84
C. Rochette-Egly
Oulad-Abdelghani M, Chazaud C, Bouillet P, Sapin V, Chambon P, Dolle P (1997) Meis2, a
novel mouse Pbx-related homeobox gene induced by retinoic acid during differentiation of P19
embryonal carcinoma cells. Dev Dyn 210:173–183
Ozsolak F, Milos PM (2011) RNA sequencing: advances, challenges and opportunities. Nat Rev
Genet 12:87–98
Padmarasu S, Himmelbach A, Mascher M, Stein N (2019) In Situ Hi-C for Plants: An Improved
Method to Detect Long-Range Chromatin Interactions. Methods Mol Biol 1933:441–472
Paschaki M, Schneider C, Rhinn M, Thibault-Carpentier C, Dembele D, Niederreither K, Dolle P
(2013) Transcriptomic analysis of murine embryos lacking endogenous retinoic acid signaling.
PLoS ONE 8:e62274
Pickering J, Wali N, Towers M (2017) Transcriptional changes in chick wing bud polarization
induced by retinoic acid. Dev Dyn 246:682–690
Preissl S, Fang R, Huang H, Zhao Y, Raviram R, Gorkin DU, Zhang Y, Sos BC, Afzal V, Dickel DE,
Kuan S, Visel A, Pennacchio LA, Zhang K, Ren B (2018) Single-nucleus analysis of accessible
chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nat
Neurosci 21:432–439
Rochette-Egly C, Germain P (2009) Dynamic and combinatorial control of gene expression by
nuclear retinoic acid receptors (RARs). Nucl Recept Signal 7:e005
Rogers MB, Rosen V, Wozney JM, Gudas LJ (1992) Bone morphogenetic proteins-2 and -4 are
involved in the retinoic acid-induced differentiation of embryonal carcinoma cells. Mol Biol Cell
3:189–196
Ruberte E, Dolle P, Chambon P, Morriss-Kay G (1991) Retinoic acid receptors and cellular retinoid
binding proteins. II. Their differential pattern of transcription during early morphogenesis in
mouse embryos. Development 111:45–60
Ruberte E, Dolle P, Krust A, Zelent A, Morriss-Kay G, Chambon P (1990) Specific spatial and
temporal distribution of retinoic acid receptor gamma transcripts during mouse embryogenesis.
Development 108:213–222
Samarut E, Gaudin C, Hughes S, Gillet B, de Bernard S, Jouve PE, Buffat L, Allot A, Lecompte
O, Berekelya L, Rochette-Egly C, Laudet V (2014) Retinoic acid receptor subtype-specific
transcriptotypes in the early zebrafish embryo. Mol Endocrinol 28:260–272
Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression
patterns with a complementary DNA microarray. Science 270:467–470
Serandour AA, Brown GD, Cohen JD, Carroll JS (2013) Development of an Illumina-based ChIPexonuclease method provides insight into FoxA1-DNA binding properties. Genome Biol 14:R147
Simandi Z, Balint BL, Poliska S, Ruhl R, Nagy L (2010) Activation of retinoic acid receptor
signaling coordinates lineage commitment of spontaneously differentiating mouse embryonic
stem cells in embryoid bodies. FEBS Lett 584:3123–3130
Sinner D, Kirilenko P, Rankin S, Wei E, Howard L, Kofron M, Heasman J, Woodland HR, Zorn AM
(2006) Global analysis of the transcriptional network controlling Xenopus endoderm formation.
Development 133:1955–1966
Skene PJ, Henikoff JG, Henikoff S (2018) Targeted in situ genome-wide profiling with high
efficiency for low cell numbers. Nat Protoc 13:1006–1019
Stocum DL (1991) Limb regeneration: a call to arms (and legs). Cell 67:5–8
Strickland S, Mahdavi V (1978) The induction of differentiation in teratocarcinoma cells by retinoic
acid. Cell 15:393–403
Strickland S, Smith KK, Marotti KR (1980) Hormonal induction of differentiation in teratocarcinoma stem cells: generation of parietal endoderm by retinoic acid and dibutyryl cAMP. Cell
21:347–355
Su D, Gudas LJ (2008) Gene expression profiling elucidates a specific role for RARgamma in
the retinoic acid-induced differentiation of F9 teratocarcinoma stem cells. Biochem Pharmacol
75:1129–1160
Taher L, Collette NM, Murugesh D, Maxwell E, Ovcharenko I, Loots GG (2011) Global gene
expression analysis of murine limb development. PLoS ONE 6:e28358
C. Rochette-Egly
Oulad-Abdelghani M, Chazaud C, Bouillet P, Sapin V, Chambon P, Dolle P (1997) Meis2, a
novel mouse Pbx-related homeobox gene induced by retinoic acid during differentiation of P19
embryonal carcinoma cells. Dev Dyn 210:173–183
Ozsolak F, Milos PM (2011) RNA sequencing: advances, challenges and opportunities. Nat Rev
Genet 12:87–98
Padmarasu S, Himmelbach A, Mascher M, Stein N (2019) In Situ Hi-C for Plants: An Improved
Method to Detect Long-Range Chromatin Interactions. Methods Mol Biol 1933:441–472
Paschaki M, Schneider C, Rhinn M, Thibault-Carpentier C, Dembele D, Niederreither K, Dolle P
(2013) Transcriptomic analysis of murine embryos lacking endogenous retinoic acid signaling.
