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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.
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.
Nucleic acid processing by the cytoplasmic exonuclease TREX1 and cytosine editing by APOBEC3B drive chromothripsis and kataegis during telomere crisis.
Genome-wide analysis in 212,453 Japanese individuals identifies loci associated with 42 diseases. Comparative analysis with European populations identifies East Asian–specific associations.
CTCF is dispensable for transdifferentiation of B cells into induced macrophages despite widespread loss of topologically associating domains. CTCF depletion impairs upregulation of inflammatory genes after endotoxin exposure by destabilizing promoter–enhancer interactions.
Cas9 expression induces DNA damage and activates the p53 pathway, and it can lead to the selection of cells with p53-inactivating mutations. Cas9 is less active in wild-type TP53 cell lines than in TP53-mutant cell lines.
Genome-wide analysis identifies 32 loci associated with breast cancer susceptibility, accounting for estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 status and tumor grade.
Genome-wide association analysis for morphological traits across 350 elite maize inbred lines in Chinese and US germplasm identifies loci and genomic regions representing the targets of selection during modern maize breeding.
Single-cell analysis of mouse hematopoietic stem cells shows that mutations in DNA methylation genes change the frequencies of erythroid versus myelomonocytic progenitors, owing to differential CpG enrichment in transcription factor binding motifs.
Whole-exome sequencing of human brain metastases from lung adenocarcinoma uncovers new drivers by comparison of somatic alteration frequencies in brain metastasis cases to those in primary lung adenocarcinomas.
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.
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.
GeVIR is a continuous gene-level metric that uses variant distribution patterns to prioritize both dominant and recessive Mendelian disease genes. GeVIR outperforms missense constraint metrics and complements loss-of-function constraint metrics.
Combined genomic and transcriptomic approaches identify the landscape of extrachromosomal circular DNA in neuroblastoma and reveal that extrachromosomal circular DNA is a major source of somatic rearrangements.
Mutations in ADAMTS19 lead to progressive heart valve disease in humans. Analysis of mice lacking Adamts19 highlights the role of a Wnt–Adamts19–Klf2 axis in proper valve function.
N6-methyladenosine (m6A) is prevalent at RNA:DNA hybrids in human pluripotent stem cells. The m6A reader YTHDF2 interacts with R-loop-enriched loci in dividing cells, and YTHDF2 loss leads to increased R-loop levels and accumulation of γH2AX.
Combining CRISPRi-FlowFISH to perturb enhancers with an activity-by-contact model to predict complex connections allows systematic mapping of enhancer–gene connections in a given cell type, on the basis of chromatin-state measurements.
Genome-wide analysis of venous thromboembolism identifies 22 new risk loci and facilitates construction of a polygenic risk score. Comparison to arterial vascular disease highlights shared pathophysiology and potential therapeutic strategies.
Genome-wide analyses identify variants near HDAC9 associated with abdominal aortic calcification and other cardiovascular phenotypes. Functional work shows that HDAC9 promotes an osteogenic vascular smooth muscle cell phenotype, enhancing calcification and reducing contractility.
Mapping long-range chromatin interactions in 27 human cell/tissue types identifies candidate target genes of 70,329 putative regulatory elements. Further analysis suggests potential regulatory function for 27,325 noncoding variants associated with 2,117 traits and diseases.