Abstract

The long-range goal of the proposed studies is to determine the functions of long non-coding RNAs in vertebrate development. The past decade has seen an explosion of genome-wide studies that have identified a plethora of previously unannotated transcripts. Among these novel transcripts, the class of long non-coding RNAs (lncRNAs) has attracted particular attention since they represent an extensive, largely unexplored component of the genome: the dark matter of the genome. The proposed study aims to perform a reverse genetic screen and analyze the function of 100 lncRNAs in zebrafish. Genomics and computational approaches have led to the identification of several hundred lncRNAs expressed during zebrafish development. 100 of these lncRNAs, selected by conservation, genomic location, expression, and chromatin profile, will be disrupted. Antisense oligonucleotides will be used to directly interfere with lncRNAs, and site-specific endonucleases (TALENs and CRISPRs) will be employed to disrupt lncRNA genes. Embryos and larvae will then undergo systematic phenotypic characterization to reveal the functions of lncRNAs. The proposed reverse genetic screen will provide the first comprehensive analysis of vertebrate lncRNA function in vivo and generate the resources for the field to reveal the roles of this mysterious class of molecules.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Type
Research Project (R01)
Project #
5R01HD076708-04
Application #
9257452
Study Section
Special Emphasis Panel (ZRG1-CB-Z (55)R)
Program Officer
Coulombe, James N
Project Start
2014-08-15
Project End
2019-04-30
Budget Start
2017-05-01
Budget End
2018-04-30
Support Year
4
Fiscal Year
2017
Total Cost
$350,675
Indirect Cost
$143,175

  Institution

Name
Harvard University
Department
Microbiology/Immun/Virology
Type
Schools of Arts and Sciences
DUNS #
082359691
City
Cambridge
State
MA
Country
United States
Zip Code
02138

  Publications

Rabani, Michal; Pieper, Lindsey; Chew, Guo-Liang et al. (2018) A Massively Parallel Reporter Assay of 3' UTR Sequences Identifies In Vivo Rules for mRNA Degradation. Mol Cell 70:565
Rabani, Michal; Pieper, Lindsey; Chew, Guo-Liang et al. (2017) A Massively Parallel Reporter Assay of 3' UTR Sequences Identifies In Vivo Rules for mRNA Degradation. Mol Cell 68:1083-1094.e5
Chew, Guo-Liang; Pauli, Andrea; Schier, Alexander F (2016) Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish. Nat Commun 7:11663
Pauli, Andrea; Montague, Tessa G; Lennox, Kim A et al. (2015) Antisense Oligonucleotide-Mediated Transcript Knockdown in Zebrafish. PLoS One 10:e0139504
Pauli, Andrea; Valen, Eivind; Schier, Alexander F (2015) Identifying (non-)coding RNAs and small peptides: challenges and opportunities. Bioessays 37:103-12