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Systematic deletions of individual imitation switch (ISWI) subunits in mouse embryonic stem cell lines highlight the role of BPTF in regulating chromatin accessibility at most CTCF sites and binding at a subset, with a modest effect on its insulating function.
Trinucleotide repeat expansions, notably CAG repeats translated into toxic polyglutamine-containing proteins, are the leading cause of spinocerebellar ataxia (SCA). New work points to a GGC repeat expansion that encodes a polyglycine-containing protein as a cause of SCA4, highlighting polyglycine disorders as an emerging human genetic disease class.
Cross-ancestry genome-wide association studies of 3,414 brain imaging phenotypes in Chinese Han and white British participants identify autosomal and X-chromosomal associations in more diverse populations.
Functional characterization of the regulatory landscape of the adjacent costimulatory genes CD28, CTLA4 and ICOS in primary human T cell subsets identifies context-dependent programs controlling this locus critical for immune homeostasis.
This study finds that CRISPR-knockout phenotypes from genome-wide screens systematically show increased similarity to knockouts of unrelated genomically proximal genes located on the same chromosome arm. Multiple lines of evidence suggest that this proximity bias is caused by telomeric truncations of chromosome arms and is consistent across cell types, labs and Cas9 delivery methods.
An analysis of somatic mutations in blood exomes from 200,618 individuals revealed previously unrecognized genes driving clonal hematopoiesis. Mutations in these genes showed age-dependent clonal expansion and their presence correlated with heightened risks of infection, death and hematological malignancy.
This study uses Strand-seq to explore the landscape of mosaic structural variants (mSVs) in human hematopoietic stem and progenitor cells from people of different ages. The analysis highlights patterns of enrichment for mSVs in specific cell types, with associated phenotypes, and suggests that clonal expansions due to mSVs are generally restricted to older individuals.
The study identifies TaSPL6-D as a negative regulator of TaHKT1;5-D and salinity tolerance in bread wheat. An insertion variation of TaSPL6-D, mainly hidden in landraces, shows the potential for breeding salt-tolerant crops.
Condensin-depleted mitotic chromosomes compartmentalize and form contacts among regulatory elements despite lacking transcription and most chromatin-associated factors. Heterochromatin protein 1 (HP1) proteins are surprisingly dispensable for compartmentalizing constitutive heterochromatin.
We adapted Tn5 transposition to reduce the amount of input DNA required for amplification-free single-molecule real-time Pacific Biosciences sequencing. We applied transposition-based library preparation in two sensitive methods for concurrently resolving genomes and epigenomes using limiting amounts of native DNA.
Cicer super-pangenome constructed using genome assemblies of eight Cicer annual wild species and two cultivated chickpea species provides insights into the genetic diversity and agronomic trait loci for chickpea improvement.
For a variety of reasons, genetic understanding of the steps leading to domestication of the nutrient-rich edible arrested inflorescence of cauliflower — its curd — has proven relatively intractable. A genomic study now unravels the details.
Characterization of seminal root number variation in the root systems of >9,000 global maize accessions and its wild relatives provides insights into root trait adaptation to environments during domestication and global expansion.
Insight from the transcriptomes of 1,032 Saccharomyces cerevisiae natural isolates emphasizes the essential contribution of accessory genes to the species-level transcriptional landscape.
Many plant products eaten daily in human diets — such as potato or banana — are polyploid and are notoriously difficult to breed. In this study, the fusion of clonal gametes from distinct diploid tomato parents is used as a blueprint for the design of polyploid genomes in crops.
By developing a modular system for precision epigenome editing, we were able to delineate the causal and quantitative role of chromatin modifications in transcription regulation. The precise effect of chromatin modifications is influenced by multiple contextual factors, including the underlying DNA sequence, transcription factor occupancy and genomic positioning.