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Articles

Studying histone inheritance in different systems using imaging-based methods and perspectives

Emily Zion, Xin Chen

Biochem Soc Trans (2023) BST20220983.

DOI: https://doi.org/10.1042/BST20220983

Published: 12 May 2023

... information, they can take on similar or different cell fates, resulting from a symmetric or asymmetric division. These fates can be modulated by epigenetic mechanisms that can alter gene expression without changing genetic information. Histone proteins, which wrap DNA into fundamental units of chromatin...

View article titled, Studying histone inheritance in different systems using imaging-based methods and perspectives

Articles

Small regulatory RNAs in rice epigenetic regulation

So Young Park, Jungnam Cho, Dong-Hoon Jeong

Biochem Soc Trans (2022) 50 (3): 1215–1225.

DOI: https://doi.org/10.1042/BST20210336

Published: 17 May 2022

...So Young Park; Jungnam Cho; Dong-Hoon Jeong Plant small RNAs (sRNAs) are short non-coding RNAs that are implicated in various regulatory processes involving post-transcriptional gene silencing and epigenetic gene regulation. In epigenetic regulation, sRNAs are primarily involved in RNA-directed DNA...

View article titled, Small regulatory RNAs in rice epigenetic regulation

Articles

Encyclopaedia of eukaryotic DNA methylation: from patterns to mechanisms and functions

Peter Sarkies

Biochem Soc Trans (2022) 50 (3): 1179–1190.

DOI: https://doi.org/10.1042/BST20210725

Published: 06 May 2022

...Peter Sarkies DNA methylation is an epigenetic modification with a very long evolutionary history. However, DNA methylation evolves surprisingly rapidly across eukaryotes. The genome-wide distribution of methylation diversifies rapidly in different lineages, and DNA methylation is lost altogether...

View article titled, Encyclopaedia of eukaryotic DNA methylation: from patterns to mechanisms and functions

Articles

Epigenetic regulation of human non-coding RNA gene transcription

Marco Morselli, Giorgio Dieci

Biochem Soc Trans (2022) 50 (2): 723–736.

DOI: https://doi.org/10.1042/BST20210860

Published: 14 March 2022

...Marco Morselli; Giorgio Dieci Recent investigations on the non-protein-coding transcriptome of human cells have revealed previously hidden layers of gene regulation relying on regulatory non-protein-coding (nc) RNAs, including the widespread ncRNA-dependent regulation of epigenetic chromatin states...

View article titled, Epigenetic regulation of human non-coding RNA gene transcription

Articles

Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits

Ulduz Vafadarshamasbi, Emma Mace, David Jordan, Peter A. Crisp

Biochem Soc Trans (2022) 50 (1): 583–596.

DOI: https://doi.org/10.1042/BST20210908

Published: 25 February 2022

... in the patterns of DNA methylation have the potential to provide for epigenetic inheritance of traits. Contemporary epigenomic technologies provide information beyond sequence variation and could supply alternative sources of trait variation for improvement in crops such as sorghum. Yet, compared with other...

View article titled, Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits

Articles

Role of macronutrient intake in the epigenetics of obesity

Priyadarshni Patel, Jeganathan Ramesh Babu, Xu Wang, Thangiah Geetha

Biochem Soc Trans (2022) 50 (1): 487–497.

DOI: https://doi.org/10.1042/BST20211069

Published: 07 January 2022

... found to this epidemic. Over the last decade, there has been a tremendous advancement in understanding the science of epigenetics, as well as a rise in public interest in learning more about the influence of diet and lifestyle choices on the health of an individual. Without affecting the underlying DNA...

View article titled, Role of macronutrient intake in the epigenetics of obesity

Articles

The tandem repeat modules of Xist lncRNA: a swiss army knife for the control of X-chromosome inactivation

Ana Cláudia Raposo, Miguel Casanova, Anne-Valerie Gendrel, Simão Teixeira da Rocha

Biochem Soc Trans (2021) 49 (6): 2549–2560.

