TY - JOUR
T1 - Transcription pausing
T2 - biological significance of thermal fluctuations biased by repetitive genomic sequences
AU - Imashimizu, Masahiko
AU - Lukatsky, David B.
N1 - Funding Information:
This work was supported by the Japan Society for the Promotion of Science (JSPS) (number 16H06692).
Publisher Copyright:
© 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
PY - 2018/5/27
Y1 - 2018/5/27
N2 - 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.
AB - 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.
KW - Brownian ratchet
KW - RNA polymerase
KW - repetitive genomic sequence
KW - thermal fluctuations
KW - transcription pausing
UR - http://www.scopus.com/inward/record.url?scp=85045856888&partnerID=8YFLogxK
U2 - 10.1080/21541264.2017.1393492
DO - 10.1080/21541264.2017.1393492
M3 - Review article
AN - SCOPUS:85045856888
SN - 2154-1264
VL - 9
SP - 196
EP - 203
JO - Transcription
JF - Transcription
IS - 3
ER -