Research articles

An RNA secondary structure (RSS) map of coding and noncoding RNA from a human family (two parents and their child) is produced; this reveals that approximately 15% of all transcribed single nucleotide variants (SNVs) alter local RNA structure, and these SNVs are depleted in certain locations, suggesting that particular RNA structures are important at those sites.

Dirac magnetic monopoles are created, directly imaged and identified in real space in the synthetic magnetic field produced by a spinor Bose–Einstein condensate.

A new high-throughput sequencing method to determine mRNA poly(A)-tail length enabled studies of individual RNAs across species and developmental stages to investigate the role of poly(A) length in translational regulation; the relationship between poly(A) length and translational efficiency shown in early embryo systems does not occur later in development, a finding that explains different regulatory consequences of microRNAs acting at different developmental times.

This study defines how a short DNA sequence, known as the PAM, is critical for target DNA interrogation by the CRISPR-associated enzyme Cas9 — DNA melting and heteroduplex formation initiate near the PAM and extend directionally through the remaining target sequence, and the PAM is also required to activate the catalytic activity of Cas9.

One of two papers describing a reprogramming phenomenon called stimulus-triggered acquisition of pluripotency (STAP) — in STAP, lineage-committed adult somatic cells are reprogrammed to pluripotency by transient exposure to low-pH treatment, and extensive analysis of the molecular features and developmental potential of STAP cells indicates that they represent a unique state of pluripotency.

A short hairpin RNA screen to identify genes that modify the action of tumour-infiltrating CD8 T cells in tumour-bearing mice pinpointed the phosphatase subunit Ppp2r2d as a new target for tumour therapy; knockdown of Ppp2r2d in T cells enabled their accumulation in tumours and significantly delayed tumour growth.

A map of the surface of a brown dwarf reveals features that suggest patchy clouds, providing the mechanism for the dispersal of atmospheric dust as brown dwarfs cool with age.

In the modern human genome, elevated Neanderthal ancestry is found at genes affecting keratin filaments, suggesting that gene flow with Neanderthals helped modern humans to adapt to non-African environments; deficiencies of Neanderthal ancestry are also found, particularly on the X chromosome and in genes expressed highly in testes, suggesting that some Neanderthal mutations were not tolerated on a modern human genetic background as they reduced male fertility.

Single-cell- and metagenomics-based study reveals two members of the candidate genus ‘Entotheonella’, symbionts of the marine sponge Theonella swinhoei; distinct biosynthetic gene clusters that account for most of the bioactive polyketides and peptides known from T. swinhoei are shown to be attributable to a single member of the T. swinhoei Y microbiome.

This paper reports integrative molecular analyses of urothelial bladder carcinoma at the DNA, RNA, and protein levels performed as part of The Cancer Genome Atlas project; recurrent mutations were found in 32 genes, including those involved in cell-cycle regulation, chromatin regulation and kinase signalling pathways; chromatin regulatory genes were more frequently mutated in urothelial carcinoma than in any other common cancer studied so far.

One of two papers describing a reprogramming phenomenon called stimulus-triggered acquisition of pluripotency (STAP) — in STAP, lineage-committed adult somatic cells are reprogrammed to pluripotency by transient exposure to low-pH treatment, and extensive analysis of the molecular features and developmental potential of STAP cells indicates that they represent a unique state of pluripotency.

A complete pre-agricultural European human genome from a ∼7,000-year-old Mesolithic skeleton suggests the existence of a common genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic, and ancestral alleles in several skin pigmentation genes suggest that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times.

Through the use of a novel three-dimensional imaging technique, used in conjunction with a multicolour reporter that allows lineage tracing and cell tracking of entire mammary ducts in vivo, bipotent stem cells are shown to have a central role in both puberty and long-term maintenance; in addition, long-lived luminal progenitor cells with a prominent role in ductal expansion are identified.

The long-term record of atmospheric carbon dioxide growth rate shows that the sensitivity of this growth rate to tropical temperature variability has increased by a factor of about two in the past five decades, and was greater when tropical land regions experienced drier conditions, implying that moisture regulates this sensitivity.

Escherichia coli K-12 performs sulphoglycolysis; heterologous expression of enzymes encoded in a ten-gene cluster present in almost all (>91%) available E. coli genomes is used to show that sulphoquinovose is catabolised through four reactions to produce dihydroxyacetone phosphate, which powers energy conservation and growth, and a sulphonate product, which is excreted.

This study shows that PADI4-mediated citrullination occurs during pluripotency and that citrullination of H1 results in loosening of chromatin compaction; furthermore, citrullination is shown to be important for the activation of stem-cell genes, for iPS cell reprogramming and to maintain pluripotent cells in the early mouse embryo.

The largest asteroid of the Solar System, (1) Ceres, has been thought to have an icy surface; here it is observed to be emitting water vapour.

Suppressing fungi in a tropical forest plant community lowers diversity by reducing the negative effects of density on seedling recruitment, and removing insects increases seedling survival and alters plant community composition; this demonstrates the crucial role of pathogens and insects in maintaining and structuring tropical forest plant diversity.

In Arabidopsis, the RNA-directed DNA methylation pathway is important for establishing and maintaining DNA methylation — here Pol V is shown to depend on SUVH2 and SUVH9, where both of these proteins are proposed to bind specifically to methylated DNA to recruit Pol V, providing a self-reinforcing loop mechanism for maintenance of RNA-directed DNA methylation.

The authors report the largest family-trio exome sequencing study of schizophrenia to date; mutations are overrepresented in genes for glutamatergic synaptic proteins and also genes mutated in autism and intellectual disability, providing insights into aetiological mechanisms and pathopshyisology shared with other neurodevelopmental disorders.