Genome-wide characterization of Foxa2 targets reveals upregulation of floor plate genes and repression of ventrolateral genes in midbrain dopaminergic progenitors.
The transcription factors Foxa1 and Foxa2 promote the specification of midbrain dopaminergic (mDA) neurons and the floor plate. Whether their role is direct has remained unclear as they also regulate the expression of Shh, which has similar roles. We characterized the Foxa2 cis-regulatory network by chromatin immunoprecipitation followed by high-throughput sequencing of mDA progenitors. This identified 9160 high-quality Foxa2 binding sites associated with 5409 genes, providing mechanistic insights into Foxa2-mediated positive and negative regulatory events. Foxa2 regulates directly and positively key determinants of mDA neurons, including Lmx1a, Lmx1b, Msx1 and Ferd3l, while negatively inhibiting transcription factors expressed in ventrolateral midbrain such as Helt, Tle4, Otx1, Sox1 and Tal2. Furthermore, Foxa2 negatively regulates extrinsic and intrinsic components of the Shh signaling pathway, possibly by binding to the same enhancer regions of co-regulated genes as Gli1. Foxa2 also regulates the expression of floor plate factors that control axon trajectories around the midline of the embryo, thereby contributing to the axon guidance function of the floor plate. Finally, this study identified multiple Foxa2-regulated enhancers that are active in the floor plate of the midbrain or along the length of the embryo in mouse and chick. This work represents the first comprehensive characterization of Foxa2 targets in mDA progenitors and provides a framework for elaborating gene regulatory networks in a functionally important progenitor population.
Department of Developmental Neurobiology, NIMR, The Ridgeway, London, NW7 1AA,  UK.
Emmanouil
E
Metzakopian
Wei
W
Lin
Mali
M
Salmon-Divon
Heidi
H
Dvinge
Elisabet
E
Andersson
Johan
J
Ericson
Thomas
T
Perlmann
Jeffrey A
JA
Whitsett
Paul
P
Bertone
Siew-Lan
SL
Ang
D000818:Animals; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics / Q000378:metabolism; D002460:Cell Line; D047369:Chromatin Immunoprecipitation; D059290:Dopaminergic Neurons / Q000378:metabolism*; D018274:Electroporation; D005838:Genotype; D051542:Hepatocyte Nuclear Factor 3-beta / Q000235:genetics / Q000378:metabolism*; D007150:Immunohistochemistry; D017403:In Situ Hybridization; D060850:LIM-Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D051957:MSX1 Transcription Factor / Q000235:genetics / Q000378:metabolism; D008636:Mesencephalon / Q000166:cytology*; D051379:Mice; D008817:Mice, Mutant Strains; D008822:Mice, Transgenic; D009363:Neoplasm Proteins / Q000235:genetics / Q000378:metabolism; D009419:Nerve Tissue Proteins / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D012097:Repressor Proteins; D055748:SOXB1 Transcription Factors / Q000235:genetics / Q000378:metabolism; D013234:Stem Cells / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
D051792:Basic Helix-Loop-Helix Proteins; D051542:Hepatocyte Nuclear Factor 3-beta; D060850:LIM-Homeodomain Proteins; D051957:MSX1 Transcription Factor; D009363:Neoplasm Proteins; D009419:Nerve Tissue Proteins; D012097:Repressor Proteins; D055748:SOXB1 Transcription Factors; D014157:Transcription Factors; C499046:Ferd3l protein, mouse; C496503:Foxa2 protein, mouse; C112149:LIM homeobox transcription factor 1 beta; C489692:Lmx1a protein, mouse; C484084:Msx1 protein, mouse; C098693:Sox1 protein, mouse; C490129:Tal2 protein, mouse