In this week's issue of Nature, which celebrates the magazine's 140th birthday, scientists from Singapore and the Netherlands use a new technique to study how genome-wide chromatin interactions affect estrogen receptor-alpha-regulated gene expression. Their method, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET), allowed them to map the chromatin interaction network bound by ER-alpha in MCF-7 breast cancer cells. Their results suggest that "ER-alpha functions by extensive chromatin looping to bring genes together for coordinated transcriptional regulation." Our sister publication, GenomeWeb Daily News, has more.
Two papers describe how NF-kappaB signaling plays a role in cancer. In one, led by MIT's Tyler Jacks, scientists found that in a mouse model of lung cancer, loss of p53 and expression of oncogenic KRAS led to NF-kappaB activation, while further tests showed that the NF-kappaB pathway is required for tumors to develop and that "this requirement depends on p53 status," they say in the abstract. Another paper led in part by Jacks and the Dana-Farber Cancer Institute's Bill Hahn used RNAi to find synthetic lethal partners of oncogenic KRAS, or "gene products that, when inhibited, result in cell death only in the presence of [oncogenic KRAS]." They found that the IkappaB kinase TBK1 and NF-kappaB signaling are necessary in KRAS mutant human cell line tumors. A News and Views story adds insight.
A paper appearing in the early online edition of Nature Biotechnology presents a new method for targeted sequencing. The method, developed by scientists at the Scripps Translational Science Institute, the University of California, San Diego, and RainDance Technologies, is based on microdroplet PCR. When the team compared their results to samples sequenced using traditional PCR on primers for 435 exons, they found that both methods resulted in the same quality data.
Finally, two papers in Nature Genetics this week report new genome sequences. First, an international consortium led by scientists at the Beijing Genomics Institute sequenced a draft of the domestic cucumber (Cucumis sativus) genome. A story at GenomeWeb Daily News reports in full. In other work, says another story at GWDN, "The genome sequence of the leprosy-causing pathogen Mycobacterium leprae is almost identical regardless of when or where the strain was collected." The paper, written in part by lead author Stewart Cole at the Ecole Polytechnique Fédérale de Lausanne, analyzes the sequence similarities between Brazilian, Indian, North American, and Thai strains of M. leprae.