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This Week in Nucleic Acids Research: Feb 2, 2011

In a paper published online in advance in Nucleic Acids Research this week, investigators at Japan's Yokohama City University show that "Hmo1 directs pre-initiation complex assembly to an appropriate site on its target gene promoters by masking a nucleosome-free region" in Saccharomyces cerevisiae. More specifically, the Yokohama City team found that "in Δhmo1 cells, the transcription start site of the Hmo1-enriched RPS5 promoter shifted upstream, while the [transcription start site] of the Hmo1-limited RPL10 promoter did not shift." In its ChIP analysis, the team found that an RPS5 "intervening region" is normally masked by Hmo1, such that it ensures accurate transcriptional initiation.

Three researchers at Michigan State University this week reports their purification of an oriC plasmid replication inhibitor, which the team says "is a truncated form of ribosomal protein L2 evidently lacking 59 amino acid residues from the C-terminal region encoded by rplB." Sundari Chodavarapu et al. also demonstrate that the truncated form of L2 "physically interacts with the N-terminal region of DnaA to inhibit initiation from oriC," which, according to their observations, occurs most likely by "interfering with DnaA oligomer formation, and the subsequent assembly of the pre-priming complex on an oriC plasmid." The UM researchers say that their in vitro results open new avenues for investigations of DnaA function and initiation frequency in vivo.

Emiko Suzuki and Manabu Nakayama at Chiba University in Japan present two site-specific recombination systems for genome engineering online in advance in Nucleic Acids Research this week. "VCre/VloxP and SCre/SloxP," Suzuki and Nakayama write, when used "in combination with Cre/loxP and Flp/FRT systems can serve as powerful tools for genome engineering, especially when used to genetically modify both alleles of a single gene in mouse and human cells."

Investigators at Germany's Justus-Liebig-University describe "the intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages" in Nucleic Acids Research this week. By sequencing cDNAs from extracellularly growing bacteria and from L. monocytogenes infected macrophages, the team cataloged "the sRNA repertoire during intracellular bacterial growth." Among other things, they found 150 putative regulatory RNAs, 71 of which were previously uncharacterized as such. In addition, the Justus-Liebig researchers found "29 regulatory RNAs, including small non-coding antisense RNAs, are specifically expressed intracellularly."

The Scan

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.