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1-46 of 46
Keywords: chromatin
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Articles
Journal:
Biochemical Journal
Biochem J (2024) 481 (21): 1497–1518.
Published: 18 October 2024
... 5 2024 30 9 2024 7 10 2024 © 2024 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2024 alternative splicing cancer chromatin epigenetics epitranscriptomics histone modifications Cancer cells employ diverse epigenetic...
Articles
In Collection
Epigenetics
Journal:
Biochemical Journal
Biochem J (2024) 481 (4): 219–244.
Published: 14 February 2024
...Ellen N. Weinzapfel; Karlie N. Fedder-Semmes; Zu-Wen Sun; Michael-Christopher Keogh The role of histone post-translational modifications (PTMs) in chromatin structure and genome function has been the subject of intense debate for more than 60 years. Though complex, the discourse can be summarized...
Articles
In Collection
Cell signaling in the 21st century
Journal:
Biochemical Journal
Biochem J (2023) 480 (1): 57–85.
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...
Articles
Journal:
Biochemical Journal
Biochem J (2022) 479 (11): 1205–1220.
Published: 13 June 2022
... in stem cells and the brain, developmentally regulated in mice and associated with several diverse malignancies in humans, including cancer, metabolic syndrome and Parkinson's disease. NUCKS1 function has been linked to modulating chromatin architecture and transcription, DNA repair and cell cycle...
Articles
In Collection
Towards systems biochemistry
Journal:
Biochemical Journal
Biochem J (2022) 479 (6): 767–786.
Published: 28 March 2022
... to hypoxia is of great importance. The family of transcription factors called Hypoxia Inducible Factors (HIFs) co-ordinate a transcriptional programme required for survival and adaptation to hypoxia. However, the effects of HIF on chromatin accessibility are currently unclear. Here, using genome wide mapping...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2021) 478 (5): 1117–1136.
Published: 10 March 2021
... and confirmed by site-directed mutagenesis. Further analysis indicates that histone interacting surface of Asf1 is highly conserved while the dimerization interface is variable. Our results identify the role of PfAsf1 as a mediator of chromatin assembly in Plasmodium falciparum, which is the causative agent...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2021) 478 (3): 511–532.
Published: 10 February 2021
...Bethany C. Taylor; Nicolas L. Young Histones are essential proteins that package the eukaryotic genome into its physiological state of nucleosomes, chromatin, and chromosomes. Post-translational modifications (PTMs) of histones are crucial to both the dynamic and persistent regulation of the genome...
Articles
Journal:
Biochemical Journal
Biochem J (2020) 477 (17): 3367–3386.
Published: 17 September 2020
...Yan Huang; Yaxin Dai; Zheng Zhou Histone chaperones include a wide variety of proteins which associate with histones and regulate chromatin structure. The classic H2A–H2B type of histone chaperones, and the chromatin remodeling complex components possessing H2A–H2B chaperone activity, show a broad...
Articles
Journal:
Biochemical Journal
Biochem J (2020) 477 (16): 3091–3104.
Published: 28 August 2020
... of the Biochemical Society 2020 alternative splicing chromatin RNA polymerase II transcription elongation Comparative genome analysis made evident that gene number cannot account for organismal complexity, a puzzle known as the G -value paradox [ 1 ], with the simple 1 mm-long nematode...
Articles
Journal:
Biochemical Journal
Biochem J (2020) 477 (5): 1033–1047.
Published: 13 March 2020
... Protein (HP1) 1 family are key players in chromatin organisation, acting as docking sites for chromatin modifiers. Here, we inactivated HP1α in HepG2 human liver carcinoma cells and showed that HP1α participated in cell proliferation. HP1α-depleted cells have a global decrease in DNA methylation...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2019) 476 (16): 2351–2354.
Published: 28 August 2019
... 8 2019 © 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2019 chromatin epigenetic histone PHD finger The eukaryotic genome is packaged in the cell nucleus in the form of chromatin, a complex of DNA and histone proteins. Chromatin...
Articles
In Collection
Editors' pick of review article highlights published in the Biochemical Journal in 2018 & 2019
Journal:
Biochemical Journal
Biochem J (2019) 476 (7): 1083–1104.
Published: 10 April 2019
... transcription and other biological processes by acting, for example, as guides that target proteins to chromatin, scaffolds that facilitate protein–protein interactions and complex formation, and orchestrators of phase-separated compartments. The study of lncRNAs has reached an exciting time, as recent advances...
Articles
Journal:
Biochemical Journal
Biochem J (2018) 475 (24): 3921–3932.
