3 Retinoic Acid-Regulated Target Genes During Development …
83
Jin W, Tang Q, Wan M, Cui K, Zhang Y, Ren G, Ni B, Sklar J, Przytycka TM, Childs R, Levens D,
Zhao K (2015) Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE
tissue samples. Nature 528:142–146
Jones-Villeneuve EM, McBurney MW, Rogers KA, Kalnins VI (1982) Retinoic acid induces
embryonal carcinoma cells to differentiate into neurons and glial cells. J Cell Biol 94:253–262
Jonk LJ, de Jonge ME, Vervaart JM, Wissink S, Kruijer W (1994) Isolation and developmental
expression of retinoic-acid-induced genes. Dev Biol 161:604–614
Kashyap V, Laursen KB, Brenet F, Viale AJ, Scandura JM, Gudas LJ (2013) RARgamma is essential
for retinoic acid induced chromatin remodeling and transcriptional activation in embryonic stem
cells. J Cell Sci 126:999–1008
Kelly DL, Rizzino A (2000) DNA microarray analyses of genes regulated during the differentiation
of embryonic stem cells. Mol Reprod Dev 56:113–123
Lalevee S, Anno YN, Chatagnon A, Samarut E, Poch O, Laudet V, Benoit G, Lecompte O, RochetteEgly C (2011) Genome-wide in silico identification of new conserved and functional retinoic acid
receptor response elements (direct repeats separated by 5 bp). J Biol Chem 286:33322–33334
LaRosa GJ, Gudas LJ (1988) Early retinoic acid-induced F9 teratocarcinoma stem cell gene ERA1: alternate splicing creates transcripts for a homeobox-containing protein and one lacking the
homeobox. Mol Cell Biol 8:3906–3917
Linney E, Dobbs-McAuliffe B, Sajadi H, Malek RL (2004) Microarray gene expression profiling
during the segmentation phase of zebrafish development. Comp Biochem Physiol C Toxicol
Pharmacol 138:351–362
Lo J, Lee S, Xu M, Liu F, Ruan H, Eun A, He Y, Ma W, Wang W, Wen Z, Peng J (2003) 15000
unique zebrafish EST clusters and their future use in microarray for profiling gene expression
patterns during embryogenesis. Genome Res 13:455–466
Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C,
Kobayashi M, Horton H, Brown EL (1996) Expression monitoring by hybridization to highdensity oligonucleotide arrays. Nat Biotechnol 14:1675–1680
Maden M (1982) Vitamin A and pattern formation in the regenerating limb. Nature 295:672–675
Mahony S, Mazzoni EO, McCuine S, Young RA, Wichterle H, Gifford DK (2011) Ligand-dependent
dynamics of retinoic acid receptor binding during early neurogenesis. Genome Biol 12:R2
Mendoza-Parra MA, Malysheva V, Mohamed Saleem MA, Lieb M, Godel A, Gronemeyer H (2016)
Reconstructed cell fate-regulatory programs in stem cells reveal hierarchies and key factors of
neurogenesis. Genome Res 26:1505–1519
Mendoza-Parra MA, Walia M, Sankar M, Gronemeyer H (2011) Dissecting the retinoid-induced
differentiation of F9 embryonal stem cells by integrative genomics. Mol Syst Biol 7:538
Morris SA, Cahan P, Li H, Zhao AM, San Roman AK, Shivdasani RA, Collins JJ, Daley GQ
(2014) Dissecting engineered cell types and enhancing cell fate conversion via Cell Net. Cell
158:889–902
Moutier E, Ye T, Choukrallah MA, Urban S, Osz J, Chatagnon A, Delacroix L, Langer D, Rochel
N, Moras D, Benoit G, Davidson I (2012) Retinoic acid receptors recognize the mouse genome
through binding elements with diverse spacing and topology. J Biol Chem 287:26328–26341
Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, Laue ED, Tanay A, Fraser P
(2013) Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502:59–
64
Nomura M, Takihara Y, Yasunaga T, Shimada K (1994) One of the retinoic acid-inducible cDNA
clones in mouse embryonal carcinoma F9 cells encodes a novel isoenzyme of fructose 1,6bisphosphatase. FEBS Lett 348:201–205
Oulad-Abdelghani M, Bouillet P, Decimo D, Gansmuller A, Heyberger S, Dolle P, Bronner S, Lutz
Y, Chambon P (1996) Characterization of a premeiotic germ cell-specific cytoplasmic protein
encoded by Stra8, a novel retinoic acid-responsive gene. J Cell Biol 135:469–477
Oulad-Abdelghani M, Chazaud C, Bouillet P, Mattei MG, Dolle P, Chambon P (1998) Stra3/lefty,
a retinoic acid-inducible novel member of the transforming growth factor-beta superfamily. Int J
