Official Title: Functional RNA Modifications Environment and Disease (FRAMED) (R01 Clinical Trial Not Allowed)
Purpose of Funding Opportunity
Chemical modifications of protein, DNA and RNA nucleoside moieties play critical roles in regulating gene expression. Emerging evidence suggests RNA modifications have substantive roles in multiple basic biological processes. Epitranscriptomics can be defined as the aggregate suite of functional biochemical modifications to the transcriptome within a cell. Recent studies in yeast, Drosophila, rodent and human models demonstrate that stressors can ?induce RNA modifications, with specific reprogramming of some regulatory RNAs.
The NIEHS seeks to solicit innovative, mechanistic research applications that are focused on how environmental exposures are associated and involved with the functional activities of RNA modifications and pathways that may be modified or misregulated, associated with adverse health outcomes and/or be useful as biomarkers of exposure and/or exposure induced pathologies.
The study of functional chemical RNA modification has identified important emerging roles in cellular regulation and gene expression. However, the impact of environmental exposures on functional RNA modifications has been relatively understudied and may present a new mechanism for enhanced understanding the relationships between exposures and the development of complex human diseases.
The NIEHS will use the R?01 mechanism to support h?y?p?o?t?h?e?s?is? d?r?i?v?e?n? research using approaches that incorporate principles of toxicology with RNA modification biological and/or chemical expertise and utilizes state of the art technologies.
February 8, 2019
April 16, 2019
May 16, 2019 by 5:00 PM local time of applicant organization. All types of non-AIDS applications allowed for this funding opportunity announcement are due on these dates.
Applicants are encouraged to apply early to allow adequate time to make any corrections to errors found in the application during the submission process by the due date.
Funding Opportunity Description
Chemical modifications are central to the field of functional RNA and emerging evidence suggests these modifications have substantive roles in basic biological processes. These processes include: embryonic stem cell differentiation, excitotoxic cell death, development, intergenerational inheritance of acquired traits, regulation of RNA stability, temperature adaptation, meiotic progression, and regulation of RNA-RNA and RNA-protein binding interactions.
A small number of covalent RNA modifications have been studied extensively, and recent evidence suggests that other newly discovered RNA chemical alterations have interesting biological and disease functions in mammals.
Moreover, recent studies have identified thousands of sites in human mRNAs modification, especially for N6-methyladenosine (m6A), suggesting an additional role in the regulation of the mRNA processing and function including alternative splicing and gene expression.
While RNA modification is emerging as an important area of research, the impacts of the environment on chemical modifications of RNA molecules (the epitranscriptome) in the development of adverse human health outcomes are relatively unexplored.
Technology advances in recent years have accelerated the detection of RNA modifications and The RNA Modification Database currently lists approximately 160 RNA modifications identified in prokaryotic and eukaryotic cells. This database also reveals that transfer (tRNAs) and ribosomal RNAs (rRNAs) are heavily modified, and many of these same modifications occur in messenger RNA and non-coding RNAs (including long non-coding and microRNAs).
The function of most of the modifications found in messenger and non-coding RNAs remains a mystery, despite their potential to influence RNA properties and functions, including RNA stability, trafficking, localization, activity (enzymatic, sensing, or regulatory), and interactions with other molecules.
The underlying importance of this emerging area for environmental health science research is rooted in RNA modifications serving as key regulatory components for multiple biological processes such as: differentiation and cell lineage determination/stem cell fate; mRNA stability, translation, splicing, transport; RNA structure; tRNA stress responses; post-transcriptional regulatory functions; and paternal inheritance. There are >60 known RNA post-transcriptional modifications in eukaryotes.
The most prevalent RNA modification in mammals is m6A (N6-methyladenosine), followed by m5C (5-methylcytosine). Recent studies now report m1A (N1-methyladenosine) is emerging as a novel mark. In addition, multiple classes of RNAs (lncRNAs, microRNAs) are proving to be major regulators of cellular functional activities, and dynamic epitranscriptomic processes regulate the actions of these regulatory RNAs. RNA methylation is dynamically controlled; for example, the m6A methyltransferase complex co-transcriptionally adds (writes) methyl marks, while m6A can be removed passively through degradation of modified RNA or via active demethylation by m6A demethylases.
These mechanisms can be rapidly deployed in response to stress challenges and importantly alter downstream protein profiles. RNA post-transcriptional modifications can control basic protein synthesis and thereby regulate a wide range of fundamental cellular processes. RNA regulatory processes are likely targets for environmental challenges and associated with disease development and thus there is an enormous potential for discovery of novel mechanisms as well as identifying new exposure responsive and/or therapeutic targets. RNA modifications may also be potentially valuable as biomarkers or signatures for toxicant exposure and/or disease progression.
Program Scope and Research Objectives
This program is intended to enhance understanding of how environmental exposures impact this layer of cellular regulation and elucidate associations between these external perturbations and adverse health outcomes. This FOA is intended to support research applications that will stimulate discovery of novel RNA modification-mediated mechanisms and biomarkers associated with environmental exposures and mechanistically tease out how/what functions/pathways may be associated with disease outcomes.
