Volume 22 Issue 2, February 2021

Corley et al. report fSHAPE, a simplified strategy for in vivo transcriptome-wide footprinting with SHAPE structure-probing techniques.

A study in Nature Biotechnology presents a library of transcription factors that are able to induce differentiation of human induced pluripotent stem cells as a resource for cell and tissue engineering.

This study reports a compendium of cell-type-specific regulatory annotations that improves the trans-ancestry portability of polygenic risk scores.

The CRISPR–Cas13 system can be used to knock down circular RNAs (circRNAs) without any impact on related mRNAs, reports a study in Nature Methods.

A new study in Nature demonstrates that re-setting the epigenetic age of retinal ganglion cells re-establishes youthful gene expression programmes and restores vision in glaucomatous and aged mice.

Two studies in Nature report regulatory roles for H1 in chromatin compaction and 3D genome organization and establish H1 mutations as a driver of tumorigenesis.

Jin et al. describe a barcoding approach for analysing metastasis, which they used to generate an organ-specific metastasis map for 500 cancer cell lines.

A study in Genome Biology uses EpiGo-KRAB to analyse the roles of H3K9me3 in genome organization and transcriptional repression and reveals the two functions may be distinct.

Fozouni et al. describe a CRISPR–Cas13a-based approach for rapid, accurate and portable detection of SARS-CoV-2 in infected individuals.

An article in Cell describes a multi-omic analysis of health risks from spaceflights that implicates mitochondrial stress and dysregulation as key drivers.

Cell–cell interactions and communication can be inferred from RNA sequencing data of, for example, ligand–receptor pairs. The authors review insights gained and the methods and tools used in studies of cell–cell interactions based on transcriptomic data.

The effects of genetic variation on the adaptive potential of species depend on the frequencies of alleles at other loci in the individual or in the population, and the patterns of spatio-temporal co-occurrence between alleles in interacting species. This Review explores these population and community genomic contexts and their direct and indirect effects on biodiversity, ecosystems and people.

Deep resequencing has revealed extreme genetic variation in mitochondrial genomes at multiple levels. This heterogeneity has implications for the origins of human mitochondrial DNA mutations as well as their impact on rare and common human diseases, including cancer.

This Perspective reviews efforts to map six different RNA modifications — pseudouridine (Ψ), 5-methylcytidine (m⁵C), N ¹-methyladenosine (m¹A), N ⁴-acetylcytidine (ac⁴C), ribose methylations (N_m) and N ⁷-methylguanosine (m⁷G) — and how they differ from N ⁶-methyladenosine (m⁶A). The authors discuss the technical and analytical challenges of characterizing the epitranscriptome and provide their own conclusions on the abundance and distribution of these modifications.