Epilepsy is one of the most common neurological disorders. It is a complex and heterogeneous disease which makes it difficult to precisely diagnose and provide effective treatment. A major and underexplored cause of complex disorders such as epilepsy could be mutations in gene regulatory elements. For example, disruption of these elements and subsequently the gene regulatory networks that are involved in brain development can lead to epilepsy subtypes such as infantile spasms (IS). However, the regulatory elements of brain expressed genes involved in IS are unknown. Using chromatin immunoprecipitation followed by deep sequencing (ChIPSeq) with active enhancer chromatin marks (H3K4me, H3K27ac, p300), we will identify potential enhancers in the mouse embryonic day 16.5 (E16.5) developing forebrain. In order to determine which genes physically interact with these potential enhancers, we will carry out chromatin interaction analysis followed by paired-end tag sequencing (ChIA-PET) on E16. 5 mouse forebrains. Candidate enhancers of genes associated with IS will be tested for forebrain enhancer expression using zebrafish and mouse transgenic enhancer assays. IS patients from two different cohorts will be screened for coding and copy number variant (CNV) mutations. Potential forebrain enhancers that are found within IS-associated CNVs will be assayed for their enhancer activity in mice. IS patients without IS-associated CNVs and coding mutations will be screened for mutations in our characterized enhancers. Potential causative enhancer mutations will be functionally assessed for their enhancer expression in mice compared to the wild type allele and for differential binding affinity to transcription factors. Combined, these results will generate a regulatory landscape of the developing mouse forebrain, identify and functionally characterize potential IS-associated gene regulatory elements, screen IS patients for mutations in these elements and provide novel functional noncoding DNA sequences for the genetic diagnosis of epilepsy. In addition, this study will serve as a model for the functional characterization of gene regulatory elements involved in other complex human diseases.

Public Health Relevance

Epilepsy is a complex and heterogeneous disease which makes it difficult to precisely diagnose and provide an effective treatment. A major cause of complex diseases, such as epilepsy, could be due to mutations in gene regulatory elements that instruct genes when, where and at what levels to turn on or off. Here, we will identify and characterize gene regulatory elements that could be associated with epilepsy and screen epilepsy patients for mutations in them, thus improving the genetic diagnosis of epilepsy.

Agency
National Institute of Health (NIH)
Institute
National Institute of Neurological Disorders and Stroke (NINDS)
Type
Research Project (R01)
Project #
3R01NS079231-02S1
Application #
8770385
Study Section
Program Officer
Fureman, Brandy E
Project Start
2012-04-01
Project End
2016-03-31
Budget Start
2013-04-01
Budget End
2014-03-31
Support Year
2
Fiscal Year
2014
Total Cost
$20,594
Indirect Cost
$7,477
Name
University of California San Francisco
Department
Pharmacology
Type
Schools of Pharmacy
DUNS #
094878337
City
San Francisco
State
CA
Country
United States
Zip Code
94143
VanderMeer, Julia E; Lozano, Reymundo; Sun, Miao et al. (2014) A novel ZRS mutation leads to preaxial polydactyly type 2 in a heterozygous form and Werner mesomelic syndrome in a homozygous form. Hum Mutat 35:945-8
Erwin, Genevieve D; Oksenberg, Nir; Truty, Rebecca M et al. (2014) Integrating diverse datasets improves developmental enhancer prediction. PLoS Comput Biol 10:e1003677
Birnbaum, Ramon Y; Patwardhan, Rupali P; Kim, Mee J et al. (2014) Systematic dissection of coding exons at single nucleotide resolution supports an additional role in cell-specific transcriptional regulation. PLoS Genet 10:e1004592
VanderMeer, Julia E; Smith, Robin P; Jones, Stacy L et al. (2014) Genome-wide identification of signaling center enhancers in the developing limb. Development 141:4194-8
Kim, Mee J; Oksenberg, Nir; Hoffmann, Thomas J et al. (2014) Functional characterization of SIM1-associated enhancers. Hum Mol Genet 23:1700-8
Oksenberg, N; Haliburton, G D E; Eckalbar, W L et al. (2014) Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes. Transl Psychiatry 4:e431
Smith, Robin P; Eckalbar, Walter L; Morrissey, Kari M et al. (2014) Genome-wide discovery of drug-dependent human liver regulatory elements. PLoS Genet 10:e1004648
Oksenberg, Nir; Ahituv, Nadav (2013) The role of AUTS2 in neurodevelopment and human evolution. Trends Genet 29:600-8
Smith, Robin P; Taher, Leila; Patwardhan, Rupali P et al. (2013) Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nat Genet 45:1021-8
Zhao, Jingjing; Shi, Hongbo; Ahituv, Nadav (2013) Classification of topological domains based on gene expression and regulation. Genome 56:415-23

Showing the most recent 10 out of 14 publications