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Modulation of chromatin architecture influences the neuronal nucleus through activity-regulated gene expression

Robert S. Porter, Shigeki Iwase

Biochem Soc Trans (2023) 51 (2): 703–713.

DOI: https://doi.org/10.1042/BST20220889

Published: 16 March 2023

...Robert S. Porter; Shigeki Iwase The disruption of chromatin-regulating genes is associated with many neurocognitive syndromes. While most of these genes are ubiquitously expressed across various cell-types, many chromatin regulators act upon activity regulated genes (ARGs) that play central roles...

View article titled, Modulation of chromatin architecture influences the neuronal nucleus through activity-regulated gene expression

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

The intricate roles of RCC1 in normal cells and cancer cells

Li Jing, Hang Fai Kwok

Biochem Soc Trans (2022) 50 (1): 83–93.

DOI: https://doi.org/10.1042/BST20210861

Published: 22 February 2022

...Li Jing; Hang Fai Kwok RCC1 (regulator of chromosome condensation 1) is a highly conserved chromatin-binding protein and the only known guanine-nucleotide exchange factor of Ran (a nuclear Ras homolog). RCC1 plays an essential role in the regulation of cell cycle-related activities such as nuclear...

View article titled, The intricate roles of RCC1 in normal cells and cancer cells

Articles

Multiple roles of Pol epsilon in eukaryotic chromosome replication

Milos A. Cvetkovic, Esther Ortega, Roberto Bellelli, Alessandro Costa

Biochem Soc Trans (2022) 50 (1): 309–320.

DOI: https://doi.org/10.1042/BST20210082

Published: 07 February 2022

... and distributed under the Creative Commons Attribution License 4.0 (CC BY) . chromatin CMG cryo-EM Ctf18 Pol epsilon replisome In all replicating systems a hexameric, ring-shaped helicase is loaded around DNA and uses the energy derived from nucleotide hydrolysis to unwind the double helix...

View article titled, Multiple roles of Pol epsilon in eukaryotic chromosome replication

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

The role of chromatin at transcription-replication conflicts as a genome safeguard

Aleix Bayona-Feliu, Andrés Aguilera

Biochem Soc Trans (2021) 49 (6): 2727–2736.

DOI: https://doi.org/10.1042/BST20210691

Published: 25 November 2021

... integrity. Increasing evidence indicates that chromatin homeostasis plays a key role in the cellular response to TRCs as well as in the preservation of genome integrity. Indeed, chromatin regulating enzymes are frequently mutated in cancer cells, a common characteristic of which is genome instability...

View article titled, The role of chromatin at transcription-replication conflicts as a genome safeguard

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

...Akhil Gargey Iragavarapu; Liqi Yao; Vignesh Kasinath Polycomb repressive complexes are a family of chromatin modifier enzymes which are critical for regulating gene expression and maintaining cell-type identity. The reversible chemical modifications of histone H3 and H2A by the Polycomb proteins...

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

... interactors. Recent advances in mapping direct interactors of histone PTMs as well as local chromatin interactomes will be highlighted, with a focus on mass-spectrometry based workflows that continue to illuminate histone-mediated PPIs in unprecedented detail. Correspondence: Antony J. Burton...

View article titled, Chemical biology approaches to study histone interactors

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

...David Llères; Yui Imaizumi; Robert Feil Different classes of non-coding RNA (ncRNA) influence the organization of chromatin. Imprinted gene domains constitute a paradigm for exploring functional long ncRNAs (lncRNAs). Almost all express an lncRNA in a parent-of-origin dependent manner. The mono...

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

Articles

Sequence determinants, function, and evolution of CpG islands

Allegra Angeloni, Ozren Bogdanovic

Biochem Soc Trans (2021) 49 (3): 1109–1119.

DOI: https://doi.org/10.1042/BST20200695

Published: 22 June 2021

... that include DNA hypomethylation, elevated CpG and GC content and the presence of transcription factor binding sites. These sequence characteristics are congruous with the recruitment of transcription factors and chromatin modifying enzymes, and transcriptional activation in general. CGIs colocalize with sites...

View article titled, Sequence determinants, function, and evolution of CpG islands

Articles

Mechanistic insights into KDM4A driven genomic instability

Nicolas L. Young, Ruhee Dere

Biochem Soc Trans (2021) 49 (1): 93–105.

