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Identification, Discovery, and Public Archiving of RNA Structural Motifs

Award Number: R01GM102515
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/01/2012
PERIOD OF PERFORMANCE END DATE: 03/31/2024

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Identification, Discovery, and Public Archiving of RNA Structural Motifs - Project Summary The non-coding RNAs (ncRNAs) play many functional roles in biological processes, such as catalysis, gene expression regulation, and RNA splicing. The various roles played by ncRNAs are determined by their charac- teristic 3D structures. RNA structural motifs are recurrent structural components in ncRNAs. The RNA structural motifs have conserved structures, and therefore, are expected to have similar biological or structural functions. For instance, the kink-turn motif is found in different kinds of ncRNAs and most of them are responsible for protein binding activities. Any alteration of the motif structures has the potential to result in loss-of-function of the RNA structural motif, and in some cases may cause severe diseases. Therefore, the study of RNA structural motif will help us to elucidate the mechanisms of many diseases and lead to the development of novel treatment strategies. Driven by the requirement of biomedical research, many computational methods have been proposed to detect instances of known motifs or to discover novel families. Recently, the rapidly increasing number of resolved RNA 3D structures urges the development of new tools to make use of the huge amount of resources in PDB. In our opinion, the large-scale dataset will support two new approaches for RNA structural motif analysis: generating proﬁles to represent motif families and to search for new instances, and identifying the structural and functional relationship among different motifs. In this proposal, we aim at devising a suite of computational methods based on these two ideas. First, we will build 3D position-speciﬁc scoring matrixes (PSSMs) as proﬁles to represent the base-pairing interactions in the discovered RNA structural motif families and develop proﬁled-based RNA structural motif search tools. Considering the fact that all the existing RNA structural motif searching programs rely on consensus, the introduction of proﬁles will create a great opportunity to improve the search accuracy. In the mean time, the new proﬁle model will provide us a formal method to describe motif families, which is very critical for the understanding of the relationship between RNA 3D structures and their functionalities. Second, we will distinguish the structural features of motif family members to identify subfamilies, and study the potential re- lationship among families to recognize clans and modules. The RNA structural motifs from different families may share similar structural features, and they can also interact with each other to perform certain speciﬁc functions. As far as we know, there is no existing research about the mentioned relationships among RNA structural motifs. Now, the de novo discovery of RNA motif families from the clustering results grants us a solid foundation for further research at both intra- and inter-family levels. With the achievement of these two goals, we also propose to build a new RNA structural motif database to incorporate all the newly discovered knowledge in this project. The tools will also be implemented as user-friendly web servers and integrated with the database to provide a well-rounded service. We expect that the proposed work will lead to better understanding of the RNA structural motifs, and signiﬁcantly promote biomedical research.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2024 ( Subtotal = $0 )
2024	2021	THE UNIVERSITY OF CENTRAL FLORIDA BOARD OF TRUSTEES	4000 CENTRAL FLORIDA BLVD	ORLANDO	FL	32816	ORANGE	USA	Biomedical Research and Research Training	000	7	9/24/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2023 ( Subtotal = $0 )
2023	2021	UNIVERSITY OF CENTRAL FLORIDA BOARD OF TRUSTEES, THE	4000 CENTRAL FLORIDA BLVD	ORLANDO	FL	32816	ORANGE	USA	Biomedical Research and Research Training	000	7	3/9/2023	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2021 ( Subtotal = $173,976 )
2021	2021	UNIVERSITY OF CENTRAL FLORIDA BOARD OF TRUSTEES, THE	4000 CENTRAL FLORIDA BLVD	ORLANDO	FL	32816	ORANGE	USA	Biomedical Research and Research Training	000	7	3/15/2021	NON-COMPETING CONTINUATION	$173,976
														Subtotal = $173,976

Issue Date FY: 2020 ( Subtotal = $174,561 )
2020	2020	UNIVERSITY OF CENTRAL FLORIDA BOARD OF TRUSTEES, THE	4000 CNTRL FLORIDA BLVD	ORLANDO	FL	32816	ORANGE	USA	Biomedical Research and Research Training	000	6	4/1/2020	NON-COMPETING CONTINUATION	$174,561
														Subtotal = $174,561

Issue Date FY: 2019 ( Subtotal = $175,117 )
2019	2019	UNIVERSITY OF CENTRAL FLORIDA BOARD OF TRUSTEES, THE	4000 CNTRL FLORIDA BLVD	ORLANDO	FL	32816	ORANGE	USA	Biomedical Research and Research Training	000	5	3/20/2019	NON-COMPETING CONTINUATION	$175,117
														Subtotal = $175,117

Issue Date FY: 2018 ( Subtotal = $175,647 )
2018	2018	UNIVERSITY OF CENTRAL FLORIDA BOARD OF TRUSTEES, THE	4000 CNTRL FLORIDA BLVD	ORLANDO	FL	32816	ORANGE	USA	Biomedical Research and Research Training	001	4	4/30/2018	COMPETING CONTINUATION	$175,647
2018	2014	UNIVERSITY OF CENTRAL FLORIDA BOARD OF TRUSTEES, THE	4000 CNTRL FLORIDA BLVD	ORLANDO	FL	32816	ORANGE	USA	Biomedical Research and Research Training	000	3	11/27/2017	NON-COMPETING CONTINUATION	$0
														Subtotal = $175,647

Issue Date FY: 2016 ( Subtotal = $0 )
2016	2014	UNIVERSITY OF CENTRAL FLORIDA	12201 RESEARCH PARKWAY	ORLANDO	FL	32826	ORANGE	USA	Biomedical Research and Research Training	000	3	7/22/2016	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2014 ( Subtotal = $168,773 )
2014	2014	UNIVERSITY OF CENTRAL FLORIDA	12201 RESEARCH PARKWAY	ORLANDO	FL	32826	ORANGE	USA	Biomedical Research and Research Training	000	3	8/14/2014	NON-COMPETING CONTINUATION	$168,773
														Subtotal = $168,773

Issue Date FY: 2013 ( Subtotal = $164,019 )
2013	2013	UNIVERSITY OF CENTRAL FLORIDA	12201 RESEARCH PARKWAY	ORLANDO	FL	32826	ORANGE	USA	Biomedical Research and Research Training	000	2	8/20/2013	NON-COMPETING CONTINUATION	$164,019
														Subtotal = $164,019

Issue Date FY: 2012 ( Subtotal = $169,158 )
2012	2012	UNIVERSITY OF CENTRAL FLORIDA	12201 RESEARCH PARKWAY	ORLANDO	FL	32826	ORANGE	USA	Biomedical Research and Research Training	000	1	8/23/2012	NEW	$169,158
														Subtotal = $169,158

Grand Total All Awards = $1,201,251

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Identification, Discovery, and Public Archiving of RNA Structural Motifs

Award Number: R01GM102515

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 09/01/2012

PERIOD OF PERFORMANCE END DATE: 03/31/2024

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