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As reported by Gagliardi et al., human papillomavirus (HPV) is found integrated within the genome in most cervical tumors, and often is associated with marked epigenetic and transcriptional activation of the surrounding chromatin. The circular arrangement shows the profile of histone modifications observed with ChIP–seq across the HPV-integration events in the cluster with the highest increase in enrichment, as shown in Fig. 5f. It is composed of data sampled from two randomly paired individuals, with tracks facing inward and outward for each individual. Individuals are paired randomly, and track colors correspond to five histone marks with epigenetic enrichment.
Gene nomenclature can be complicated, and the official naming of genes requires rational standards to avoid confusion and to maximize clarity. The HUGO Gene Nomenclature Committee has released updated guidelines for the naming of human genes, and we encourage the community to adopt these recommendations.
Genomes are highly organized in space and time. Compartments, topologically associating domains (TADs) and loops are three dimensional (3D) genome features that have been extensively studied. Among these three levels of organization, TADs have sparked the most debate. New microscopy data shed light on how TADs and their leaky borders contribute to gene regulation.
Standardized gene naming is crucial for effective communication about genes, and as genomics becomes increasingly important in health care, the need for a consistent language to refer to human genes becomes ever more essential. Here, we present the current HUGO Gene Nomenclature Committee (HGNC) guidelines for naming not only protein-coding genes but also RNA genes and pseudogenes, and we outline the changes in approach and ethos that have resulted from the discoveries of the past few decades.
This Perspective discusses the need for mechanistic and quantitative understanding of the ecological and evolutionary dynamics of tumor growth to inform strategies for earlier detection, diagnosis and treatment of cancer.
Computational analyses integrating whole-genome sequencing, cardiac epigenomic data and RNA-binding-protein data identify a role for noncoding de novo mutations in congenital heart disease.
Whole-genome bisulfite sequencing along with whole-genome and transcriptome sequencing of 100 prostate cancer metastases identifies genomic regions that are differentially methylated during disease progression and a novel epigenomic subtype.
Analyses of epigenomic datasets spanning transitions from normal prostate epithelium to localized prostate cancer to metastases show that latent developmental programs are reactivated in metastatic disease and that prostate lineage-specific regulatory elements are strongly enriched for prostate cancer risk heritability.
Genomic analysis of 118 cervical tumors from Ugandan individuals identifies HPV-clade-specific differences in tumor DNA methylation, regulatory-region-associated histone marks, gene expression and pathway dysregulation.
A new computational method integrates whole-genome sequencing and transcriptomic data to identify regulatory noncoding variants in an individual cancer genome.
Whole-genome bisulfite sequencing analysis of human embryonic stem cells shows that DNMT3 deficiency leads to global and local demethylation, which depends on TET activity. Dynamic loci overlap with putative somatic enhancers that are highly methylated in ESCs.
Cells lacking TET proteins and DNMT3A and DNMT3B show that DNMT1 has imprecise maintenance activity and weak de novo activity leading to spontaneous ‘epimutations’. These epimutations can be corrected through a neighbor-guided mechanism.
A combination of super-resolution microscopy and Oligopaint technology shows that TAD boundaries are variable at the single-cell level. Loss of cohesin, in contrast to WAPL or CTCF depletion, reduces interactions across boundaries and alters transcriptional bursting of genes near boundaries.
Genome-wide detection of inversions in great ape genomes by using long-read sequencing and single-cell DNA template strand sequencing (Strand-seq) expands the number of known ape inversions and identifies several regions that have recurrently toggled between a direct and an inverted state during primate evolution.
The HDL method improves the precision in genetic correlation estimation over LD score regression when applied to GWAS summary statistics of complex traits from the UK Biobank.