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Keywords: chromatin
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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...
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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
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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
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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...
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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...
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Biochem J (2020) 477 (16): 3091–3104.
Published: 28 August 2020
...’ was due to differences in the elongation rates of the RNAPIIs transcribing from these promoters which, in turn, affected the probability of SRSF1 binding to the nascent mRNA. alternative splicing chromatin RNA polymerase II transcription elongation Comparative genome analysis made evident...
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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
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...
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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...
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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...
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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...
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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...
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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
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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...
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Biochem J (2013) 450 (3): 433–442.
Published: 28 February 2013
... ]. The ING1 gene is located at the chromosomal location 13q34 and encodes four potential alternatively spliced isoforms, all containing a highly conserved PHD (plant homeodomain), commonly found in chromatin regulatory proteins [ 2 , 3 ]. ING1a and ING1b are expressed in almost all cell types, including...
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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...
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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
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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
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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...
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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...
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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
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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
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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 s.rocha@dundee.ac.uk ). 29 5...
Includes: Multimedia, Supplementary data
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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...
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Biochem J (2008) 409 (3): 651–656.
Published: 15 January 2008
... giorgio.camilloni@uniroma1.it ). 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 Cells were grown...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...