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Systematic analysis of highly rearranged balancer chromosomes in Drosophila shows that extensive changes to chromatin topology affect the expression of only a subset of genes.
Multi-region sequencing of 35 primary uveal melanomas and their matched metastases yields new insights into the genetics and evolution of these tumors and provides potential biomarkers for progression and therapy.
Application of SuRE reporter technology to survey the effect of 5.9 million SNPs in the human genome on enhancer and promoter activity identifies over 30,000 SNPs that alter the activity of putative regulatory elements.
Comprehensive CRISPR mutagenesis targeting all members of the NuRD complex identifies a specific subcomplex required for fetal globin silencing and informs a rational targeting strategy for elevating globin levels while avoiding cytotoxicity.
Promoter capture Hi-C maps in human pancreatic islets identify more than 1,300 three-dimensional regulatory hubs, linking diabetes-associated enhancers to their target genes. Genetic variation in hubs impacts insulin secretion heritability.
Whole-genome sequencing and association analysis of 270 Epstein–Barr virus (EBV) isolates from China identify two non-synonymous EBV variants within BALF2 that are strongly associated with the risk of nasopharyngeal carcinoma.
Analysis of evolutionary dynamics of colorectal cancers and paired distant brain or liver metastases provides evidence that early disseminated cancer cells seed metastases before the carcinoma is clinically detectable.
The authors present a method for determining 3D protein structures using high-throughput mutation experiments. Pairs of residues with the largest positive epistasis are sufficient to determine the 3D fold.
This method predicts three-dimensional protein structures based on the activity of mutant variants. The approach relies on quantifying genetic interactions between mutations to infer direct contacts between residues.
Trans-ancestry meta-analysis of estimated glomerular filtration rate (eGFR) from 1,046,070 individuals identifies 264 associated loci, providing a resource of molecular targets for translational research of chronic kidney disease.
A high-quality reference genome of the maize SK inbred line and analyses between the tropical SK line and two other maize genomes, B73 and Mo17, provide insights into structural variation and crop improvement.
Similarity regression is an improved method for predicting transcription factor motifs, enabling analysis of DNA-binding motifs across eukaryotes and an expansion of the Cis-BP database of measured and predicted transcription factor motifs.
Analyses of 2,083 globally distributed group A Streptococcus (GAS) genomes enable the development of a compendium of all GAS vaccine antigen sequences, providing a platform for population-genomics-informed vaccine design.
Swapping the Xist/Tsix transcriptional units and placing their promoters in each other’s topologically associating domain shows that the topological partitioning of the X-inactivation center is critical to ensure proper X inactivation during development.
Application of a deep-learning-based framework shows that individuals with autism spectrum disorder (ASD) harbor regulation-disrupting mutations of higher functional impact than those in unaffected siblings and identifies a convergent genetic landscape of coding and noncoding de novo mutations in ASD.
The folate pathway enzyme MTHFD1 is recruited to chromatin by BRD4. Inhibition of BRD4 or MTHFD1 similarly changes nuclear metabolite composition and gene expression, and dual inhibition synergistically impairs cancer cell viability.
CRISPR screens identify JNK–JUN family genes as repressors of definitive endoderm differentiation in human pluripotent stem cells. JUN co-occupies stem cell enhancers with OCT4, NANOG, SMAD2 and SMAD3 and inhibits the exit from pluripotency.
Release of paused Pol II at specific intronic loci or chromatin domains favors the formation of abnormal DNA recombination, leading to cancer-associated chromosomal translocations.
A tomato pan-genome constructed from genome sequences of 725 tomato accessions captures 4,873 genes absent from the reference genome and identifies a rare allele of TomLoxC regulating fruit flavor.
Genome-wide analysis identifies 30 loci associated with bipolar disorder, allowing for comparisons of shared genes and pathways with other psychiatric disorders, including schizophrenia and depression.