RT Journal Article
SR Electronic
T1 Identification and characterization of cis-regulatory elements for photoreceptor type-specific transcription in zebrafish
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 683284
DO 10.1101/683284
A1 Wei Fang
A1 Yi Wen
A1 Xiangyun Wei
YR 2019
UL http://biorxiv.org/content/early/2019/06/27/683284.abstract
AB 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.