This week in Genome Biology, Japanese researchers performed the first genome-wide analysis of EGR-1 binding sites. While it's known that EGR-1 plays a role in monocytic differentiation, their technique allowed them to further describe how. Using ChIP-chip and combining the results with newly reported FANTOM4 data, they found that EGR-1 binding sites are "highly co-localized with CpG islands, acetylated histone H3 lysine 9 binding sites, and CAGE tag clusters," they write in the abstract.
Scientists also looked at the transcriptional features of genomic regulatory blocks. Combining CAGE tag mapping of transcription start sites, expression data, sequence, and epigenetic information, they found that GRB genes are different in that they have "longer CpG islands, a higher number and wider spacing of alternative transcription start sites, and a distinct composition of transcription factor binding sites in their core/proximal promoters."
Patrick Duffy at the University of Washington and the Seattle Biomedical Research Institute has trained high-throughput techniques on studying the malaria sporozoite. He and his team found that the malaria parasite sporozoite proteome changes during maturation, revealing proteins specifically expressed in the stage that infects the human host, he says in the abstract.
Josee Dostie's lab at McGill has developed a suite of computer programs for identifying genome-wide chromatin conformation signatures with 5C technology. In particular, they found that dynamic HoxA cluster chromatin conformation signatures are linked to cell differentiation, suggesting that these signatures could serve as novel disease biomarkers.