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Two BAH-domain-containing proteins (SHL and EBS) form a complex with EMF1, reading and effecting the H3K27me3 mark in Arabidopsis. The BAH-EMF1c complex thus shows PRC1-like functions in higher plants.
Sequencing and de novo assembly of the maize W22 reference genome enable accurate placement of Mutator (Mu) and Dissociation (Ds) transposable element insertions, providing a foundation for maize functional genomics and transposon biology.
The de novo genome assembly of maize line Mo17 and comparative analysis with other sequenced maize lines show extensive gene-order variations. This study provides insights into maize evolution and has implications for improving maize hybrid lines.
Coding variants in peptidylglycine α-amidating monooxygenase (PAM) associated with type 2 diabetes risk negatively impact overall PAM activity via defects in expression and catalytic function, resulting in reduced insulin content and altered dynamics of insulin secretion.
A coupled knockdown-editing screen shows that CRISPR–Cas9 editing in human cells requires the Fanconi anemia pathway, which acts by diverting double-strand break repair away from non-homologous end joining toward single-strand template repair.
The authors use genome editing and live imaging to visualize physical enhancer–promoter interaction and transcription at the single-cell level in Drosophila embryos. They show that sustained proximity of an enhancer to its target is required for transcription.
Using common variants in six non-human primate species, the authors train a deep neural network that identifies pathogenic mutations in patients with rare disease with 88% accuracy and enables the discovery of 14 new candidate genes in intellectual disability.
A high-throughput method for functional SNP identification uses enzymatic restriction to detect altered regulatory protein binding and identifies 148 candidate fSNPs associated with juvenile idiopathic arthritis, including two that regulate STAT4 via the regulatory proteins SATB2 and H1.2.
ExPecto is a deep learning–based framework that can predict the tissue-specific transcriptional effects of mutations on the basis of DNA sequence alone. ExPecto can prioritize causal variants from GWAS loci and be used to predict the disease risk of a variant.
Multi-contact 4C (MC-4C) sequencing analyzes multi-way conformations of individual alleles. MC-4C identifies the β-globin superenhancer as a hub that can accommodate two genes simultaneously and shows that CTCF-anchored loops collide in WAPL-depleted cells.
Analysis of ATAC-seq and RNA-seq data from stimulated T cells identifies genetic variants that disrupt transcription factor binding sites within ATAC-seq peaks. ATAC quantitative trait loci (ATAC-QTLs) are enriched for autoimmune disease-associated variants.
The assembly of the genome of the koala provides insights into its adaptive biology and identifies gene expansions that contribute to its ability to detoxify eucalyptus-derived compounds and perceive plant secondary metabolites.
Integration of expression quantitative trait locus (eQTL) data from the Genotype-Tissue Expression project with genome-wide association study data shows that eQTLs are enriched for trait associations in disease-relevant tissues.
A transcriptome-wide association study identifies associations of genetically predicted gene expression with breast cancer risk. This analysis finds 48 candidate genes implicated in breast cancer susceptibility, including 14 at novel loci.
An integrated experimental-computational approach evaluates the impact of de novo missense mutations on protein–protein interactions. This interactome-based framework can be used to identify and prioritize disease-associated missense mutations.
The roles of of Gorab in the Golgi and in centriole structure and function can be separated mutationally in Drosophila. Complexed to Sas6 in the centriolar cartwheel, Gorab is essential for mitotic centriole duplication in the fly.
The authors describe the MiCEE complex, which comprises Mirlet7d ncRNA duplexes bound by C1D, the RNA exosome complex, and PRC2. MiCEE regulates bidirectionally transcribed loci and nucleolar organization.
The authors show that the transcription factor Grainy head (Grh) is necessary and sufficient for opening of epithelial enhancers, but not for their activation. Grh is shown to function as a pioneer factor, displacing nucleosomes and paving the way for other transcription factors to activate enhancers.