DOI: https://doi.org/10.1042/BST20191219

Published: 25 January 2021

...Nicolas L. Young; Ruhee Dere Alterations in global epigenetic signatures on chromatin are well established to contribute to tumor initiation and progression. Chromatin methylation status modulates several key cellular processes that maintain the integrity of the genome. KDM4A, a demethylase...

View article titled, Mechanistic insights into KDM4A driven genomic instability

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

... 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) . cell fate chromatin Dppa2/4 epigenetic priming epigenetics plasticity Mammalian development starts with a single...

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

Articles

Nuclear import of histones

Natalia Elisa Bernardes, Yuh Min Chook

Biochem Soc Trans (2020) 48 (6): 2753–2767.

DOI: https://doi.org/10.1042/BST20200572

Published: 10 December 2020

... License 4.0 (CC BY-NC-ND) . Open access for this article was enabled by the participation of the University of Texas Southwestern Medical Centre in an all-inclusive Read & Publish pilot with Portland Press and the Biochemical Society under a transformative agreement with EBSCO. chromatin...

View article titled, Nuclear import of histones

Articles

RNA matchmaking in chromatin regulation

Stephen K. Wu, Justin T. Roberts, Maggie M. Balas, Aaron M. Johnson

Biochem Soc Trans (2020) 48 (6): 2467–2481.

DOI: https://doi.org/10.1042/BST20191225

Published: 27 November 2020

...Stephen K. Wu; Justin T. Roberts; Maggie M. Balas; Aaron M. Johnson Beyond being the product of gene expression, RNA can also influence the regulation of chromatin. The majority of the human genome has the capacity to be transcribed and the majority of the non-protein-coding transcripts made by RNA...

View article titled, RNA matchmaking in chromatin regulation

Articles

Architectural RNA in chromatin organization

Jitendra Thakur, Steven Henikoff

Biochem Soc Trans (2020) 48 (5): 1967–1978.

DOI: https://doi.org/10.1042/BST20191226

Published: 08 September 2020

...Jitendra Thakur; Steven Henikoff RNA plays a well-established architectural role in the formation of membraneless interchromatin nuclear bodies. However, a less well-known role of RNA is in organizing chromatin, whereby specific RNAs have been found to recruit chromatin modifier proteins. Whether...

View article titled, Architectural RNA in chromatin organization

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

... organisation and affect chromatin conformation. However, there are important differences between the domain architectures of SMC proteins and SMCHD1, which distinguish SMCHD1 as a non-canonical member of the family. In the last year, the crystal structures of the two key domains crucial to SMCHD1 function...

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

Articles

How do histone modifications contribute to transgenerational epigenetic inheritance in C. elegans ?

In Collection

Embryonic development

Rachel M. Woodhouse, Alyson Ashe

Biochem Soc Trans (2020) 48 (3): 1019–1034.

DOI: https://doi.org/10.1042/BST20190944

Published: 15 June 2020

... in C. elegans . We describe the role of repressive histone marks, histone methyltransferases, and associated chromatin factors in heritable gene silencing, and discuss recent developments and unanswered questions in how these factors integrate with other known TEI mechanisms. We also review...

View article titled, How do histone modifications contribute to transgenerational epigenetic inheritance in C. elegans ?

Articles

Three-dimensional genome rewiring during the development of antibody-secreting cells

Wing Fuk Chan, Timothy M. Johanson, Rhys S. Allan

Biochem Soc Trans (2020) 48 (3): 1109–1119.

DOI: https://doi.org/10.1042/BST20191104

Published: 26 May 2020

... morphological and functional alterations that begin early after antigenic stimulation. These include chromatin restructuring that is critical in regulating gene expression, DNA rearrangement and other cellular processes. Here we outline the recent understanding of the three-dimensional architecture...

View article titled, Three-dimensional genome rewiring during the development of antibody-secreting cells

Articles

Gene transcription and chromatin regulation in hypoxia

Michael Batie, Sonia Rocha

Biochem Soc Trans (2020) 48 (3): 1121–1128.

DOI: https://doi.org/10.1042/BST20191106

Published: 05 May 2020

...-dependent effects on chromatin structure. Correspondence: Michael Batie ( m.batie@liverpool.ac.uk ) and Sonia Rocha ( s.rocha@liverpool.ac.uk ) 17 3 2020 2 4 2020 6 4 2020 © 2020 The Author(s) 2020 This is an open access article published by Portland Press Limited on behalf...

View article titled, Gene transcription and chromatin regulation in hypoxia

Articles

Cell signaling and cytomegalovirus reactivation: what do Src family kinases have to do with it?

Matthew B. Reeves

Biochem Soc Trans (2020) 48 (2): 667–675.

DOI: https://doi.org/10.1042/BST20191110

Published: 20 April 2020

... of gene regulation. Indeed, the demonstration that the latent viral genome is associated with chromatin in naturally infected individuals provides a clear mechanism for the control of HCMV latency and reactivation [ 10 ]. A reductionist view of latency and reactivation is that it is hallmarked...

View article titled, Cell signaling and cytomegalovirus reactivation: what do Src family kinases have to do with it?

Articles

New insights into the evolutionary conservation of the sole PIKK pseudokinase Tra1/TRRAP

Alberto Elías-Villalobos, Philippe Fort, Dominique Helmlinger

Biochem Soc Trans (2019) 47 (6): 1597–1608.

DOI: https://doi.org/10.1042/BST20180496

Published: 26 November 2019

... and NuA4/TIP60 complex assembly and recruitment to chromatin. We further discuss its evolutionary history within the PIKK family and highlight recent findings that reveal the importance of molecular chaperones in pseudokinase folding, function, and conservation. In spite of their sequence similarity...

View article titled, New insights into the evolutionary conservation of the sole PIKK pseudokinase Tra1/TRRAP

Articles

Packaging development: how chromatin controls transcription in zebrafish embryogenesis

In Collection

Embryonic development

Julia A. Horsfield

Biochem Soc Trans (2019) 47 (2): 713–724.

DOI: https://doi.org/10.1042/BST20180617

Published: 05 April 2019

... depend on other factors such as DNA methylation, the presence of particular histone variants and post-translational modifications of histones. Collectively, factors that modify DNA or affect its packaging and accessibility contribute to a chromatin landscape that helps to control the timely expression...

View article titled, Packaging development: how chromatin controls transcription in zebrafish embryogenesis

Articles

United colours of chromatin? Developmental genome organisation in flies

Caroline Delandre, Owen J. Marshall

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

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

Published: 22 March 2019

...Caroline Delandre; Owen J. Marshall The organisation of DNA into differing forms of packaging, or chromatin, controls many of the cell fate decisions during development. Although early studies focused on individual forms of chromatin, in the last decade more holistic studies have attempted...

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

Articles

The role of chromosome segregation and nuclear organisation in human subfertility

Katie E. Fowler, Anjali A. Mandawala, Darren K. Griffin

Biochem Soc Trans (2019) 47 (1): 425–432.

DOI: https://doi.org/10.1042/BST20180231

Published: 07 February 2019

... of the haploid genome. Faithful chromosome segregation is thus crucial, as is an ordered spatio-temporal ‘dance’ of packing a large amount of chromatin into a very small space. Ergo, when the process goes wrong, this is associated with an improper chromosome number, nuclear position and/or chromatin damage...

View article titled, The role of chromosome segregation and nuclear organisation in human subfertility

Articles

Regulation of ATP-dependent chromatin remodelers: accelerators/brakes, anchors and sensors

Somnath Paul, Blaine Bartholomew

Biochem Soc Trans (2018) 46 (6): 1423–1430.

DOI: https://doi.org/10.1042/BST20180043

Published: 22 November 2018

...Somnath Paul; Blaine Bartholomew All ATP-dependent chromatin remodelers have a DNA translocase domain that moves along double-stranded DNA when hydrolyzing ATP, which is the key action leading to DNA moving through nucleosomes. Recent structural and biochemical data from a variety of different...

View article titled, Regulation of ATP-dependent chromatin remodelers: accelerators/brakes, anchors and sensors

Articles

Nucleosome-level 3D organization of the genome

Masae Ohno, David G. Priest, Yuichi Taniguchi

Biochem Soc Trans (2018) 46 (3): 491–501.

DOI: https://doi.org/10.1042/BST20170388

Published: 06 April 2018

... The Author(s). 2018 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) . chromatin chromatin conformation capture epigenomics structural analysis Figure...

View article titled, Nucleosome-level 3D organization of the genome

Articles

Protein phosphatases at the nuclear envelope

Raquel Sales Gil, Ines J. de Castro, Jerusalem Berihun, Paola Vagnarelli

Biochem Soc Trans (2018) 46 (1): 173–182.

DOI: https://doi.org/10.1042/BST20170139

Published: 06 February 2018

... on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) . chromatin nuclear envelopes nucleus protein phosphatases In higher eukaryotes, the nucleus is heavily remodelled during mitosis; this leads to the formation of mitotic...

View article titled, Protein phosphatases at the nuclear envelope

Articles

The 10-nm chromatin fiber and its relationship to interphase chromosome organization

Jeffrey C. Hansen, Mark Connolly, Charles J. McDonald, Anyu Pan, Anna Pryamkova, Kyle Ray, Erik Seidel, Sachiko Tamura, Ryan Rogge, Kazuhiro Maeshima

Biochem Soc Trans (2018) 46 (1): 67–76.

DOI: https://doi.org/10.1042/BST20170101

Published: 20 December 2017

... of the 10-nm chromatin fiber, but not the regular 30-nm fiber. We hypothesize that the hierarchical globular organization of an interphase chromosome is fundamentally established by the self-interacting properties of a 10-nm zig-zag array of nucleosomes, while histone post-translational modifications...

View article titled, The 10-nm chromatin fiber and its relationship to interphase chromosome organization

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

The links between chromatin spatial organization and biological function

Alejandro Rodriguez, Pernilla Bjerling

Biochem Soc Trans (2013) 41 (6): 1634–1639.

DOI: https://doi.org/10.1042/BST20130213

Published: 20 November 2013

...Alejandro Rodriguez; Pernilla Bjerling During the last few years, there has been a rapid increase in our knowledge of how chromatin is organized inside the nucleus. Techniques such as FISH (fluorescence in situ hybridization) have proved that chromosomes organize themselves in so-called CTs...

View article titled, The links between chromatin spatial organization and biological function

Articles

A snapshot of Snf2 enzymes in fission yeast

Punit Prasad, Karl Ekwall

Biochem Soc Trans (2013) 41 (6): 1640–1647.

DOI: https://doi.org/10.1042/BST20130145

Published: 20 November 2013

...Punit Prasad; Karl Ekwall Eukaryotic chromatin is remodelled by the evolutionarily conserved Snf2 family of enzymes in an ATP-dependent manner. Several Snf2 enzymes are part of CRCs (chromatin remodelling complexes). In the present review we focus our attention on the functions of Snf2 enzymes...

View article titled, A snapshot of Snf2 enzymes in fission yeast

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

Resolving the functions of peptidylprolyl isomerases: insights from the mutagenesis of the nuclear FKBP25 enzyme

Geoff Gudavicius, Heddy Soufari, Santosh Upadhyay, Cameron D. Mackereth, Christopher J. Nelson

Biochem Soc Trans (2013) 41 (3): 761–768.

DOI: https://doi.org/10.1042/BST20130013

Published: 23 May 2013

...Geoff Gudavicius; Heddy Soufari; Santosh Upadhyay; Cameron D. Mackereth; Christopher J. Nelson Peptidylprolyl isomerases have been implicated in chromatin regulation through their association with histones, chromatin-modifying enzymes and DNA-binding transcription factors. As with other post...

View article titled, Resolving the functions of peptidylprolyl isomerases: insights from the mutagenesis of the nuclear FKBP25 enzyme

Articles

CHD4 in the DNA-damage response and cell cycle progression: not so NuRDy now

Aoife O’Shaughnessy, Brian Hendrich

Biochem Soc Trans (2013) 41 (3): 777–782.

DOI: https://doi.org/10.1042/BST20130027

Published: 23 May 2013

.../licenses/by/3.0/ ) which permits unrestricted use, distribution and reproduction in any medium, provided the original work is properly cited. cell cycle chromatin chromodomain helicase DNA-binding 4 (CHD4) DNA damage DNA repair nucleosome remodelling and deacetylation (NuRD) The CHD3...

View article titled, CHD4 in the DNA-damage response and cell cycle progression: not so NuRDy now

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

... correspondence should be addressed (email llewelyn.roderick@babraham.ac.uk ). 1 2 2013 © The Authors Journal compilation © 2013 Biochemical Society 2013 cardiac hypertrophy chromatin epigenetics histone histone methylation The mammalian heart is a remarkable organ that, by its...

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

...Hannah K. Long; Neil P. Blackledge; Robert J. Klose Vertebrate DNA can be chemically modified by methylation of the 5 position of the cytosine base in the context of CpG dinucleotides. This modification creates a binding site for MBD (methyl-CpG-binding domain) proteins which target chromatin...