Dev Biol 42:23–32
83
Jin W, Tang Q, Wan M, Cui K, Zhang Y, Ren G, Ni B, Sklar J, Przytycka TM, Childs R, Levens D,
Zhao K (2015) Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE
tissue samples. Nature 528:142–146
Jones-Villeneuve EM, McBurney MW, Rogers KA, Kalnins VI (1982) Retinoic acid induces
embryonal carcinoma cells to differentiate into neurons and glial cells. J Cell Biol 94:253–262
Jonk LJ, de Jonge ME, Vervaart JM, Wissink S, Kruijer W (1994) Isolation and developmental
expression of retinoic-acid-induced genes. Dev Biol 161:604–614
Kashyap V, Laursen KB, Brenet F, Viale AJ, Scandura JM, Gudas LJ (2013) RARgamma is essential
for retinoic acid induced chromatin remodeling and transcriptional activation in embryonic stem
cells. J Cell Sci 126:999–1008
Kelly DL, Rizzino A (2000) DNA microarray analyses of genes regulated during the differentiation
of embryonic stem cells. Mol Reprod Dev 56:113–123
Lalevee S, Anno YN, Chatagnon A, Samarut E, Poch O, Laudet V, Benoit G, Lecompte O, RochetteEgly C (2011) Genome-wide in silico identification of new conserved and functional retinoic acid
receptor response elements (direct repeats separated by 5 bp). J Biol Chem 286:33322–33334
LaRosa GJ, Gudas LJ (1988) Early retinoic acid-induced F9 teratocarcinoma stem cell gene ERA1: alternate splicing creates transcripts for a homeobox-containing protein and one lacking the
homeobox. Mol Cell Biol 8:3906–3917
Linney E, Dobbs-McAuliffe B, Sajadi H, Malek RL (2004) Microarray gene expression profiling
during the segmentation phase of zebrafish development. Comp Biochem Physiol C Toxicol
Pharmacol 138:351–362
Lo J, Lee S, Xu M, Liu F, Ruan H, Eun A, He Y, Ma W, Wang W, Wen Z, Peng J (2003) 15000
unique zebrafish EST clusters and their future use in microarray for profiling gene expression
patterns during embryogenesis. Genome Res 13:455–466
Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C,
Kobayashi M, Horton H, Brown EL (1996) Expression monitoring by hybridization to highdensity oligonucleotide arrays. Nat Biotechnol 14:1675–1680
Maden M (1982) Vitamin A and pattern formation in the regenerating limb. Nature 295:672–675
Mahony S, Mazzoni EO, McCuine S, Young RA, Wichterle H, Gifford DK (2011) Ligand-dependent
dynamics of retinoic acid receptor binding during early neurogenesis. Genome Biol 12:R2
Mendoza-Parra MA, Malysheva V, Mohamed Saleem MA, Lieb M, Godel A, Gronemeyer H (2016)
Reconstructed cell fate-regulatory programs in stem cells reveal hierarchies and key factors of
neurogenesis. Genome Res 26:1505–1519
Mendoza-Parra MA, Walia M, Sankar M, Gronemeyer H (2011) Dissecting the retinoid-induced
differentiation of F9 embryonal stem cells by integrative genomics. Mol Syst Biol 7:538
Morris SA, Cahan P, Li H, Zhao AM, San Roman AK, Shivdasani RA, Collins JJ, Daley GQ
(2014) Dissecting engineered cell types and enhancing cell fate conversion via Cell Net. Cell
158:889–902
Moutier E, Ye T, Choukrallah MA, Urban S, Osz J, Chatagnon A, Delacroix L, Langer D, Rochel
N, Moras D, Benoit G, Davidson I (2012) Retinoic acid receptors recognize the mouse genome
through binding elements with diverse spacing and topology. J Biol Chem 287:26328–26341
Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, Laue ED, Tanay A, Fraser P
(2013) Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502:59–
64
Nomura M, Takihara Y, Yasunaga T, Shimada K (1994) One of the retinoic acid-inducible cDNA
clones in mouse embryonal carcinoma F9 cells encodes a novel isoenzyme of fructose 1,6bisphosphatase. FEBS Lett 348:201–205
Oulad-Abdelghani M, Bouillet P, Decimo D, Gansmuller A, Heyberger S, Dolle P, Bronner S, Lutz
Y, Chambon P (1996) Characterization of a premeiotic germ cell-specific cytoplasmic protein
encoded by Stra8, a novel retinoic acid-responsive gene. J Cell Biol 135:469–477
Oulad-Abdelghani M, Chazaud C, Bouillet P, Mattei MG, Dolle P, Chambon P (1998) Stra3/lefty,
a retinoic acid-inducible novel member of the transforming growth factor-beta superfamily. Int J
Dev Biol 42:23–32