Epigenomics articles within Nature Communications

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  • Article
    | Open Access

    ATAC-seq measures chromatin accessibility as a proxy for the activity of DNA regulatory regions across the genome. Here the authors present AtacWorks, a deep learning tool to denoise and identify accessible chromatin regions from low cell count, low-coverage, or low-quality ATAC-seq data.

    • Avantika Lal
    • , Zachary D. Chiang
    •  & Jason D. Buenrostro

  • Article
    | Open Access

    The NCI-60 cancer cell line panel covers multiple cancer types but has not been extensively investigated at the epigenetic level. Here, the authors present H3K4me3, H3K27ac, H3K9me3, and H4K20me3 ChIP-Seq analysis of the cell lines, and describe features of chromatin states and integrative analyses of expression, epigenetic and genetic mutation data.

    • Lijin K. Gopi
    •  & Benjamin L. Kidder

  • Article
    | Open Access

    Single cell analysis of transposase-accessible chromatin is deepening our understanding on the origins of cellular diversity, yet methods are limited by data sparsity. Here, the authors introduce SnapATAC, a pipeline to resolve cellular heterogeneity and reveal candidate regulatory elements across different cell populations.

    • Rongxin Fang
    • , Sebastian Preissl
    •  & Bing Ren

  • Article
    | Open Access

    Interaction between transcription factors and chromatin is fundamental for genome organization and regulation. Here, the authors use information theory to measure signatures of organized chromatin resulting from transcription factor-chromatin interactions, termed chromatin information enrichment, and find that variations in the information encoded in chromatin architecture reflects functional biological variation.

    • Ricardo D’Oliveira Albanus
    • , Yasuhiro Kyono
    •  & Stephen C. J. Parker

  • Article
    | Open Access

    Spatial orientation of cells in an interconnected network is lost in high-throughput single-cell epigenomic assays. Here the authors present sciMAP-ATAC to produce spatially resolved single-cell ATAC-seq data.

    • Casey A. Thornton
    • , Ryan M. Mulqueen
    •  & Andrew C. Adey

  • Article
    | Open Access

    Boundaries of topologically associated domains in genomes are marked by CTCF and cohesin binding. Here the authors predict CTCF interaction specificity by building a simple mathematical model with features including loop competition and extrusion.

    • Wang Xi
    •  & Michael A. Beer

  • Article
    | Open Access

    Aberrant gain of DNA methylation at CpG islands is frequently observed in colorectal tumours. Here the authors use ectopically integrated CpG islands in colorectal cancer cells and find that aberrantly methylated CpG islands are subject to low levels of de novo DNA methylation, and that instead de novo DNA methylation activity is targeted primarily to CpG islands marked by the histone modification H3K36me3.

    • Roza H. Ali Masalmeh
    • , Francesca Taglini
    •  & Duncan Sproul

  • Article
    | Open Access

    It is known that invasive lung adenocarcinomas evolve from pre-cancerous dysplastic lesions. In this study, the authors show that evolution of pre-cancerous lesions is accompanied by DNA methylation alterations, and that global hypomethylation correlates with immune infiltration, mutational burden and copy number alterations.

    • Xin Hu
    • , Marcos R. Estecio
    •  & Jianjun Zhang

  • Article
    | Open Access

    Here, the authors introduce Cell Heterogeneity–Adjusted cLonal Methylation (CHALM) as a methylation quantification method that considers the heterogeneity of sequenced bulk cells. They apply CHALM to methylation datasets to detect differentially methylated genes that exhibit distinct biological functions supporting underlying mechanisms.

    • Jianfeng Xu
    • , Jiejun Shi
    •  & Wei Li

  • Article
    | Open Access

    Enhancers shape gene expression patterns and are involved in disease pathogenesis. Here the authors demonstrate a strategy to screen functional regulatory elements for non-coding RNAs ― illustrated with miR-146a ― and link autoimmune disease risk genetic variants to autoimmune disease etiology.

    • Guojun Hou
    • , Isaac T. W. Harley
    •  & Nan Shen

  • Article
    | Open Access

    Genome-wide maps of evolutionary constraint and large-scale compendia of epigenomic and transcription factor data provide complementary information for genome annotation. Here, the authors develop the Constrained Non-Exonic Predictor (CNEP) that enables better understanding of their relationship.

