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Retinoic Acid-Regulated Target Genes During Development: Integrative Genomics Analysis

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The Biochemistry of Retinoid Signaling III

Part of the book series: Subcellular Biochemistry ((SCBI,volume 95))

Abstract

Retinoic acid (RA), a major natural active metabolite of vitamin A (VA) is well known to play critical roles in embryonic development. The effects of RA are mediated by nuclear receptors (RARs), which regulate the expression of gene batteries involved in cell growth and differentiation. Since the early 1990s several laboratories have focused on understanding how RA-regulated genes and RAR binding sites operate by studying the differentiation of embryonal carcinoma cells and embryonic stem cells. The development of hybridization-based microarray technology and high performance software analysis programs has allowed the characterization of thousands of RA-regulated genes. During the two last decades, publication of the genome sequence of various organisms has allowed advances in massive parallel sequencing and bioinformatics analysis of genome-wide data sets. These new generation sequencing (NGS) technologies have revolutionized the field by providing a global integrated picture of RA-regulated gene networks and the regulatory programs involved in cell fate decisions during embryonal carcinoma and embryonic stem cells differentiation. Now the challenge is to reconstruct the RA-regulated gene networks at the single cell level during the development of specialized embryonic tissues.

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Abbreviations

CRABP:

Cellular Retinoic Acid Binding Protein

ChIP:

Chromatin Immunoprecipitation

ChIp-Chip:

ChIP-on-chip

ChIP-seq:

ChIP coupled to massive parallel sequencing

DNA-chip:

DNA microarrays

ECC:

Embryonal carcinoma cell

ESC:

Embryonic Stem Cell

KO:

Knock Out

NGS:

Next Generation Sequencing

PCR:

Polymerase Chain Reaction

RT-PCR:

Reverse Transcriptase PCR

qPCR:

Quantitative PCR

RNA-seq:

RNA sequencing (whole transcriptome sequencing using NGS)

RA:

Retinoic Acid

RAR:

Retinoic Acid Receptor

RARE:

Retinoic Acid Response Element

RXR:

Retinoid X Receptor

TF:

Transcription factor

Transcriptome:

All transcribed RNAs produced in one or a population of cells

VAD:

Vitamin A deficiency

WT:

Wild Type

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  1. Université de Strasbourg, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM, U964, CNRS, UMR7104, 1 rue Laurent Fries, BP 10142, 67404, Illkirch Cedex, France

    Cecile Rochette-Egly

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  1. Cecile Rochette-Egly
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Correspondence to Cecile Rochette-Egly .

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  1. Maine Medical Center Research Institute, Scarborough, ME, USA

    Mary Ann Asson-Batres

  2. Département of Functional Génomics and Cancer, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), Illkirch, France

    Cecile Rochette-Egly

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Rochette-Egly, C. (2020). Retinoic Acid-Regulated Target Genes During Development: Integrative Genomics Analysis. In: Asson-Batres, M., Rochette-Egly, C. (eds) The Biochemistry of Retinoid Signaling III. Subcellular Biochemistry, vol 95. Springer, Cham. https://doi.org/10.1007/978-3-030-42282-0_3

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