DOI: https://doi.org/10.1042/BST20210253

Published: 09 December 2021

... of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) . chromatin epigenetics lncRNA tandem repeat X-chromosome inactivation X - i nactive- s pecific t ranscript ( Xist ) is a l ong n on- c oding RNA (lncRNA) responsible for X - C hromosome...

View article titled, The tandem repeat modules of Xist lncRNA: a swiss army knife for the control of X-chromosome inactivation

Articles

Structural insights into the interactions of Polycomb Repressive Complex 2 with chromatin

Akhil Gargey Iragavarapu, Liqi Yao, Vignesh Kasinath

Biochem Soc Trans (2021) 49 (6): 2639–2653.

DOI: https://doi.org/10.1042/BST20210450

Published: 08 November 2021

... of the Biochemical Society 2021 chromatin cryo-electron microscopy epigenetics eukaryotic gene expression transcription Eukaryotic cells pack their DNA (∼6 billion bases) into the small volume of the nucleus (1 × 10 2 –1 × 10 5 µm 3 ) by organizing their DNA into complex but defined structures...

View article titled, Structural insights into the interactions of Polycomb Repressive Complex 2 with chromatin

Articles

Chemical biology approaches to study histone interactors

Antony J. Burton, Ghaith M. Hamza, Andrew X. Zhang, Tom W. Muir

Biochem Soc Trans (2021) 49 (5): 2431–2441.

DOI: https://doi.org/10.1042/BST20210772

Published: 28 October 2021

...-translational modification. Perturbation to these networks leads to genomic instability and disease, presenting epigenetic proteins as key therapeutic targets. This mini-review will describe progress in mapping the combinatorial histone PTM landscape, and recent chemical biology approaches to map histone...

View article titled, Chemical biology approaches to study histone interactors

Articles

To export, or not to export: how nuclear export factor variants resolve Piwi's dilemma

Sheng Wang, Xiaohua Lu, Ding Qiu, Yang Yu

Biochem Soc Trans (2021) 49 (5): 2073–2079.

DOI: https://doi.org/10.1042/BST20201171

Published: 13 October 2021

... by Portland Press Limited on behalf of the Biochemical Society 2021 epigenetics gene silencing piRNA transposons Genome integrity of eukaryotes is constantly challenged by parasitic transposable elements [ 1–8 ]. To defend germline genomes, small RNAs guide their associated Argonaute proteins...

View article titled, To export, or not to export: how nuclear export factor variants resolve Piwi's dilemma

Articles

Exploring chromatin structural roles of non-coding RNAs at imprinted domains

David Llères, Yui Imaizumi, Robert Feil

Biochem Soc Trans (2021) 49 (4): 1867–1879.

DOI: https://doi.org/10.1042/BST20210758

Published: 02 August 2021

...@igmm.cnrs.fr ) 19 5 2021 5 7 2021 6 7 2021 © 2021 The Author(s) 2021 This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) . chromatin CTCF epigenetics...

View article titled, Exploring chromatin structural roles of non-coding RNAs at imprinted domains

Articles

The MLL3/4 H3K4 methyltransferase complex in establishing an active enhancer landscape

Lan-Hsin Wang, Marvin Angelo E. Aberin, Sean Wu, Shu-Ping Wang

Biochem Soc Trans (2021) 49 (3): 1041–1054.

DOI: https://doi.org/10.1042/BST20191164

Published: 22 June 2021

... 4.0 (CC BY-NC-ND) . cancer enhancer epigenetics gene expression and regulation H3K4 histone lysine methyltransferase Precise gene regulation is required for the correct cellular identity in multicellular organisms. However, aberrant gene expression often leads to detrimental...

View article titled, The MLL3/4 H3K4 methyltransferase complex in establishing an active enhancer landscape

Articles

Nutrient regulation of the flow of genetic information by O-GlcNAcylation

Yi Zhu, Gerald W. Hart

Biochem Soc Trans (2021) 49 (2): 867–880.

