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An α-helical region conserved among FOXA pioneer factors interacts with core histones and promotes chromatin opening in vitro. This region also promotes chromatin opening in early mouse embryos and is required for normal development.
Replacement of lysine 4 or 36 with alanine in histone H3.3 impairs ESC differentiation and induces widespread gene expression changes. Expression of H3.3K4A, but not H3.3K36A, leads to H3.3 depletion, reduces remodeler binding and increases RNA polymerase II activity.
Analysis of whole-genome doubling (WGD) by using cancer sequencing data combined with simulations of tumor evolution suggests that there is negative selection against homozygous loss of essential genes before WGD but not after.
Chromatin interaction analysis identifies PRC2-bound silencers in mESCs, which, when deleted in mice, can lead to developmental phenotypes. Silencers in pluripotent cells can transition into active tissue-specific enhancers during development.
A genome-wide screen identifies silencer regions in human cells. Deletion of silencers linked to the transporter genes ABCC2 and ABCG2 causes their up-regulation and chemo-resistance.
Deep mRNA sequencing at eight time points during memory CD4+ T cell activation identifies widespread dynamic allele-specific expression events that are enriched in HLA and other autoimmune disease loci.
Naphthyridine-azaquinolone specifically binds slipped-CAG DNA intermediates, induces contractions of expanded repeats and reduces mutant HTT protein aggregates in cell and animal models of Huntington’s disease.
Analysis of whole-genome sequencing data across 2,658 tumors spanning 38 cancer types shows that chromothripsis is pervasive, with a frequency of more than 50% in several cancer types, contributing to oncogene amplification, gene inactivation and cancer genome evolution.
Viral pathogen load in cancer genomes is estimated through analysis of sequencing data from 2,656 tumors across 35 cancer types using multiple pathogen-detection pipelines, identifying viruses in 382 genomic and 68 transcriptome datasets.
Analysis of mitochondrial genomes (mtDNA) by using whole-genome sequencing data from 2,658 cancer samples across 38 cancer types identifies hypermutated mtDNA cases, frequent somatic nuclear transfer of mtDNA and high variability of mtDNA copy number in many cancers.
A pan-cancer genomic analysis reports the effects of structural variations on chromatin domains (TADs). Most TAD disruptions do not result in appreciable changes in expression of nearby genes.
An analysis of 2,954 genomes from 38 cancer subtypes identified 19,166 retrotransposition events in 35% of samples. Aberrant LINE-1 retrotranspositions can lead to the deletion of tumor-suppressor genes as well as the amplification of oncogenes.
A mouse model that combines nitrosamide exposure with inducible, tissue-specific TP53 alterations is used to generate premalignant gastric organoids and provides insights into the development of gastric premalignancy.
MutPanning is a new method to detect cancer driver genes that identifies genes with an excess of mutations in unusual nucleotide contexts. Applying this to whole-exome sequencing data from 11,873 tumor–normal pairs identifies 460 driver genes.
Genomic and transcriptomic analysis of lung adenocarcinoma (LUAD) in Asia indicates that Asian LUADs have fewer mutations, lower driver prevalence and fewer copy number alterations than European LUADs.
Multitrait genome-wide analysis of glaucoma and related phenotypes identifies new risk loci and enables development of a polygenic risk score to predict disease susceptibility and key clinical outcomes.
Genome-wide association analysis of 1,172 urinary metabolites identifies 240 metabolite–locus associations that when combined with UK Biobank data suggest novel metabolic mediators of disease and markers of disease risk.
Experiments in developing human erythroid cells show that LIN28B controls hemoglobin switching by directly suppressing BCL11A translation, independently of its role in regulating let-7 microRNA biogenesis.
Whole-genome sequencing, transcriptome sequencing and single-cell analysis of primary and metastatic pancreatic adenocarcinoma identify molecular subtypes and intratumor heterogeneity.
A CRISPR–CAS9 screen, analysis of patient data, and functional in vivo and in vitro experiments identify a critical role for ARID1A in determining breast luminal cell identity and endocrine therapeutic response in estrogen-receptor-positive breast cancer.