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This Week in Genome Biology: Apr 22, 2009

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.

The Scan

NFTs for Genome Sharing

Nature News writes that non-fungible tokens could be a way for people to profit from sharing genomic data.

Wastewater Warning System

Time magazine writes that cities and college campuses are monitoring sewage for SARS-CoV-2, an approach officials hope lasts beyond COVID-19.

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.