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This Week in PNAS: Sep 17, 2013

In the early, online edition of the Proceedings of the National Academy of Sciences, an international team led by investigators at the University of Lausanne describes a whole-genome sequencing-based search for new culprits in retinitis pigmentosa, a progressive degenerative disease that can eventually lead to blindness. By sequencing the genomes of eight North American and eight Japanese individuals with autosomal recessive forms of retinitis pigmentosa and comparing the sequences with those from 69 unaffected individuals, the researchers narrowed in on suspicious mutations in seven genes already implicated in the disease. They also detected a frameshift mutation affecting a new retinitis pigmentosa gene, NEK2, which was linked to retina-related features in follow-up zebrafish experiments.

Researchers from the Massachusetts Institute of Technology and the University of Texas at San Antonio report on a set of developmental genes that appear prepared to spring into action in mouse sperm and egg cells, despite remaining silent. Using RNA sequencing as well as chromatin immunoprecipitation sequencing experiments focused on H3K4me3 and H3K27me3 — chromatin marks that are typically found at the promoters of actively expressed genes and repressed genes, respectively — the team tracked down silent-but-poised developmental genes in both male and female mouse germ cells. "[A]lthough these genes are never expressed in the germ cells themselves," the study's authors say, "they maintain a chromatin state usually associated with the potential for rapid gene activation. We propose that maintenance of this poised state in the germ cells contributes to the generation of totipotency in the fertilized zygote."

A family of transcription factors best known for their role in animal development may have appeared early in evolution, prior to the metazoan split, according to another PNAS study. A Spanish-led team searched available eukaryotic genome and transcriptome data, searching for sequences that resembled T-box transcription factor genes. Indeed, the search uncovered several T-box genes — including a homolog of Brachyury — in fungi and other non-metazoan organisms. Through a series of follow-up experiments, researchers found clues suggesting T-box diversification and target specification evolved in the metazoan lineage in concert with changes to co-factors that interact with the transcription factors.