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Keywords: epigenetics
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Articles

Characterizing crosstalk in epigenetic signaling to understand disease physiology

In Collection
Cell signaling in the 21st century
Joanna K. Lempiäinen, Benjamin A. Garcia
Journal: Biochemical Journal
Biochem J (2023) 480 (1): 57–85.
DOI: https://doi.org/10.1042/BCJ20220550
Published: 11 January 2023
...Joanna K. Lempiäinen; Benjamin A. Garcia Epigenetics, the inheritance of genomic information independent of DNA sequence, controls the interpretation of extracellular and intracellular signals in cell homeostasis, proliferation and differentiation. On the chromatin level, signal transduction leads...
View article titled, Characterizing crosstalk in <span class="search-highlight">epigenetic</span> signaling to understand disease physiology
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Articles

The roles of epigenetics in cancer progression and metastasis

Jocelyn F. Chen, Qin Yan
Journal: Biochemical Journal
Biochem J (2021) 478 (17): 3373–3393.
DOI: https://doi.org/10.1042/BCJ20210084
Published: 14 September 2021
... sequencing studies. Emerging evidence suggests that key steps of metastasis are controlled by reversible epigenetic mechanisms, which can be targeted to prevent and treat the metastatic disease. A variety of epigenetic mechanisms were identified to regulate metastasis, including the well-studied DNA...
View article titled, The roles of <span class="search-highlight">epigenetics</span> in cancer progression and metastasis
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Articles

Epigenetic dynamics of the thermogenic gene program of adipocytes

In Collection
Adipose biology
Danielle Yi, Hai P. Nguyen, Hei Sook Sul
Journal: Biochemical Journal
Biochem J (2020) 477 (6): 1137–1148.
DOI: https://doi.org/10.1042/BCJ20190599
Published: 27 March 2020
..., these transcription factors recruit epigenetic factors, such as LSD1 and MLL3/4, for specific histone signatures to establish the favorable chromatin landscape. In this review, we discuss advances made in understanding the molecular mechanism underlying the thermogenic gene program, particularly epigenetic regulation...
View article titled, <span class="search-highlight">Epigenetic</span> dynamics of the thermogenic gene program of adipocytes
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Articles

lncRedibly versatile: biochemical and biological functions of long noncoding RNAs

In Collection
Editors' pick of review article highlights published in the Biochemical Journal in 2018 & 2019
Emily J. Shields, Ana F. Petracovici, Roberto Bonasio
Journal: Biochemical Journal
Biochem J (2019) 476 (7): 1083–1104.
DOI: https://doi.org/10.1042/BCJ20180440
Published: 10 April 2019
... and organismal contexts, including development and disease. Correspondence: Roberto Bonasio ( roberto@bonasiolab.org ) 29 12 2018 28 2 2019 19 3 2019 © 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2019 chromatin epigenetics gene...
View article titled, lncRedibly versatile: biochemical and biological functions of long noncoding RNAs
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Articles

Lead induces the up-regulation of the protein arginine methyltransferase 5 possibly by its promoter demethylation

Krishna Ghosh, Biji Chatterjee, Santosh R. Kanade
Journal: Biochemical Journal
Biochem J (2018) 475 (16): 2653–2666.
DOI: https://doi.org/10.1042/BCJ20180009
Published: 29 August 2018
...Krishna Ghosh; Biji Chatterjee; Santosh R. Kanade The studies on lead (Pb) exposure linking to epigenetic modulations are caused by its differential actions on global DNA methylation and histone modifications. These epigenetic changes may result in increased accessibility of the transcription...
View article titled, Lead induces the up-regulation of the protein arginine methyltransferase 5 possibly by its promoter demethylation
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Includes: Supplementary data
Articles

The role of interactions of long non-coding RNAs and heterogeneous nuclear ribonucleoproteins in regulating cellular functions

Xinghui Sun, Mohamed Sham Shihabudeen Haider Ali, Matthew Moran
Journal: Biochemical Journal
Biochem J (2017) 474 (17): 2925–2935.
DOI: https://doi.org/10.1042/BCJ20170280
Published: 11 August 2017
... 4 2017 21 6 2017 26 6 2017 © 2017 The Author(s) 2017 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-NC-ND) . epigenetics eukaryotic gene...
View article titled, The role of interactions of long non-coding RNAs and heterogeneous nuclear ribonucleoproteins in regulating cellular functions
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Articles

Potential mechanisms linking SIRT activity and hypoxic 2-hydroxyglutarate generation: no role for direct enzyme (de)acetylation

