TY - JOUR
T1 - G-quadruplexes involving both strands of genomic DNA are highly abundant and colocalize with functional sites in the human genome
AU - Kudlicki, Andrzej S.
N1 - Publisher Copyright:
© 2016 Andrzej S Kudlicki. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2016/1/4
Y1 - 2016/1/4
N2 - The G-quadruplex is a non-canonical DNA structure biologically significant in DNA replication, transcription and telomere stability. To date, only G4s with all guanines originating from the same strand of DNA have been considered in the context of the human nuclear genome. Here, I discuss interstrand topological configurations of G-quadruplex DNA, consisting of guanines from both strands of genomic DNA; an algorithm is presented for predicting such structures. I have identified over 550,000 non-overlapping interstrand Gquadruplex forming sequences in the human genome - significantly more than intrastrand configurations. Functional analysis of interstrand G-quadruplex sites shows strong association with transcription initiation, the results are consistent with the XPB and XPD transcriptional helicases binding only to G-quadruplex DNA with interstrand topology. Interstrand quadruplexes are also enriched in origin of replication sites. Several topology classes of interstrand quadruplex-forming sequences are possible, and different topologies are enriched in different types of structural elements. The list of interstrand quadruplex forming sequences, and the computer program used for their prediction are available at the web address http://moment.utmb.edu/allquads.
AB - The G-quadruplex is a non-canonical DNA structure biologically significant in DNA replication, transcription and telomere stability. To date, only G4s with all guanines originating from the same strand of DNA have been considered in the context of the human nuclear genome. Here, I discuss interstrand topological configurations of G-quadruplex DNA, consisting of guanines from both strands of genomic DNA; an algorithm is presented for predicting such structures. I have identified over 550,000 non-overlapping interstrand Gquadruplex forming sequences in the human genome - significantly more than intrastrand configurations. Functional analysis of interstrand G-quadruplex sites shows strong association with transcription initiation, the results are consistent with the XPB and XPD transcriptional helicases binding only to G-quadruplex DNA with interstrand topology. Interstrand quadruplexes are also enriched in origin of replication sites. Several topology classes of interstrand quadruplex-forming sequences are possible, and different topologies are enriched in different types of structural elements. The list of interstrand quadruplex forming sequences, and the computer program used for their prediction are available at the web address http://moment.utmb.edu/allquads.
UR - http://www.scopus.com/inward/record.url?scp=84954042292&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84954042292&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0146174
DO - 10.1371/journal.pone.0146174
M3 - Article
C2 - 26727593
AN - SCOPUS:84954042292
SN - 1932-6203
VL - 11
JO - PloS one
JF - PloS one
IS - 1
M1 - e0146174
ER -