Transcriptomics articles from across Nature Portfolio

KDM7A restrains fibrotic macrophage polarization and lung fibrosis. Loss of Kdm7a drives transcriptional and metabolic reprogramming toward Fib-Mac states, expands Fib-Macs, and exacerbates bleomycin-induced fibrosis, consistent with reduced KDM7A in human disease. Mechanistically, Kdm7a loss increases H3K27me2 at the Tlr8 enhancer, reduces TLR8 expression, and promotes Fib-Mac polarization.

This study reports that de novo germline missense variants in SF3B1, distinct from the somatic variants frequently observed in cancer, cause a neurodevelopmental disorder and disrupt global RNA splicing.

Single-cell RNA sequencing and assay for transposase-accessible chromatin using sequencing profiling of human retinal samples from diverse ancestries create an epitranscriptomic atlas characterizing over 130 cell types. Integration with genome-wide association study and expression quantitative trait loci data provides further insights into gene regulation and disease etiology.

The changing cellular, transcriptional, and genomic landscape of human lung aging can be characterized using single-cell RNA sequencing. Here, the authors show that lung aging is cell-type dyssynchronous, with alveolar epithelial and endothelial cells exhibiting the greatest changes in gene expression, transcriptional entropy, and a high level of somatic mutations.

Using single-cell transcriptomics and functional analyses, the authors identify a specialized neural network in the male schistosome gynecophoric canal and show that lsamp maintains its integrity, enabling intersex communication and female reproductive maturation.

Scientists have transformed enigmatic cell structures, called vaults, into storage units for messenger RNA molecules.

In this Tools of the Trade article, Yubao Cheng discusses the development of RAEFISH (reverse-padlock amplicon-encoding fluorescence in situ hybridization), a method that enables spatial transcriptomics with both single-molecule spatial resolution and genome-wide coverage.

In this Tools of the Trade article, Moritz Schaefer introduces CellWhisperer, a multimodal machine learning model and software tool for the chat-based interrogation of single-cell RNA sequencing datasets.

The plant cell wall makes the preparation of high-quality cells for single-cell RNA sequencing challenging. To tackle this issue, we developed FX-Cell, a method that enables the enzymatic digestion of the cell wall at high temperatures to result in high-quality single plant cells for transcriptome analysis.