University of Hong Kong researchers present a new method dubbed SpliceNet in Nucleic Acids Research that aims to infer isoform-specific co-expression networks from RNA-seq data. SpliceNet first looks at the expression of genes and isoforms as multivariate variables and then relies on a large dimensional trace test to uncover any pairwise dependencies and construct co-expression networks with isoform-level resolution. The researchers say that SpliceNet can also be used infer splicing isoform network changes that arise between normal and diseased samples.
National Institute of Diabetes and Digestive and Kidney Diseases researchers report on Metaseq, a Python-based software library that enables users to load various genomic data formats into standard Python ones for analysis. In their test case of the software, the NIDDKD researchers brought together RIP- and ChIP-seq data from Shep and the core gypsy insulator protein Su(Hw) from two Drosophila cell lines. From this, they found that Shep associates with chromatin co-transcriptionally, but that it is also recruited to trans insulator complexes where it has a negative function.
Researchers from the University of Basel report in Nucleic Acid Research that they identified a number of transcription factors whose activity is influenced by embryonic microRNAs and that could help maintain pluripotency. In particular, they found that the transcription factor IRF2 TF is upregulated in the absence of the embryonic miRNAs and that the nuclear concentration of RelA — which is part of the NF-κB pathway — increases when stimulated by TNF-α. The researchers say their results provide a glimpse into the role of miRNAs in the regulatory circuitry of embryonic stem cells.