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Super-resolution microscopy identifies sub-topologically associating domain (TAD) nanodomains and intercellular heterogeneity in TAD conformation and insulation. Cohesin or CTCF depletion regulates distinct types of chromatin contacts at the TAD but not nanodomain level.
Analysis of two independent cohorts of patients with Bardet–Biedl syndrome (BBS) with known recessive biallelic pathogenic mutations in one of 17 BBS genes shows an enrichment of rare nonsynonymous secondary variants in the same gene set, with significant over-representation of secondary alleles in chaperonin-encoding genes.
Haplotype-resolved assembly of a heterozygous diploid potato, RH89-039-16, and identification of deleterious mutations provide insights into the genome organization and breeding of a clonally propagated diploid species.
LSD1 promotes FOXA1 chromatin binding by demethylating lysine 270 of FOXA1 in prostate cancer cells. LSD1 inhibition decreases growth of prostate cancer cells.
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.