Volume 49 Issue 2, February 2017

A CRISPR screen conducted in a CD4⁺ T cell leukemia line has identified host factors required for HIV infection but dispensable for cellular survival. The results highlight sulfation on the HIV co-receptor CCR5 and cellular aggregation as potential targets for therapeutic intervention.

The chromatin scaffolding protein SMCHD1 (structural maintenance of chromosomes flexible hinge domain containing 1) was previously shown to have diverse roles in X-chromosome inactivation, imprinting and double-strand break repair, and mutations in SMCHD1 contribute to a type of muscular dystrophy. Now, development of the nose and eyes is added to its list of functions.

Four studies in this issue report new mechanisms underlying the function of the chromatin remodeling SWI/SNF complex in controlling gene expression and suppressing tumor development, providing valuable insights into the treatment of cancers harboring mutations in genes encoding SWI/SNF complex subunits.

Nada Jabado, Jacek Majewski and colleagues identify mutations in multiple histone H3 genes causing recurrent p.Lys36Met alterations in head and neck squamous cell carcinomas. They show that tumors with these p.Lys36Met alterations correspond to a specific DNA methylation cluster along with tumors harboring previously described mutations in NSD1.

Carl Anderson, Jeffrey Barrett and colleagues use whole-genome sequencing and imputation to explore the genetic architecture of inflammatory bowel disease. They identify a low-frequency missense variant in ADCY7 that doubles risk of ulcerative colitis and detect a burden of very rare, damaging missense variants in known Crohn's disease risk genes.

Nir Hacohen, Bruce Walker, David Sabatini, Eric Lander and colleagues perform a CRISPR–Cas9-based screen for host factors that are required for HIV infection. They identify two known and three novel factors that are necessary for viral infection but that are not required for cell viability, making them potential targets for antiviral therapy.

Jaroslaw Maciejewski, Seishi Ogawa and colleagues examine the clonal dynamics of myelodysplastic syndromes (MDS) by analyzing whole-exome and targeted sequencing data from a large patient collection. They find that progression steps previously defined by pathologic criteria are accompanied by distinct molecular changes, and they show that driver genes can be classified into molecular subtypes differentially associated with low-risk MDS, high-risk MDS or secondary acute myeloid leukemia.

Gerald Crabtree, Cigall Kadoch and colleagues report that BAF complexes oppose PRC by rapid, ATP-dependent eviction in the absence of Pol II occupancy, transcription or replication, leading to the formation of accessible chromatin. They also find that tumor-suppressor and oncogenic mutations in BAF subunits result in differential effects on PRC eviction.

Manju Kurian and colleagues report heterozygous variants in KMT2B in 27 unrelated individuals with a complex progressive childhood-onset dystonia, often associated with a typical facial appearance. Their findings highlight a clinically recognizable form of dystonia and demonstrate a crucial role for KMT2B in the physiological control of voluntary movement.

Michael Talkowski, David FitzPatrick, Erica Davis and colleagues report rare inherited or de novo missense variants in SMCHD1 in arhinia patients. Some of the same mutations in SMCHD1 are known to cause a phenotypically distinct muscular dystrophy disorder, FSHD2, and the distinct clinical features of the two disorders suggests that additional genes interact with SMCHD1 to cause arhinia.

Jeanne Amiel, Bernd Wollnik, Bruno Reversade and colleagues report de novo missense mutations in SMCHD1 in patients with Bosma arhinia microphthalmia syndrome (BAMS) and isolated arhinia. Mechanistic studies support a key role for SMCHD1 in nasal development and suggest that the mutations in patients may function via a gain-of-function mechanism.

Jeffrey Barrett, Carl Anderson and colleagues report the results of a large genome-wide association study of inflammatory bowel disease. They identify 25 new genome-wide significant loci, 3 of which contain integrin genes, and find that the associated variants at several of these loci are correlated with expression changes in response to immune stimulus.

James Lee, Kenneth Smith and colleagues report a within-cases genome-wide association analysis for Crohn's disease to identify genetic loci specifically associated with disease severity and outcome. They find four loci associated with prognosis, none of which is associated with susceptibility to Crohn's disease.

Konstantinos Lazaridis, Carl Anderson and colleagues report results of a genome-wide association study of primary sclerosing cholangitis (PSC). They identify four new susceptibility loci for PSC and quantify the correlation of common genetic variation shared between PSC and inflammatory bowel diseases.

Richa Saxena and colleagues report genome-wide association analyses of sleep disturbance traits in the UK Biobank cohort. They discover loci associated with insomnia symptoms and excessive daytime sleepiness and identify genetic correlations with several neuropsychiatric and metabolic traits.

Gerald Crabtree, Keji Zhao and colleagues report that recurrent disease-associated mutations in SMARCA4 result in increased PRC1 deposition and activity. Using an in cellula assay, they find that the BAF (mSWI/SNF) complex directly evicts PRC from chromatin via an ATP-dependent mechanism and that this occurs within minutes of BAF occupancy.

Charles Roberts, Peter Park, Bradley Bernstein and colleagues examine the consequences of SMARCB1 loss on enhancer landscapes in human rhabdoid tumors. They show that SMARCB1 is essential for the integrity and abundance of SWI/SNF complexes and facilitates their targeting to appropriate enhancers.

Charles Roberts and colleagues show that deletion of Arid1a from mouse intestinal epithelium results in invasive adenocarcinomas resembling human colorectal cancer. They further show that ARID1A loss impairs SWI/SNF targeting and enhancer-mediated gene regulation.

Yun Song and colleagues present SMC++, a statistical method for population history inference capable of analyzing unphased whole genomes and sample sizes much larger than can be analyzed by current methods. The authors apply SMC++ to sequence data from human, Drosophila and finch populations.

James Liley, John Todd and Chris Wallace present a statistical method for determining whether disease-associated variants have different effect sizes in phenotypically defined subgroups of disease cases. The test can be combined with existing methods to determine whether genetic heterogeneity is driven by population stratification or by different mechanisms of disease pathology.