Moreover, the FOA encourages toxicologists to embrace this approach in mechanistic studies of exposure-induced disease. Mounting evidence from recent studies in yeast, Drosophila and rodent models demonstrates stressors afford changes in RNA levels via specific types of ribo modifications, with specific epitranscriptomic reprogramming of some regulatory RNAs.
As the number of biological roles associated with RNA modification grows, it is reasonable to consider that minor perturbations to the cellular epitranscriptome could severely compromise/alter gene expression patterns to better accommodate /mitigate the exogenous insults and contribute to global dysfunction associated with an adverse outcome pathway (AOPs).
There is a growing literature that mechanistically implicates stress-induced RNA modifications with stressor associated phenotypes. These stressors include UV radiation , high fat diet (Zhang et al., Nat Cell Biol, 2018), low fat diet as well as a battery of other ROS inducing agents, e.g., H2O2, MMS (Methyl methanesulfonate), NaAsO2 . Intriguingly, these studies implicate the potential for other ROS inducing environmental exposures to be mechanistically implicated in RNA modification-mediated phenotypic outcomes. Currently, very little is known regarding the identity of aberrantly modified RNA transcripts.
The study of RNA damage/alteration patterns directly caused by toxicants such as methylating or oxidizing compounds represents another untapped area of study linking epitranscriptomics research with environmental health and risk-assessment studies. This line of investigation has the potential to reveal novel biomarkers for environmental exposure as well uncover novel mechanisms of RNA stability/integrity that are crucial for organismal homeostasis.
This RFA will support research focusing on functional consequences of toxicant exposures as they relate to the role of RNA modifications. Applications are solicited that propose employment of state of the art technologies including but not limited to: mass spectrometry-based approaches that permit simultaneous identification and quantitation of levels of multiple specific epitranscriptomic marks in purified total RNA as well as specific RNA species (mRNA, tRNA, rRNA, lncRNA, miRNA, and small RNAs).
The FOA also encourages approaches that include established methods for mapping several different epitranscriptomic modifications, including but not limited to chemical pull down methods, single base resolution mapping approaches and RNA specific CRISPR-cas platforms.
Specific research questions that may be addressed include but are not limited to the following:
- What are exposure-associated alterations in readers, writers, and erasers of reversible RNA modifications?
- What are the functional consequences of exposure-associated alterations in readers, writers, and erasers of reversible RNA modifications?
- How are the stability and dynamics of RNA modifications altered by environmental exposures?
- What are the dynamics of the epitranscriptome over the course of exposure-associated disease development?
- Are the ratios of modified vs. unmodified RNAs altered in response to exposure and subsequent disease progression?
- How are signal transduction pathways impacted by perturbed RNA modifications?
- Do environmental exposures change the subcellular localization of modified RNAs?
- How may the specific substrates and target sites for RNA-modifying enzymes be altered by environmental exposures?
- Can modified ncRNAs serve as potential biomarkers of exposure/disease?
- Is there a combinatorial code for RNA modifications? Is the combinatorial code disrupted by exposure? Can changed combinatorial codes serve as signatures or biomarkers of exposure or exposure associated disease.
All model organisms including but not limited to Drosophila, yeast, worms, fish, as well as human cells, cell lines or 3D organ cultures are appropriate for use, however, NIEHS will prioritize support for applications that are relevant to exposure associated human pathologies.
1. Eligible Applicants
Higher Education Institutions
- Public/State Controlled Institutions of Higher Education
- Private Institutions of Higher Education
The following types of Higher Education Institutions are always encouraged to apply for NIH support as Public or Private Institutions of Higher Education:
- Hispanic-serving Institutions
- Historically Black Colleges and Universities (HBCUs)
- Tribally Controlled Colleges and Universities (TCCUs)
- Alaska Native and Native Hawaiian Serving Institutions
- Asian American Native American Pacific Islander Serving Institutions (AANAPISIs)
Nonprofits Other Than Institutions of Higher Education
- Nonprofits with 501(c)(3) IRS Status (Other than Institutions of Higher Education)
- Nonprofits without 501(c)(3) IRS Status (Other than Institutions of Higher Education)
- Small Businesses
- For-Profit Organizations (Other than Small Businesses)
- State Governments
- County Governments
- City or Township Governments
- Special District Governments
- Indian/Native American Tribal Governments (Federally Recognized)
- Indian/Native American Tribal Governments (Other than Federally Recognized)
- Eligible Agencies of the Federal Government
- U.S. Territory or Possession
- Independent School Districts
- Public Housing Authorities/Indian Housing Authorities
- Native American Tribal Organizations (other than Federally recognized tribal governments)
- Faith-based or Community-based Organizations
- Regional Organizations
- Non-domestic (non-U.S.) Entities (Foreign Institutions)