In the early, online version of Genome Biology this week, members of the Catfish Genome Consortium report that they have put together a collection of nearly half a million catfish expressed sequence tags using data for eight channel catfish and four blue catfish as well as previous data. In the process, they identified some 300,000 potential catfish SNPs and nearly 15,000 unique catfish genes. "The EST resource should be valuable for identification of microsatellites, genome annotation, large-scale expression analysis, and comparative genome analysis," they write. "The inter- and intra- specific SNPs identified from all catfish EST dataset assembly will greatly benefit the catfish introgression breeding program and whole genome association studies."
A University of California at San Diego research team describes their method for finding transcription factor binding sites across the genome, demonstrating the validity of this approach using 13 transcription factors in mouse embryonic stem cells. The approach, which they dubbed "chromatin-based integrated approach" or Chromia, integrates sequence data (such as transcription factor binding motifs) and chromatin signatures at regulatory elements.
German researchers report on a database called PhenomiR that houses information on microRNA expression. The database includes information from 542 studies, providing a resource for understanding how miRNA regulation shifts during certain biological processes or disease. "This comprehensive repository for the first time allows a large-scale statistical analysis of aspects like genomic localization of deregulated miRNAs or influence of the sample origin," they write.
Joanna Bridger and her co-workers explore how chromosome position changes in human primary fibroblast cells coerced into a growth arrest. They found that this chromosome re-positioning uses energy and takes less than a quarter of an hour to complete. "These findings demonstrate that genome organization in interphase nuclei is altered considerably when cells leave the proliferative cell cycle," they write, "and that re-positioning of chromosomes relies on efficient functioning of an active nuclear motor complex that contains nuclear myosin 1beta."