Sergiy M. Nadtochiy, Yves T. Wang, Jimmy Zhang, Keith Nehrke, Xenia Schafer, Kevin Welle, Sina Ghaemmaghami, Josh Munger, Paul S. Brookes
Journal: Biochemical Journal
Biochem J (2017) 474 (16): 2829–2839.
DOI: https://doi.org/10.1042/BCJ20170389
Published: 10 August 2017
...Sergiy M. Nadtochiy; Yves T. Wang; Jimmy Zhang; Keith Nehrke; Xenia Schafer; Kevin Welle; Sina Ghaemmaghami; Josh Munger; Paul S. Brookes 2-Hydroxyglutarate (2-HG) is a hypoxic metabolite with potentially important epigenetic signaling roles. The mechanisms underlying 2-HG generation are poorly...
View article titled, Potential mechanisms linking SIRT activity and hypoxic 2-hydroxyglutarate generation: no role for direct enzyme (de)acetylation
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Articles

Structural basis of molecular recognition of helical histone H3 tail by PHD finger domains

Alessio Bortoluzzi, Anastasia Amato, Xavier Lucas, Manuel Blank, Alessio Ciulli
Journal: Biochemical Journal
Biochem J (2017) 474 (10): 1633–1651.
DOI: https://doi.org/10.1042/BCJ20161053
Published: 04 May 2017
...Alessio Bortoluzzi; Anastasia Amato; Xavier Lucas; Manuel Blank; Alessio Ciulli The plant homeodomain (PHD) fingers are among the largest family of epigenetic domains, first characterized as readers of methylated H3K4. Readout of histone post-translational modifications by PHDs has been the subject...
View article titled, Structural basis of molecular recognition of helical histone H3 tail by PHD finger domains
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Includes: Supplementary data
Articles

A saga of cancer epigenetics: linking epigenetics to alternative splicing

Sathiya Pandi Narayanan, Smriti Singh, Sanjeev Shukla
Journal: Biochemical Journal
Biochem J (2017) 474 (6): 885–896.
DOI: https://doi.org/10.1042/BCJ20161047
Published: 07 March 2017
... known that several diseases are a direct and indirect consequence of aberrant splicing events in humans. In addition to the conventional mode of alternative splicing regulation by ‘ cis ’ RNA-binding sites and ‘ trans’ RNA-binding proteins, recent literature provides enormous evidence for epigenetic...
View article titled, A saga of cancer <span class="search-highlight">epigenetics</span>: linking <span class="search-highlight">epigenetics</span> to alternative splicing
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Articles

GFI1 functions in transcriptional control and cell fate determination require SNAG domain methylation to recruit LSD1

Matthew Velinder, Jason Singer, Diana Bareyan, Jessica Meznarich, Christopher M. Tracy, James M. Fulcher, David McClellan, Helena Lucente, Sarah Franklin, Sunil Sharma, Michael E. Engel
Journal: Biochemical Journal
Biochem J (2016) 473 (19): 3355–3369.
DOI: https://doi.org/10.1042/BCJ20160558
Published: 27 September 2016
..., *** <0.0005, **** <0.00005). cancer epigenetics GFI1 LSD1 methylation transcription Growth factor independence 1 (GFI1) is a transcriptional repressor and master regulator of normal and malignant hematopoiesis. GFI1 is comprised of a 20 amino acid N-terminal Snail/GFI1 (SNAG) domain, a C...
View article titled, GFI1 functions in transcriptional control and cell fate determination require SNAG domain methylation to recruit LSD1
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Includes: Supplementary data
Articles

Targeting polyamine metabolism for cancer therapy and prevention

Tracy R. Murray-Stewart, Patrick M. Woster, Robert A. Casero, Jr
Journal: Biochemical Journal
Biochem J (2016) 473 (19): 2937–2953.
DOI: https://doi.org/10.1042/BCJ20160383
Published: 27 September 2016
... activity of several polyamine analogs; MTA is produced from decarboxylated S -adenosylmethionine by the activity of both spermidine and spermine synthases. cancer therapy chemoprevention epigenetics polyamines reactive oxygen species spermine oxidase Polyamines have been implicated...
View article titled, Targeting polyamine metabolism for cancer therapy and prevention
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Articles

