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This Week in Nucleic Acids Research: Nov 26, 2014

A team from Japan characterized more than two dozen lung adenocarcinoma cell lines using a combination of whole-genome sequencing, RNA sequencing, bisulfite sequencing, and chromatin immunoprecipitation sequencing to look at everything from somatic mutation patterns and transcriptional profiles to methylation and histone marks. In the 26 lung adenocarcinoma cell lines, the researchers identified hundreds of coding and splice site mutations, along with thousands of methylation or histone mark changes and more than 13,500 alterations affecting apparent regulatory regions. "Unexpectedly, we found that the aberrant expression was associated with various causative events," they write, "which are characteristically gene-dependent."

For another Nucleic Acids Research study, investigators from the European Molecular Biology Laboratory and elsewhere explain how they used proteomic, transcriptomic, and experimental biochemical data to augment their annotation of the genome of Chaetomium thermophilum, a thermophilic, filamentous fungus that's sometimes used as a model in structural biology studies. By incorporating these additional sources of information, the team was able to tweak gene annotation, revising thousands of gene profiles, uncovering previously undetected genes, and predicting function for some genes that were poorly characterized in the past.

A China-led team introduces an online, open-access database called DoGSD that contains SNPs found in the canidae family. The site currently houses roughly 19 million SNPs identified in dozens of domesticated dog and grey wolf genomes through published and unpublished genotyping and whole-genome sequencing studies. The variant collection includes information found in 34 indigenous Chinese dog genomes, the study's authors note, "which represent a key phase in dog domestication" not found in prior dog SNP databases. "We will keep up with whole-genome SNP data releases and update DoGSD in a timely manner with new released data from population studies of dogs and wolves either by our own research groups or from publicly available resources," they write.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.