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Genomics In The Journals: May 12, 2011

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – A sequencing study in the Proceedings of the National Academy of Sciences is offering clues about the ecology, physiology, and bioactive secondary metabolite repertoire of the filamentous cyanobacterium Lyngbya majuscula. Researchers used Sanger and Roche 454 strategies to sequence the draft genome of a Caribbean L. majuscula strain that's known to produce a tubulin polymerization-inhibiting anti-cancer compound, as well as a compound called barbamide that kills mollusks. Analysis of the 8.5 million base genome turned up 293,000 nucleotides that apparently contribute to secondary metabolite production, they noted, along with other sequences contributing to the cyanobacterium's marine lifestyle.

"The true natural product potential and life strategies of Lyngbya strains are poorly understood because of phylogenetic ambiguity, lack of genomic information, and their close association with heterotrophic bacteria and other cyanobacteria," senior author Lena Gerwick, a marine biotechnology and biomedicine researcher at the University of California at San Diego, and co-authors wrote.

"Our analysis revealed a complex gene regulatory network, including a large number of sigma factors and other regulatory proteins, indicating an enhanced ability for environmental adaptation or microbial associations," they added.

Baylor College of Medicine researchers used transcriptome sequencing to hunt down recurrent RNA chimeras in human prostate cancer in another PNAS study. From 20 prostate cancer transcriptomes and transcriptomes for 10 benign, matched tissue samples, the team found thousands of chimeric RNAs. In follow-up studies homing in on a few dozen chimeric RNAs that seemed most likely to contribute to prostate cancer, the team found 27 that were recurrent in prostate cancer samples but not found in unaffected control transcriptomes. Among them: TMEM79-SMG5, a chimeric RNA they believe may hold potential as a prostate cancer biomarker.

In the Journal of the American Medical Association, an MD Anderson Cancer Center-led team reports on a genomic signature coinciding with recurrence-free survival for individuals with an invasive form of breast cancer. As part of a prospective, multi-center study, the researchers did gene expression profiling of ERBB2-negative breast tumors from 310 newly diagnosed with breast cancer patients being treated with sequential taxane and anthracycline-based chemotherapy. In the process, the team tracked down gene expression signatures that corresponded to chemoresistance and chemosensitivity — results that they confirmed in another 198 individuals with breast cancer. By combining these signatures with other clinical information, such as estrogen receptor status and predicted endocrine sensitivity, they then came up with an algorithm that appears to hold promise for predicting relapse-free survival.

Genetic variants in the Drosophila melanogaster mitochondrial genome can influence the way nuclear genes are expressed in male flies, according to a Science study. Swedish and Australian researchers tossed five different versions of the Drosophila mitochondrial genome into fruit flies with the same nuclear genome sequences and used Affymetrix GeneChip Drosophila Genome 2.0 microarrays to compare nuclear gene expression patterns in the flies. Although female flies showed few nuclear gene expression differences related to their mitochondrial sequence, the researchers explained, a significant subset of male transcripts were differentially expressed depending on the version of the mitochondrial genome that they carried.

"Mitochondrial polymorphism had few effects on nuclear gene expression in females but major effects in males, modifying nearly 10 percent of transcripts," the study authors wrote, noting that "[t]hese were mostly male-biased in expression, with enrichment hotspots in the testes and accessory glands."

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.

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