In PLoS One this week, researchers in the US and China describe their mRMR feature selection and analysis method to predict protein domain. The team combined the techniques of random forest, maximum relevance minimum redundancy, and incremental feature selection, and incorporated physicochemical and biochemical properties, sequence conservation, residual disorder, secondary structure, and solvent accessibility to make their predictions. "The overall success rate achieved by the new method on an independent dataset was around 73 percent, which was about 28-40 percent higher than those by the existing method on the same benchmark dataset," the team writes. This new method could become a new tool for protein domain annotation, they add.
In PLoS Biology this week, researchers at Case Western Reserve University report that the DEAD-box RNA helicase Dhh1 promotes RNA decapping. The team found that Dhh1 represses translation in vivo after initiation, and independent of initiation factors eIF4E and eIF3b. In addition, the team found an association between Dhh1 on an mRNA and the accumulation of ribosomes on the transcript. "Endogenous Dhh1 accompanies slowly translocating polyribosomes," the authors write. "Dhh1 activates decapping in response to impaired ribosome elongation. Together, these findings suggest that changes in ribosome transit rate represent a key event in the decapping and turnover of mRNA."
In PLoS Genetics this week, researchers in Europe and Japan report that the non-specific lethal, or NSL, complex regulates housekeeping genes in Drosophila. The team performed a ChIP-seq analysis of four NSL complex members in the genome of Drosophila melanogaster, and found that 85.5 percent of NSL-bound genes are constitutively expressed across different cell types. "We find that an increased abundance of the histone modifications H4K16ac, H3K4me2, H3K4me3, and H3K9ac in gene promoter regions is characteristic of NSL-targeted genes," the team writes. "Furthermore, we show that these genes have a well-defined nucleosome free region and broad transcription initiation patterns." They also performed ChIP-seq analyses of RNA polymerase II in NSL1- and NSL3-depleted cells, and found that both NSL proteins are required for recruitment of Pol II to NSL target gene promoters. "The observed Pol II reduction coincides with compromised binding of TBP and TFIIB to target promoters, indicating that the NSL complex is required for optimal recruitment of the pre-initiation complex on target genes," the team says. These findings suggest that the MOF-containing NSL complex regulates the housekeeping genes in the flies through modulation of Pol II transcription initiation, they add.
And in PLoS Biology this week, researchers in Canada report that p180 promotes the ribosome-independent localization of a subset of mRNA to the endoplasmic reticulum. Using a mass spectrometry analysis of proteins that associate with ER-bound polysomes, the team identified mRNA receptors that may mediate an alternative mechanism for the targeting of transcripts to the endoplasmic reticulum. "We demonstrate that p180 over-expression can enhance the association of generic mRNAs with the ER," the team says. "We then show that p180 contains a lysine-rich region that can directly interact with RNA in vitro." It is likely, they add, that this alternative pathway enhances the fidelity of protein sorting and localizes mRNAs to subdomains of the endoplasmic reticulum.