    • Olivera Grujic
    • , Tanya N. Phung
    •  & Jason Ernst

  • Article
    | Open Access

    DNA 5-hydroxymethylcytosine (5hmC) modification is associated with gene transcription and used as a mark of mammalian development. Here the authors report a comprehensive 5hmC tissue map and analysis of 5hmC genomic distributions in 19 human tissues derived from 10 organ systems, thus providing insights into the role of 5hmC in tissue-specific development.

    • Xiao-Long Cui
    • , Ji Nie
    •  & Chuan He

  • Article
    | Open Access

    Active and passive demethylation pathways have been implicated in the genome-wide erasure of 5mC accompanying mammalian preimplantation development. Here the authors reveal a recently evolved, mammalian-specific pathway in which global hypomethylation is achieved by the coupling of active and passive demethylation.

    • Christopher B. Mulholland
    • , Atsuya Nishiyama
    •  & Heinrich Leonhardt

  • Article
    | Open Access

    Systemic sclerosis (SSc) is a disease with manifestation in the skin and immune etiology, but the pathogenic immune cell types remain unidentified. Here the authors use ATAC-seq to profile chromatin landscapes of skin samples from patients with SSc to implicate skin dendritic cells for having the strongest disease-associated epigenetic changes.

    • Qian Liu
    • , Lisa C. Zaba
    •  & Howard Y. Chang

  • Article
    | Open Access

    MYCN amplification is common in neuroblastomas. Here the authors analyse the MYCN amplicon structure and its epigenetic regulation by integrating short- and longread genomic and epigenomic data and find two classes of MYCN amplicons in neuroblastomas, one driven by local enhancers and the other by hijacking of distal regulatory elements.

    • Konstantin Helmsauer
    • , Maria E. Valieva
    •  & Richard P. Koche

  • Article
    | Open Access

    Here, the authors perform ATAC-seq on four distinct cell populations from three different regions of the human brain, finding that chromatin accessibility varies greatly by cell type and less by brain region. This study reveals differences in biological function and gene regulation, as well as overlap of genetic variants associated with schizophrenia and other neuropsychiatric traits.

    • Mads E. Hauberg
    • , Jordi Creus-Muncunill
    •  & Panos Roussos

  • Article
    | Open Access

    Human memory B cells differentiate from naïve B cells and can express different immunoglobulin (Ig) isotypes resulted from class-switch recombination. Here the authors describe, using transcriptional and epigenetic data from human memory B cells and integrated multi-omics analyses, the differentiation regulation and trajectory of IgG+, IgA+ and IgD+ memory B cells.

    • Justin B. Moroney
    • , Anusha Vasudev
    •  & Paolo Casali

  • Article
    | Open Access

    The histone variant mutation H3.3-G34W occurs in the majority of giant cell tumor of bone (GCTB). By profiling patient-derived GCTB tumor cells, the authors show that this mutation associates with epigenetic alterations in heterochromatic and bivalent regions that contribute to an impaired osteogenic differentiation and the osteolytic phenotype of GCTB.

    • Pavlo Lutsik
    • , Annika Baude
    •  & Christoph Plass

  • Article
    | Open Access

    Allele-specific measurements can reveal differences in DNA methylation between homologous alleles associated with changes in genetic sequence. Here, the authors develop a method for detecting allele specific methylation events within haplotypes of linked SNPs, compare it with existing methods, and show it identifies haplotypes for which the genetic variant carries significant information about the methylation state of the allele of origin.

    • J. Abante
    • , Y. Fang
    •  & J. Goutsias

  • Article
    | Open Access

    Chromatin state underlies cellular function, and transcription factor binding patterns along with epigenetic marks define chromatin state. Here the authors show that the histone chaperone ANP32E functions through regulation of H2A.Z to restrict genome-wide chromatin accessibility and to inhibit gene transcriptional activation.

    • Kristin E. Murphy
    • , Fanju W. Meng
    •  & Patrick J. Murphy

  • Article
    | Open Access

    Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impaired social interactions with repetitive and restrictive behaviours. Here the authors integrate mRNA expression, miRNA expression, DNA methylation, and histone acetylation datasets from a collection of post mortem brain tissues and identify a convergent molecular subtype of ASD.