DOI: https://doi.org/10.1042/BST20200769

Published: 26 March 2021

... ( yzhu@uga.edu ) or Gerald W. Hart ( gerald.hart@uga.edu ) 15 1 2021 1 3 2021 3 3 2021 © 2021 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2021 DNA synthesis and repair epigenetics O-GlcNAc post translational modification...

View article titled, Nutrient regulation of the flow of genetic information by O-GlcNAcylation

Articles

Using computational modelling to reveal mechanisms of epigenetic Polycomb control

Cecilia Lövkvist, Martin Howard

Biochem Soc Trans (2021) 49 (1): 71–77.

DOI: https://doi.org/10.1042/BST20190955

Published: 22 February 2021

... epigenetic memory elements of PRC2-mediated silencing. As these marks are stored locally in the chromatin, PRC2-based memory is a cis -acting system. A key feature of stable epigenetic memory in cis is PRC2-mediated, self-reinforcing feedback from K27-methylated histones onto nearby histones in a read-write...

View article titled, Using computational modelling to reveal mechanisms of epigenetic Polycomb control

Articles

Keeping your options open: insights from Dppa2/4 into how epigenetic priming factors promote cell plasticity

Mélanie A. Eckersley-Maslin

Biochem Soc Trans (2020) 48 (6): 2891–2902.

DOI: https://doi.org/10.1042/BST20200873

Published: 18 December 2020

...Mélanie A. Eckersley-Maslin The concept of cellular plasticity is particularly apt in early embryonic development, where there is a tug-of-war between the stability and flexibility of cell identity. This balance is controlled in part through epigenetic mechanisms. Epigenetic plasticity dictates how...

View article titled, Keeping your options open: insights from Dppa2/4 into how epigenetic priming factors promote cell plasticity

Articles

Epigenetic plasticity, selection, and tumorigenesis

William A. Flavahan

Biochem Soc Trans (2020) 48 (4): 1609–1621.

DOI: https://doi.org/10.1042/BST20191215

Published: 14 August 2020

...William A. Flavahan Epigenetic processes converge on chromatin in order to direct a cell's gene expression profile. This includes both maintaining a stable cell identity, but also priming the cell for specific controlled transitions, such as differentiation or response to stimuli. In cancer...

View article titled, Epigenetic plasticity, selection, and tumorigenesis

Articles

Relating SMCHD1 structure to its function in epigenetic silencing

In Collection

Protein structure and function

Alexandra D. Gurzau, Marnie E. Blewitt, Peter E. Czabotar, James M. Murphy, Richard W. Birkinshaw

Biochem Soc Trans (2020) 48 (4): 1751–1763.

DOI: https://doi.org/10.1042/BST20200242

Published: 11 August 2020

...Alexandra D. Gurzau; Marnie E. Blewitt; Peter E. Czabotar; James M. Murphy; Richard W. Birkinshaw The structural maintenance of chromosomes hinge domain containing protein 1 (SMCHD1) is a large multidomain protein involved in epigenetic gene silencing. Variations in the SMCHD1 gene are associated...

View article titled, Relating SMCHD1 structure to its function in epigenetic silencing

Caroline Delandre, Owen J. Marshall

Biochem Soc Trans (2019) 47 (2): 691–700.

DOI: https://doi.org/10.1042/BST20180605

Published: 22 March 2019

.... Correspondence: Owen J. Marshall ( owen.marshall@utas.edu.au ) 4 1 2019 21 2 2019 22 2 2019 © 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2019 chromatin developmental biology Drosophila melanogaster epigenetics...

View article titled, United colours of chromatin? Developmental genome organisation in flies

Articles

Chromatin modulation and gene regulation in plants: insight about PRC1 function

Qiannan Wang, Wen-Hui Shen

Biochem Soc Trans (2018) 46 (4): 957–966.

DOI: https://doi.org/10.1042/BST20170576

Published: 31 July 2018

... ) or Wen-Hui Shen ( wen-hui.shen@ibmp-cnrs.unistra.fr ) 21 4 2018 24 5 2018 25 5 2018 © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2018 Arabidopsis thaliana chromatin remodeling epigenetics gene transcription histone H2A...

