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This Week in Nucleic Acids Research: Mar 21, 2012

In Nucleic Acids Research this week, researchers in Belgium and France report that LSD1 and CTIP2 work together to promote HIV-1 transcriptional silencing. In previous studies, the team showed that CTIP2 forces heterochromatin formation and HIV-1 gene silencing. In this study, the team shows that LSD1 represses HIV-1 transcription and viral expression in cooperation with CTIP2. "We show that recruitment of LSD1 at the HIV-1 proximal promoter is associated with both H3K4me3 and H3K9me3 epigenetic marks," the authors add. "Our data suggest that LSD1-induced H3K4 trimethylation is linked to hSET1 recruitment at the integrated provirus."

Also in Nucleic Acids Research this week, a team of US and European researchers present their genome-wide transcriptome analysis of the Xanthomonas plant pathogen. The team used a differential RNA sequencing method to automatically generate comprehensive transcription start site maps. "We report 1421 putative TSSs in the Xcv genome," they write. "Genes in Xcv exhibit a poorly conserved — 10 promoter element and no consensus Shine-Dalgarno sequence. Moreover, 14% of all mRNAs are leaderless and 13% of them have unusually long 5'-UTRs."

Researchers in South Korea describe their biochemical studies of the Saccharomyces cerevisiae Mph1 helicase in Nucleic Acids Research this week. In order to understand the ATPase/helicase role of Mph1, the team characterized the helicase activity, and focused on its effect on DNA junction structures. "Consistent with its 3' to 5' directionality, Mph1 displaced 3'-flap substrates in double-fixed or equilibrating flap substrates," the authors write. "Surprisingly, Mph1 displaced the 5'-flap strand more efficiently than the 3'flap strand from double-flap substrates, which is not expected for a 3–5' DNA helicase." The researchers say that the helicase/ATPase activity of Mph1 may play a role in "converting multiple-stranded DNA structures into structures cleavable by processing enzymes such as Fen1."

Finally in Nucleic Acids Research this week, researchers at the University of Wisconsin-Madison report their findings from a study of the regulation of 6S RNA by pRNA synthesis. "Escherichia coli 6S RNA accumulates to high levels during stationary phase, and has been shown to bea released from Eσ70 during exit from stationary phase by a process in which 6S RNA serves as a template for Eσ70 to generate product RNAs," the authors write. In this study, they show that pRNA synthesis occurs and that it is an important mechanism of 6S RNA function, "required for cells to exit stationary phase efficiently in both E. coli and B. subtilis."

The Scan

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Can't Be Used

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PLOS Papers on Frozen Shoulder GWAS, Epstein-Barr Effects on Immune Cell Epigenetics, More

In PLOS this week: genome-wide association study of frozen shoulder, epigenetic patterns of Epstein-Barr-infected B lymphocyte cells, and more.