Transcription pausing: biological significance of thermal fluctuations biased by repetitive genomic sequences

Masahiko Imashimizu, David B. Lukatsky

Research output: Contribution to journalReview articlepeer-review

2 Scopus citations

Abstract

Transcription of DNA by RNA polymerase (RNAP) takes place in a cell environment dominated by thermal fluctuations. How are transcription reactions including initiation, elongation, and termination on genomic DNA so well-controlled during such fluctuations? A recent statistical mechanical approach using high-throughput sequencing data reveals that repetitive DNA sequence elements embedded into a genomic sequence provide the key mechanism to functionally bias the fluctuations of transcription elongation complexes. In particular, during elongation pausing, such repetitive sequence elements can increase the magnitude of one-dimensional diffusion of the RNAP enzyme on the DNA upstream of the pausing site, generating a large variation in the dwell times of RNAP pausing under the control of these genomic signals.

Original languageEnglish
Pages (from-to)196-203
Number of pages8
JournalTranscription
Volume9
Issue number3
DOIs
StatePublished - 27 May 2018

Keywords

  • Brownian ratchet
  • RNA polymerase
  • repetitive genomic sequence
  • thermal fluctuations
  • transcription pausing

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