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This Week in Nucleic Acids Research: Jul 21, 2010

In the most recent issue of Nucleic Acids Research, investigators in Germany show that "expression profiling in organisms lacking any genome or transcriptome sequence information is feasible by combining Illumina's mRNA-seq technology with a novel bioinformatics pipeline that integrates assembled and annotated Chinese hamster ovary sequences with information derived from related organisms." Using this methodology, the authors interrogated CHO cells and identified sequences for more than 13,000 genes — including about 5,000 novel genes. The team suggests that "more than 6,000 transcript sequences are predicted to be complete, as they covered [greater than] 95 percent of the corresponding mouse orthologs."

Investigators at the Polish Academy of Sciences investigate the presence of trinucleotide repeats in the human genome and exome. The team found 32,448 TNRs and 878 TNR-containing genes; some triplet repeats, they show, "specifically CNG, are over-represented, while CTT, ATC, AAC and AAT are under-represented in exons," evoking the possibility that "the occurrence of TNRs in exons is not random, but undergoes positive or negative selective pressure," the authors write. The team also suggests that "TNR polymorphisms should be considered a priority in association studies."

A University of Colorado-led team demonstrates that "ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives." In characterizing the relationship between "16 rRNA gene sequence similarity and overall levels of gene conservation in four groups of species," the team found that specialist bacteria in the gut "share fewer genes than is typical for genomes that come from non-gut environments, but at longer phylogenetic distances gut bacteria are more similar to each other than are genomes at equivalent evolutionary distances from non-gut environments." The authors write that their work bolsters the idea that, "despite considerable interpersonal variation in species content, there is surprising functional convergence in the microbiome of different humans."

Also, researchers at the University of Georgia and Rockefeller University show that "two thymidine hydroxylases differentially regulate the formation of glucosylated DNA at regions flanking polymerase II polycistronic transcription units throughout the genome of Trypanosoma brucei." Using high-throughput sequencing, the team localized JBP1 and JBP2 — both of which are "capable of stimulation de novo J-synthesis," at telomeric regions in T. brucei. "This genome-wide analysis revealed an enrichment of base J at regions flanking polymerase II polycistronic transcription units (Pol II PTUs) throughout the T. brucei genome," the team writes.

The Scan

Alzheimer's Risk Gene Among Women

CNN reports that researchers have found that variants in MGMT contribute to Alzheimer's disease risk among women but not men.

Still Hanging Around

The Guardian writes that persistent pockets of SARS-CoV-2 in the body could contribute to long COVID.

Through a Little Spit

Enteric viruses like norovirus may also be transmitted through saliva, not just the fecal-oral route, according to New Scientist.

Nature Papers Present Method to Detect Full Transcriptome, Viruses Infecting Asgard Archaea, More

In Nature this week: VASA-seq approach to detect full transcriptome, analysis of viruses infecting Asgard archaea, and more.