    • Gokul Ramaswami
    • , Hyejung Won
    •  & Daniel H. Geschwind

  • Article
    | Open Access

    Smoking-associated DNA methylation changes in whole blood have been reported by many EWAS. Here, the authors use a cell-type deconvolution algorithm to identify cell-type specific DNA methylation signals in seven EWAS, identifying lineage-specific smoking-associated DNA methylation changes.

    • Chenglong You
    • , Sijie Wu
    •  & Andrew E. Teschendorff

  • Article
    | Open Access

    Epigenetic mechanisms have emerged as contributors to the molecular impairments caused by exposure to environmental factors such as abused substances. Here the authors perform epigenetic profiling of the striatum and identify the tyrosine kinase FYN is an important driver of neurodegenerative-like pathology and drug-taking behaviour.

    • Gabor Egervari
    • , Diana Akpoyibo
    •  & Yasmin L. Hurd

  • Article
    | Open Access

    Although Huntington’s disease (HD) is a well-studied genetic disorder, less is known about the epigenetic changes underlying it. Here, the authors characterize DNA methylation levels in tissues from patients, a mouse huntingtin (Htt) gene knock-in model, and a transgenic HTT sheep model, and provide evidence that HD is accompanied by DNA methylation changes in these three species.

    • Ake T. Lu
    • , Pritika Narayan
    •  & Steve Horvath

  • Article
    | Open Access

    Histone methyltransferase, DOTL1 is implicated in the pathogenesis of MLL-rearranged leukemia, however, not much is known of its role in prostate cancer (PCa). Here, the authors report that DOTL1 inhibition suppresses both androgen receptor and MYC pathways in a negative feed forward manner to reduce growth of AR-positive PCa.

    • R. Vatapalli
    • , V. Sagar
    •  & S. A. Abdulkadir

  • Article
    | Open Access

    The shoot apical meristem of flowering plants transitions from forming leaves to floral organs. Here Higo et al. show that DNA methylation of many transposons that are hypermethylated in gametes is established in the SAM before flowering, suggesting it protects against harmful transposition long before germ cell differentiation.

    • Asuka Higo
    • , Noriko Saihara
    •  & Hiroyuki Tsuji

  • Article
    | Open Access

    Acute kidney injury is a major health problem amongst hospitalized patients. Here the authors provide a comprehensive characterization of enhancer and super-enhancer elements, and the transcription factor motifs associated with these elements in response to kidney injury in vivo; providing insight into the regulation of kidney repair.

    • Julia Wilflingseder
    • , Michaela Willi
    •  & Joseph V. Bonventre

  • 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

    Linking epigenetic marks to clinical outcomes promises insight into the underlying processes. Here, the authors introduce a statistical approach to estimate associations between a phenotype and all epigenetic probes jointly, and to estimate the proportion of variation captured by epigenetic effects.

    • Daniel Trejo Banos
    • , Daniel L. McCartney
    •  & Matthew R. Robinson

  • Article
    | Open Access

    Local activity of the DNA methylation machinery remains poorly understood. Here, the authors present a theoretical and experimental framework to infer methylation and demethylation rates at genome scale in mouse embryonic stem cells, finding that maintenance methylation activity is reduced at transcription factor binding sites, while methylation turnover is elevated in transcribed gene bodies.

    • Paul Adrian Ginno
    • , Dimos Gaidatzis
    •  & Dirk Schübeler

  • Article
    | Open Access

    DNA methylation is an epigenetic marker in all domains of life. Here, Jeudy et al., using single-molecule realtime sequencing, determine DNA methylation patterns in giant viruses and evolutionary analysis of virus encoded DNA methyltransferases suggests that they affect viral fitness.

    • Sandra Jeudy
    • , Sofia Rigou
    •  & Matthieu Legendre

  • Article
    | Open Access

    Comprehensive epigenomic maps of various rice varieties are still unavailable. Here, the authors report the development of eChIP as a fast and low-input upgrade of regular plant ChIP-seq protocol for epigenome analysis of 20 rice varieties and annotate over 80% of the genome with different epigenome properties for transcriptional regulation.

