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Mendelian randomization (MR) and colocalization analyses are used to estimate causal effects of 1,002 plasma proteins on 225 phenotypes. Evidence from drug developmental programs shows that target-indication pairs with MR and colocalization support were more likely to be approved, highlighting the value of this approach for prioritizing therapeutic targets.
The role of N6-methyladenosine (m6A) is still not fully understood. Two new studies advance understanding of this RNA modification. One shows that m6A modification of nascent messenger RNA promotes transcription by recruiting the histone H3 K9 demethylase KDM3B. Another study identifies genetic variants that affect m6A deposition and human disease.
Binding of RNA to the gene expression regulator Polycomb repressive complex 2 (PRC2) has been proposed to antagonize PRC2’s chromatin recruitment. A new study now shows that RNA is in fact critical for correct recruitment of PRC2 at its target genes in human pluripotent stem cells and suggests that interplay of PRC2 and RNA can fine-tune PRC2’s regulatory role.
Increasing amounts of crop genomic resources, along with new technical achievements in genome analysis, can facilitate basic and translational research in agriculture, and expand the ability to meet the global challenge of food production and security.
MOBSTER is an approach for subclonal reconstruction of tumors from cancer genomics data on the basis of models that combine machine learning with evolutionary theory, thus leading to more accurate evolutionary histories of tumors.
Insertion of a tissue-invariant chromatin domain boundary into 16 ectopic loci leads to various structural phenotypes, which depend on local chromatin features, CTCF binding and transcriptional status.
LSD1 promotes FOXA1 chromatin binding by demethylating lysine 270 of FOXA1 in prostate cancer cells. LSD1 inhibition decreases growth of prostate cancer cells.
STAAR is a powerful rare variant association test that incorporates variant functional categories and complementary functional annotations using a dynamic weighting scheme based on annotation principal components. STAAR accounts for population structure and relatedness and is scalable for analyzing large whole-genome sequencing studies.
Single-cell RNA-seq and in vivo lineage tracing identify unique luminal progenitors in the mouse prostate that can contribute to regeneration and oncogenesis. Single-cell RNA-seq analysis of human prostate identifies a similar cell population.
METTL3-induced deposition of N6-methyladenosine (m6A) in RNA correlates with removal of H3K9me2 genome wide. The m6A reader YTHDC1 recruits the H3K9me2 demethylase KDM3B to chromatin.
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.
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.
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.
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 statistical framework to classify mutagenesis clusters identifies a novel, diffuse hypermutation pattern, named omikli, that is induced by APOBEC3 and associated with mismatch-repair activity.
Quantitative ChIP–seq analysis maps G-quadruplex (G4) DNA structures in breast cancer patient-derived tumor xenograft (PDTX) models. G4-based subtypes highlight additional tumor heterogeneity in the integrative cluster (IC) system.
De novo genome assemblies of four European flint maize lines and comparison with two US Corn Belt genomes provide insights into the dynamics of intraspecies variation in repeat and gene content in maize genomes.