Published: 14 December 2018
...Grace E. Adams; Aditya Chandru; Shaun M. Cowley At face value, the Sin3 histone deacetylase (HDAC) complex appears to be a prototypical co-repressor complex, that is, a multi-protein complex recruited to chromatin by DNA bound repressor proteins to facilitate local histone deacetylation...
Articles
Journal:
Biochemical Journal
Biochem J (2017) 474 (20): 3455–3469.
Published: 05 October 2017
...Qingtang Shen; Nissrine Beyrouthy; Laura Matabishi-Bibi; Catherine Dargemont The ISWI class of proteins consists of a family of chromatin remodeling ATPases that is ubiquitous in eukaryotes and predominantly functions to slide nucleosomes laterally. The yeast Saccharomyces cerevisiae Isw1 partners...
Articles
Journal:
Biochemical Journal
Biochem J (2014) 462 (3): 385–395.
Published: 22 August 2014
... that gene expression is co-ordinated by changes in transcription and translation in hypoxia, much less is known about how chromatin changes allow for transcription to take place. The missing link between co-ordinating chromatin structure and the hypoxia-induced transcriptional programme could be in the form...
Articles
Journal:
Biochemical Journal
Biochem J (2014) 461 (3): 477–486.
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...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2014) 458 (1): 153–158.
Published: 20 January 2014
.... However, to perform these functions, they need to occupy their sites in chromatin. In the present study, we have systematically assessed TALE binding to chromatin substrates and find that in vitro TALEs bind to their target site on nucleosomes at the more accessible entry/exit sites...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2013) 451 (1): 13–23.
Published: 14 March 2013
.... It is becoming apparent that a major role of DNA modification is to act as a relatively stable, and mitotically heritable, template that contributes to the establishment and maintenance of chromatin states. In this regard, interplay is emerging between DNA methylation and the PcG (Polycomb group) proteins, which...
Articles
Journal:
Biochemical Journal
Biochem J (2013) 450 (3): 433–442.
Published: 28 February 2013
... To whom correspondence should be addressed (email [email protected] ). 24 10 2012 13 12 2012 18 12 2012 © The Authors Journal compilation © 2013 Biochemical Society 2013 acetylation chromatin epigenetics inhibitor of growth (ING) stress tumour suppressor The ING...
Articles
Journal:
Biochemical Journal
Biochem J (2013) 449 (3): 567–579.
Published: 09 January 2013
...Catherine B. Millar Chromatin acts as an organizer and indexer of genomic DNA and is a highly dynamic and regulated structure with properties directly related to its constituent parts. Histone variants are abundant components of chromatin that replace canonical histones in a subset of nucleosomes...
Articles
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.
Published: 14 December 2012
... and reproduction in any medium, provided the original work is properly cited. chromatin epigenetics FAD-dependent oxidase histone modification transcriptional repression The term ‘epigenetic’ refers to heritable changes regulating gene expression that are not a result of changes...
Includes: Supplementary data
Articles
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.
Published: 24 February 2012
...Gráinne Barkess; Yuri Postnikov; Chrisanne D. Campos; Shivam Mishra; Gokula Mohan; Sakshi Verma; Michael Bustin; Katherine L. West HMGNs are nucleosome-binding proteins that alter the pattern of histone modifications and modulate the binding of linker histones to chromatin. The HMGN3 family member...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2011) 439 (3): 487–502.
Published: 13 October 2011
... nucleosome and a derepressed state that is nucleosome-free. These two chromatin states are inherited stably through many cell divisions. According to the model described in the present paper, the role of H2A.Z is to facilitate the addition and removal of promoter nucleosomes and to prevent the formation...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2011) 434 (2): 333–342.
Published: 11 February 2011
... of chromatin-modifying complexes, PRC1 (Polycomb repressive complex 1) and PRC2–4. In Drosophila , PRC2 contains the H3K27 histone methyltransferase E(Z) whose trimethylation activity towards PcG target genes is stimulated by PCL (Polycomb-like). In the present study, we have examined hPCL3 , one of its three...
Articles
Hiroko Inoue, Stavros Giannakopoulos, Christopher N. Parkhurst, Tatsushi Matsumura, Evelyn A. Kono, Takako Furukawa, Naoko Tanese
Journal:
Biochemical Journal
Biochem J (2011) 434 (1): 83–92.
Published: 27 January 2011
...Hiroko Inoue; Stavros Giannakopoulos; Christopher N. Parkhurst; Tatsushi Matsumura; Evelyn A. Kono; Takako Furukawa; Naoko Tanese The largest subunit of the mammalian SWI/SNF-A or BAF (BRG1-associated factor) chromatin-remodelling complex is encoded by two related cDNAs hOsa1 / BAF250a and hOsa2...
