Chromatin analysis articles within Nature Communications

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  • Article
    | Open Access

    Conducting epigenomic studies on FFPE samples is traditionally challenging due to chromatin damage caused due to exposure to formaldehyde. Here, the authors show that an optimisation of their previous CUTAC method allows the production of high-resolution maps of regulatory elements from FFPE samples.

    • Steven Henikoff
    • , Jorja G. Henikoff
    •  & Eric C. Holland

  • Article
    | Open Access

    Limited work has been done on concurrent C-to-G and A-to-G base editing. Here the authors test how a number of chromatin-associated factors affect base editing and show that HMGN1 enhanced the efficiency; by fusing HMGN1 to GBE and ABE they develop a CRISPR-based dual-function A-to-G and C-to-G base editor (GGBE).

    • Chao Yang
    • , Zhenzhen Ma
    •  & Xueli Zhang

  • Article
    | Open Access

    Here the authors present the low input capture Hi-C (liCHi-C) method, a cost-effective, flexible method to map and robustly compare promoter interactomes at high resolution. liCHi-C identifies new disease-associated genes and structural variants to ultimately illuminate their pathogenic effects.

    • Laureano Tomás-Daza
    • , Llorenç Rovirosa
    •  & Biola M. Javierre

  • Article
    | Open Access

    It is currently not clear how architectural proteins orchestrate chromatin looping at different scales of genome organisation. Here the authors report Hi-TrAC as a proximity ligation-free method to profile genome-wide chromatin interactions at single nucleosome resolution among regulatory elements.

    • Shuai Liu
    • , Yaqiang Cao
    •  & Keji Zhao

  • Article
    | Open Access

    The contractile properties of adult myofibers are shaped by their Myosin heavy chain isoform content. Here the authors show that a super enhancer controls the spatiotemporal expression of the genes at the fast myosin heavy chain locus by DNA looping and that this expression profile is recapitulated in a rainbow transgenic mouse model of the locus.

    • Matthieu Dos Santos
    • , Stéphanie Backer
    •  & Pascal Maire

  • Article
    | Open Access

    The effect of ATP-dependent chromatin remodelers on 3D genome organization has not been well studied. Here the authors employ in situ Hi-C with an auxin-inducible degron system to degrade chromatin remodelers in yeast to find that the 3D structure of chromatin collapses in their absence. The chromatin remodeling can modulate 3D architecture depending on chromosomal context and cell cycle stage.

    • Hyelim Jo
    • , Taemook Kim
    •  & Daeyoup Lee

  • Article
    | Open Access

    The authors present epiScanpy: a computational framework for the analysis of single-cell epigenomic data, both ATAC-seq and DNA methylation data, with examples for clustering, cell type identification, trajectory learning and atlas integration - and show its performance in distinguishing cell types.

    • Anna Danese
    • , Maria L. Richter
    •  & Maria Colomé-Tatché

  • Article
    | Open Access

    Mesomelic dysplasia, a severe shortening and bending of the limb, has been linked to rearrangements in the HoxD cluster in humans and mice. Here the authors engineer a 1 Mb inversion including the HoxD gene cluster and use this model to provide a mechanistic framework to understand and unify the molecular origins of human mesomelic dysplasia associated with 2q31.

    • Christopher Chase Bolt
    • , Lucille Lopez-Delisle
    •  & Denis Duboule

  • Article
    | Open Access

    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
    | Open Access

    Histone variant H2A.Z has been suggested to contribute to the regulation of promoter accessibility. Here, the authors present high-depth maps of the position and accessibility of H2A.Z-containing nucleosomes for human Pol II promoters and provide evidence that H2A.Z has multiple and distinct roles in regulating gene expression dependent upon its location in a promoter.

    • Lauren Cole
    • , Sebastian Kurscheid
    •  & David J. Tremethick

  • Article
    | Open Access

    Extensive epigenetic reprogramming occurs during preimplantation embryo development. Here the authors develop a single cell multiomics sequencing technology that enables profiling of genome-wide chromatin accessibility, DNA methylation and RNA expression in the same individual cell and apply this method to study mouse preimplantation embryos.

    • Yang Wang
    • , Peng Yuan
    •  & Liying Yan

  • Article
    | Open Access

    Genetic elements that control inflammatory gene expression are not fully elucidated. Here the authors conduct a multi-species analysis of chromatin landscape and NF-κB binding in response to the proinflammatory cytokine TNFα, finding that conserved NF-κB bound regions are linked to enhancer activity and disease.

    • Azad Alizada
    • , Nadiya Khyzha
    •  & Michael D. Wilson

  • Article
    | Open Access

    Mast cells are critical effectors of allergic inflammation and protection against parasitic infections. Here the authors demonstrate that GATA2 promotes chromatin accessibility at the super-enhancers of mast cell identity genes and primes both typical and super-enhancers at genes that respond to antigenic stimulation.

    • Yapeng Li
    • , Junfeng Gao
    •  & Hua Huang

  • Article
    | Open Access

    The role of BRD4 and Mediator in regulating enhancer-promoter interactions is poorly understood. Here the authors find that treatment with BET inhibitors or pharmacological degradation of BRD4 disrupts transcription while having very little effect on enhancer-promoter interactions.

    • Nicholas T. Crump
    • , Erica Ballabio
    •  & Thomas A. Milne

  • Article
    | Open Access

    Genomes are partitioned into topologically associating domains (TADs). Here the authors present single-nucleus Hi-C maps in Drosophila at 10 kb resolution, demonstrating the presence of chromatin compartments in individual nuclei, and partitioning of the genome into non-hierarchical TADs at the scale of 100 kb, which resembles population TAD profiles.

