Reviews & Analysis

Orchids have captured imaginations worldwide for hundreds of years. The publication of the moth orchid genome sequence opens the door to a greater understanding of orchid morphological evolution and physiological adaptation.

Bacterial whole-genome sequencing of longitudinally collected isolates enables the investigation of evolutionary trajectories, which may inform both the prevention and treatment of human-associated pathogen infections. A new study explores the adaptation of multiple lineages of Pseudomonas aeruginosa to the lungs of young patients with cystic fibrosis and finds evidence of convergent molecular evolution and historical contingencies.

Betalains are bright red and yellow pigments, which are produced in only one order of plants, the Caryophyllales, and replace the more familiar anthocyanin pigments. The evolutionary origin of betalain production is a mystery, but a new study has identified the first regulator of betalain production and discovered a previously unknown link between the two pigment pathways.

Jason Lieb and Sebastian Pott review the identification and composition of super-enhancers and ask whether super-enhancers are a new, conceptually distinct regulatory entity.

Febrile seizures can arise in response to fevers induced by viral infection or as an adverse reaction to live-virus vaccines such as measles, mumps and rubella (MMR) vaccination. A new study has now identified common genetic variants influencing susceptibility to febrile seizures, including two loci specifically associated with MMR-related events.

A new study detects unstable nascent RNAs and uncovers thousands of transcription initiation sites in promoters and enhancers. Detailed analysis shows that these initiation sites have a similar architecture and that they are differentiated by post-transcriptional regulation rather than transcription initiation.

Characterization of the mutational landscape of tumors is important to understanding disease etiology but does not provide mechanistic insight into the functional role of specific mutations. A new study introduces a statistical mechanical framework that draws on biophysical data from SH2 domain–phosphoprotein interactions to predict the functional effects of mutations in cancer.

A new study identifies homozygous missense mutations in SGOL1, which encodes a component of the cohesin complex, in a newly described disorder termed Chronic Atrial and Intestinal Dysrhythmia (CAID) syndrome. These findings implicate cohesin in the regulation of intrinsic cardiac and intestinal rhythm and further expand the growing group of disorders termed the cohesinopathies.

A new study identifies rare mutations in SPRTN that cause a novel progeroid syndrome. The results point to an unexpected function of SPRTN and bring insight to the mechanisms that link premature aging and cancer.

The histone-modifying PRC2 complex has an ambiguous role in cancer, bearing both oncogenic and tumor-suppressive features depending on cell type. Studies of malignant peripheral nerve sheath tumors (MPNSTs) have now identified loss-of-function mutations altering PRC2 subunits, leading to the amplification of Ras-driven transcription and conferring vulnerability to BRD4 inhibitors.

The NLRC4 inflammasome mediates the rapid release of proinflammatory cytokines in response to various microbial stimuli, but its role in the pathology of human diseases remains unknown. Two new studies now report gain-of-function mutations in the NLRC4 gene that cosegregate with distinct autoinflammatory syndromes in affected families.

Meiotic tetrad analysis is a powerful tool for analyzing all four products of a single meiosis. A new method for tetrad analysis in mammals provides valuable insights into the mechanisms that mediate the exchange of DNA sequences between homologs during meiosis and their influence on the evolution of recombination hotspots.

A new study compares the copy number variants (CNVs) in 29,085 children with developmental delay to those in 19,584 healthy controls, providing a valuable compilation of such data. The phenotypic variability and wide range of penetrance for these variants present societal challenges regarding how these findings might be incorporated into newborn screening, early intervention and, perhaps, carrier testing and prenatal diagnosis.

The domestication of African rice, Oryza glaberrima, occurred separately from that of the much more widespread Asian rice species Oryza sativa. Analysis of the whole-genome sequence for O. glaberrima shows the extent to which the same genes were involved in these distinct but parallel evolutionary events.

A new study describes a tool, Lentihop, for somatic insertional mutagenesis in human cells and uses this system in combination with cancer genome data to define new genes and pathways involved in sarcoma development. Gene discovery in this way suggests that we are far from a complete catalog of cancer drivers.

Polycomb/Trithorax response elements (PRE/TREs) are genetic elements that can stably silence or activate genes. A new study describes how long noncoding RNAs (lncRNAs) transcribed from opposite strands of the Drosophila melanogaster vestigial PRE/TRE throw the switch between these two opposing epigenetic states.

The influence of Epstein-Barr virus (EBV) on cancer is not well understood. High-throughput sequencing of nasopharyngeal carcinoma (NPC) illustrates the influences of EBV on oncogenesis and identifies driver pathways that might be therapeutically useful for NPC treatment.

An international effort, the 1000 bull genomes project, aims to resequence the genomes of a large number of key ancestor bulls of the most important domestic cattle breeds. A new study reports on the first results of this important initiative based on the analysis of the first 234 bovine whole-genome sequences.

The genetic determinants of progression from premalignant Barrett's esophagus to esophageal adenocarcinoma are not known. A new study reports genomic sequence analyses of this progression and uses the insights gained to identify high-risk Barrett's esophagus in a new non-endoscopic test.

Two new studies report genomic data on three species of whipworm, soil-transmitted parasitic worms responsible for trichuriasis. These genomes provide insights into host-pathogen interactions and potential for new drug targets for helminth therapy.