In Genome Biology this week, a team of researchers in Germany compared target genes of TFIIB and NC2 transcription factors in human B cells and analyzed the associated core promoter architectures. TFIIB occupancy is positively correlated with gene expression, the researchers write, and the majority of promoters are GC-rich and lack defined core promoter elements. They also found that NC2 binds to a highly related target gene set. "TFIIB and NC2 are global players that occupy active genes," the team writes. "Preinitiation complex formation is independent of core elements at the majority of genes."
Also in Genome Biology this week, researchers from Johns Hopkins University and NIH used testes isolated from a Drosophila bag of marbles mutant strain, with undifferentiated germ cells, to study the endogenous chromatin structure of undifferentiated cells using ChIP-seq. The researchers' genome-wide analysis indicated that most differentiation-associated genes in undifferentiated cells lack an active chromatin mark and an initiative Pol II. However, the team writes, they are associated with either the repressive H3K27me3 mark or no detectable mark at all.
An international team of researchers report their study on the transcription of non-coding RNAs in eukaryotic genomes in the budding yeast cell cycle. The researchers discovered 523 antisense transcripts, 135 unannotated intergenic non-coding RNAs, and 109 cell cycle-regulated protein-coding genes that had not previously been shown to cycle. "Our dataset ... reveals periodic expression of both protein-coding and non-coding RNA and profiles the expression of non-annotated RNAs throughout the cell cycle for the first time," the researchers write. "This data enables hypothesis-driven mechanistic studies concerning the functions of non-coding RNAs."
Researchers from the Dana-Farber Cancer Institute and Harvard Medical School report their findings on the impact of human 5'UTR introns on gene expression in Genome Biology this week. They found that the most highly-expressed genes tend to have short 5'UTR introns and observed that genes in special functional categories have an uneven distribution of 5'UTR introns. The team also analyzed the evolution of 5'UTR introns in non-receptor protein tyrosine kinases, and identified a conserved DNA motif enriched within the 5'UTR introns of human NRTKs. "Our results suggest that human 5'UTR introns enhance the expression of some genes in a length-dependent manner," the researchers write.