The effects of chromatin organization on variation in mutation rates in the genome

Nature Reviews. Genetics
Kateryna D Makova, Ross C Hardison

Abstract

The variation in local rates of mutations can affect both the evolution of genes and their function in normal and cancer cells. Deciphering the molecular determinants of this variation will be aided by the elucidation of distinct types of mutations, as they differ in regional preferences and in associations with genomic features. Chromatin organization contributes to regional variation in mutation rates, but its contribution differs among mutation types. In both germline and somatic mutations, base substitutions are more abundant in regions of closed chromatin, perhaps reflecting error accumulation late in replication. By contrast, a distinctive mutational state with very high levels of insertions and deletions (indels) and substitutions is enriched in regions of open chromatin. These associations indicate an intricate interplay between the nucleotide sequence of DNA and its dynamic packaging into chromatin, and have important implications for current biomedical research. This Review focuses on recent studies showing associations between chromatin state and mutation rates, including pairwise and multivariate investigations of germline and somatic (particularly cancer) mutations.

References

Feb 17, 1968·Nature·M Kimura
Jun 19, 1981·Science·M Ehrlich, R Y Wang
Aug 7, 1998·Journal of Molecular Evolution·W Makalowski, M S Boguski
Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Nov 22, 2001·Proceedings of the National Academy of Sciences of the United States of America·F ChiaromonteR C Hardison
Feb 2, 2002·Nature Reviews. Genetics·Rhea Vallente Samonte, Evan E Eichler
Feb 16, 2002·Science·Job DekkerNancy Kleckner
Aug 10, 2002·Science·Jeffrey A BaileyEvan E Eichler
Mar 4, 2003·Nature Genetics·Phil GreenEric D Green
Jun 26, 2003·Nucleic Acids Research·William H MajorosSteven L Salzberg
Aug 26, 2003·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jia Li, Webb Miller
Nov 14, 2003·Genome Research·Elizabeth LouieJacek Majewski
Oct 8, 2004·Nature Biotechnology·Sean R Eddy
Jul 19, 2005·Genome Research·Daniel J Gaffney, Peter D Keightley
Sep 6, 2005·Genome Research·Ines HellmannSusan E Ptak
May 11, 2007·BMC Evolutionary Biology·James G D PrendergastColin A M Semple
May 25, 2007·Nature·Peter Fraser, Wendy Bickmore
Oct 19, 2007·PLoS Computational Biology·Erika M KvikstadKateryna D Makova
Nov 7, 2007·Nature Structural & Molecular Biology·Bradley R Cairns
Nov 23, 2007·Genome Research·Yogeshwar D KelkarKateryna D Makova
May 2, 2008·Genome Biology·Svitlana TyekuchevaFrancesca Chiaromonte
May 9, 2008·Genome Research·Paz Polak, Peter F Arndt
Oct 28, 2008·Trends in Genetics : TIG·Stefan WashietlNick Goldman
Nov 1, 2008·Molecular Biology and Evolution·Carina F MugalMartin Peifer
Nov 8, 2008·PLoS Genetics·Tobias WarneckeLaurence D Hurst
Mar 17, 2009·Nature Genetics·John A StamatoyannopoulosShamil R Sunyaev
Feb 6, 2010·Genome Research·Louise LaurentChia-Lin Wei
May 26, 2010·Epigenetics & Chromatin·Asaf Hellman, Andrew Chess
Dec 1, 2010·Nature Reviews. Genetics·Vicky W ZhouBradley E Bernstein
Jan 12, 2011·Nature Reviews. Genetics·Christian Beisel, Renato Paro
Mar 15, 2011·Nature Structural & Molecular Biology·Michael Y TolstorukovPeter J Park
Mar 24, 2011·Genome Biology·Guruprasad AnandaKateryna D Makova
Mar 29, 2011·Nature·Jason ErnstBradley E Bernstein
Sep 10, 2011·Genome Research·James G D Prendergast, Colin A M Semple
Sep 29, 2011·Human Mutation·Alan HodgkinsonAdam Eyre-Walker

❮ Previous
Next ❯

Citations

Feb 19, 2016·Nucleus·Dana Branzei, Barnabas Szakal
Apr 10, 2016·Current Opinion in Cell Biology·Dana Branzei, Ivan Psakhye
Jul 8, 2015·Nature Reviews. Genetics·Darren J Burgess
Jun 21, 2016·Nature Genetics·Jakob M GoldmannJohn E Niederhuber
Jul 31, 2016·BMC Genomics·Guénola DrillonAlain Arneodo
Oct 25, 2016·Scientific Reports·Tatiana V TatarinovaNickolai Alexandrov
Jan 31, 2017·Biophysical Journal·Marco TompitakHelmut Schiessel
Apr 21, 2018·PLoS Computational Biology·Reuben M BuckleyDavid L Adelson
Sep 9, 2017·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Didier Auboeuf
May 22, 2018·Nanoscale·Rebekah J KaradeemaDmitry M Kolpashchikov
Nov 22, 2017·The Plant Journal : for Cell and Molecular Biology·Ryan F McCormickJohn E Mullet
Jun 30, 2018·The Journal of Biological Chemistry·Homa RahnamounShannon M Lauberth
Oct 21, 2018·Genome Research·Armande Ang HoulePhilip Awadalla
Oct 27, 2018·Nucleic Acids Research·Morad M Mokhtar, Mohamed A M Atia
Feb 20, 2019·Endocrine-related Cancer·Peder Rustøen Braadland, Alfonso Urbanucci
Dec 6, 2018·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Cheuk-Ting LawChun-Ming Wong
Mar 13, 2019·International Journal of Cancer. Journal International Du Cancer·Stefano MeucciStefano Cacciatore
Aug 9, 2017·Nature Reviews. Immunology·Edze R WestraAngus Buckling
Dec 29, 2016·EMBO Molecular Medicine·Didier Leroy
Dec 8, 2015·G3 : Genes - Genomes - Genetics·Karl M GlastadBrendan G Hunt
Oct 2, 2017·Genome Medicine·Arpit Mishra, R David Hawkins
Jun 7, 2019·Current Opinion in Hematology·Zhenrui LiLinheng Li
Feb 12, 2020·Molecular Biology and Evolution·Yubin YanRuolin Yang
Apr 2, 2020·Genome Biology and Evolution·Kohta YoshidaJun Kitano

❮ Previous
Next ❯

Related Concepts

Related Feeds

Cancer Epigenetics and Chromatin (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 chromatin and its role in cancer epigenetics please follow this feed to learn more.

Cancer Epigenetics Chromatin Complexes (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 chromatin complexes and their role in cancer epigenetics.

© 2022 Meta ULC. All rights reserved