View article titled, Chromatin modulation and gene regulation in plants: insight about PRC1 function

Articles

Studying X chromosome inactivation in the single-cell genomic era

Andrew Keniry, Marnie E. Blewitt

Biochem Soc Trans (2018) 46 (3): 577–586.

DOI: https://doi.org/10.1042/BST20170346

Published: 20 April 2018

...Andrew Keniry; Marnie E. Blewitt Single-cell genomics is set to revolutionise our understanding of how epigenetic silencing works; by studying specific epigenetic marks or chromatin conformations in single cells, it is possible to ask whether they cause transcriptional silencing or are instead...

View article titled, Studying X chromosome inactivation in the single-cell genomic era

Articles

O-GlcNAcylation and chromatin remodeling in mammals: an up-to-date overview

Maïté Leturcq, Tony Lefebvre, Anne-Sophie Vercoutter-Edouart

Biochem Soc Trans (2017) 45 (2): 323–338.

DOI: https://doi.org/10.1042/BST20160388

Published: 13 April 2017

...Maïté Leturcq; Tony Lefebvre; Anne-Sophie Vercoutter-Edouart Post-translational modifications of histones and the dynamic DNA methylation cycle are finely regulated by a myriad of chromatin-binding factors and chromatin-modifying enzymes. Epigenetic modifications ensure local changes...

View article titled, O-GlcNAcylation and chromatin remodeling in mammals: an up-to-date overview

Articles

Protein acetylation as a means to regulate protein function in tune with metabolic state

Lei Shi, Benjamin P. Tu

Biochem Soc Trans (2014) 42 (4): 1037–1042.

DOI: https://doi.org/10.1042/BST20140135

Published: 11 August 2014

... 2014 acetyl-CoA acetylation epigenetics metabolism Fundamental aspects of the regulation of cell growth and proliferation remain incompletely understood. In investigations of the mechanisms of cell growth control, researchers have tended to focus on biological macromolecules...

View article titled, Protein acetylation as a means to regulate protein function in tune with metabolic state

Articles

Regulation of the 2-oxoglutarate-dependent dioxygenases and implications for cancer

Margreet C.M. Vissers, Caroline Kuiper, Gabi U. Dachs

Biochem Soc Trans (2014) 42 (4): 945–951.

DOI: https://doi.org/10.1042/BST20140118

Published: 11 August 2014

...Margreet C.M. Vissers; Caroline Kuiper; Gabi U. Dachs There is growing interest in the family of 2-OG (2-oxoglutarate)-dependent dioxygenase enzymes that catalyse the hydroxylation of a wide range of organic targets. Members of this family that regulate the cell's hypoxic response and epigenetic...

View article titled, Regulation of the 2-oxoglutarate-dependent dioxygenases and implications for cancer

Articles

Depression during pregnancy: molecular regulations of mothers’ and children's behaviour

Carmine M. Pariante

Biochem Soc Trans (2014) 42 (2): 582–586.

DOI: https://doi.org/10.1042/BST20130246

Published: 20 March 2014

... the suffering of the next generation. 1 email carmine.pariante@kcl.ac.uk 15 10 2013 © The Authors Journal compilation © 2014 Biochemical Society 2014 cortisol depression epigenetics hypothalamic–pituitary–adrenal axis intergenerational transmission maternal care pregnancy...

View article titled, Depression during pregnancy: molecular regulations of mothers’ and children's behaviour

Articles

HDAC inhibitors as cognitive enhancers in fear, anxiety and trauma therapy: where do we stand?

Nigel Whittle, Nicolas Singewald

Biochem Soc Trans (2014) 42 (2): 569–581.

DOI: https://doi.org/10.1042/BST20130233

Published: 20 March 2014

... and boosting mechanisms underlying learning, drug development in this field aims at designing CBT-augmenting compounds that help to overcome extinction learning deficits, promote long-term fear inhibition and thus support relapse prevention. Progress in revealing the role of epigenetic regulation of specific...

View article titled, HDAC inhibitors as cognitive enhancers in fear, anxiety and trauma therapy: where do we stand?

