Eukaryotic genomes are packaged into chromatin, which regulates the function of proteins that mediate transcriptional activity and other essential processes, including recombination and the faithful segregation of the genome during mitosis and meiosis. The goal of this proposal is to identify discrete elements that regulate chromatin structure and function in the nematode C. elegans, a model metazoan of central importance in large-scale genomic research and gene function discovery. We will first use ChlP-chip and related methods to map the genomic distributions of selected histone modifications and chromosome-associated proteins, and then use that information, in combination with data from other modENCODE groups, to build quantitative models of chromatin function. Specifically, we will: 1. Identify and technically validate functional elements that control chromatin and chromosome behavior. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. An efficient pipeline design will facilitate identification and validation of the different classes of functional elements associated with these targets and will integrate the results with the well-annotated C. elegans genome. 2. Biologically validate identified functional elements and build integrated, quantitative models of chromosome function. We will integrate information generated in Aim 1 with existing knowledge on the biology of the targets, perform ChlP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions. Achieving these goals in the context of the ongoing expansion and rich history of C. elegans research will provide an important milestone in meeting the challenge of using genome sequence information to understand and predict biological functions.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project--Cooperative Agreements (U01)
Project #
3U01HG004270-04S1
Application #
8236003
Study Section
Special Emphasis Panel (ZHG1-HGR-P (J1))
Program Officer
Feingold, Elise A
Project Start
2007-05-04
Project End
2013-03-31
Budget Start
2011-04-01
Budget End
2013-03-31
Support Year
4
Fiscal Year
2011
Total Cost
$1,783,660
Indirect Cost
Name
University of North Carolina Chapel Hill
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
608195277
City
Chapel Hill
State
NC
Country
United States
Zip Code
27599
Jeffers, Tess E; Lieb, Jason D (2017) Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans. Genome Res 27:75-86
Garrigues, Jacob M; Sidoli, Simone; Garcia, Benjamin A et al. (2015) Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2. Genome Res 25:76-88
Latorre, Isabel; Chesney, Michael A; Garrigues, Jacob M et al. (2015) The DREAM complex promotes gene body H2A.Z for target repression. Genes Dev 29:495-500
Ho, Joshua W K; Jung, Youngsook L; Liu, Tao et al. (2014) Comparative analysis of metazoan chromatin organization. Nature 512:449-52
Ikegami, Kohta; Lieb, Jason D (2013) Integral nuclear pore proteins bind to Pol III-transcribed genes and are required for Pol III transcript processing in C. elegans. Mol Cell 51:840-9
Berkseth, Matt; Ikegami, Kohta; Arur, Swathi et al. (2013) TRA-1 ChIP-seq reveals regulators of sexual differentiation and multilevel feedback in nematode sex determination. Proc Natl Acad Sci U S A 110:16033-8
Chen, Ron A-J; Down, Thomas A; Stempor, Przemyslaw et al. (2013) The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures. Genome Res 23:1339-47
Gassmann, Reto; Rechtsteiner, Andreas; Yuen, Karen W et al. (2012) An inverse relationship to germline transcription defines centromeric chromatin in C. elegans. Nature 484:534-7
Vielle, Anne; Lang, Jackie; Dong, Yan et al. (2012) H4K20me1 contributes to downregulation of X-linked genes for C. elegans dosage compensation. PLoS Genet 8:e1002933
Chen, Yiwen; Negre, Nicolas; Li, Qunhua et al. (2012) Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods 9:609-14

Showing the most recent 10 out of 25 publications