Project title: Form and function of our Janus faced genome The conversion of RNA into DNA via reverse transcription has transformed the human genome: insertion of RNA-derived DNA copies has roughly doubled the mass of our hereditary material. However, integration of reverse transcribed RNAs is an inefficient process, even for the most successful genomic parasites (e.g. retroviruses, retrotransposons, and pseudogenes). The reverse transcribed copies that fail to integrate may be considered microcosms of the Roman god Janus: with one face, they gaze towards the past as an imperfect copy of a previous life (i.e. the RNA they are derived from), and with another face, they look towards the future, capable of directing the fate of their molecular environment. Remarkably, the identity and function of these genomic misfits that lie outside the confines of the traditional landscape of DNA is largely unexplored, but expected to be vast and powerful. We find that endogenous cDNA formation (i.e. reverse transcribed DNA derived from host RNA) is robust and has important biological and disease-modifying function. Blocking reverse transcription prevents endogenous cDNA formation, and interestingly, also blocks an endogenous cDNA-mediated mouse model of blindness. Here, we will extend these observations to systematically analyze the host-derived reverse transcriptome to produce the first draft atlas of the identity and function of endogenous cDNA, in health and disease. We will also experimentally demonstrate the relevance of endogenous cDNA to molecular and metabolic pathways, and provide an alternate explanation of toxicity attributed nucleoside reverse transcriptase inhibitors (e.g. peripheral neuropathy and developmental defects). We expect our work to demonstrate that the collision of host-derived RNA and the bidirectional flow of genetic information produces a powerful regulatory class of hereto underappreciated molecules that control health and disease, and can be harnessed to understand and manipulate basic tenets of cellular biology.

Public Health Relevance

Form and function of our Janus faced genome The Roman god Janus is said to have two faces on either side of his head - one which faces forward, staring into the future and one which faces backwards, gazing towards the past. In much the same way, genetic information within an organism contains not only the blueprints needed to ensure its current and future fitness, but also a distinct form: an imperfect copy of a previous life.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
NIH Director’s Pioneer Award (NDPA) (DP1)
Project #
1DP1GM114862-01
Application #
8754832
Study Section
Special Emphasis Panel (ZRG1-BCMB-N (50))
Program Officer
Gorospe, Rafael
Project Start
2014-09-30
Project End
2019-07-31
Budget Start
2014-09-30
Budget End
2015-07-31
Support Year
1
Fiscal Year
2014
Total Cost
$750,250
Indirect Cost
$250,250
Name
University of Kentucky
Department
Ophthalmology
Type
Schools of Medicine
DUNS #
939017877
City
Lexington
State
KY
Country
United States
Zip Code
40506
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Fowler, Benjamin J; Gelfand, Bradley D; Kim, Younghee et al. (2014) Nucleoside reverse transcriptase inhibitors possess intrinsic anti-inflammatory activity. Science 346:1000-3