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The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, D....

By Yi-Chieh Wu,Matthew D. Rasmussen,Mukul S. Bansal,Manolis Kellis--Nature Publishing Group--2016-01-10
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The nuclear factor κB (NF-κΒ) subunits RelA, RelB, cRel, p50, and p52 are each critical for B cell development and function. To systematically characterize their responses to canonical and noncanonical NF-κB pathway activity, we performed chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) analysis in lymphoblastoid B cell lines (LCLs....

By Bo Zhao,Luis A. Barrera,Ina Ersing,Bradford Willox,Hannah Greenfeld,Hufeng Zhou,Sarah B. Mollo,Tom Sh--Elsevier--2016-01-10
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The mechanisms contributing to transcription-associated genomic instability are both complex and incompletely understood. Although R-loops are normal transcriptional intermediates, they are also associated with genomic instability. Here, we show that BRCA1 is recruited to R-loops that form normally over a subset of transcription termination regions. There it mediates th....

By Elodie Hatchi,Konstantina Skourti-Stathaki,Steffen Ventz,Luca Pinello,Angela Yen,Kinga Kamienia--Elsevier--2016-01-10
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The seasonal variability of the polar stratospheric vortex is studied in a simplified AGCM driven by specified equilibrium temperature distributions. Seasonal variations in equilibrium temperature are imposed in the stratosphere only, enabling the study of stratosphere–troposphere coupling on seasonal time scales, without the complication of an internal tropospheric s....

By Aditi Sheshadri,R. Alan Plumb,Edwin P. Gerber--American Meteorological Society--2016-01-10
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Genetic studies of type 1 diabetes (T1D) have identified 50 susceptibility regions, finding major pathways contributing to risk, with some loci shared across immune disorders. To make genetic comparisons across autoimmune disorders as informative as possible, a dense genotyping array, the Immunochip, was developed, from which we identified four new T1D-associated region....

By Suna Onengut-Gumuscu,Wei-Min Chen,Oliver Burren,Emily Farber,Michal Szpak,Ellen Schofield--Nature Publishing Group--2016-01-10
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Objective We explore the role of DNA methylation in Alzheimer's disease (AD). To elucidate where DNA methylation falls along the causal pathway linking risk factors to disease, we examine causal models to assess its role in the pathology of AD. Methods DNA methylation profiles were generated in 740 brain samples using the Illumina HumanMet450K beadset. We focused our an....

By Lori B. Chibnik,Lei Yu,Gyan Srivastava,Julie A. Schneider,Manolis Kellis,David A. Bennett,Philip De --American Neurological Association--2016-01-10
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DNMT3L, a member of DNA methyltransferases family, is present only in mammals. As it provides specificity to the action of de novo methyltransferases, DNMT3A and DNMT3B and interacts with histone H3, DNMT3L has been invoked as the molecule that can read the histone code and translate it into DNA methylation. It plays an important role in the initiation of genomic imprin....

By Partha Pratim Das,David A. Hendrix,Effie Apostolou,Alice H. Buchner,Matthew C. Canver,S Beyaz--Elsevier--2016-01-10
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Aging is one of the most important biological processes and is a known risk factor for many age-related diseases in human. Studying age-related transcriptomic changes in tissues across the whole body can provide valuable information for a holistic understanding of this fundamental process. In this work, we catalogue age-related gene expression changes in nine tissues fr....

By Lucas D. Ward,Pouya Kheradpour,Benjamin Iriarte,Manolis Kellis--Nature Publishing Group--2016-01-10
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We introduce far-infrared graphene plasmonic crystals. Periodic structural perturbation—in a proof-of-concept form of hexagonal lattice of apertures—of a continuous graphene medium alters delocalized plasmonic dynamics, creating plasmonic bands in a manner akin to photonic crystals. Fourier transform infrared spectroscopy demonstrates band formation, where far-infra....

By Kitty Y. M. Yeung,Jingyee Chee,Hosang Yoon,Yi Song,Jing Kong,Donhee Ham--American Chemical Society (ACS)--2016-01-10
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As a new two-dimensional layered material, black phosphorus (BP) is a very promising material for nanoelectronics and optoelectronics. We use Raman spectroscopy and first-principles theory to characterize and understand the low-frequency (LF) interlayer breathing modes (<100 cm[superscript –1]) in few-layer BP for the first time. Using a laser polarization dependence ....

By Xi Ling,Liangbo Liang,Shengxi Huang,Alexander A. Puretzky,David B. Geohegan,Bobby G. Sumpter--American Chemical Society (ACS)--2016-01-10
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Conventionally, engineers have employed rigid materials to fabricate precise, predictable robotic systems, which are easily modelled as rigid members connected at discrete joints. Natural systems, however, often match or exceed the performance of robotic systems with deformable bodies. Cephalopods, for example, achieve amazing feats of manipulation and locomotion withou....

By Michael T. Tolley,Daniela L. Rus--Nature Publishing Group--2016-01-08
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Understanding nitrogen metabolism in plants holds promise for future agricultural improvements. Chellamuthu et al. now identify a feedback regulation in plant nitrogen metabolism through glutamine sensing. This mechanism appears to be conserved from algae to flowering plants with a few surprising exceptions.....

By Timothy Robert Fallon,Jing-Ke Weng--Elsevier--2016-01-08
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