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This cartoon depicts a genomic ‘neighborhood’ with houses and apartments representing genes. The mailbox ‘promoters’ and mRNA mailtruck are all wired into a complex network of cis-regulatory elements depicted as power plants, lighting each of the homes to different levels. A new approach called HCR–FlowFISHallows researchers to use CRISPR to perturb these elements, quantifying and mapping how they connect to genes.
Genome-wide association studies have identified genetic variants in maternal and fetal genomes associated with early-life growth traits but have been limited by the paucity of large-scale family-based cohorts that would enable the resolution of informative transmissions between parents and their offspring. A new study uses extensive pedigree data from the Icelandic population to identify genetic effects on birth weight that differ according to parental origin and to demarcate distinct contributions from the maternal intrauterine environment and offspring genetics on fetal growth.
Metastable epialleles refer to loci with variable methylation states among individuals without underlying genetic differences. Although these loci have generally been assumed to be vulnerable to environmental influence, a new study reports their remarkable metastable epigenetic robustness toward a range of physiological, chemical and dietary disruptions in mammals.
Analysis of whole-genome sequence data from 3,474 families finds an excess of private, likely gene-disrupting variants in individuals with autism. These variants are under purifying selection and suggest candidate genes not previously associated with autism.
Genome-wide association analyses using parental and offspring genotypes provide insights into fetal and maternal genetic effects on fetal growth. The results show that maternal and fetal genomes influence birth weight through distinct mechanisms.
An integrative analysis of single-nucleus assay for transposase-accessible chromatin with sequencing and RNA sequencing in normal and Alzheimer’s disease brain tissue identifies cell-type-specific cis-regulatory elements and candidate target genes at disease-associated loci.
Analysis of 129 N6-methyladenosine (m6A) profiles across 4 tissues (brain, lung, muscle and heart) identifies 8,843 tissue-specific and 469 tissue-shared m6A quantitative trait loci (QTLs). Of these, 184 m6A QTLs colocalize with GWAS signals.
HCR–FlowFISH is a new approach to characterize CRISPR-perturbed cis-regulatory elements (CREs) via accurate quantification of native transcripts, alongside CRISPR activity screen analysis (CASA), a hierarchical Bayesian model to quantify CRE activity.
Introduction of hereditary persistence of fetal hemoglobin variants into the γ-globin promoter by using CRISPR mutagenesis and editing provides insights into transcription factor interplay, with implications for gene therapies targeting this element.
The use of natural killer (NK) cells in immunotherapy as an alternative to allogeneic T cells is gaining ground. Here, two genome-scale high-throughput platforms are used to identify genes that modulate the sensitivity of multiple solid tumor cell lines to NK-mediated killing.
The oncohistone H3.3-K27M decreases chromatin accessibility and H3K27ac at some active enhancers and downregulates nearby neurodevelopmental genes, while increasing transcriptional repression of a subset of PRC2-bound neurodevelopment genes.
Variably methylated intracisternal A particle (VM-IAP) retrotransposons are stable across the murine lifespan. VM-IAP retrotransposons are unaffected by maternal exposure to the endocrine disruptor bisphenol A, an obesogenic diet or methyl donor supplementation.
Fourier Mixture Regression (FMR) is a method for estimating common-variant effect-size distributions. Applying FMR to summary statistics for complex traits from the UK Biobank shows that heritability is spread across a wide range of effect sizes.
Haplotype-resolved genome assembly of an Oolong tea cultivar Tieguanyin and population genomic analyses of 190 Camellia accessions provide insights into the evolutionary history of the tea plant Camellia sinensis.
Imputation of rare coding variants in the UK Biobank enables association and fine-mapping analyses of rare (minor allele frequency (MAF) = 0.00005) genotypes, identifying 600 new variant–trait associations, including long allelic series in individual genes.