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Genome Technology s Peer Review: A Weekly Forum of Recently Published Journal Articles: Feb 8, 2005

Following is a description of a recently published research paper recommended by a scientist involved in integrated biology. The recommender, Dick McCombie, is at Cold Spring Harbor Laboratory. This installment was reported and written by Meredith Salisbury, Genome Technology editor.

 

For a complete list of recommended papers, read  Genome Technology, a GenomeWeb News sister publication.


"Transcriptional regulatory code of a eukaryotic genome," Christopher Harbison, Benjamin Gordon, Tong Ihn Lee, Nicola Rinaldi, Kenzie MacIsaac, Timothy Danford, Nancy Hannett, Jean-Bosco Tagne, David Reynolds, Jane Yoo, Ezra Jennings, Julia Zeitlinger, Dmitry Pokholok, Manolis Kellis, Alex Rolfe, Ken Takusagawa, Eric Lander, David Gifford, Ernest Fraenkel, and Richard Young. Nature. 2004; 431 (02 Sept): 99-104.

 

The authors report having used the sequence elements bound by regulators in certain circumstances and conserved among yeast strains to construct a map of the transcriptional regulatory code of yeast. They note that comparative genomics has been used to find potential cis-regulatory sequences in the yeast genome based on phylogenetic conservation, but that such studies remain inconclusive as to whether and when transcriptional regulators occupy the discovered binding sites. The paper includes discussion of "the organization of regulatory elements in promoters and the environment-dependent use of these elements by regulators," according to the abstract. Authors add that "environment-specific use of regulatory elements predicts mechanistic models for the function of a large population of yeast's transcriptional regulators."

 

Dick McCombie recommends this paper for being one of the first real looks at genome-wide regulation of transcription and transcription-factor binding in a eukaryotic organism.

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.