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Analyses of population-level variation in gene and enhancer expression in the human brain characterize the gene–enhancer regulome and the regulatory mechanisms of transcribed enhancers in neuropsychiatric diseases.
Single-cell DNA sequencing data are generated from human neurons using primary template-directed amplification and analyzed using SCAN2, an improved genotyping tool. Indels are enriched in neuronal regulatory elements and may be deleterious.
Oncogenes commonly amplify on circular extrachromosomal DNA (ecDNA) molecules in cancer. We show that ecDNA shapes each of the foundational principles of Darwinian evolution — random inheritance by descent, enhanced variation through random segregation, and selection — and thereby promotes rapid genome change, treatment resistance and poor outcomes for patients with cancer.
Clonal expansion of DNMT3A-mutant hematopoietic stem cells is a risk factor for myeloid malignancies and other morbidities. A new study uses multi-modal single-cell genomics to characterize the myeloid differentiation bias of DNMT3A-mutated clones, and finds preferential hypomethylation of binding motifs for key transcriptional regulators.
SAIGE-GENE+ performs set-based rare variant association tests with improved type 1 error control and computational efficiency by collapsing ultra-rare variants and conducting multiple tests corresponding to different minor allele frequency cutoffs and annotations.
Multi-modality single-cell sequencing determines genotype, transcriptome and methylome information in cells from individuals with DNMT3A R882 mutated clonal hematopoiesis, allowing for the comparison of mutant and wild-type cells from the same individuals.
A high-quality genome assembly of pea cultivar ZW6 and pan-genome analyses provide insights into pea genome evolution and domestication as well as genomic resources for pea improvement.
Random segregation of extrachromosomal DNA contributes to intratumoral heterogeneity and facilitates the rapid adaptation of human tumor cells to anticancer drugs.
In this issue, Deng and colleagues show that the RNA m6A modification reader FXR1 recruits DNA 5-methylcytosine dioxygenase TET1 to genomic regions in order to demethylate DNA, which highlights a crosstalk between RNA methylation and DNA methylation in chromatin.
Multi-ancestry meta-analyses of genome-wide association studies for self-reported physical activity during leisure time, leisure screen time, sedentary commuting and sedentary behavior at work identify 99 loci associated with at least one of these traits.
Cistrome-wide association study (CWAS) is an approach for nominating variants that impact traits through effects on chromatin state. CWAS performed on 307 prostate cistromes identifies candidate loci for prostate cancer and androgen-related traits.
METTL3-dependent RNA N6-methyladenosine (m6A) deposition can lead to DNA demethylation. The m6A reader FXR1 recruits DNA 5-methylcytosine dioxygenase TET1 to chromatin, which is linked to chromatin accessibility and gene transcription.
Migration can increase regional differences in both DNA variants and environmental factors that are associated with socio-economic status. Without controlling for geography, associations between genes and complex traits will therefore include effects of environmental differences between high-income and low-income regions.
The genetic landscape of human induced pluripotent stem cells (iPSCs) is strongly influenced by the somatic cells of origin, and mutational signatures directly reflect pre-reprogramming and post-reprogramming mutagenic processes. BCOR mutations are recurrent and have functional consequences for the differentiation capacity of iPSCs.
In our study of 83 tissue samples from 31 patients with pancreatic cancer receiving different treatment regimens, we directly identified normal cells transitioning to a tumor state. Single-cell technologies enabled us to observe how the tumor and the surrounding environment work together to create a treatment-resistant niche.
We comprehensively define the genomic landscape of pediatric acute lymphoblastic leukemia (ALL) in the largest cohort assembled to date, and identify new driver genes and biological pathways that are targeted by genetic alteration. These findings serve as a road map to improve our understanding of disease development and identify therapeutic targets in pediatric ALL.
scDRS associates individual cells in scRNA-seq with disease by scoring single-cell transcriptomes using GWAS gene signatures. Applied to 74 GWAS and 1.3 million single-cell profiles, scDRS identifies specific cellular subpopulations associated with these diseases.
A genomic and transcriptomic analysis of 2,754 childhood acute lymphoblastic leukemias identifies 376 putative driver genes, and associations between disease subtypes and prognosis.