PUBLICATION

Identification and Characterization of Cis-Regulatory Elements for Photoreceptor-Type-Specific Transcription in ZebraFish

Authors
Fang, W., Wen, Y., Wei, X.
ID
ZDB-PUB-191202-10
Date
2020
Source
Methods in molecular biology (Clifton, N.J.)   2092: 123-145 (Chapter)
Registered Authors
Fang, Wei, Wei, Xiangyun
Keywords
Apical polarity genes, Bioinformatics, CREs, Cis-regulatory elements, Gene expression regulation, Photoreceptor, Retina, Teleost, Transcription factors, Zebrafish, mpp5a, mpp5b, nagie oko, ponli
MeSH Terms
  • Animals
  • Enhancer Elements, Genetic/genetics
  • Promoter Regions, Genetic/genetics
  • Regulatory Elements, Transcriptional/genetics*
  • Regulatory Sequences, Nucleic Acid/genetics
  • Retinal Cone Photoreceptor Cells/physiology*
  • Transcription, Genetic/genetics*
  • Zebrafish/genetics*
  • Zebrafish Proteins/genetics
PubMed
31786786 Full text @ Meth. Mol. Biol.
Citation
Fang, W., Wen, Y., Wei, X. (2020) Identification and Characterization of Cis-Regulatory Elements for Photoreceptor-Type-Specific Transcription in ZebraFish. Methods in molecular biology (Clifton, N.J.). 2092:123-145.
Abstract
Tissue-specific or cell-type-specific transcription of protein-coding genes is controlled by both trans-regulatory elements (TREs) and cis-regulatory elements (CREs). However, it is challenging to identify TREs and CREs, which are unknown for most genes. Here, we describe a protocol for identifying two types of transcription-activating CREs-core promoters and enhancers-of zebrafish photoreceptor type-specific genes. This protocol is composed of three phases: bioinformatic prediction, experimental validation, and characterization of the CREs. To better illustrate the principles and logic of this protocol, we exemplify it with the discovery of the core promoter and enhancer of the mpp5b apical polarity gene (also known as ponli), whose red, green, and blue (RGB) cone-specific transcription requires its enhancer, a member of the rainbow enhancer family. While exemplified with an RGB-cone-specific gene, this protocol is general and can be used to identify the core promoters and enhancers of other protein-coding genes.
Genes / Markers
Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
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