Expanding the Encyclopedia of DNA Elements (ENCODE) in the Human and Model Organisms (U54) | Apply Online

Opportunity Summary:

This funding opportunity, RFA HG 11 024, is a National Institutes of Health (NIH) cooperative agreement (U54) focused on expanding the Encyclopedia of DNA Elements (ENCODE) effort in humans and extending parallel resources in well-studied model organisms (often associated with modENCODE). The core idea behind ENCODE and modENCODE is that a genome is more than a list of genes: it contains many types of functional DNA elements that influence when, where, and how genes are used, including regulatory regions such as promoters, enhancers, silencers, insulators, transcription factor binding sites, chromatin states, and other biochemical signatures tied to gene control. Over time, the ENCODE and modENCODE projects built widely used catalogs of these elements, and the research community increasingly relies on them both for basic biology and for interpreting genetic and genomic results related to disease, especially when disease-associated variants fall outside protein-coding regions. This announcement seeks to push those catalogs much closer to completeness by using state-of-the-art, high-throughput, and cost-efficient experimental and computational approaches.

The goal of the program is not simply incremental data generation, but a major expansion of reference resources that the broader community can use. Applicants are expected to propose research projects that can scale, produce high-quality datasets, and add substantial new coverage of functional elements across the human genome and selected model organism genomes. The emphasis on "as complete catalogs as is feasible" signals that projects should be designed with breadth and systematic coverage in mind, rather than small, isolated case studies. At the time this opportunity was released, relevant approaches typically included genome-wide assays that measure chromatin accessibility, protein-DNA interactions, histone modifications, transcription and RNA processing, DNA methylation, and other molecular readouts that help define functional regulatory landscapes across cell types, tissues, developmental stages, or experimental conditions. Although the announcement text provided here does not enumerate specific assays, the intent clearly centers on comprehensive mapping using modern, efficient platforms and strong quality control so the resulting resources are reliable and reusable.

A defining feature of the FOA is that awards will operate as part of a single, coordinated Research Network that consolidates the existing ENCODE and modENCODE research consortia. In practical terms, that means funded groups are expected to collaborate rather than work in isolation, aligning on common standards and shared goals. Because the mechanism is a cooperative agreement, NIH staff typically play an active role beyond normal grant stewardship, which often includes substantial programmatic involvement in coordination, milestone tracking, data release expectations, and cross-site integration. The network structure implies that successful projects should be prepared to adopt consortium-wide experimental standards, metadata requirements, benchmarking and validation practices, and rapid data sharing norms so that datasets generated by different centers can be compared and integrated into unified public resources.

Financially, the FOA listed an estimated total funding amount of $23,000,000. It is categorized under Health and aligns with CFDA 93.172 (Human Genome Research). There is no cost sharing or matching requirement stated. The funding instrument is discretionary, and the mechanism (U54) typically supports large, multi-component efforts that can include coordinated research cores, production pipelines, analysis teams, and consortium participation activities, reflecting the scale and infrastructure needed for high-throughput functional genomics.

Eligibility is broad and includes many types of organizations, spanning public and private institutions of higher education, public and state-controlled universities, nonprofit organizations (with or without 501(c)(3) status), for-profit organizations (other than small businesses), small businesses, and multiple levels of government (state, county, city/township, special district governments), as well as tribal governments and tribal organizations. The eligibility section also explicitly includes institutions serving specific communities and regions, such as Alaska Native and Native Hawaiian Serving Institutions, Hispanic Serving Institutions, Historically Black Colleges and Universities (HBCUs), Tribally Controlled Colleges and Universities (TCCUs), faith-based or community-based organizations, regional organizations, and U.S. territories or possessions, along with eligible federal agencies. This wide eligibility reflects the consortium nature of ENCODE-style work, where different kinds of organizations may contribute specialized expertise, platforms, or resources.

Timing details indicate the opportunity was posted October 4, 2011, created November 16, 2011, with an original closing date of December 6, 2011, later extended to December 21, 2011, and archived January 21, 2012. While these dates show the FOA is historical, the program description captures a major phase of ENCODE/modENCODE expansion aimed at producing broadly accessible, standardized functional genomics reference maps that help the scientific community interpret genome function and connect noncoding variation to biological mechanisms and disease. For full official requirements, consortium expectations, and application instructions, the FOA pointed applicants to the NIH grants page listed in the additional information link.

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Next opportunity: Data Analysis and Coordination Center for the Encyclopedia of DNA Elements (ENCODE) (U41)

Previous opportunity: Governors Institute for Community Design, Request for Proposals (RFP)

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