Structure and function of histone methylation-binding proteins in plants

Yanli Liu, Jinrong Min
Journal: Biochemical Journal
Biochem J (2016) 473 (12): 1663–1680.
DOI: https://doi.org/10.1042/BCJ20160123
Published: 10 June 2016
... since mutations of some cage residues destroy the DNA methylation activity of CMT3 in vivo ( Figure 2 E) [ 66 ]. epigenetics histone methylation readers histone post-translational modifications In eukaryotes, gene expression is under the control of elaborate modulation of chromatin...
View article titled, Structure and function of histone methylation-binding proteins in plants
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Articles

The cancer-promoting gene fatty acid-binding protein 5 ( FABP5 ) is epigenetically regulated during human prostate carcinogenesis

Koichiro Kawaguchi, Ayumi Kinameri, Shunsuke Suzuki, Shogo Senga, Youqiang Ke, Hiroshi Fujii
Journal: Biochemical Journal
Biochem J (2016) 473 (4): 449–461.
DOI: https://doi.org/10.1042/BJ20150926
Published: 09 February 2016
... statistically significant. © 2016 Authors; published by Portland Press Limited 2016 The DNA methylation status of CpG islands in the FABP5 promoter is critical for its expression. Epigenetic regulation of FABP5 gene expression plays an important role during human prostate carcinogenesis...
View article titled, The cancer-promoting gene fatty acid-binding protein 5 ( FABP5 ) is <span class="search-highlight">epigenetically</span> regulated during human prostate carcinogenesis
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Includes: Supplementary data
Articles

PAQR3 modulates H3K4 trimethylation by spatial modulation of the regulatory subunits of COMPASS-like complexes in mammalian cells

Chunchun Liu, Yuxue Zhang, Yongfan Hou, Liqiang Shen, Yinlong Li, Weiwei Guo, Daqian Xu, Gaigai Liu, Zilong Zhao, Kaiyang Man, Yi Pan, Zhenzhen Wang, Yan Chen
Journal: Biochemical Journal
Biochem J (2015) 467 (3): 415–424.
DOI: https://doi.org/10.1042/BJ20141392
Published: 17 April 2015
...Chunchun Liu; Yuxue Zhang; Yongfan Hou; Liqiang Shen; Yinlong Li; Weiwei Guo; Daqian Xu; Gaigai Liu; Zilong Zhao; Kaiyang Man; Yi Pan; Zhenzhen Wang; Yan Chen Epigenetic control via histone methylation is important in transcriptional regulation and occurs in the nucleus. However, this process can...
View article titled, PAQR3 modulates H3K4 trimethylation by spatial modulation of the regulatory subunits of COMPASS-like complexes in mammalian cells
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Articles

Observed bromodomain flexibility reveals histone peptide- and small molecule ligand-compatible forms of ATAD2

Guillaume Poncet-Montange, Yanai Zhan, Jennifer P. Bardenhagen, Alessia Petrocchi, Elisabetta Leo, Xi Shi, Gilbert R. Lee, IV, Paul G. Leonard, Mary K. Geck Do, Mario G. Cardozo, Jannik N. Andersen, Wylie S. Palmer, Philip Jones, John E. Ladbury
Journal: Biochemical Journal
Biochem J (2015) 466 (2): 337–346.
DOI: https://doi.org/10.1042/BJ20140933
Published: 20 February 2015
... emerges as an attractive therapeutic approach in cancer. Overexpression of ATAD2 (ATPase family AAA domain-containing 2 isoform A) in cancer cells is associated with poor prognosis making the bromodomain of ATAD2 a promising epigenetic therapeutic target. In the development of an in vitro assay...
View article titled, Observed bromodomain flexibility reveals histone peptide- and small molecule ligand-compatible forms of ATAD2
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Includes: Supplementary data
Articles

Holocarboxylase synthetase interacts physically with nuclear receptor co-repressor, histone deacetylase 1 and a novel splicing variant of histone deacetylase 1 to repress repeats

Dandan Liu, Janos Zempleni
Journal: Biochemical Journal
Biochem J (2014) 461 (3): 477–486.
DOI: https://doi.org/10.1042/BJ20131208
Published: 10 July 2014
...Dandan Liu; Janos Zempleni HLCS (holocarboxylase synthetase) is a nuclear protein that catalyses the binding of biotin to distinct lysine residues in chromatin proteins. HLCS-dependent epigenetic marks are over-represented in repressed genomic loci, particularly in repeats. Evidence is mounting...
View article titled, Holocarboxylase synthetase interacts physically with nuclear receptor co-repressor, histone deacetylase 1 and a novel splicing variant of histone deacetylase 1 to repress repeats
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Articles

Characterization of the histone methyltransferase PRDM9 using biochemical, biophysical and chemical biology techniques

