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Analysis of human tumor datasets shows that all features that appear significantly associated with immunotherapy response and survival may be collapsed into five latent factors: tumor mutation burden, T cell effective infiltration, TGF-β activity in the microenvironment, prior treatment and tumor proliferative potential.

Massively parallel reporter assays in four plant species show that transcriptional regulatory elements are position dependent with enrichment downstream of the transcription start site, particularly GATC motifs with strong effects in vascular plants.

MILTON uses phenotype information in the UK Biobank to identify clinical biomarkers and other quantitative traits that characterize diseases. It then constructs augmented cohorts by predicting undiagnosed individuals, improving power to discover gene–disease relationships.

Microfluidics-assisted grid chips for spatial transcriptome sequencing (MAGIC-seq) is a spatial transcriptomics method combining multiple-grid microfluidic design and prefabricated DNA arrays for increased throughput and reduced cost, with applications for large fields of view and 3D spatial mapping.

Hi-C analysis identifies Xist-separated megadomains (X-megadomains) on the inactive X chromosome in mouse early embryos. Cohesin loading at Xist regulatory elements promotes X-megadomain formation and restricts nearby gene activity.

Integration of genome-wide association analysis of 406,504 individuals in the UK Biobank and scATAC–seq data reveals that variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function.

Calls for more diverse data in genetics studies typically fall short of offering further guidance. Here we summarize a policy framework from the Global Alliance for Genomics and Health designed to fill this gap. The framework prompts researchers to consider both what types of diversity are needed and why, and how aims can be achieved through choices made throughout the data life cycle.

CRISPR screen identifies coactivators of the androgen receptor (AR) complex, including NSD2. NSD2 contributes to AR cistrome reprogramming during prostate cancer progression, and its degradation via a novel PROTAC reduces prostate cancer cell viability in vitro.

High-quality genome of the modern soybean cultivar Nongdadou2 and deep resequencing of 547 accessions provide insights into the role of structural variations in soybean improvement.

Loss of MEN1 affects tumor growth, varing with the components of the tumor microenvironment. These tumors show redistribution of MLL1 on chromatin and the activation of a viral mimicry response.

Spatial molecular imaging analysis of human pancreatic adenocarcinomas describes multicellular neighborhoods in the tumor microenvironment. Ligand–receptor analysis using optimal transport-based SCOTIA identifies interleukin-6 as a mediator of chemoresistance.

Epigenetic therapy triggers myriad transposable elements to generate new antigens that could prime tumor cells for immunotherapy. A study of glioblastoma discovers indiscriminate activation in healthy cells as well, and presents a more selective strategy for potential therapeutic targeting.

Genomic analyses suggest that ~15% of transcript molecules are spliced into unproductive transcripts targeted by nonsense-mediated decay, which have a larger effect on gene expression than previously thought.

Treatment of primary glioblastoma cell lines with epigenetic therapy reactivates transposable elements (TEs). TE-derived transcripts can produce human leukocyte antigen class I-presented antigens, which could potentially be therapeutically targeted.

Gene-based rare variant analyses for 601 diseases across 748,879 individuals from three biobanks identify 363 significant associations and highlight important considerations for multi-ancestry and cross-biobank sequencing studies.

Yin Yang 1 (YY1) aids in the formation of enhancer–promoter (E–P) loops independently of cohesin. YY1 maintains a subset of E–P interactions in interphase and establishes an overlapping yet distinct set after mitotic exit.