Articles
Catherine Chailleux, Sandrine Tyteca, Christophe Papin, François Boudsocq, Nadine Puget, Céline Courilleau, Mikhaïl Grigoriev, Yvan Canitrot, Didier Trouche
Journal:
Biochemical Journal
Biochem J (2010) 426 (3): 365–371.
Published: 24 February 2010
...Catherine Chailleux; Sandrine Tyteca; Christophe Papin; François Boudsocq; Nadine Puget; Céline Courilleau; Mikhaïl Grigoriev; Yvan Canitrot; Didier Trouche Chromatin modifications and chromatin-modifying enzymes are believed to play a major role in the process of DNA repair. The histone acetyl...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2008) 414 (3): 327–341.
Published: 27 August 2008
... The Authors Journal compilation © 2008 Biochemical Society 2008 chromatin gene expression microRNA nervous system synaptic plasticity transcription The brain is the most complex organ in the human body, containing the largest diversity of cell types of any organ. Collectively, cells...
Includes: Multimedia, Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2008) 414 (1): 19–29.
Published: 29 July 2008
... integrate with HIF and how other cellular pathways such as chromatin remodelling, translation regulation and microRNA induction, contribute to the co-ordinated cellular response observed following hypoxic stress. 1 To whom correspondence should be addressed (email [email protected] ). 29 5...
Includes: Multimedia, Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2008) 410 (2): 381–389.
Published: 12 February 2008
...Elisabetta Albi; Remo Lazzarini; Mariapia Viola Magni It is known that phospholipids represent a minor component of chromatin. It has been highlighted recently that these lipids are metabolized directly inside the nucleus, thanks to the presence of enzymes related to their metabolism...
Articles
Journal:
Biochemical Journal
Biochem J (2008) 409 (3): 651–656.
Published: 15 January 2008
... [email protected] ). 6 7 2007 18 10 2007 30 10 2007 30 10 2007 © The Authors Journal compilation © 2008 Biochemical Society 2008 chromatin DNA structure DNA topoisomerase I nucleosome Saccharomyces cerevisiae trinucleotide repeats DNA topology...
Articles
Journal:
Biochemical Journal
Biochem J (2007) 405 (3): 541–545.
Published: 13 July 2007
... in regulating higher order chromatin structures in vivo . Here, we analyse the ability of a number of synthetic polyamine analogues to potentiate formation of higher order chromatin structures in vitro . We find that a class of long-chain polyamines called oligoamines are potent inducers of nucleosomal array...
Articles
Journal:
Biochemical Journal
Biochem J (2007) 404 (2): 289–298.
Published: 14 May 2007
... that the N-terminal domain of MAML1 directly interacts with both p300 and histones, and the p300–MAML1 complex specifically acetylates histone H3 and H4 tails in chromatin. Furthermore, p300 acetylates MAML1 and evolutionarily conserved lysine residues in the MAML1 N-terminus are direct substrates for p300...
Articles
Journal:
Biochemical Journal
Biochem J (2007) 402 (1): 71–80.
Published: 25 January 2007
... structures such as chromatin, the nuclear envelope and the nucleoli. Thirdly, Ca 2+ -dependent accumulation of both calmodulin and the C-terminal calmodulin lobe occurs in the nucleoli. The N-terminal lobe of calmodulin does not show significant binding to subnuclear structures although, similarly to the C...
Articles
Journal:
Biochemical Journal
Biochem J (2006) 400 (3): 573–582.
Published: 28 November 2006
... involved in mediating DNA repair have transcriptional regulatory domains, and as demonstrated for BRCA1 these regulatory domains are important in mediating the functions of these proteins. These transcriptional regulatory processes involve modification of chromatin, and recent evidence has clearly...
Articles
Journal:
Biochemical Journal
Biochem J (2006) 398 (3): 461–467.
Published: 29 August 2006
... proteins. We observed physical interactions of CNOT2 with several subunits of the SMRT/NCoR–HDAC3 complex. Our results show that the SMRT/NCoR–HDAC3 complex is a cofactor of CNOT2-mediated repression and suggest that transcriptional regulation by the Ccr4–Not complex involves regulation of chromatin...
Articles
Journal:
Biochemical Journal
Biochem J (2005) 388 (1): e1.
Published: 10 May 2005
... picture of the cellular responses to DNA damage. In this issue of the Biochemical Journal , a proteomics approach was used by Lee et al. to identify proteins that bind to chromatin in a DNA damage-inducible manner. The proteins identified, nucleophosmin, hnRNP C1 (heterogeneous nuclear ribonucleoprotein...
