publication types

  • Comparative Study
  • Meta-Analysis

MeSH terms

  • Cell Nucleus / metabolism*
  • Computational Biology
  • Databases, Genetic
  • Exosome Multienzyme Ribonuclease Complex / genetics
  • Exosome Multienzyme Ribonuclease Complex / metabolism
  • HeLa Cells
  • Humans
  • Phosphorylation
  • Polyadenylation
  • RNA Interference
  • RNA Polymerase II / metabolism
  • RNA Precursors / genetics
  • RNA Precursors / metabolism*
  • RNA Processing, Post-Transcriptional*
  • RNA Splicing
  • RNA Stability
  • RNA, Long Noncoding / genetics
  • RNA, Long Noncoding / metabolism*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • Transcription, Genetic*
  • Transfection


  • RNA Precursors
  • RNA, Long Noncoding
  • RNA, Messenger
  • RNA Polymerase II
  • Exosome Multienzyme Ribonuclease Complex