Single-cell Profiling of Regulatory Element and Gene Activity in Relationship to Genome Function (UM1 Clinical Trial Not Allowed) | RFA HG 20 045

Frequently Asked Questions (FAQs)

What is the purpose of NIH RFA HG 20 045?

This funding opportunity supports the creation of specialized "Mapping Centers" to produce detailed single-cell, multi-omics maps of genome activity in human and mouse. The goal is to identify which genes and regulatory DNA elements are active in specific cell types and states, rather than relying on averaged "bulk tissue" signals.

What are "Mapping Centers" expected to produce?

Mapping Centers are expected to generate high-resolution, single-cell, multi-omics maps that show genome activity, including which genes are expressed and which regulatory DNA elements (such as enhancers and promoters) are active, across human and mouse genomes.

Why does the FOA emphasize single-cell approaches instead of bulk tissue measurements?

Bulk tissue measurements average signals across many cells, which can mask important differences between cell types and cell states. Single-cell approaches enable researchers to connect patterns of gene expression and regulatory element usage to specific cell identities, developmental stages, and cell fate decisions.

What does "multi-omics" mean in the context of this opportunity?

In this FOA, "multi-omics" refers to integrated measurements that may combine gene expression readouts with chromatin or other regulatory readouts. This supports linking regulatory element activity (for example, active enhancers or promoters) to transcriptional outputs in the same cells or closely matched cellular populations.

What types of genomic features are specifically highlighted as "active" parts of the genome?

The FOA highlights enhancers, promoters, and other regulatory elements as examples of active genome components that Mapping Centers should map and link to the genes they control.

What is meant by capturing "biochemical signatures of active genomic regions"?

The FOA emphasizes using high-throughput, state-of-the-art methods that capture biochemical signatures indicating which genomic regions are active, while preserving key contextual information about the cells being measured.

What kinds of "context" should Mapping Centers preserve in their data?

The FOA emphasizes preserving biological context (such as cell identity or lineage). When possible, it also encourages preserving spatial context, meaning information about where a cell is located within a tissue.

Why are both human and mouse included?

By generating maps in both species, the program supports cross-species comparisons to distinguish conserved regulatory mechanisms from species-specific ones. This can help interpret mouse models of human biology and disease.

How does this program aim to deepen understanding of genome function?

The program aims to link active regulatory DNA elements to the genes they control and to the cellular programs they influence. This helps explain how gene regulation drives cell type- and state-specific functions and how genome regulation relates to development and cell fate decisions.

What type of award mechanism is used for this opportunity?

Awards are issued as a Cooperative Agreement (UM1), which indicates substantial NIH involvement in coordinating and shaping the overall effort.

What does it mean that this is a Cooperative Agreement (UM1)?

It means NIH is expected to be substantially involved in the project beyond providing funding, including coordination and involvement consistent with a consortium-based program.

What consortium will funded Mapping Centers join?

Funded Mapping Centers will become part of the Impact of Genomic Variation on Function (IGVF) Consortium.

What is the IGVF Consortium focus, as described in the listing?

The IGVF Consortium is described as a collaborative program focused on accelerating understanding of how genetic variation influences genome function and, ultimately, human health and disease.

What collaboration and coordination expectations are described for Mapping Centers?

Centers are expected to work closely with each other and with other IGVF components to align experimental strategies, coordinate data generation and analysis plans, and support interoperable and comparable datasets.

Why does the FOA stress standards and interoperability across sites?

The FOA indicates the value of these maps increases when centers use compatible standards and when data can be integrated across sites, enabling a more comprehensive view of regulatory activity and gene control across many cell types and conditions.

Is this opportunity open to clinical trials?

No. The opportunity is explicitly listed as "Clinical Trial Not Allowed," which indicates applications should focus on functional genomics and mapping work rather than interventional clinical studies.

What is the NIH health activity area / CFDA number listed for this opportunity?

The opportunity is classified under CFDA 93.172.

Who is the sponsor of this funding opportunity?

The sponsor listed is the National Institutes of Health (NIH).

When was this funding opportunity originally posted?

The source listing indicates it was created on August 3, 2020.

What is the original closing date shown in the listing?

The original closing date shown is November 4, 2020.

What types of organizations are eligible to apply?

Eligible applicants are broad and include many types of U.S. organizations and governments, including state, county, city/township governments, and special districts; public and private institutions of higher education; independent school districts; tribal governments and organizations (including federally recognized tribes and other tribal organizations); public housing authorities/Indian housing authorities; nonprofits (with or without 501(c)(3) status); for-profit organizations (including small businesses and other for-profits); and other entities.

Are institutions like HBCUs, HSIs, and Tribal Colleges specifically encouraged or included?

Yes. The FOA highlights additional eligible groups such as Historically Black Colleges and Universities (HBCUs), Hispanic-serving institutions (HSIs), Tribally Controlled Colleges and Universities, Alaska Native and Native Hawaiian Serving Institutions, and Asian American Native American Pacific Islander Serving Institutions.

Are faith-based or community-based organizations included in eligible applicants?

Yes. The FOA explicitly lists faith-based or community-based organizations among eligible groups.

Can non-U.S. (foreign) organizations apply?

Yes. The FOA includes non-U.S. (foreign) organizations among eligible groups.

Are U.S. territories or possessions included in eligibility?

Yes. The FOA includes U.S. territories or possessions among eligible groups.

Does the listing provide an award ceiling or the expected number of awards?

No. The source listing does not specify an award ceiling or the expected number of awards.

What does the listing imply about the scale and responsibilities of funded projects?

While specific funding amounts and award counts are not provided, the consortium-based structure and "Mapping Center" model imply center-scale efforts. Responsibilities are described as extending beyond local data production to include active consortium participation, shared approaches, and coordinated dissemination of data and analyses.

What is the overarching scientific theme of the Mapping Center work described?

The overarching theme is to connect regulatory DNA activity and gene expression to cell type- and state-specific programs, and to support understanding of genome function and the effects of genomic variation by generating coordinated, comparable datasets across the consortium.