Articles
Journal:
Biochemical Journal
Biochem J (2005) 388 (1): 7–15.
Published: 10 May 2005
... severe to be tolerated. Evidence indicates that, upon generation of DNA DSBs, many nuclear proteins that are involved in DNA repair and checkpoints are recruited to chromatin around the DNA lesions. In the present study we used a proteomics approach to identify DNA-damage-induced chromatin-binding...
Articles
Journal:
Biochemical Journal
Biochem J (2005) 387 (1): 257–269.
Published: 22 March 2005
... (retinoblastoma) family proteins, and on the other, chromatin-directed histone deacetylase activity that is recruited to the cyclin A promoter early in the cell cycle in association with these RB proteins. This dual regulation maintains transcriptional silence of the cyclin A locus until its transcription...
Articles
Journal:
Biochemical Journal
Biochem J (2004) 383 (2): 249–257.
Published: 08 October 2004
... region was localized to 158 bp flanking the transcriptional start sites. By gel shift and chromatin immunoprecipitation assays, USF (upstream stimulatory factor), Sp1 and Ikaros-related proteins were bound to consensus elements (one E-box, two GC-box and three Ikaros) within this region. The functional...
Articles
Journal:
Biochemical Journal
Biochem J (2004) 377 (3): 641–651.
Published: 01 February 2004
...Wenzheng ZHANG; Yoshihide HAYASHIZAKI; Bruce C. KONE Recently, a new class of histone methyltransferases that plays an indirect role in chromatin silencing by targeting a conserved lysine residue in the nucleosome core was described, namely the Dot1 (disruptor of telomeric silencing) family [Feng...
Articles
Journal:
Biochemical Journal
Biochem J (2004) 377 (3): 809–818.
Published: 01 February 2004
..., although the cis - and trans -regulatory factors controlling mouse hepatocyte iNOS expression have been well-characterized, the local changes in chromatin structure that accompany activation of iNOS gene transcription have not been considered. In the present study, we demonstrate that (1) in the absence...
Articles
Liu YANG, Qi MEI, Anna ZIELINSKA-KWIATKOWSKA, Yoshito MATSUI, Michael L. BLACKBURN, Daniel BENEDETTI, Anton A. KRUMM, Gerald J. TABORSKY, Jr, Howard A. CHANSKY
Journal:
Biochemical Journal
Biochem J (2003) 369 (3): 651–657.
Published: 01 February 2003
... -related gene)-associated protein with a SET ( s uppressor of variegation, e nhancer of zest and t rithorax) domain (ESET) that was found to have the activity of a histone H3-specific methyltransferase. In the present study, we investigated the interaction of ESET with other chromatin remodelling factors...
Articles
Journal:
Biochemical Journal
Biochem J (2002) 364 (1): 255–264.
Published: 08 May 2002
...Adam F.L. HURLSTONE; Ivan A. OLAVE; Nick BARKER; Mascha van NOORT; Hans CLEVERS A highly conserved multisubunit enzymic complex, SWI/SNF, participates in the regulation of eukaryote gene expression through its ability to remodel chromatin. While a single component of SWI/SNF, Swi2 or a related...
Articles
Journal:
Biochemical Journal
Biochem J (2001) 356 (2): 297–310.
Published: 24 May 2001
... observations regarding the dynamic properties of chromatin, mRNA and nuclear proteins, and we consider the implications these findings have for the organization of nuclear processes and gene expression. Finally, we speculate that self-organization might play a substantial role in establishing and maintaining...
Articles
Journal:
Biochemical Journal
Biochem J (2001) 356 (1): 1–10.
Published: 08 May 2001
... cytosine methylation and chromatin remodelling, result in alterations in gene expression which, in turn, affects the phenotype of the organism. Recent evidence, from our work and that of others in mice, suggests that these epigenetic modifications, which in the past were thought to be cleared and reset...
Articles
Violeta MORIN, Freddy DIAZ, Martin MONTECINO, Linda FOTHERGILL-GILMORE, Marcia PUCHI, Maria IMSCHENETZKY
Journal:
Biochemical Journal
Biochem J (1999) 343 (1): 95–98.
Published: 24 September 1999
...Violeta MORIN; Freddy DIAZ; Martin MONTECINO; Linda FOTHERGILL-GILMORE; Marcia PUCHI; Maria IMSCHENETZKY Fertilization in sea urchins is followed by the replacement of sperm-specific histones by cleavage-stage histone variants recruited from maternal stores. Such remodelling of zygote chromatin...
