Pax6 Interactions with chromatin and identification of its novel direct target genes in lens and forebrain
| Autor: | Tessa Walcher, Jie Huang, David C. Beebe, Jovica Ninkovic, Jiri Zavadil, Magdalena Götz, Ying Yang, Deyou Zheng, Ales Cvekl, Ariel Vitenzon, Qing Xie, Louise Wolf |
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| Jazyk: | angličtina |
| Rok vydání: | 2013 |
| Předmět: |
PAX6 Transcription Factor
Visual System lcsh:Medicine Gene Expression Biochemistry Mice 0302 clinical medicine Gene expression Molecular Cell Biology Paired Box Transcription Factors lcsh:Science 0303 health sciences Multidisciplinary Genomics Chromatin Sensory Systems Functional Genomics Epigenetics Research Article Protein Binding Chromatin Immunoprecipitation endocrine system Biology Cell fate determination 03 medical and health sciences Prosencephalon DNA-binding proteins Lens Crystalline Genetics Animals Gene Networks Eye Proteins Gene Transcription factor ChIA-PET 030304 developmental biology Homeodomain Proteins lcsh:R Proteins Computational Biology Promoter Molecular Development Molecular biology eye diseases Repressor Proteins lcsh:Q sense organs Genome Expression Analysis Chromatin immunoprecipitation Organism Development 030217 neurology & neurosurgery Developmental Biology Neuroscience |
| Zdroj: | PLoS ONE 8:e54507 (2013) PLoS ONE PLoS ONE, Vol 8, Iss 1, p e54507 (2013) |
| Popis: | Pax6 encodes a specific DNA-binding transcription factor that regulates the development of multiple organs, including the eye, brain and pancreas. Previous studies have shown that Pax6 regulates the entire process of ocular lens development. In the developing forebrain, Pax6 is expressed in ventricular zone precursor cells and in specific populations of neurons; absence of Pax6 results in disrupted cell proliferation and cell fate specification in telencephalon. In the pancreas, Pax6 is essential for the differentiation of alpha-, beta- and delta-islet cells. To elucidate molecular roles of Pax6, chromatin immunoprecipitation experiments combined with high-density oligonucleotide array hybridizations (ChIP-chip) were performed using three distinct sources of chromatin (lens, forebrain and beta-cells). ChIP-chip studies, performed as biological triplicates, identified a total of 5,260 promoters occupied by Pax6. 1,001 (133) of these promoter regions were shared between at least two (three) distinct chromatin sources, respectively. In lens chromatin, 2,335 promoters were bound by Pax6. RNA expression profiling from Pax6(+/-) lenses combined with in vivo Pax6-binding data yielded 76 putative Pax6-direct targets, including the Gaa, Isl1, Kif1b, Mtmr2, Pcsk1n, and Snca genes. RNA and ChIP data were validated for all these genes. In lens cells, reporter assays established Kib1b and Snca as Pax6 activated and repressed genes, respectively. In situ hybridization revealed reduced expression of these genes in E14 cerebral cortex. Moreover, we examined differentially expressed transcripts between E9.5 wild type and Pax6(-/-) lens placodes that suggested Efnb2, Fat4, Has2, Nav1, and Trpm3 as novel Pax6-direct targets. Collectively, the present studies, through the identification of Pax6-direct target genes, provide novel insights into the molecular mechanisms of Pax6 gene control during mouse embryonic development. In addition, the present data demonstrate that Pax6 interacts preferentially with promoter regions in a tissue-specific fashion. Nevertheless, nearly 20% of the regions identified are accessible to Pax6 in multiple tissues. |
| Databáze: | OpenAIRE |
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