    • Lun Zhao
    • , Liang Xie
    •  & Xingwang Li

  • Article
    | Open Access

    Characterization of the distance over which TF binding influences gene expression is important for inferring target genes. Here the authors study this relationship using thousands of genomic data sets, finding two classes of TFs with distinct ranges of regulatory influence modulated by chromatin states of topologically associated domains.

    • Chen-Hao Chen
    • , Rongbin Zheng
    •  & X. Shirley Liu

  • Article
    | Open Access

    Inflammatory bowel disease (IBD) has been linked to host-microbiota interactions. Here, the authors investigate mucosa-associated microbiota using endoscopically-targeted biopsies from inflamed and non-inflamed colon in patients with Crohn’s disease and ulcerative colitis, finding associations with inflammation and host epigenomic alterations.

    • F. J. Ryan
    • , A. M. Ahern
    •  & M. J. Claesson

  • Article
    | Open Access

    While genome-wide association studies have yielded thousands of trait-associated loci, identifying causal variants remains challenging. Here, the authors perform seven genomics assays in various cell types to prioritize genetic variants in the TNFAIP3 locus, and report high-priority variants within disease-associated haplotypes.

    • John P. Ray
    • , Carl G. de Boer
    •  & Nir Hacohen

  • Article
    | Open Access

    Parkinson’s disease (PD) is a common neurodegenerative disorder with a complex etiology involving genetics and the environment. Here, Vallerga et al. identify two CpG probes associated with PD in a blood cell type-corrected epigenome-wide meta-analysis, implicating the SLC7A11 gene as a plausible biological target.

    • Costanza L. Vallerga
    • , Futao Zhang
    •  & Jacob Gratten

  • Article
    | Open Access

    How traits specific to modern humans have evolved is difficult to study. Here, Gokhman et al. compare measured and reconstructed DNA methylation maps of present-day humans, archaic humans and chimpanzees and find that genes that affect vocal tract and facial anatomy show methylation changes between archaic and modern humans.

    • David Gokhman
    • , Malka Nissim-Rafinia
    •  & Liran Carmel

  • Article
    | Open Access

    Identification of silencer elements by computational or experimental approaches in a genome-wide manner is still challenging. Here authors define uncharacterized cis-regulatory elements (CREs) in human and mouse genomes likely containing silencer elements, and test them in cells using massively parallel reporter assays to identify silencer elements that showed silencer activity.

    • Naresh Doni Jayavelu
    • , Ajay Jajodia
    •  & R. David Hawkins

  • Article
    | Open Access

    Somatic mutations in MED12 have been implicated as the causal genetic lesion in the majority of uterine leiomyomas. Here, the authors profile the chromatin landscape of matched normal and leiomyoma tissues and find that changes in enhancer acetylation, enhancer-promoter interaction strength, differential enhancer usage and transcription factor AP-1 occupancy are significant drivers of transcriptional dysregulation in MED12 mutant leiomyomas.

    • Mthabisi B. Moyo
    • , J. Brandon Parker
    •  & Debabrata Chakravarti

  • Article
    | Open Access

    Ibrutinib, a Bruton tyrosine kinase inhibitor, provides effective treatment for chronic lymphocytic leukemia (CLL). Here, the authors describe time-dependent molecular changes to malignant cells and to the immune system in patients undergoing ibrutinib therapy, with can be used for therapy monitoring.

    • André F. Rendeiro
    • , Thomas Krausgruber
    •  & Christoph Bock

  • Article
    | Open Access

    DNA methylation is associated with complex traits and the expression of genes and proteins. Here, Zaghlool et al. perform epigenome-wide association studies for 1,123 plasma proteins, replicate obtained protein (p)QTMs in an independent cohort and find overlap of pQTMs with expression QTMs and previously reported disease associations.

    • Shaza B. Zaghlool
    • , Brigitte Kühnel
    •  & Karsten Suhre

  • Article
    | Open Access

    The edematous form of severe acute childhood malnutrition (ESAM) presents with more severe multi-organ dysfunction than non-edematous SAM (NESAM). Here the authors assess genome-wide DNA methylation in buccal cells of SAM children and find that ESAM is characterized by hypomethylation at genes associated with disorders of nutrition and metabolism, including fatty liver and diabetes.

    • Katharina V. Schulze
    • , Shanker Swaminathan
    •  & Neil A. Hanchard

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