Xiaoying Koh-Stenta, Joma Joy, Anders Poulsen, Rong Li, Yvonne Tan, Yoonjung Shim, Jung-Hyun Min, Liling Wu, Anna Ngo, Jianhe Peng, Wei Guang Seetoh, Jing Cao, John Liang Kuan Wee, Perlyn Zekui Kwek, Alvin Hung, Umayal Lakshmanan, Horst Flotow, Ernesto Guccione, Jeffrey Hill
Journal: Biochemical Journal
Biochem J (2014) 461 (2): 323–334.
DOI: https://doi.org/10.1042/BJ20140374
Published: 26 June 2014
..., and demonstrated its chemical tractability in a compound library screen. Significantly, our data indicate that PRDM9 has broader activities than previously recognized. biochemical characterization chemical biology enzyme kinetics epigenetics high-throughput screen histone methyltransferase PRDM protein...
View article titled, Characterization of the histone methyltransferase PRDM9 using biochemical, biophysical and chemical biology techniques
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Includes: Supplementary data
Articles

Convergent evolution of chromatin modification by structurally distinct enzymes: comparative enzymology of histone H3 Lys 27 methylation by human polycomb repressive complex 2 and vSET

Brooke M. Swalm, Kenneth K. Hallenbeck, Christina R. Majer, Lei Jin, Margaret Porter Scott, Mikel P. Moyer, Robert A. Copeland, Tim J. Wigle
Journal: Biochemical Journal
Biochem J (2013) 453 (2): 241–247.
DOI: https://doi.org/10.1042/BJ20130439
Published: 28 June 2013
...Brooke M. Swalm; Kenneth K. Hallenbeck; Christina R. Majer; Lei Jin; Margaret Porter Scott; Mikel P. Moyer; Robert A. Copeland; Tim J. Wigle H3K27 (histone H3 Lys 27 ) methylation is an important epigenetic modification that regulates gene transcription. In humans, EZH (enhancer of zeste homologue...
View article titled, Convergent evolution of chromatin modification by structurally distinct enzymes: comparative enzymology of histone H3 Lys 27 methylation by human polycomb repressive complex 2 and vSET
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Articles

RegulatING chromatin regulators: post-translational modification of the ING family of epigenetic regulators

Shankha Satpathy, Arash Nabbi, Karl Riabowol
Journal: Biochemical Journal
Biochem J (2013) 450 (3): 433–442.
DOI: https://doi.org/10.1042/BJ20121632
Published: 28 February 2013
...Shankha Satpathy; Arash Nabbi; Karl Riabowol The five human ING genes encode at least 15 splicing isoforms, most of which affect cell growth, differentiation and apoptosis through their ability to alter gene expression by epigenetic mechanisms. Since their discovery in 1996, ING proteins have been...
View article titled, RegulatING chromatin regulators: post-translational modification of the ING family of <span class="search-highlight">epigenetic</span> regulators
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Articles

Loss of LSD1 (lysine-specific demethylase 1) suppresses growth and alters gene expression of human colon cancer cells in a p53- and DNMT1(DNA methyltransferase 1)-independent manner

Lihua Jin, Christin L. Hanigan, Yu Wu, Wei Wang, Ben Ho Park, Patrick M. Woster, Robert A. Casero, Jr
Journal: Biochemical Journal
Biochem J (2013) 449 (2): 459–468.
DOI: https://doi.org/10.1042/BJ20121360
Published: 14 December 2012
...Lihua Jin; Christin L. Hanigan; Yu Wu; Wei Wang; Ben Ho Park; Patrick M. Woster; Robert A. Casero, Jr Epigenetic silencing of gene expression is important in cancer. Aberrant DNA CpG island hypermethylation and histone modifications are involved in the aberrant silencing of tumour-suppressor genes...
View article titled, Loss of LSD1 (lysine-specific demethylase 1) suppresses growth and alters gene expression of human colon cancer cells in a p53- and DNMT1(DNA methyltransferase 1)-independent manner
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Includes: Supplementary data
Articles

Antidepressants inhibit DNA methyltransferase 1 through reducing G9a levels

Nicole Zimmermann, Jürgen Zschocke, Tatjana Perisic, Shuang Yu, Florian Holsboer, Theo Rein
Journal: Biochemical Journal
Biochem J (2012) 448 (1): 93–102.
DOI: https://doi.org/10.1042/BJ20120674
Published: 18 October 2012
...Nicole Zimmermann; Jürgen Zschocke; Tatjana Perisic; Shuang Yu; Florian Holsboer; Theo Rein The discovery of epigenetic processes as possible pivotal regulatory mechanisms in psychiatric diseases raised the question of how psychoactive drugs may impact the epigenetic machinery. In the present study...
View article titled, Antidepressants inhibit DNA methyltransferase 1 through reducing G9a levels
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Articles

