In Genome Research this week, Katie Pollard at UCSF is first author on work that used computational methods to find nucleotide substitution rates that are either faster or slower than the neutral rate. Bundling four statistical, phylogenetic tests – "a likelihood ratio test, a score test, a test based on exact distributions of numbers of substitutions, and the Genomic Evolutionary Rate Profiling (GERP) test" – into a freely available program called phyloP, they were able to apply the methods to 36 mammalian species, where "they all appear to be capable of fairly good sensitivity with low false positive rates in detecting strong selection at individual nucleotides, moderate selection in 3 bp elements, and weaker or clade-specific selection in longer elements," says the abstract.
A team at Oregon State University has performed genome-wide mapping of alternative splice variants in Arabidopsis thaliana. Using Illumina to perform RNA-seq, they found that at least 42 percent of introns are alternatively spliced and that alternative isoforms with premature termination codons make up the majority of these. Further experiments revealed that nonsense-mediated mRNA decay and regulated unproductive splicing and translation "may be widespread in plants and may play important roles in regulating gene expression," they write.
Stanford University's Arend Sidow is lead author on a paper that presents ProPhylER, "a next-generation curated proteome resource that uses comparative sequence analysis to predict constraint and mutation impact for eukaryotic proteins." ProPhylER has almost 9,000 clusters of related proteins and offers two interfaces, the ProPhylER interface, which "displays predictive analyses in sequence space," and CrystalPainter, which "maps evolutionary constraints onto solved protein structures."
Finally, research led in part by UMass's Oliver Rando has created a method for finding nucleosome positions from deep sequencing data and applied it to chromatin maps of S. cerevisiae. Looking at "digestion series where nucleosomes are isolated from under- and over-digested chromatin," they found that some nucleosomes are more susceptible or resistant to overdigestion, "with promoter nucleosomes easily digested and mid-coding region nucleosomes being quite stable." Their resource will hopefully provide more tools for future nucleosome mapping experiments, they say.