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This Week in Nature: Feb 19, 2015

A collection of studies from the Roadmap Epigenomics Program appears in Nature this week, offering new insights into these genetic modifications in a variety of human cell types. The program examined samples from both adult and embryonic cells and tissues, with researchers mapping how the epigenome varies and functions in different biological settings. In one paper, a Massachusetts Institute of Technology-led team examined 111 reference human epigenomes, highlighting similarities and differences, and identifying genetic variants associated with 58 complex traits. A Broad Institute-led group showed that DNA methylation influences stem cell differentiation into neural cells, while a University of California, San Diego-led group showed how chromatic modification also has a role in stem cell differentiation. Investigators from the University of Washington and the Broad, meanwhile, published data linking epigenomic profiles to cancer-associated mutation patterns and showed how this information can be used to identify the cell of origin for an individual tumor. Another MIT group examined the epigenomics of Alzheimer's disease and showed that a genetic predisposition to the condition may be associated with immune functions, while the symptomatic changes in neuronal activity are most influenced by non-genetic factors.

Meanwhile, in Nature Biotechnology, University of California, Los Angeles' Jason Ernst and MIT's Manolis Kellis publish the results of a large-scale imputation of epigenomic datasets, providing comprehensive human regulatory region annotation across different tissues. Also in Nature Biotechnology, a Washington University in St. Louis-led team publish a letter detailing the epigenomic annotation of genetic variants using the Roadmap Epigenome Browser, which integrates data from both the NIH Roadmap Epigenomics Consortium and ENCODE.

And in Nature Communications, a group from the Baylor College of Medicine described an analysis of the 111 reference epigenomics from the Roadmap Epigenomics project that revealed tissue-specific regulation by long non-coding RNAs, while in Nature Communications, a multi-institute team generated epigenomic and transcriptional profiles from human breast cell types from healthy individuals to define the events that led to breast cell differentiation.

GenomeWeb has more on these Roadmap Epigenomics Project studies here.

Also this week, in Nature Protocols, Salk Institute researchers describe the preparation of a MethylC-sequencing library for base-resolution whole-genome bisulfate sequencing.

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.