High-Throughput Analysis of Retinal Cis-Regulatory Networks by Massively Parallel Reporter Assays

Inez Y. Oh; Shiming Chen

doi:10.1007/978-3-030-27378-1_59

High-Throughput Analysis of Retinal Cis-Regulatory Networks by Massively Parallel Reporter Assays

Inez Y. Oh, Shiming Chen

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

3 Scopus citations

Abstract

Inherited retinal degenerations are diverse and debilitating blinding diseases. Genetic tests and exome sequencing have identified mutations in many protein-coding genes associated with such diseases, but causal sequence variants remain to be found in many retinopathy cases. Since 99% of our genome does not code for protein but contains cis-regulatory elements (CREs) that regulate the expression of essential genes, CRE variants might hold the answer for some of these cases. However, identifying functional CREs within the noncoding genome and predicting the pathogenicity of CRE variants pose a significant challenge. Here, we review the development of massively parallel reporter assays in the mouse retina, its use in dissecting retinal cis-regulatory networks, and its potential application for developing therapies.

Original language	English
Title of host publication	Advances in Experimental Medicine and Biology
Publisher	Springer
Pages	359-364
Number of pages	6
DOIs	https://doi.org/10.1007/978-3-030-27378-1_59
State	Published - 2019

Publication series

Name	Advances in Experimental Medicine and Biology
Volume	1185
ISSN (Print)	0065-2598
ISSN (Electronic)	2214-8019

Keywords

CRE-seq
CRX
Cis-regulatory element
High-throughput functional analysis
Massively parallel reporter assay (MPRA)
NRL
Noncoding DNA
Retina transcription factor
Transcriptional regulation

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10.1007/978-3-030-27378-1_59

Cite this

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title = "High-Throughput Analysis of Retinal Cis-Regulatory Networks by Massively Parallel Reporter Assays",

abstract = "Inherited retinal degenerations are diverse and debilitating blinding diseases. Genetic tests and exome sequencing have identified mutations in many protein-coding genes associated with such diseases, but causal sequence variants remain to be found in many retinopathy cases. Since 99% of our genome does not code for protein but contains cis-regulatory elements (CREs) that regulate the expression of essential genes, CRE variants might hold the answer for some of these cases. However, identifying functional CREs within the noncoding genome and predicting the pathogenicity of CRE variants pose a significant challenge. Here, we review the development of massively parallel reporter assays in the mouse retina, its use in dissecting retinal cis-regulatory networks, and its potential application for developing therapies.",

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AU - Chen, Shiming

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N2 - Inherited retinal degenerations are diverse and debilitating blinding diseases. Genetic tests and exome sequencing have identified mutations in many protein-coding genes associated with such diseases, but causal sequence variants remain to be found in many retinopathy cases. Since 99% of our genome does not code for protein but contains cis-regulatory elements (CREs) that regulate the expression of essential genes, CRE variants might hold the answer for some of these cases. However, identifying functional CREs within the noncoding genome and predicting the pathogenicity of CRE variants pose a significant challenge. Here, we review the development of massively parallel reporter assays in the mouse retina, its use in dissecting retinal cis-regulatory networks, and its potential application for developing therapies.

AB - Inherited retinal degenerations are diverse and debilitating blinding diseases. Genetic tests and exome sequencing have identified mutations in many protein-coding genes associated with such diseases, but causal sequence variants remain to be found in many retinopathy cases. Since 99% of our genome does not code for protein but contains cis-regulatory elements (CREs) that regulate the expression of essential genes, CRE variants might hold the answer for some of these cases. However, identifying functional CREs within the noncoding genome and predicting the pathogenicity of CRE variants pose a significant challenge. Here, we review the development of massively parallel reporter assays in the mouse retina, its use in dissecting retinal cis-regulatory networks, and its potential application for developing therapies.

KW - CRE-seq

KW - CRX

KW - Cis-regulatory element

KW - High-throughput functional analysis

KW - Massively parallel reporter assay (MPRA)

KW - NRL

KW - Noncoding DNA

KW - Retina transcription factor

KW - Transcriptional regulation

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T3 - Advances in Experimental Medicine and Biology

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EP - 364

BT - Advances in Experimental Medicine and Biology

PB - Springer

ER -

High-Throughput Analysis of Retinal Cis-Regulatory Networks by Massively Parallel Reporter Assays

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