This application describes a project that aims to answer the question, do some parts of the human genome function by virtue of their structure, and not directly by their nucleotide sequence? To address this question a structural map of the 30 Mb of the ENCODE regions of human genomic DNA, at single-nucleotide resolution, has been produced, based on hydroxyl radical cleavage patterns of DNA. A freely available database, ORChID (OH Radical Cleavage Intensity Database), was constructed to house hydroxyl radical cleavage data. An algorithm was developed to predict the hydroxyl radical cleavage pattern of any DNA sequence to high accuracy. This algorithm was applied to the ENCODE regions of the human genome, and the resulting data were deposited in the UCSC genome browser. This dataset of DNA structural data can be searched for structural patterns in genomic DNA that may be associated with biological function. The first objective of this project is to develop high-throughput methods for collecting hydroxyl radical cleavage data, to enhance the predictive power of the ORChID database. The second objective is to locate structural features in human genomic DNA that are under selective evolutionary pressure, but for which the exact nucleotide sequence is not under selection. Experimental data production and informatics pipelines, data verification and validation protocols, and plans for data deposition are detailed in the application.

Public Health Relevance

The aim of this research is to understand how the local shape and structure of DNA, and not just the sequence of nucleotides, contribute to the storage and readout of the information that is contained in the human genome. This work will lead to a deeper understanding of how the human genome works, a necessary step in the next phase of genome-based medicine.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
2R01HG003541-04A1
Application #
7462575
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Good, Peter J
Project Start
2004-09-29
Project End
2011-06-30
Budget Start
2009-09-22
Budget End
2010-06-30
Support Year
4
Fiscal Year
2009
Total Cost
$500,000
Indirect Cost
Name
Boston University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
049435266
City
Boston
State
MA
Country
United States
Zip Code
02215
ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74
Bishop, Eric P; Rohs, Remo; Parker, Stephen C J et al. (2011) A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. ACS Chem Biol 6:1314-20
Parker, Stephen C J; Tullius, Thomas D (2011) DNA shape, genetic codes, and evolution. Curr Opin Struct Biol 21:342-7
Parker, Stephen C J; Harlap, Aaron; Tullius, Thomas D (2011) A computational method to search for DNA structural motifs in functional genomic elements. Methods Mol Biol 759:367-79
Parker, Stephen C J; Hansen, Loren; Abaan, Hatice Ozel et al. (2009) Local DNA topography correlates with functional noncoding regions of the human genome. Science 324:389-92
Parker, Stephen C J; Margulies, Elliott H; Tullius, Thomas D (2008) The relationship between fine scale DNA structure, GC content, and functional elements in 1% of the human genome. Genome Inform 20:199-211
(2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816
Greenbaum, Jason A; Parker, Stephen C J; Tullius, Thomas D (2007) Detection of DNA structural motifs in functional genomic elements. Genome Res 17:940-6
Greenbaum, Jason A; Pang, Bo; Tullius, Thomas D (2007) Construction of a genome-scale structural map at single-nucleotide resolution. Genome Res 17:947-53