Pax6 Interactions with Chromatin and Identification of Its Novel Direct Target Genes in Lens and Forebrain

Qing Xie, Ying Yang, Jie Huang, Jovica Ninkovic, Tessa Walcher, Louise Wolf, Ariel Vitenzon, Deyou Zheng, Magdalena Götz, David C. Beebe, Jiri Zavadil, Ales Cvekl

Research output: Contribution to journalArticle

48 Citations (Scopus)

Abstract

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 α-, β- and δ-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 β-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.

Original languageEnglish (US)
Article numbere54507
JournalPLoS One
Volume8
Issue number1
DOIs
StatePublished - Jan 14 2013

Fingerprint

Prosencephalon
Lens
Lenses
Chromatin
chromatin
Genes
brain
promoter regions
genes
Genetic Promoter Regions
pancreas
Pancreas
RNA
cells
eye lens
Telencephalon
Crystalline Lens
Tissue
Chromatin Immunoprecipitation
cerebral cortex

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Pax6 Interactions with Chromatin and Identification of Its Novel Direct Target Genes in Lens and Forebrain. / Xie, Qing; Yang, Ying; Huang, Jie; Ninkovic, Jovica; Walcher, Tessa; Wolf, Louise; Vitenzon, Ariel; Zheng, Deyou; Götz, Magdalena; Beebe, David C.; Zavadil, Jiri; Cvekl, Ales.

In: PLoS One, Vol. 8, No. 1, e54507, 14.01.2013.

Research output: Contribution to journalArticle

Xie, Q, Yang, Y, Huang, J, Ninkovic, J, Walcher, T, Wolf, L, Vitenzon, A, Zheng, D, Götz, M, Beebe, DC, Zavadil, J & Cvekl, A 2013, 'Pax6 Interactions with Chromatin and Identification of Its Novel Direct Target Genes in Lens and Forebrain', PLoS One, vol. 8, no. 1, e54507. https://doi.org/10.1371/journal.pone.0054507
Xie, Qing ; Yang, Ying ; Huang, Jie ; Ninkovic, Jovica ; Walcher, Tessa ; Wolf, Louise ; Vitenzon, Ariel ; Zheng, Deyou ; Götz, Magdalena ; Beebe, David C. ; Zavadil, Jiri ; Cvekl, Ales. / Pax6 Interactions with Chromatin and Identification of Its Novel Direct Target Genes in Lens and Forebrain. In: PLoS One. 2013 ; Vol. 8, No. 1.
@article{3103af6004fa43ef9abf850340873aa7,
title = "Pax6 Interactions with Chromatin and Identification of Its Novel Direct Target Genes in Lens and Forebrain",
abstract = "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 α-, β- and δ-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 β-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.",
author = "Qing Xie and Ying Yang and Jie Huang and Jovica Ninkovic and Tessa Walcher and Louise Wolf and Ariel Vitenzon and Deyou Zheng and Magdalena G{\"o}tz and Beebe, {David C.} and Jiri Zavadil and Ales Cvekl",
year = "2013",
month = "1",
day = "14",
doi = "10.1371/journal.pone.0054507",
language = "English (US)",
volume = "8",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "1",

}

TY - JOUR

T1 - Pax6 Interactions with Chromatin and Identification of Its Novel Direct Target Genes in Lens and Forebrain

AU - Xie, Qing

AU - Yang, Ying

AU - Huang, Jie

AU - Ninkovic, Jovica

AU - Walcher, Tessa

AU - Wolf, Louise

AU - Vitenzon, Ariel

AU - Zheng, Deyou

AU - Götz, Magdalena

AU - Beebe, David C.

AU - Zavadil, Jiri

AU - Cvekl, Ales

PY - 2013/1/14

Y1 - 2013/1/14

N2 - 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 α-, β- and δ-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 β-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.

AB - 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 α-, β- and δ-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 β-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.

UR - http://www.scopus.com/inward/record.url?scp=84872308179&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84872308179&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0054507

DO - 10.1371/journal.pone.0054507

M3 - Article

VL - 8

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 1

M1 - e54507

ER -