PUBLICATION
Genomic selection identifies vertebrate transcription factor Fezf2 binding sites and target genes
- Authors
- Chen, L., Zheng, J., Yang, N., Li, H., and Guo, S.
- ID
- ZDB-PUB-110511-17
- Date
- 2011
- Source
- The Journal of biological chemistry 286(21): 18641-18649 (Journal)
- Registered Authors
- Chen, Lishan, Guo, Su, Yang, Nan
- Keywords
- brain, development, DNA binding protein, transcription target genes, zebrafish
- MeSH Terms
-
- Animals
- DNA/genetics
- DNA/metabolism
- HEK293 Cells
- Humans
- Microcephaly/genetics
- Microcephaly/metabolism
- Mutation
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/metabolism*
- Prosencephalon/embryology*
- Response Elements/physiology*
- SELEX Aptamer Technique
- Transcription Factors/genetics
- Transcription Factors/metabolism*
- Transcription, Genetic
- Zebrafish/embryology*
- Zebrafish/genetics
- Zebrafish Proteins/genetics
- Zebrafish Proteins/metabolism*
- PubMed
- 21471212 Full text @ J. Biol. Chem.
Citation
Chen, L., Zheng, J., Yang, N., Li, H., and Guo, S. (2011) Genomic selection identifies vertebrate transcription factor Fezf2 binding sites and target genes. The Journal of biological chemistry. 286(21):18641-18649.
Abstract
Identification of transcription factor targets is critical to understanding gene regulatory networks. Here we uncover transcription factor binding sites and target genes employing systematic evolution of ligands by exponential enrichment (SELEX). Instead of selecting randomly synthesized DNA oligonucleotides as in most SELEX studies, we utilized zebrafish genomic DNA to isolate fragments bound by Fezf2, an evolutionarily conserved gene critical for vertebrate forebrain development. This is, to our knowledge, the first time that SELEX is applied to a vertebrate genome. Computational analysis of bound genomic fragments predicted a core consensus-binding site, which identified response elements that mediated Fezf2-dependent transcription both in vitro and in vivo. Fezf2-bound fragments were enriched for conserved sequences. Surprisingly, ~20% of these fragments overlapped well-annotated protein-coding exons. Through loss-of-function, gain-of-function and chromatin immunoprecipitation, we further identified and validated eomesa/tbr2 and lhx2b as biologically relevant target genes of Fezf2. Mutations in eomesa/tbr2 cause microcephaly in humans, while lhx2b is a critical regulator of cell fate and axonal targeting in the developing forebrain. These results demonstrate the feasibility of employing genomic SELEX to identify vertebrate transcription factor binding sites and target genes and reveal Fezf2 as a transcription activator and a candidate for evaluation in human microcephaly.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping