Histone analysis articles within Nature Communications

Featured

• Article
  05 November 2022 | Open Access

  Learning the histone codes with large genomic windows and three-dimensional chromatin interactions using transformer

  Existing deep learning-based approaches for the prediction of gene expression by histone modifications (HMs) can only focus on narrow and linear genomic regions around promoters. Here, the authors address these problems by developing a transformer-based deep learning architecture named Chromoformer.

  • Dohoon Lee
  • , Jeewon Yang
  •  & Sun Kim

• Article
  08 June 2021 | Open Access

  HIRA stabilizes skeletal muscle lineage identity

  The epigenetic mechanisms coordinating the maintenance of adult cellular lineages remain poorly understood. Here the authors demonstrate that HIRA, a H3.3 histone chaperone, establishes the chromatin landscape required for skeletal muscle cell identity.

  • Joana Esteves de Lima
  • , Reem Bou Akar
  •  & Frédéric Relaix

• Article
  11 January 2021 | Open Access

  Transcription shapes genome-wide histone acetylation patterns

  Histone acetylation is a ubiquitous hallmark of transcription. Here the authors provide evidence that the majority of histone acetylation is dependent on transcription, specifically due to the requirement of RNAPII for the recruitment and activity of histone acetyltransferases.

  • Benjamin J. E. Martin
  • , Julie Brind’Amour
  •  & LeAnn J. Howe

• Article
  04 January 2021 | Open Access

  Hydroxamic acid-modified peptide microarrays for profiling isozyme-selective interactions and inhibition of histone deacetylases

  Current histone microarrays cannot be used to directly study the transient interactions of histone deacetylases (HDACs). Here, the authors show that hydroxamic acid-modified microarrays can capture HDACs, provide insights into their substrate specificity, and serve to develop peptide inhibitors.

  • Carlos Moreno-Yruela
  • , Michael Bæk
  •  & Christian A. Olsen

• Article
  08 December 2020 | Open Access

  An epigenetic gene silencing pathway selectively acting on transgenic DNA in the green alga Chlamydomonas

  Strong transgene suppression has been observed in Chlamydomonas reinhardtii, but the underlying mechanism is unknown. Here, the authors identify a sirtuin-type histone deacetylase that selectively acts on transgenic DNA to repress gene expression by assembling a repressive chromatin structure composed of deacetylated histones.

  • Juliane Neupert
  • , Sean D. Gallaher
  •  & Ralph Bock

• Article
  09 October 2020 | Open Access

  An embryonic stem cell-specific heterochromatin state promotes core histone exchange in the absence of DNA accessibility

  Nucleosome turnover concomitant with incorporation of the histone variant H3.3 is a hallmark of regulatory regions in the animal genome. Here, the authors demonstrate that fast histone turnover and H3.3 incorporation defines a dynamic heterochromatin state in pluripotent stem cells.

  • Carmen Navarro
  • , Jing Lyu
  •  & Simon J. Elsässer

• Article
  26 July 2019 | Open Access

  Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition

  The SWI2/SNF2-Related 1 chromatin remodeling complex (SWR1-C) is important for gene regulation, but its composition remains largely uncharacterized in plants. Here, the authors report that methyl-CpG-binding domain 9 (MBD9) is a SWR1-C interacting protein required for histone H2A.Z deposition in Arabidopsis.

  • Magdalena E. Potok
  • , Yafei Wang
  •  & Steven E. Jacobsen

• Article
  18 September 2018 | Open Access

  Paf1 and Ctr9 subcomplex formation is essential for Paf1 complex assembly and functional regulation

  The evolutionarily conserved multifunctional polymerase-associated factor 1 (Paf1) complex plays an essential role in gene regulation. Here, the authors report two structures of the human and yeast Ctr9/Paf1 subcomplexes, and find that this is essential for Paf1 complex assembly and function.

  • Ying Xie
  • , Minying Zheng
  •  & Jiafu Long

• Article
  11 April 2018 | Open Access

  Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration

  Incorporation of histone H3 variant H3.3 into chromatin regulates transcription. Here the authors find that H3.3 sub-variant H3mm7 is required for skeletal muscle regeneration and that H3mm7 nucleosomes are unstable and exhibit higher mobility, with H3mm7 promoting open chromatin around promoters.

  • Akihito Harada
  • , Kazumitsu Maehara
  •  & Yasuyuki Ohkawa

• Article
  26 March 2018 | Open Access

  A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons

  The limited size of some neuronal types and their entangled environment renders it difficult to study their transcription regulation. Here the authors present a comparative analysis of histone modifications and transcription in dopaminergic and serotonergic neurons and embryonic neural progenitors.

  • Erik Södersten
  • , Konstantinos Toskas
  •  & Johan Holmberg

• Article
  12 December 2017 | Open Access

  H3K14ac is linked to methylation of H3K9 by the triple Tudor domain of SETDB1

  SETDB1 is a histone methyltransferase that generates H3K9me3 marks in euchromatic regions. Here the authors show that the triple Tudor domain (3TD) of SETDB1 binds histone H3 tails containing K14 acetylation combined with K9 methylation, and that the K9me–K14ac modification defines a novel chromatin state enriched at SETDB1 binding sites.

  • Renata Z. Jurkowska
  • , Su Qin
  •  & Albert Jeltsch