Although frequently predicted to play critical roles in regulatory control, the nature and identity of functional noncoding sequences require comprehensive investigation. The inability to readily impute the functions of noncoding sequences, or the impact of variation therein significantly hampers attempts to investigate potential associations between noncoding variation and disease susceptibility. The purpose of this grant is to systematically examine the regulatory potential of conserved noncoding sequences at a single human disease locus, RET. RET is a critical gene in the genesis and maintenance of multiple organ systems and a major susceptibility locus in multiple human disorders. This proposal has 3 major aims. First, we will use computational, in vitro and molecular analyses to identify S60 conserved noncoding regulatory sequences at RET, and begin to define critical sequences therein. Second, we will determine the biologic relevance of 3 identified regulatory sequences using plasmid-based transgenesis in mice to examine their in vivo regulatory function. Third, we will specifically examine the disease relevance of a single identified regulatory noncoding sequence. We will delete the selected sequence from a wild-type human BAG encompassing RET and compare the ability of wild-type and mutant transgenic mouse strains to complement the Ret null phenotype in mice. This proposal will yield insights into the nature of functional noncoding sequences at RET and in doing so provide a foundation for increasingly comprehensive investigation of putatively functional sequences at this and other disease loci. The central aim of this proposal is to begin to uncover the nature and identity of regulatory sequences through the systematic implementation of functional genetic analyses at the RET locus. ? ? ?

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM071648-02
Application #
7196404
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Anderson, Richard A
Project Start
2006-04-01
Project End
2011-03-31
Budget Start
2007-04-01
Budget End
2008-03-31
Support Year
2
Fiscal Year
2007
Total Cost
$299,976
Indirect Cost
Name
Johns Hopkins University
Department
Genetics
Type
Schools of Medicine
DUNS #
001910777
City
Baltimore
State
MD
Country
United States
Zip Code
21218
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Fufa, Temesgen D; Harris, Melissa L; Watkins-Chow, Dawn E et al. (2015) Genomic analysis reveals distinct mechanisms and functional classes of SOX10-regulated genes in melanocytes. Hum Mol Genet 24:5433-50
Praetorius, Christian; Grill, Christine; Stacey, Simon N et al. (2013) A polymorphism in IRF4 affects human pigmentation through a tyrosinase-dependent MITF/TFAP2A pathway. Cell 155:1022-33
Gorkin, David U; Lee, Dongwon; Reed, Xylena et al. (2012) Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes. Genome Res 22:2290-301
Hodonsky, Chani J; Kleinbrink, Erica L; Charney, Kira N et al. (2012) SOX10 regulates expression of the SH3-domain kinase binding protein 1 (Sh3kbp1) locus in Schwann cells via an alternative promoter. Mol Cell Neurosci 49:85-96
Harden, Maegan V; Pereiro, Luisa; Ramialison, Mirana et al. (2012) Close association of olfactory placode precursors and cranial neural crest cells does not predestine cell mixing. Dev Dyn 241:1143-54
Cox, Jane A; McAdow, Anthony R; Dinitz, Amy E et al. (2011) A zebrafish SKIV2L2-enhancer trap line provides a useful tool for the study of peripheral sensory circuit development. Gene Expr Patterns 11:409-14
Prasad, Megana K; Reed, Xylena; Gorkin, David U et al. (2011) SOX10 directly modulates ERBB3 transcription via an intronic neural crest enhancer. BMC Dev Biol 11:40
Stine, Zachary E; McGaughey, David M; Bessling, Seneca L et al. (2011) Steroid hormone modulation of RET through two estrogen responsive enhancers in breast cancer. Hum Mol Genet 20:3746-56
Antonellis, Anthony; Dennis, Megan Y; Burzynski, Grzegorz et al. (2010) A rare myelin protein zero (MPZ) variant alters enhancer activity in vitro and in vivo. PLoS One 5:e14346

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