Genome-wide colocalization of RNA-DNA interactions and fusion RNA pairs

Proceedings of the National Academy of Sciences of the United States of America
Zhangming YanSheng Zhong


Fusion transcripts are used as biomarkers in companion diagnoses. Although more than 15,000 fusion RNAs have been identified from diverse cancer types, few common features have been reported. Here, we compared 16,410 fusion transcripts detected in cancer (from a published cohort of 9,966 tumor samples of 33 cancer types) with genome-wide RNA-DNA interactions mapped in two normal, noncancerous cell types [using iMARGI, an enhanced version of the mapping of RNA-genome interactions (MARGI) assay]. Among the top 10 most significant RNA-DNA interactions in normal cells, 5 colocalized with the gene pairs that formed fusion RNAs in cancer. Furthermore, throughout the genome, the frequency of a gene pair to exhibit RNA-DNA interactions is positively correlated with the probability of this gene pair to present documented fusion transcripts in cancer. To test whether RNA-DNA interactions in normal cells are predictive of fusion RNAs, we analyzed these in a validation cohort of 96 lung cancer samples using RNA sequencing (RNA-seq). Thirty-seven of 42 fusion transcripts in the validation cohort were found to exhibit RNA-DNA interactions in normal cells. Finally, by combining RNA-seq, single-molecule RNA FISH, and DNA FISH, we detected a ca...Continue Reading


Sep 23, 2008·Nature Methods·Arjun RajSanjay Tyagi
Nov 19, 2008·PathoGenetics·Wenli GuJames R Lupski
Jan 17, 2009·The American Journal of Pathology·Maria Paola MartelliBrunangelo Falini
Sep 11, 2012·Nature Methods·Harmen J G van de WerkenWouter de Laat
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Aug 21, 2013·Nature Protocols·Anna LyubimovaAlexander van Oudenaarden
Aug 21, 2013·PLoS Computational Biology·Michael LawrenceVincent J Carey
Jan 1, 2014·Cell Reports·Stefan SemrauAlexander van Oudenaarden
Mar 29, 2014·PloS One·Fatu Badiane MarkeyMona Batish
Apr 4, 2014·Bioinformatics·W Torres-GarciaRoel G W Verhaak
Jun 16, 2014·Breast Cancer Research and Treatment·Katherine E VarleyRichard M Myers
Sep 11, 2014·Nature Communications·Nicolas StranskyChristoph Lengauer
Dec 17, 2014·Oncogene·Kosuke YoshiharaRoel G W Verhaak
May 23, 2015·Nature Reviews. Cancer·Fredrik MertensFelix Mitelman
May 29, 2015·Genome Medicine·Nadia M DavidsonAlicia Oshlack
Aug 27, 2015·Genome Biology·Takashi NaganoPeter Fraser
Dec 3, 2015·BMC Genomics·John LaiJyotsna Batra
Dec 20, 2015·Genome Medicine·Chandan Kumar-SinhaArul M Chinnaiyan
May 22, 2016·Bioinformatics·Zuguang GuMatthias Schlesner
Jun 25, 2016·Nature Communications·Tri C NguyenSheng Zhong
Dec 2, 2016·Nucleic Acids Research·Simon A ForbesPeter J Campbell
Feb 22, 2017·Current Biology : CB·Bharat SridharSheng Zhong
Feb 26, 2017·F1000Research·Tiago C SilvaHoutan Noushmehr
Mar 30, 2017·Microbial Genomics·Silvia ArgimónDavid M Aanensen
Nov 4, 2017·Nucleic Acids Research·Xin HuRoel G W Verhaak
Nov 28, 2017·PLoS Computational Biology·Ruolin Liu, Julie Dickerson
Jan 23, 2018·Biochimica Et Biophysica Acta. Reviews on Cancer·Xiaofeng DaiJianying Zhang
Jul 19, 2018·Genome Biology·Xiaoyi CaoSheng Zhong


Oct 18, 2019·Nature Protocols·Weixin WuSheng Zhong
Aug 9, 2020·Nature Reviews. Genetics·Dali ZongAndré Nussenzweig
Mar 30, 2020·Science China. Life Sciences·Cong LiuZhihua Zhang
May 31, 2020·Non-coding RNA·Masaki Kato, Piero Carninci
Sep 26, 2020·Nucleic Acids Research·Volodymyr TsybulskyiIrmtraud M Meyer
Oct 17, 2020·Nature Communications·Riccardo CalandrelliSheng Zhong
Dec 14, 2019·Genes & Diseases·Hao WuHui Li

Methods Mentioned

membrane filtration
fluorescence imaging

Related Concepts

Related Feeds

CZI Human Cell Atlas Seed Network

The aim of the Human Cell Atlas (HCA) is to build reference maps of all human cells in order to enhance our understanding of health and disease. The Seed Networks for the HCA project aims to bring together collaborators with different areas of expertise in order to facilitate the development of the HCA. Find the latest research from members of the HCA Seed Networks here.

Related Papers

Zhongguo fei ai za zhi = Chinese journal of lung cancer
Tong YangJun Chen
The American Journal of Pathology
Hiroyuki Mano, Kengo Takeuchi
Zhonghua bing li xue za zhi Chinese journal of pathology
Lu WangRen-sheng Lai
Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases
Xun Wang, Chun-Xue Bai
© 2021 Meta ULC. All rights reserved