PLoS ONE 8:e62274
Pickering J, Wali N, Towers M (2017) Transcriptional changes in chick wing bud polarization
induced by retinoic acid. Dev Dyn 246:682–690
Preissl S, Fang R, Huang H, Zhao Y, Raviram R, Gorkin DU, Zhang Y, Sos BC, Afzal V, Dickel DE,
Kuan S, Visel A, Pennacchio LA, Zhang K, Ren B (2018) Single-nucleus analysis of accessible
chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nat
Neurosci 21:432–439
Rochette-Egly C, Germain P (2009) Dynamic and combinatorial control of gene expression by
nuclear retinoic acid receptors (RARs). Nucl Recept Signal 7:e005
Rogers MB, Rosen V, Wozney JM, Gudas LJ (1992) Bone morphogenetic proteins-2 and -4 are
involved in the retinoic acid-induced differentiation of embryonal carcinoma cells. Mol Biol Cell
3:189–196
Ruberte E, Dolle P, Chambon P, Morriss-Kay G (1991) Retinoic acid receptors and cellular retinoid
binding proteins. II. Their differential pattern of transcription during early morphogenesis in
mouse embryos. Development 111:45–60
Ruberte E, Dolle P, Krust A, Zelent A, Morriss-Kay G, Chambon P (1990) Specific spatial and
temporal distribution of retinoic acid receptor gamma transcripts during mouse embryogenesis.
Development 108:213–222
Samarut E, Gaudin C, Hughes S, Gillet B, de Bernard S, Jouve PE, Buffat L, Allot A, Lecompte
O, Berekelya L, Rochette-Egly C, Laudet V (2014) Retinoic acid receptor subtype-specific
transcriptotypes in the early zebrafish embryo. Mol Endocrinol 28:260–272
Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression
patterns with a complementary DNA microarray. Science 270:467–470
Serandour AA, Brown GD, Cohen JD, Carroll JS (2013) Development of an Illumina-based ChIPexonuclease method provides insight into FoxA1-DNA binding properties. Genome Biol 14:R147
Simandi Z, Balint BL, Poliska S, Ruhl R, Nagy L (2010) Activation of retinoic acid receptor
signaling coordinates lineage commitment of spontaneously differentiating mouse embryonic
stem cells in embryoid bodies. FEBS Lett 584:3123–3130
Sinner D, Kirilenko P, Rankin S, Wei E, Howard L, Kofron M, Heasman J, Woodland HR, Zorn AM
(2006) Global analysis of the transcriptional network controlling Xenopus endoderm formation.
Development 133:1955–1966
Skene PJ, Henikoff JG, Henikoff S (2018) Targeted in situ genome-wide profiling with high
efficiency for low cell numbers. Nat Protoc 13:1006–1019
Stocum DL (1991) Limb regeneration: a call to arms (and legs). Cell 67:5–8
Strickland S, Mahdavi V (1978) The induction of differentiation in teratocarcinoma cells by retinoic
acid. Cell 15:393–403
Strickland S, Smith KK, Marotti KR (1980) Hormonal induction of differentiation in teratocarcinoma stem cells: generation of parietal endoderm by retinoic acid and dibutyryl cAMP. Cell
21:347–355
Su D, Gudas LJ (2008) Gene expression profiling elucidates a specific role for RARgamma in
the retinoic acid-induced differentiation of F9 teratocarcinoma stem cells. Biochem Pharmacol
75:1129–1160
Taher L, Collette NM, Murugesh D, Maxwell E, Ovcharenko I, Loots GG (2011) Global gene
expression analysis of murine limb development. PLoS ONE 6:e28358