R01HG012216

Extensive Multiplexing of Protein Nucleic-Acid Interactions to Comprehensively Study Gene Expression Regulation from Chromatin to mRNA Degradation - Project Summary

Gene expression is tightly controlled at both the RNA and protein level by mechanisms involving chromatin modification, transcriptional regulation, mRNA splicing, processing, translation, and degradation. Each of these processes is regulated by nucleic acid-protein interactions (DNA-protein and RNA-protein). Accordingly, there have been tremendous efforts in the scientific community to comprehensively map these interactions, including major international research efforts (e.g., ENCODE, Roadmap Epigenomics) focused on generating reference maps for specific cell types.

However, because these binding maps are highly specific for individual cell types, there is a critical need to enable the generation of comprehensive genomic maps for any cell type of interest – including primary cell types, disease models, or other rare cell populations – within an individual lab. This goal remains challenging because existing assays can only map interactions of a single protein at a time and are therefore prohibitively expensive.

To address these issues, this proposal will develop a highly innovative technology based on our Split-Pool Barcoding Strategy (SPRITE) that maps multiway protein-nucleic acid interactions using high-throughput sequencing. The proposed HI-P technology will be used to establish:

(I) A highly multiplexed eCLIP-seq method to map up to hundreds of RNA binding proteins simultaneously to their RNA binding sites,
(II) A highly multiplexed ChIP-seq method to map up to hundreds of DNA binding proteins and histone modifications to their DNA binding sites, and
(III) Methods to map these multiple protein-nucleic acid interactions across many samples, among these rare cell types, simultaneously.

The proposed technology represents a major advance – it will dramatically increase the scale of existing methods and create new capabilities that are currently not possible. These tools will empower individual researchers to generate detailed genomic datasets in specific biological and disease contexts that are comparable in size and complexity to those generated by the ENCODE project at a tiny fraction of its cost.

More generally, we anticipate that these tools will lead to critical new insights into gene regulation and human disease.

The Trustees Of Columbia University In The City Of New York

NHGRI SUPPORTS THE DEVELOPMENT OF RESOURCES AND TECHNOLOGIES THAT WILL ACCELERATE GENOME RESEARCH AND ITS APPLICATION TO HUMAN HEALTH AND GENOMIC MEDICINE. A CRITICAL PART OF THE NHGRI MISSION CONTINUES TO BE THE STUDY OF THE ETHICAL, LEGAL AND SOCIAL IMPLICATIONS (ELSI) OF GENOME RESEARCH. NHGRI ALSO SUPPORTS THE TRAINING AND CAREER DEVELOPMENT OF INVESTIGATORS AND THE DISSEMINATION OF GENOME INFORMATION TO THE PUBLIC AND TO HEALTH PROFESSIONALS. THE SMALL BUSINESS INNOVATION RESEARCH (SBIR) PROGRAM IS USED TO INCREASE PRIVATE SECTOR COMMERCIALIZATION OF INNOVATIONS DERIVED FROM FEDERAL RESEARCH AND DEVELOPMENT, TO INCREASE SMALL BUSINESS PARTICIPATION IN FEDERAL RESEARCH AND DEVELOPMENT, AND TO FOSTER AND ENCOURAGE PARTICIPATION OF SOCIALLY AND ECONOMICALLY DISADVANTAGED SMALL BUSINESS CONCERNS AND WOMEN-OWNED SMALL BUSINESS CONCERNS IN TECHNOLOGICAL INNOVATION. THE SMALL BUSINESS TECHNOLOGY TRANSFER (STTR) PROGRAM IS USED TO FOSTER SCIENTIFIC AND TECHNOLOGICAL INNOVATION THROUGH COOPERATIVE RESEARCH AND DEVELOPMENT CARRIED OUT BETWEEN SMALL BUSINESS CONCERNS AND RESEARCH INSTITUTIONS, TO FOSTER TECHNOLOGY TRANSFER BETWEEN SMALL BUSINESS CONCERNS AND RESEARCH INSTITUTIONS, TO INCREASE PRIVATE SECTOR COMMERCIALIZATION OF INNOVATIONS DERIVED FROM FEDERAL RESEARCH AND DEVELOPMENT, AND TO FOSTER AND ENCOURAGE PARTICIPATION OF SOCIALLY AND ECONOMICALLY DISADVANTAGED SMALL BUSINESS CONCERNS AND WOMEN-OWNED SMALL BUSINESS CONCERNS IN TECHNOLOGICAL INNOVATION.

93.172 - Human Genome Research

National Human Genome Research Institute (NHGRI) [HHS - NIH]

New York, New York 100272346 United States

Single Zip Code

NIH Research Project Grant (Parent R01 Clinical Trial Not Allowed) (PA-20-185)

Amendment Since initial award the total obligations have increased 364% from $664,649 to $3,086,952.