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

Articles

DNA thermodynamics shape chromosome organization and topology

Andrew A. Travers, Georgi Muskhelishvili

Biochem Soc Trans (2013) 41 (2): 548–553.

DOI: https://doi.org/10.1042/BST20120334

Published: 21 March 2013

...Andrew A. Travers; Georgi Muskhelishvili How much information is encoded in the DNA sequence of an organism? We argue that the informational, mechanical and topological properties of DNA are interdependent and act together to specify the primary characteristics of genetic organization and chromatin...

View article titled, DNA thermodynamics shape chromosome organization and topology

Articles

Topological Aspects of DNA Function and Protein Folding

Andrzej Stasiak, Andrew D. Bates, Dorothy E. Buck, Sarah A. Harris, De Witt Sumners

Biochem Soc Trans (2013) 41 (2): 491–493.

DOI: https://doi.org/10.1042/BST20130006

Published: 21 March 2013

... ( andrzej.stasiak@unil.ch ). 24 1 2013 © The Authors Journal compilation © 2013 Biochemical Society 2013 catenane chromatin chromosome DNA knot protein folding recombinase supercoiling topoisomerase The structure and function of DNA and proteins are affected by the topology...

View article titled, Topological Aspects of DNA Function and Protein Folding

Articles

Structure and dynamics of the crenarchaeal nucleoid

Rosalie P.C. Driessen, Remus Th. Dame

Biochem Soc Trans (2013) 41 (1): 321–325.

DOI: https://doi.org/10.1042/BST20120336

Published: 29 January 2013

...Rosalie P.C. Driessen; Remus Th. Dame Crenarchaeal genomes are organized into a compact nucleoid by a set of small chromatin proteins. Although there is little knowledge of chromatin structure in Archaea, similarities between crenarchaeal and bacterial chromatin proteins suggest that organization...

View article titled, Structure and dynamics of the crenarchaeal nucleoid

Articles

Nucleosome recognition and spacing by chromatin remodelling factor ISW1a

Timothy J. Richmond

Biochem Soc Trans (2012) 40 (2): 347–350.

DOI: https://doi.org/10.1042/BST20110748

Published: 21 March 2012

...Timothy J. Richmond Nucleosomes are actively positioned along DNA by ATP-dependent, chromatin remodelling factors. A structural model for the ISW1a chromatin remodelling factor from Saccharomyces cerevisiae in complex with a dinucleosome substrate was constructed from the X-ray structures of ISW1a...

View article titled, Nucleosome recognition and spacing by chromatin remodelling factor ISW1a

Articles

DNA structure, nucleosome placement and chromatin remodelling: a perspective

Andrew A. Travers, Cédric Vaillant, Alain Arneodo, Georgi Muskhelishvili

Biochem Soc Trans (2012) 40 (2): 335–340.

DOI: https://doi.org/10.1042/BST20110757

Published: 21 March 2012

...Andrew A. Travers; Cédric Vaillant; Alain Arneodo; Georgi Muskhelishvili A major question in chromatin biology is to what extent the sequence of DNA directly determines the genetic and chromatin organization of a eukaryotic genome? We consider two aspects to this question: the DNA sequence...

View article titled, DNA structure, nucleosome placement and chromatin remodelling: a perspective

Articles

Deciphering how the chromatin factor RCC1 recognizes the nucleosome: the importance of individuals in the scientific discovery process

Song Tan

Biochem Soc Trans (2012) 40 (2): 351–356.

DOI: https://doi.org/10.1042/BST20110734

Published: 21 March 2012

...Song Tan The nucleosome repeating unit of chromatin is the target of chromatin enzymes and factors that regulate gene activity in a eukaryotic cell. How the nucleosome is recognized by chromatin enzymes and factors is poorly understood, even though such interaction is fundamental to gene regulation...

View article titled, Deciphering how the chromatin factor RCC1 recognizes the nucleosome: the importance of individuals in the scientific discovery process

Articles

Histone marks: repairing DNA breaks within the context of chromatin

Kyle M. Miller, Stephen P. Jackson

Biochem Soc Trans (2012) 40 (2): 370–376.

DOI: https://doi.org/10.1042/BST20110747

Published: 21 March 2012

...Kyle M. Miller; Stephen P. Jackson Inherited or acquired defects in detecting, signalling or repairing DNA damage are associated with various human pathologies, including immunodeficiencies, neurodegenerative diseases and various forms of cancer. Nuclear DNA is packaged into chromatin and therefore...