Articles

Epigenetic Mechanisms in Development and Disease

Adele Murrell, Paul J. Hurd, Ian C. Wood

Biochem Soc Trans (2013) 41 (3): 697–699.

DOI: https://doi.org/10.1042/BST20130051

Published: 23 May 2013

...Adele Murrell; Paul J. Hurd; Ian C. Wood Our advances in technology allow us to sequence DNA to uncover genetic differences not only between individuals, but also between normal and diseased cells within an individual. However, there is still a lot we have yet to understand regarding the epigenetic...

View article titled, Epigenetic Mechanisms in Development and Disease

Articles

Could lncRNAs contribute to β-cell identity and its loss in Type 2 diabetes?

Timothy J. Pullen, Guy A. Rutter

Biochem Soc Trans (2013) 41 (3): 797–801.

DOI: https://doi.org/10.1042/BST20120355

Published: 23 May 2013

... in the mechanisms which define and maintain β-cell identity. The advent of genome-wide analyses of chromatin modifications has highlighted the role of epigenetic factors in determining cell identity. There is also evidence from both human populations and animal models for an epigenetic component in susceptibility...

View article titled, Could lncRNAs contribute to β-cell identity and its loss in Type 2 diabetes?

Articles

Cross-talk among epigenetic modifications: lessons from histone arginine methylation

Diego Molina-Serrano, Vassia Schiza, Antonis Kirmizis

Biochem Soc Trans (2013) 41 (3): 751–759.

DOI: https://doi.org/10.1042/BST20130003

Published: 23 May 2013

...Diego Molina-Serrano; Vassia Schiza; Antonis Kirmizis Epigenetic modifications, including those occurring on DNA and on histone proteins, control gene expression by establishing and maintaining different chromatin states. In recent years, it has become apparent that epigenetic modifications do...

View article titled, Cross-talk among epigenetic modifications: lessons from histone arginine methylation

Articles

The impact of culture on epigenetic properties of pluripotent stem cells and pre-implantation embryos

Kirsten R. McEwen, Harry G. Leitch, Rachel Amouroux, Petra Hajkova

Biochem Soc Trans (2013) 41 (3): 711–719.

DOI: https://doi.org/10.1042/BST20130049

Published: 23 May 2013

... of pluripotent cells in vitro . Recent studies have, however, found that the choice of culture condition has a significant impact on epigenetic profiles of cultured pluripotent cells. Mouse and human ESCs (embryonic stem cells) show substantial epigenetic differences that are dependent on the culture condition...

View article titled, The impact of culture on epigenetic properties of pluripotent stem cells and pre-implantation embryos

Articles

The role of histone deacetylases in rheumatoid arthritis fibroblast-like synoviocytes

Sarah Hawtree, Munitta Muthana, Anthony G. Wilson

Biochem Soc Trans (2013) 41 (3): 783–788.

DOI: https://doi.org/10.1042/BST20130053

Published: 23 May 2013

...-transformed, auto-aggressive phenotype typified by loss of contact inhibition, reduced apoptosis and the production of matrix-degrading enzymes. The mechanisms involved in the development of this phenotype are unclear; however, increasing evidence implicates alterations in the epigenetic regulation of gene...

View article titled, The role of histone deacetylases in rheumatoid arthritis fibroblast-like synoviocytes

Articles

Epigenetics in the heart: the role of histone modifications in cardiac remodelling

Asmita Tingare, Bernard Thienpont, H. Llewelyn Roderick

Biochem Soc Trans (2013) 41 (3): 789–796.

DOI: https://doi.org/10.1042/BST20130012

Published: 23 May 2013

... expression programme is largely driven through epigenetic mechanisms such as post-translational histone modifications and DNA methylation. In the last few years, the distinct functions of histone modifications and of the enzymes catalysing their formation have begun to be elucidated in processes important...

View article titled, Epigenetics in the heart: the role of histone modifications in cardiac remodelling

Articles

ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection

Hannah K. Long, Neil P. Blackledge, Robert J. Klose

Biochem Soc Trans (2013) 41 (3): 727–740.

