Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq

ELife
Jason G Dumelie, Samie R Jaffrey

Abstract

R-loops are features of chromatin consisting of a strand of DNA hybridized to RNA, as well as the expelled complementary DNA strand. R-loops are enriched at promoters where they have recently been shown to have important roles in modifying gene expression. However, the location of promoter-associated R-loops and the genomic domains they perturb to modify gene expression remain unclear. To resolve this issue, we developed a bisulfite-based approach, bisDRIP-seq, to map R-loops across the genome at near-nucleotide resolution in MCF-7 cells. We found the location of promoter-associated R-loops is dependent on the presence of introns. In intron-containing genes, R-loops are bounded between the transcription start site and the first exon-intron junction. In intronless genes, the 3' boundary displays gene-specific heterogeneity. Moreover, intronless genes are often associated with promoter-associated R-loop formation. Together, these studies provide a high-resolution map of R-loops and identify gene structure as a critical determinant of R-loop formation.

References

Jun 11, 1979·Nucleic Acids Research·D B KabackN Davidson
Feb 11, 1975·Biochemistry·T S Hsieh, J C Wang
Mar 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·M FrommerC L Paul
May 1, 1986·Journal of Immunological Methods·S J BoguslawskiR J Carrico
Feb 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·R L BrinsterR D Palmiter
Oct 4, 1972·Journal of the American Chemical Society·S M KupchanR F Bryan
May 1, 1981·Cell·L M HerefordC S McLaughlin
Aug 15, 1996·Nucleic Acids Research·R LandgrafD S Sigman
Nov 26, 1999·Gene·Z Dominski, W F Marzluff
Mar 15, 2006·The Journal of Cell Biology·Ji-Long LiuJoseph G Gall
Feb 1, 1967·Proceedings of the National Academy of Sciences of the United States of America·E Robbins, T W Borun
Apr 29, 2006·Nature Genetics·Piero CarninciYoshihide Hayashizaki
Mar 11, 2008·Cell·Dustin E SchonesKeji Zhao
Oct 18, 2008·Nature Reviews. Genetics·William F MarzluffRobert J Duronio
Dec 21, 2010·Nature Cell Biology·Yuntao S MaoDavid L Spector
Jan 12, 2011·Nature Biotechnology·James T RobinsonJill P Mesirov
Feb 1, 2011·Nature Chemical Biology·Denis V TitovJun O Liu
Apr 16, 2011·Bioinformatics·Felix Krueger, Simon R Andrews
Sep 15, 2011·Gene·Amel LouhichiAhmed Rebaï
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Mar 7, 2012·Nature Reviews. Genetics·Boris LenhardPiero Carninci
Apr 21, 2012·Briefings in Bioinformatics·Helga ThorvaldsdóttirJill P Mesirov
Jul 31, 2012·Cell Reports·Nicole I BiebersteinKarla M Neugebauer
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Sep 8, 2012·Genome Research·Jennifer HarrowTim J Hubbard
May 3, 2013·Genome Research·Nasun HahW Lee Kraus
May 28, 2013·Cell·Fedor KouzineRafael Casellas
Jun 21, 2013·Journal of Molecular Recognition : JMR·Damilola D PhillipsClinton E Leysath
Nov 1, 2013·Molecular Biology of the Cell·Tetsuro HiroseGérard Pierron
Jan 18, 2014·Nature Reviews. Genetics·David SimsChris P Ponting
Nov 10, 2015·Nature Structural & Molecular Biology·Poshen B ChenThomas G Fazzio
Nov 22, 2015·Nucleic Acids Research·Matthew L SpeirW James Kent

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Citations

Apr 17, 2018·Médecine sciences : M/S·Benoit Palancade
Nov 14, 2017·Nature Reviews. Genetics·Katharine H Wrighton
Oct 12, 2018·Proceedings of the National Academy of Sciences of the United States of America·Sonia SilvaAndrés Aguilera
Dec 18, 2019·The Journal of Biological Chemistry·Youssef A HegazyElizabeth J Tran
Jan 17, 2020·Current Protocols in Molecular Biology·Qingqing Yan, Kavitha Sarma
Mar 9, 2020·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Rachel J O'Neill
Jun 17, 2020·Nucleic Acids Research·Magdalena P CrossleyKarlene A Cimprich
Jul 4, 2020·Journal of Cellular Physiology·Cheng PengYandong Zhang
Feb 6, 2020·Cold Spring Harbor Symposia on Quantitative Biology·Tomohiro YamazakiTetsuro Hirose
Feb 2, 2020·Nature Reviews. Molecular Cell Biology·Christof Niehrs, Brian Luke
Apr 12, 2019·The Biochemical Journal·Emily J ShieldsRoberto Bonasio
Oct 3, 2019·Critical Reviews in Biochemistry and Molecular Biology·Tanya T Paull
Mar 7, 2020·International Journal of Molecular Sciences·Giulia Maria NavaFederico Lazzaro
Mar 19, 2020·Journal of Biomedical Science·Chia-Yu GuhHsueh-Ping Chu
Aug 9, 2020·Nature Reviews. Genetics·Dali ZongAndré Nussenzweig
Dec 30, 2020·International Journal of Molecular Sciences·Ilaria Rosso, Fabrizio d'Adda di Fagagna
Feb 28, 2020·Journal of Molecular Biology·Maika MaligFrederic Chedin
Feb 19, 2021·Science Advances·Kang WangKaiwei Liang
Mar 12, 2021·Nucleic Acids Research·Elena A Kouzminova, Andrei Kuzminov
Apr 27, 2021·Non-coding RNA Research·Zhenxing SongChuan Huang
May 1, 2021·International Journal of Molecular Sciences·Zuzana NascakovaJana Dobrovolna
Jun 12, 2021·Journal of Experimental Botany·Jingjing GaoWenli Zhang
Jul 31, 2021·Nucleic Acids Research·Wei YuanYanzhong Yang
Aug 31, 2021·Biochimica Et Biophysica Acta. Gene Regulatory Mechanisms·Arum Kim, Gang Greg Wang

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Datasets Mentioned

BETA
GSM1067414
GSM1067415
GSM1720613
GSM1720614
GSM1720615
GSM1720616

Methods Mentioned

BETA
immunoprecipitation
DRIP-seq
using
bisDRIP-seq
GRO-seq
RNA-seq
ChIP
eCLIP
DRIPc-seq
deamination

Software Mentioned

Bowtie2
CASAVA
bisDRIP
Python
metaplot
seq
bisDRIPseqmetaplotanalysis
R random
fANCOVA
violin

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