View article titled, Histone marks: repairing DNA breaks within the context of chromatin

Articles

Active nucleosome positioning beyond intrinsic biophysics is revealed by in vitro reconstitution

Philipp Korber

Biochem Soc Trans (2012) 40 (2): 377–382.

DOI: https://doi.org/10.1042/BST20110730

Published: 21 March 2012

... for active packing of nucleosomes against the 5′ ends of genes rather than statistical positioning. A first extract fractionation identified a direct, specific, necessary, but not sufficient role for the RSC (remodels the structure of chromatin) remodelling enzyme. Collectively, nucleosome positioning...

View article titled, Active nucleosome positioning beyond intrinsic biophysics is revealed by in vitro reconstitution

Articles

The role of nesprins as multifunctional organizers in the nucleus and the cytoskeleton

Angelika A. Noegel, Sascha Neumann

Biochem Soc Trans (2011) 39 (6): 1725–1728.

DOI: https://doi.org/10.1042/BST20110668

Published: 21 November 2011

... The Authors Journal compilation © 2011 Biochemical Society 2011 α-catenin chromatin laminopathy linker of nucleoskeleton and cytoskeleton complex (LINC complex) nesprin Wnt signalling wound healing The nature of the NE (nuclear envelope) is of fundamental interest in cell biology...

View article titled, The role of nesprins as multifunctional organizers in the nucleus and the cytoskeleton

Articles

The nuclear lamina and heterochromatin: a complex relationship

Erin M. Bank, Yosef Gruenbaum

Biochem Soc Trans (2011) 39 (6): 1705–1709.

DOI: https://doi.org/10.1042/BST20110603

Published: 21 November 2011

..., providing a potential mechanism for how these mutations lead to tissue-specific diseases. Many components of the nuclear lamina are directly linked to chromatin via interactions with DNA, transcription factors, histones and histone-modifying enzymes. Together, these interactions form a network...

View article titled, The nuclear lamina and heterochromatin: a complex relationship

Articles

Nucleoid-associated proteins in Crenarchaea

Rosalie P.C. Driessen, Remus Th. Dame

Biochem Soc Trans (2011) 39 (1): 116–121.

DOI: https://doi.org/10.1042/BST0390116

Published: 19 January 2011

... by which they modulate the genome do seem to be functionally conserved across kingdoms. On a generic level, architectural proteins can be classified based on their structural effect as DNA benders, DNA bridgers or DNA wrappers. Although chromatin organization in archaea has not been studied extensively...

View article titled, Nucleoid-associated proteins in Crenarchaea

Articles

Alternative polyadenylation of antisense RNAs and flowering time control

Csaba Hornyik, Céline Duc, Katarzyna Rataj, Lionel C. Terzi, Gordon G. Simpson

Biochem Soc Trans (2010) 38 (4): 1077–1081.

DOI: https://doi.org/10.1042/BST0381077

Published: 26 July 2010

... -acting regulators of alternative cleavage and polyadenylation. FCA and FPA directly associate with chromatin at the locus encoding the floral repressor FLC, but appear to control FLC transcription by mediating alternative polyadenylation of embedded non-coding antisense RNAs. These findings prompt the re...

View article titled, Alternative polyadenylation of antisense RNAs and flowering time control

Articles

Male gamete biology in flowering plants

Scott D. Russell, Xiaoping Gou, Xiaoping Wei, Tong Yuan

Biochem Soc Trans (2010) 38 (2): 598–603.

DOI: https://doi.org/10.1042/BST0380598

Published: 22 March 2010

... of paternal effects. However, as more is known about molecular expression of chromatin-modifying proteins, ubiquitin pathway proteins and transcription factors in sperm cells, as well as their ability to achieve effect by intaglio expression, passing transcripts directly into translation, the role of the male...

View article titled, Male gamete biology in flowering plants

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Lamins: ‘structure goes cycling’

Mirta Boban, Juliane Braun, Roland Foisner

Biochem Soc Trans (2010) 38 (1): 301–306.

DOI: https://doi.org/10.1042/BST0380301

Published: 19 January 2010

...@meduniwien.ac.at ). 29 10 2009 © The Authors Journal compilation © 2010 Biochemical Society 2010 cell proliferation chromatin lamin mitosis nuclear assembly nuclear envelope Transition of proliferating cells from G 1 - to S-phase marks an irreversible event committing cells...

View article titled, Lamins: ‘structure goes cycling’

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