DOI: https://doi.org/10.1042/BST20130028

Published: 23 May 2013

... of the Creative Commons Attribution Licence (CC-BY) ( http://creativecommons.org/licenses/by/3.0/ ) which permits unrestricted use, distribution and reproduction in any medium, provided the original work is properly cited. chromatin CpG island DNA demethylation DNA methylation epigenetics transcription...

View article titled, ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection

Articles

Do age-related changes in DNA methylation play a role in the development of age-related diseases?

Sanne D. van Otterdijk, John C. Mathers, Gordon Strathdee

Biochem Soc Trans (2013) 41 (3): 803–807.

DOI: https://doi.org/10.1042/BST20120358

Published: 23 May 2013

...Sanne D. van Otterdijk; John C. Mathers; Gordon Strathdee DNA methylation is an important epigenetic mechanism in mammalian cells. It occurs almost exclusively at CpG sites and has a key role in a number of biological processes. It plays an important part in regulating chromatin structure and has...

View article titled, Do age-related changes in DNA methylation play a role in the development of age-related diseases?

Articles

The reversal of epigenetic silencing of the EBV genome is regulated by viral bZIP protein

Questa H. Karlsson, Celine Schelcher, Elizabeth Verrall, Carlo Petosa, Alison J. Sinclair

Biochem Soc Trans (2008) 36 (4): 637–639.

DOI: https://doi.org/10.1042/BST0360637

Published: 22 July 2008

... this epigenetic silencing is overturned. A key event is the activation of the viral protein Zta with three ZREs (Zta-response elements) from the BRLF1 promoter (referred to as Rp). Two of these ZREs contain CpG motifs and are methylated in the latent genome. Biochemical analyses and molecular modelling of Zta...

View article titled, The reversal of epigenetic silencing of the EBV genome is regulated by viral bZIP protein

Articles

Genome plasticity in the mouse oocyte and early embryo

A.E. Peaston, B.B. Knowles, K.W. Hutchison

Biochem Soc Trans (2007) 35 (3): 618–622.

DOI: https://doi.org/10.1042/BST0350618

Published: 22 May 2007

... libraries. These retrotransposons can act as alternative promoters and first exons for diverse genes, synchronizing their expression. Heritable genetic change due to replication of these retrotransposons probably occurs specifically in oocytes and early embryos. ERVs are usually epigenetically silenced...

View article titled, Genome plasticity in the mouse oocyte and early embryo

Articles

Does everything now make (anti)sense?

J.A. Timmons, L. Good

Biochem Soc Trans (2006) 34 (6): 1148–1150.

DOI: https://doi.org/10.1042/BST0341148

Published: 25 October 2006

.... Sorek R. Sanderson C.M. Casari G. Trends Biochem Sci. 2004 29 88 94 1 To whom correspondence should be addressed (email Jamie.Timmons@ki.se ). 11 7 2006 © 2006 The Biochemical Society 2006 biodiversity epigenetics imprinting natural antisense non...

View article titled, Does everything now make (anti)sense?

Articles

Methylation of the ESR1 CpG island in the colorectal mucosa is an ‘all or nothing’ process in healthy human colon, and is accelerated by dietary folate supplementation in the mouse

N.J. Belshaw, G.O. Elliott, E.A. Williams, J.C. Mathers, L. Buckley, B. Bahari, I.T. Johnson

Biochem Soc Trans (2005) 33 (4): 709–711.

DOI: https://doi.org/10.1042/BST0330709

Published: 01 August 2005

... The Biochemical Society 2005 Methylation of cytosine within the CpG islands of gene promoter regions is now recognized as an important epigenetic regulator of gene expression [ 3 ]. One context in which this phenomenon is known to be particularly important is during ‘stepwise’ carcinogenesis...

View article titled, Methylation of the ESR1 CpG island in the colorectal mucosa is an ‘all or nothing’ process in healthy human colon, and is accelerated by dietary folate supplementation in the mouse

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