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Funding Update: Dec 15, 2009

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Sequencing-Related NSF Grants Awarded Oct. 27 — Dec. 14, 2009

2010 Project: Arabidopsis 2010: Transcriptomes for Functional and Evolutionary Studies

Start Date: Dec. 1, 2009
Expires: Nov. 30, 2011
Awarded Amount to Date: $608,755
Principal Investigator: Richard Clark
Sponsor: University of Utah

In this project, the investigators will generate a resource to address the fundamental question of how differences in DNA sequences among individuals lead to the production of different RNA molecules. To do this, the investigators will exploit newly developed technologies, including second-generation DNA sequencing methods, to characterize in a highly cost-effective manner the majority of RNA molecules from 19 diverse strains of the model plant Arabidopsis thaliana, for which sequenced genomes are available.

According to the investigators, this project will increase understanding of how genetic variation affects RNA levels, and hence how DNA differences lead to trait differences. Specifically, the resource will allow investigators to understand the regulation of genes relevant to a multitude of traits of critical importance for agriculture. The sequence data that will be generated by the project will be deposited in GenBank.


Arabidopsis 2010: High-resolution Mapping of Regulatory DNA

Start Date: Dec. 1, 2009
Expires: Nov. 30, 2010
Awarded Amount to Date: $635,303
Principal Investigator: John Stamatoyannopoulos
Sponsor: University of Washington

At the DNA level, gene regulatory signals are encoded by regulatory elements that comprise clustered recognition sites for DNA binding proteins. However, the location and function of the vast majority of Arabidopsis regulatory sequences is currently obscure. In this project, novel high-throughput epigenomic technologies — digital DNaseI mapping and digital genomic footprinting — will be applied to map and characterize regulatory DNA across the A. thaliana genome at nucleotide resolution. Because gene regulatory programs vary widely both between different cell types and within a cell type during differentiation, the project will encompass multiple developmental stages and tissues of a reference strain. As sessile organisms, plants integrate many cues into appropriate developmental and stress responses, most of which rely on major re-programming gene regulatory responses. Regulatory DNA involved in such responses will therefore be mapped through study of standard stress conditions. At the population level, most phenotypic variation is likely to derive from non-coding genetic variation. By systematically extending maps of regulatory DNA across both diverse A. thaliana accessions and related species, the project will expose relationships between genotypic variation and gene regulatory programs on a genome-wide scale. The resulting data will provide insight into endogenous and environmentally-responsive plant regulatory programs, and will accelerate the identification of functional non-coding variation underlying relevant phenotypic variation, according to the grantees.

The Scan

For Better Odds

Bloomberg reports that a child has been born following polygenic risk score screening as an embryo.

Booster Decision Expected

The New York Times reports the US Food and Drug Administration is expected to authorize a booster dose of the Pfizer-BioNTech SARS-CoV-2 vaccine this week for individuals over 65 or at high risk.

Snipping HIV Out

The Philadelphia Inquirer reports Temple University researchers are to test a gene-editing approach for treating HIV.

PLOS Papers on Cancer Risk Scores, Typhoid Fever in Colombia, Streptococcus Protection

In PLOS this week: application of cancer polygenic risk scores across ancestries, genetic diversity of typhoid fever-causing Salmonella, and more.