    • Sergey V. Ulianov
    • , Vlada V. Zakharova
    •  & Sergey V. Razin

  • Article
    | Open Access

    Hutchinson-Gilford progeria syndrome is a genetic disease where an aberrant form of Lamin A disrupts chromatin by interfering with lamina associated domains. Here, the authors present the SAMMY-seq, a method for genome-wide characterization of heterochromatin dynamics and detect early stage alterations of heterochromatin structure in progeria primary fibroblasts, accompained by Polycomb dysfunctions.

    • Endre Sebestyén
    • , Fabrizia Marullo
    •  & Chiara Lanzuolo

  • Article
    | Open Access

    Senescence is a state of stable proliferative arrest. Here, the authors perform Hi-C analysis on oncogenic RAS-induced senescence in human fibroblasts and characterize the changes in the 3D genome folding associated with the senescence-specific gene expression profile, which are mediated in part through cohesin redistribution on chromatin.

    • Ioana Olan
    • , Aled J. Parry
    •  & Masashi Narita

  • Article
    | Open Access

    T cells are a major cell type involved in systemic lupus erythematosus (SLE). Here, the authors use promoter capture-C and ATAC-seq in human follicular T helper cells to identify SLE genes distant from GWAS loci (via 3D interaction) and validate the function of key regulatory elements and genes in vitro.

    • Chun Su
    • , Matthew E. Johnson
    •  & Andrew D. Wells

  • Article
    | Open Access

    Epstein-Barr virus (EBV) episomes tether to the host chromosome via EBNA1. Here, using circular chromosome conformation capture (4C), Kim et al. identify attachment sites and show that EBV episomes preferentially associate with transcriptionally silenced genes in Burkitt lymphoma cells.

    • Kyoung-Dong Kim
    • , Hideki Tanizawa
    •  & Paul M. Lieberman

  • Article
    | Open Access

    Understanding gene regulation will require mapping specific chromain features in a small number of cells at high resolution. Here the authors describe CUT&Tag, which uses antibody-mediated tethering of Tn5 transposase to a chromatin protein to generate high resolution libraries.

    • Hatice S. Kaya-Okur
    • , Steven J. Wu
    •  & Steven Henikoff

  • Article
    | Open Access

    Chromatin conformation studies are limited by the large amounts of starting material required to perform current protocols. Here the authors present Low-C, a Hi-C method for low amounts of input material and produce Low-C maps from primary B-cells of a diffuse large B-cell lymphoma patient, demonstrating the suitability of Low-C to analyse rare cell populations.

    • Noelia Díaz
    • , Kai Kruse
    •  & Juan M. Vaquerizas

  • Article
    | Open Access

    Cellular heterogeneity in cancer is complex and difficult to study. Here, the authors introduce Protein-indexed Assay of Transposase Accessible Chromatin (Pi-ATAC), which combines single cell chromatin and proteomic profiling to provide deep insight into the tumor microenvironment, and reveal the role of hypoxia in shaping the regulome of a subset of breast cancer cells in vivo.

    • Xingqi Chen
    • , Ulrike M. Litzenburger
    •  & Howard Y. Chang

  • Article
    | Open Access

    Mitosis poses a challenge for transcriptional programs, as it is thought that several proteins lose binding on condensed chromosomes. Here, the authors analyze the chromatin-bound proteome through the cell cycle, revealing retention of most transcription factors and preservation of the regulatory landscape.

    • Paul Adrian Ginno
    • , Lukas Burger
    •  & Dirk Schübeler

  • Article
    | Open Access

    Relationships between DNA methylation and transcription, and methylation and DNA accessibility can be probed but interrogating all three in the same single cells has not been possible. Here, the authors report the first single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling.

    • Stephen J. Clark
    • , Ricard Argelaguet
    •  & Wolf Reik

  • Article
    | Open Access

    Understanding the link between epigenetic marks and gene regulation requires the development of new tools to directly manipulate chromatin. Here the authors demonstrate a Cas9-based system to recruit chromatin remodelers to loci of interest, allowing rapid, reversible manipulation of epigenetic states.

    • Simon M. G. Braun
    • , Jacob G. Kirkland
    •  & Gerald R. Crabtree

  • Article
    | Open Access

    Chromatin architecture is a key regulator of transcriptional processes, however current methods to investigate it have technical limitations. Here, the authors describe a novel chromatin capture technique, CATCH, which can be used to identify and characterize complex genomic interaction networks.

    • Ryan J. Bourgo
    • , Hari Singhal
    •  & Geoffrey L. Greene

  • Article
    | Open Access

    A tumour’s cell of origin may influence tumour progression and response to therapy. Here, the authors demonstrate that the cell of origin determines the aggressiveness of AML in a mouse model and identify unique biomarkers of the specific leukaemia cell of origin by profiling open chromatin regions of AML samples.

    • Joshy George
    • , Asli Uyar
    •  & Jennifer J. Trowbridge

  • Article
    | Open Access

    Chromosomes contain large heterochromatin domains. Here, the authors measure the kinetics of heterochromatin formation in fission yeast and show both global and local feedbacks by nucleosome-bound enzymes are important for formation and stability of the large heterochromatin domains.

    • Michaela J. Obersriebnig
    • , Emil M. H. Pallesen
    •  & Geneviève Thon

  • Article |

    Epigenetic alterations alter chromatin structure and gene expression and are known contributors to cancer development. Here, Muratani et al.profile multiple epigenetic chromatin marks in primary gastric cancers and identify hundreds of altered promoters and enhancers that drive the gene expression program in these malignancies.

    • Masafumi Muratani
    • , Niantao Deng
    •  & Patrick Tan

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