Reviews & Analysis

Stem cell regulation is critical to the development of all multicellular organisms; in plants, stem cell niches reside in meristems. Two newly identified plant genes establish a novel signaling feedback from the incipient leaf primordia back to the meristem that is required to regulate stem cell proliferation.

The genome sequence of carrot (Daucus carota L.) is the first completed for an Apiaceae species, furthering knowledge of the evolution of the important euasterid II clade. Analyzing the whole-genome sequence allowed for the identification of a gene that may regulate the accumulation of carotenoids in the root.

Studies of the Y chromosome over the past few decades have opened a window into the history of our species, through the reconstruction and exploitation of a patrilineal (Y-genealogical) tree based on several hundred single-nucleotide variants (SNVs). A new study validates, refines and extends this tree by incorporating >65,000 Y-linked variants identified in 1,244 men representing worldwide diversity.

How epigenetic regulators find their specific targets remains a challenging question. Two parallel studies show that REF6, a plant H3K27me3 demethylase, binds a specific DNA motif via its zinc-finger domains and recruits the SWI/SNF-type ATPase BRAHMA, demonstrating a sequence-specific recruitment mechanism for a chromatin-modifying complex.

A new mouse model linking diabetes, insulin secretion and autoimmunity with a high-fat diet supports a shared mechanism for type 1 (T1D) and type 2 (T2D) diabetes. In this model, the protein secretion system of insulin-producing pancreatic beta cells is stressed, leading to increased beta cell apoptosis and diabetes via reduced levels of the transcription factor GLIS3, a pathogenic pathway that can be mimicked by a high-fat diet.

Determining how the evolving genome-wide map of distal regulatory elements is connected with target genes has remained a significant challenge, despite progress in understanding chromatin architecture and regulation. A new study presents a computational approach for predicting distal element–gene interactions.

How maternal diet influences offspring metabolism is unclear, as it is difficult to distinguish between the effects of the in utero environment and epigenetic factors contributed by the oocyte. In a mouse model of high-fat diet, a new study teases apart these mechanisms by using in vitro fertilization and shows that susceptibility of offspring to metabolic disorder can likely be attributed to epigenetic inheritance via the oocyte.

A new study compares DNA methylation profiles in developing zebrafish, Xenopus tropicalis and mice and suggests roles for Tet proteins in demethylating conserved gene enhancers during the phylotypic period of early development. These findings provide an epigenetic underpinning for the 'hourglass' model.

Teleosts have emerged as important model organisms, yet their ancestrally duplicated genomes sometimes complicate developmental genetic analyses and comparisons to humans. A new genome sequence of spotted gar, a fish related to teleosts but lacking a duplicated genome, now helps to bridge human and teleost biology.

Polymorphism of haptoglobin in human serum was first discovered over 60 years ago. A new paper characterizes the complex structural variation at the HP locus in detail and, by using imputation from flanking SNP genotype data, shows that it affects blood cholesterol levels.

The recently discovered chromatin compartments called topologically associating domains (TADs) are essential for the three-dimensional organization of regulatory interactions driving gene expression. A new study documents the emergence of a TAD flanking the amphioxus Hox cluster, prefiguring the vertebrate anterior Hox TAD and preceding the appearance of the concurring posterior Hox TAD.

Current efforts in cellular disease modeling and regenerative medicine are limited by the paucity of cell types that can be generated in the laboratory. A new study introduces a computational framework, Mogrify, that uses network biology to predict combinations of transcription factors necessary for direct conversion between human cell types to ameliorate this issue.

The integration of large, well-sampled collections of bacterial isolates with genomics and experimental methods provides opportunities for 'top-down' discovery of the genetic basis of phenotypes of interest. In a new report, the authors apply this approach to investigate the heterogeneity in manifestations of disease caused by Listeria monocytogenes and demonstrate that a previously uncharacterized cellobiose PTS system is involved in central nervous system infection.

The idea that pollinators are in large part responsible for the diversity of flowering plants dates back more than 150 years to Darwin's work, but even modern scientists have struggled to identify specific 'speciation genes' and determine how they influenced flower-pollinator interactions. A new study proposes that a series of mutations in a single gene controlling floral chemicals influenced pollinator preferences, likely resulting in speciation, bringing us closer to finding a speciation gene.

The Legionella genus includes opportunistic human pathogenic species that invade human cells using effector proteins that evolved during association with their natural amoeba hosts. A new study compares the genomes of 41 Legionella species to identify nearly 6,000 effectors, providing insight into these species' evolution and pathogenic lifestyles.

Plant pathogens can evolve new host specificities and overcome host resistances over surprisingly few generations, a process that is greatly accelerated by agricultural practices. A new study provides a striking example in which the rapid emergence of a new pathogen via introgressive hybridization mirrors the evolution of a hybrid cereal crop.