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As we age, our cells acquire DNA mutations, resulting in cell-to-cell genomic heterogeneity. We characterized the landscape of mitochondrial DNA (mtDNA) heterogeneity in healthy human cells. Our observations provide deeper insight into the frequency of new mitochondrial mutations and the mechanisms that propagate low-level mutations in mtDNA over a lifetime.
Clones expressing variants of the X-chromosome-linked STAG2 gene only form lymphocytes in the absence of Stag2WT clones. Interactions between epigenetic clones can thus modulate the impact of X-chromosome-linked genetic diversity in a cell-type-specific manner.
Nearly 50% of the sequence of mammalian genomes is derived from mobile elements that inserted into the genome over millions of years of evolution. A recent mobile element insertion, found only in some individuals with European genetic ancestry, contributes to decreased skin pigmentation and increased sunburn frequency and skin cancer risk.
We present a multi-omic map of the human kidney in health and disease, using single-cell RNA, single-nuclei RNA, single-nuclei assay for transposase-accessible chromatin sequencing, spot-based and single-cell spatial transcriptomics. This comprehensive approach enables an in-depth understanding of the microenvironments in the diseased kidney.
Genomic analysis identifies an SVA retrotransposon insertion in an intron of ASIP as a likely causal variant influencing human pigmentation. This insertion appears to mitigate the effects of an older, nonpolymorphic SVA insertion in the same intron.
Allele-specific DNA methylation data in whole blood from 7,179 individuals sequenced by Nanopore, and gene expression profiles from 896 samples, show that DNA sequence variability accounts for most of the correlation between CpG methylation and gene expression.
This Review explores the challenges and strategies for developing gapless telomere-to-telomere genome assemblies to enhance our understanding of genome organization and improve crops through genome-assisted breeding or gene editing.
A spatial transcriptomic analysis of healthy kidneys and those from individuals with chronic kidney disease characterizes the fibrotic microenvironment and highlights features that could be used to predict prognosis.
Single-cell analyses in RAD21-depleted mouse embryonic stem cells show that cohesin limits the coexpression of genes located in different accessible chromatin domains on the same chromosome by preventing co-bursting and blocking spatial mixing of different transcriptional hubs.
Genotype prediction from RNA sequencing (RNA-seq) data has become widespread, but there is a lack of clarity in current policy and inconsistency in data handling. To address this we call for a framework consisting of registered access for RNA-seq data, controlled access for genotypes, a code of conduct and enhanced downstream protections.
Inactivation of somatic SMC complexes in Caenorhabditis elegans shows that condensin I is the major long-range genome loop extruder, while cohesin forms small loops. Inactivation of cohesin, condensin II and condensin I/IDC causes minor transcriptional changes in autosomes.
Analysis of 2,096 single-cell clones from three tissues of 31 healthy donors characterizes mitochondrial DNA mosaicism and highlights the following two origins of mtDNA variants: heteroplasmy in the fertilized egg and postzygotic mutations.
Exome sequencing within a structured diagnostic process for rare diseases in Germany shows how facial image analysis and machine learning can guide variant prioritization and uncover many ultrarare diseases.
A European ancestry genome-wide meta-analysis of pregnancy-associated bleeding traits identifies five novel loci associated with postpartum hemorrhage, but none with early bleeding. Functional analysis highlights a role for progesterone receptor-mediated signaling.
A multiomic approach profiles the three-dimensional, epigenetic and mutational landscapes of 80 metastatic prostate cancer biopsies. Hi-C experiments identify an extrachromosomal circular DNA at the AR locus associated with therapy resistance.
Genetic constraint identifies genes under selection against loss-of-function, but existing methods are inaccurate for shorter genes. A new study overcomes this key limitation to ascribe more confident predictions to all human protein-coding genes.