In a paper published online in advance in Nature this week, an international team led by investigators at Imperial College London shows that the homing endonuclease gene I-Sce1 "can substantially increase its transmission to the progeny in transgenic mosquitoes of the human malaria vector Anopheles gambiae." More specifically, I-Sce1 quickly invades mosquito populations such that it validates mathematical models of homing endonuclease gene transmission dynamics. In addition, "expression of I-SceI in the male germline induces high rates of site-specific chromosomal cleavage and gene conversion, which results in the gain of the I-SceI gene, and underlies the observed genetic drive," the team writes.
Members of Europe's MetaHIT Consortium, along with their international colleagues, this week break the human gut microbiome into three main enterotypes – those that are dominated by Bacteroides, Prevotella, and Ruminococcus. "The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities," the team writes, adding that "data-driven marker genes or functional modules can be identified for each of these host properties." Daily Scan's sister publication GenomeWeb Daily News has more on this study.
In another Nature paper published online this week, an international team led by researchers at SAIC-Frederick in Maryland suggests that "the −35 SNP is not the causal variant for differential HLA-C expression," but rather that "variation within the 3′ untranslated region of HLA-C regulates binding of the microRNA hsa-miR-148 to its target site," such that it is "strongly" associated with HIV control. The 3’ UTR variant, the authors add, may add "to the effects of genetic variation encoding the peptide-binding region of the HLA class I loci."
Over in Nature Genetics, a team led by researchers at the National Cancer Center Research Institute in Tokyo presents a "high-resolution characterization of a hepatocellular carcinoma genome." The researchers sequenced a hepatitis C virus-positive hepatocellular carcinoma to 36-fold coverage, and matched lymphocytes to a maximum of 28-fold coverage. They identified more than 11,000 somatic substitutions in the tumor genome, for which they used gene annotation enrichment analysis to validate 63 non-synonymous substitutions. The team also validated 22 chromosomal rearrangements, which it says are responsible for "four fusion transcripts that had altered transcriptional regulation or promoter activity." Overall, the team says that its analysis of the virus-associated cancer genome "identified previously uncharacterized mutation patterns, intra-chromosomal rearrangements and fusion genes, as well as genetic heterogeneity within the tumor."