Single-cell transcriptogenomics reveals transcriptional exclusion of ENU-mutated alleles

Mutation Research. Fundamental and Molecular Mechanisms of Mutagenesis
Wenge LiJan Vijg

Abstract

Recently, great progress has been made in single cell genomics and transcriptomics. Here, we present an integrative method, termed single-cell transcriptogenomics (SCTG), in which whole exome sequencing and RNA-seq is performed concurrently on single cells. This methodology enables one to track germline and somatic variants directly from the genome to the transcriptome in individual cells. Mouse embryonic fibroblasts were treated with the powerful mutagen ethylnitrosourea (ENU) and subjected to SCTG. Interestingly, while germline variants were found to be transcribed in an allelically balanced fashion, a significantly different pattern of allelic exclusion was observed for ENU-mutant variants. These results suggest that the adverse effects of induced mutations, in contrast to germline variants, may be mitigated by allelically biased transcription. They also illustrate how SCTG can be instrumental in the direct assessment of phenotypic consequences of genomic variants.

References

Sep 27, 2000·Proceedings of the National Academy of Sciences of the United States of America·J H Bielas, J A Heddle
Nov 21, 2000·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·S L Rutherford
Mar 30, 2002·Nature Biotechnology·Christoph A KleinGert Riethmüller
Oct 31, 2006·Nucleic Acids Research·Claudia H Hartmann, Christoph A Klein
Nov 4, 2006·Cell·Sophie E PoloGeneviève Almouzni
Mar 14, 2007·Annual Review of Biochemistry·Yao-Fu ChangMiles F Wilkinson
Jun 23, 2007·BMC Molecular Biology·K Ryo TakahasiYoichi Gondo
Nov 17, 2007·Science·Alexander GimelbrantAndrew Chess
Jun 24, 2008·Human Mutation·Arkadiusz PiotrowskiJan P Dumanski
Oct 30, 2008·Cell·Arjun Raj, Alexander van Oudenaarden
Nov 13, 2008·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Lioudmila V SharovaMinoru S H Ko
Apr 8, 2009·Nature Methods·Fuchou TangM Azim Surani
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Feb 12, 2010·Bioinformatics·Thomas D Wu, Serban Nacu
Mar 3, 2010·Annual Review of Biochemistry·Kazuko Nishikura
Apr 1, 2010·Nature Methods·Ivan A AdzhubeiShamil R Sunyaev
Jun 3, 2010·Cold Spring Harbor Protocols·Matthias Meyer, Martin Kircher
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Nov 5, 2010·Annual Review of Genetics·Daniel F JaroszSusan Lindquist
Jan 12, 2011·Nature Biotechnology·James T RobinsonJill P Mesirov
Apr 1, 2011·Nature Methods·Fuchou TangM Azim Surani
Jun 15, 2011·Nature Genetics·Donald F ConradUNKNOWN 1000 Genomes Project
Jul 29, 2011·Nature·Ryan D MorinMarco A Marra
Sep 17, 2011·Nature·Thomas M KeaneDavid J Adams
Nov 1, 2011·Nature·J Kenneth BaillieGeoffrey J Faulkner
Nov 17, 2011·Nucleic Acids Research·Michael GundryJan Vijg
Jul 24, 2012·Nature Biotechnology·Daniel RamsköldRickard Sandberg
Sep 4, 2012·Cell Reports·Tamar HashimshonyItai Yanai
Sep 6, 2012·Current Opinion in Cell Biology·Davood Sabour, Hans R Schöler
Sep 8, 2012·Science·Matthew T MauranoJohn A Stamatoyannopoulos
Oct 16, 2012·Proceedings of the National Academy of Sciences of the United States of America·Roy D DarLeor S Weinberger
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Feb 12, 2013·Nature Biotechnology·Kristian CibulskisGad Getz
Jul 31, 2013·Nature Reviews. Genetics·Ehud ShapiroSten Linnarsson
Sep 24, 2013·Nature Methods·Simone PicelliRickard Sandberg
Sep 24, 2013·Nature Methods·Philip BrenneckeMarcus G Heisler

❮ Previous
Next ❯

Citations

Jun 27, 2015·Human Molecular Genetics·Quin F Wills, Adam J Mead
Jan 18, 2018·Briefings in Functional Genomics·Mark W E J FiersStein Aerts
May 5, 2018·Annual Review of Genomics and Human Genetics·Lia ChappellThierry Voet
Jun 18, 2017·Frontiers in Genetics·Sören Müller, Aaron Diaz
Sep 16, 2020·Experimental & Molecular Medicine·Jean FanFan Zhang
Aug 11, 2020·Computational and Structural Biotechnology Journal·Xinlin HuJing Qin
Mar 13, 2021·Ageing Research Reviews·Jan Vijg
Aug 21, 2020·Trends in Biotechnology·Anjun MaQin Ma

❮ Previous
Next ❯

Related Concepts

Related Feeds

Cancer Epigenetics and Senescence (Keystone)

Epigenetic changes are present and dysregulated in many cancers, including DNA methylation, non-coding RNA segments and post-translational protein modifications. The epigenetic changes may be involved in regulating senescence in cancer cells. This feed captures the latest research on cancer epigenetics and senescence.

Cancer Epigenetics & Metabolism (Keystone)

Epigenetic changes are present and dysregulated in many cancers, including DNA methylation, non-coding RNA segments and post-translational protein modifications. The epigenetic changes may or may not provide advantages for the cancer cells. This feed focuses on the relationship between cell metabolism, epigenetics and tumor differentiation.

Cancer Genomics (Keystone)

Cancer genomics approaches employ high-throughput technologies to identify the complete catalog of somatic alterations that characterize the genome, transcriptome and epigenome of cohorts of tumor samples. Discover the latest research using such technologies in this feed.

Cancer -Omics

A variety of different high-throughput technologies can be used to identify the complete catalog of changes that characterize the molecular profile of cohorts of tumor samples. Discover the latest insights gained from cancer 'omics' in this feed.

Related Papers

Rinshō shinkeigaku = Clinical neurology
Karen Nuytemans, Jeffery M Vance
Nature Biotechnology
Siddharth S DeyAlexander van Oudenaarden
Environmental Microbiology
Howard Ochman
© 2022 Meta ULC. All rights reserved