Chapter 3
Retinoic Acid-Regulated Target Genes
During Development: Integrative
Genomics Analysis
Cecile Rochette-Egly
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.
Keywords Vitamin A · Retinoic acid · Retinoids · Development · Differentiation ·
Embryonic · Retinoic acid-regulated · Gene networks · Transcriptome · New
generation sequencing · NGS · Embryonal carcinoma cells · Embryonic stem cells
Abbreviations
CRABP
Cellular Retinoic Acid Binding Protein
ChIP
Chromatin Immunoprecipitation
C. Rochette-Egly (B)
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
e-mail: cegly@igbmc.fr
© Springer Nature Switzerland AG 2020
M. A. Asson-Batres and C. Rochette-Egly (eds.), The Biochemistry of Retinoid
Signaling III, Subcellular Biochemistry 95,
https://doi.org/10.1007/978-3-030-42282-0_3
57
Retinoic Acid-Regulated Target Genes
During Development: Integrative
Genomics Analysis
Cecile Rochette-Egly
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.
Keywords Vitamin A · Retinoic acid · Retinoids · Development · Differentiation ·
Embryonic · Retinoic acid-regulated · Gene networks · Transcriptome · New
generation sequencing · NGS · Embryonal carcinoma cells · Embryonic stem cells
Abbreviations
CRABP
Cellular Retinoic Acid Binding Protein
ChIP
Chromatin Immunoprecipitation
C. Rochette-Egly (B)
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
e-mail: cegly@igbmc.fr
© Springer Nature Switzerland AG 2020
M. A. Asson-Batres and C. Rochette-Egly (eds.), The Biochemistry of Retinoid
Signaling III, Subcellular Biochemistry 95,
https://doi.org/10.1007/978-3-030-42282-0_3
57