Gene expression articles from across Nature Portfolio

IBDverse is a single-cell RNA atlas of terminal ileal biopsies comprising 1.1 million cells from 111 patients with Crohn’s disease and 232 healthy participants. Analysis of the data identifies genes, pathways and cell populations associated with the disease and implicates inflammatory monocytes and macrophages in disease susceptibility.

Epigenetic regulation in NPM1c-mutated acute myeloid leukemia (AML) is poorly understood. Here, the authors show that ESCO2 loss accelerates NPM1-mutated AML by disrupting cohesin and NuRD complexes on chromatin and thereby increasing the expression of genes linked to leukemia self-renewal.

This research utilized multi-omics data from 1,274 adolescents to identify transdiagnostic biomarkers for neuropsychiatric disorders, employing genome-wide analyses and Mendelian randomization to uncover causal pathways linking immune dysregulation to psychiatric conditions and revealing potential therapeutic targets.

Here they show that zebrafish fast-twitch muscle structure is sensitive to reduced myosin light chain dosage. The light chain mutants’ behavioral defects are mitigated by slow-twitch muscle hypertrophy. Rescue by the human homolog suggests functional conservation.

Single-cell mapping of cis-expression quantitative trait loci in inflammatory bowel disease revealed distal, enhancer-enriched variants detected at the cell-type level more frequently co-localize with genome-wide association study loci than those identified at the tissue level.

In this Comment, Patricia Wittkopp revisits assumptions that cis-regulatory mutations are weakly pleiotropic, ultimately calling for more data to assess the extent to which they are less pleiotropic and deleterious than trans-regulatory mutations.

In this Tools of the Trade article, Yu-Kai Chao describes TimeVault, an inducible system that can store transcriptomes at defined time points, enabling temporal changes in transcriptional state to be linked to biological events.

Non-transgenic crop improvement via cis-regulatory editing is limited by rare activating alleles and incomplete promoter maps. A massively parallel reporter assay in sorghum protoplasts quantifies more than 30,000 CRISPR-mimicking variants across three photosynthesis genes, finely mapping cis-regulatory modules and pinpointing compact edits that drive upregulated protein production.

In this Journal Club, Yousuf A. Khan recounts a landmark study published in 1985 by Jacks and Varmus that documented programmed ribosomal frameshifting in retroviruses, which later inspired Yousuf to search for this phenomenon in vertebrates.

Oculopharyngodistal myopathy and oculopharyngeal myopathy with leukoencephalopathy are diseases caused by 50–200 repeats of the GGC DNA motif located in diverse sequences annotated as non-coding. This work shows that these repeats are embedded in previously unrecognized open reading frames, leading to their translation into novel and toxic polyglycine proteins.