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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.
Perturbation of RNA–PRC2 interaction in human pluripotent stem cells disrupts PRC2 chromatin occupancy and localization genome wide. PRC2–RNA interactions contribute to cardiomyocyte differentiation.
A new computational method integrates whole-genome sequencing and transcriptomic data to identify regulatory noncoding variants in an individual cancer genome.
Male mice lacking piRNAs from a conserved locus on chromosome 6 (pi6) produce sperm with defects in capacitation and egg fertilization. pi6 piRNAs repress mRNAs required for sperm function.
Quantitative trait locus (QTL) mapping of N6-methyladenosine (m6A) in human cells highlights the role of RNA-binding proteins, RNA secondary structure and context-dependent m6A effects. m6A QTLs are enriched in loci associated with immune and blood-related traits.
Longitudinal single-cell analysis of transcription and DNA methylation dynamics in cancer cell lines suggests a clonally stable epigenetic memory. Colon cancer cells show a spectrum of epithelial-to-mesenchymal identities that seems independent of genetic variation.
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.
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 association meta-analyses among 1.4 million individuals identify 318 new risk loci for type 2 diabetes and provide insight into the contribution of these risk variants to diabetes-related vascular outcomes.
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.
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.
Analysis with alleles encoding pharmacologically degradable Mediator subunits shows that Mediator acts as a global coactivator that facilitates transcription globally but is acutely required for cell-type-specific gene regulatory circuits.
Immunogenomic analyses of advanced high-grade serous ovarian cancer samples before and after neoadjuvant chemotherapy show that the tumor–immune microenvironment is intrinsically heterogeneous and that chemotherapy induces local immune activation.
CAUSE is a new Mendelian randomization method that accounts for correlated and uncorrelated horizontal pleiotropic effects. CAUSE is more robust to correlated pleiotropy than other methods and avoids identifying unlikely causal relationships.
Analysis of metastases using a mathematical framework and multi-region sampling data shows that lymph node metastases have higher levels of intratumor heterogeneity than distant metastases, and that these form via different evolutionary mechanisms.
Single-cell RNA sequencing of colorectal tumors highlights associations between lineage-related gene expression signatures and specific stromal and immune cell populations.
Mediated expression score regression (MESC) is a new method that estimates disease heritability mediated by the cis genetic component of gene expression levels by using summary statistics from GWAS and eQTL studies.
Analysis of whole-exome sequencing data from paired primary tumors and metastases from patients with breast, colorectal and lung cancer identifies clonal remodeling associated with therapy and few metastasis-private clonal mutations, consistent with early metastatic seeding.
Deep sequencing and lineage tracing analysis of esophageal epithelium of mutagen-treated aging mice leads to a model in which the proliferative advantage of positively selected mutations depends on the competitive fitness of neighboring cells.
A CRISPR screen for MLL2-dependent transcription identifies a compensatory repressive mechanism involving PRC2 and DNA methylation. PRC2 inactivation or DNA demethylation activates gene expression in the absence of H3K4me3.