Structural characterization of the mechanism leading to recognition of Alu elements by the Z-RNA-binding domain of ADAR1

Project: Research project

Project Details

Description

DNA represents the repository of our genetic makeup, but its many copies into RNA constitute the actual blueprint for life. These RNA copies start off as exact DNA transcripts, but they later get altered in precise ways that end up determining the fate of the cell. The swap of a very common RNA building block (adenosine or A) to a less common one (inosine or I). Such editing of cellular RNAs helps a cell distinguish between self and non-self RNAs. If that mechanism is corrupted, the immune system can be compromised, or auto-immune diseases may arise and misediting is also observed in cancerous cells. The biological pathway leading to such modifications is complex because not every A needs to or should be turned into an I. A single protein enzyme called ADAR1 is responsible for selecting the modification site, as well as for catalyzing the chemical reaction that leads to 'editing of A to I'. The catalysis part is understood, but how ADAR1 recognizes a particular site in an RNA molecule remains a mystery. This project is grounded in the hypothesis that a region in ADAR1 is key for recognizing where exactly editing should occur on RNA. That region is known to selectively bind to a rare left-handed form of RNA. This proposal will use advanced NMR methods to monitor the transition from A-form to Z-form RNA, combined with techniques such as isothermal calorimetry and circular dichroism to localize where on natural RNA this part of long ADAR1 binds. The project will then delineate the signature for recognition by ADAR1, through pinpointing the steps leading to a fully assembled complex. This project will in corporate research into course modules and train graduate, undergraduate, and high school students from underrepresented communities.

RNA editing of cellular RNAs helps a cell distinguish between self and non-self RNAs. Editing of adenosines into inosines (A-to-I) is generally catalyzed by the 'adenosine deaminase acting on RNA-1' protein (ADAR1) at primate-specific Alu retrotransposons. A-to-I editing is augmented upon infection, primarily through the interferon-induced longer isoform of ADAR1 that comprises a Z-DNA/Z-RNA binding domain named 'Zα' at its N-terminus. Z-RNA in the form of repeats of cytosine and guanosine (CpG) in a left-handed double-helical conformation has been found in cells, but the prevalence of such structures and their exact role are unknown. In addition, many —if not most— regions proposed to adopt a Z conformation do not resemble regular (CpG)n. How these local Z-RNA conformations are generated within A-form helices, stabilized, and regulated by Zα of ADAR1 (acting in synergy with the downstream Zβ domain), as well as their exact role in the function of these RNAs, remain unknown. This project will test the hypothesis that the binding of Zα to Alu elements plays an essential role during the editing process with the overall goal of achieving structural and dynamic characterization of the formation of A-Z RNA junctions and their recognition by Zα(-Zβ) across transcriptomes. This project is supported by the Molecular Biophysics Cluster of the Division of Molecular and Cellular Biosciences.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

StatusActive
Effective start/end date7/15/226/30/26

Funding

  • National Science Foundation: $1,000,000.00

Fingerprint

Explore the research topics touched on by this project. These labels are generated based on the underlying awards/grants. Together they form a unique fingerprint.