Dynamics of plant histone modifications in response to DNA damage

Georgina E. Drury, Adam A. Dowle, David A. Ashford, Wanda M. Waterworth, Jerry Thomas, Christopher E. West
Journal: Biochemical Journal
Biochem J (2012) 445 (3): 393–401.
DOI: https://doi.org/10.1042/BJ20111956
Published: 13 July 2012
... Biochemical Society 2012 Arabidopsis DNA double-strand break DNA repair epigenetics recombination Histones are subject to post-translational modification which residue-specific modification determines chromatin structure or function, including acetylation, phosphorylation, methylation...
View article titled, Dynamics of plant histone modifications in response to DNA damage
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Articles

The chromatin-binding protein HMGN3 stimulates histone acetylation and transcription across the Glyt1 gene

Gráinne Barkess, Yuri Postnikov, Chrisanne D. Campos, Shivam Mishra, Gokula Mohan, Sakshi Verma, Michael Bustin, Katherine L. West
Journal: Biochemical Journal
Biochem J (2012) 442 (3): 495–505.
DOI: https://doi.org/10.1042/BJ20111502
Published: 24 February 2012
... chromatin elongation epigenetics HMGN p300/CREB (cAMP-response-element-binding protein)-binding protein-associated factor (PCAF) Figure 1 Overexpression of Hmgn3b and Hmgn3a in Hepa-1 cells ( a ) Schematic diagram of HMGN3a and its shorter splice form, HMGN3b. The two NLS, the NBD...
View article titled, The chromatin-binding protein HMGN3 stimulates histone acetylation and transcription across the Glyt1 gene
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Articles

ADP-ribose polymers localized on Ctcf–Parp1–Dnmt1 complex prevent methylation of Ctcf target sites

Michele Zampieri, Tiziana Guastafierro, Roberta Calabrese, Fabio Ciccarone, Maria G. Bacalini, Anna Reale, Mariagrazia Perilli, Claudio Passananti, Paola Caiafa
Journal: Biochemical Journal
Biochem J (2012) 441 (2): 645–652.
DOI: https://doi.org/10.1042/BJ20111417
Published: 21 December 2011
...-ribosylates itself and, in turn, inhibits DNA methylation via non-covalent interaction between its ADP-ribose polymers and Dnmt1. By such a mechanism, Ctcf may preserve the epigenetic pattern at promoters of important housekeeping genes. The results of the present study showed Dnmt1 as a new protein partner...
View article titled, ADP-ribose polymers localized on Ctcf–Parp1–Dnmt1 complex prevent methylation of Ctcf target sites
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Includes: Supplementary data
Articles

The histone variant H2A.Z interconverts two stable epigenetic chromatin states

Jin Zhao, Wee Leng Siew, Weiqi Sun, Norbert Lehming
Journal: Biochemical Journal
Biochem J (2011) 439 (3): 487–502.
DOI: https://doi.org/10.1042/BJ20110791
Published: 13 October 2011
... repression of the GAL1 promoter. With the help of a fusion of the URA3 ORF (open reading frame) to the GAL1 promoter, we were able to detect two different epigenetic transcription states of the GAL1 promoter in glucose-grown cells lacking H2A.Z: a repressed state that is occupied by a H2A-containing...
View article titled, The histone variant H2A.Z interconverts two stable <span class="search-highlight">epigenetic</span> chromatin states
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Includes: Supplementary data
Articles

Functional characterization of human Polycomb-like 3 isoforms identifies them as components of distinct EZH2 protein complexes

Gaylor Boulay, Claire Rosnoblet, Cateline Guérardel, Pierre-Olivier Angrand, Dominique Leprince
Journal: Biochemical Journal
Biochem J (2011) 434 (2): 333–342.
DOI: https://doi.org/10.1042/BJ20100944
Published: 11 February 2011
...Gaylor Boulay; Claire Rosnoblet; Cateline Guérardel; Pierre-Olivier Angrand; Dominique Leprince PcG (Polycomb group) proteins are conserved transcriptional repressors essential to regulate cell fate and to maintain epigenetic cellular memory. They work in concert through two main families...
View article titled, Functional characterization of human Polycomb-like 3 isoforms identifies them as components of distinct EZH2 protein complexes
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