Sequencing articles from across Nature Portfolio

Pseudouridine (Ψ) is an abundant modification in human small RNA but the substrate specificity of its synthesis enzymes (PUSs) remains elusive. Here, the authors quantitatively profile Ψ map in small RNA, identify the substrates of PUSs and reveal unexpected PUSs interplay in tRNA pseudouridylation.

Here the authors report that a missense variant in ASCL5 causes lobodontia, a rare dental anomaly. Genetic analysis and mouse models confirm that the variant disrupts tooth and jaw development, overturning previous theories and defining the genetic basis of this rare condition.

High spatial resolution is essential for resolving cellular and subcellular organization in tissues. Here, authors present Seq-Scope-X, which integrates tissue expansion with Seq-Scope to achieve an order-of-magnitude improvement in resolution of spatial transcriptomics and proteomics.

The successful implementation of genomic newborn screening involves a wide array of ethical, legal and social implications of great complexity. The authors outline key decision points and highlight a GA4GH policy tool to support responsible, trustworthy implementation within diverse public health systems globally.

In this Tools of the Trade article, Qin Wu discusses the development of SPARK-seq (single-cell perturbation-driven aptamer recognition and kinetics sequencing), a method that enables high-throughput identification of aptamer–target pairs.

In this Tools of the Trade article, Mariani (Bulyk Lab) describes the development of PIONEAR-Seq, a method designed to explore how genome composition influences transcription factor binding, particularly in the context of nucleosomes and other genomic elements.

We present SpaHDmap, a deep learning framework that integrates histology images with spatial transcriptomic data to derive high-resolution and interpretable spatial metagenes. We demonstrate that SpaHDmap effectively generates fine-grained spatial metagenes, reveals refined spatial structures and enables joint analysis of multiple samples across different experimental conditions.

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.