3 Retinoic Acid-Regulated Target Genes During Development …
81
Bakken TE, Hodge RD, Miller JA, Yao Z, Nguyen TN, Aevermann B, Barkan E, Bertagnolli D,
Casper T, Dee N, Garren E, Goldy J, Graybuck LT, Kroll M, Lasken RS, Lathia K, Parry S, Rimorin
C, Scheuermann RH, Schork NJ et al (2018) Single-nucleus and single-cell transcriptomes
compared in matched cortical cell types. PLoS ONE 13:e0209648
Balmer JE, Blomhoff R (2002) Gene expression regulation by retinoic acid. J Lipid Res 43:1773–
1808
Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J (2012) Hi-C: a comprehensive
technique to capture the conformation of genomes. Methods 58:268–276
Benbrook DM, Chambon P, Rochette-Egly C, Asson-Batres MA (2014) History of retinoic acid
receptors. Subcell Biochem 70:1–20
Bibel M, Richter J, Schrenk K, Tucker KL, Staiger V, Korte M, Goetz M, Barde YA (2004)
Differentiation of mouse embryonic stem cells into a defined neuronal lineage. Nat Neurosci
7:1003–1009
Blat Y, Kleckner N (1999) Cohesins bind to preferential sites along yeast chromosome III, with
differential regulation along arms versus the centric region. Cell 98:249–259
Bouillet P, Chazaud C, Oulad-Abdelghani M, Dolle P, Chambon P (1995a) Sequence and expression
pattern of the Stra7 (Gbx-2) homeobox-containing gene induced by retinoic acid in P19 embryonal
carcinoma cells. Dev Dyn 204: 372-82
Bouillet P, Oulad-Abdelghani M, Vicaire S, Garnier JM, Schuhbaur B, Dolle P, Chambon P (1995b)
Efficient cloning of cDNAs of retinoic acid-responsive genes in P19 embryonal carcinoma cells
and characterization of a novel mouse gene, Stra1 (mouse LERK-2/Eplg2). Dev Biol 170: 420-33
Bouillet P, Oulad-Abdelghani M, Ward SJ, Bronner S, Chambon P, Dolle P (1996) A new mouse
member of the Wnt gene family, mWnt-8, is expressed during early embryogenesis and is
ectopically induced by retinoic acid. Mech Dev 58:141–152
Bouillet P, Sapin V, Chazaud C, Messaddeq N, Decimo D, Dolle P, Chambon P (1997) Developmental expression pattern of Stra6, a retinoic acid-responsive gene encoding a new type of membrane
protein. Mech Dev 63:173–186
Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L, Kirschner MW, Klein AM (2018) The
dynamics of gene expression in vertebrate embryogenesis at single-cell resolution. Science 360
Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ (2013) Transposition of native
chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins
and nucleosome position. Nat Methods 10:1213–1218
Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf
WJ (2015) Single-cell chromatin accessibility reveals principles of regulatory variation. Nature
523:486–490
Bumgarner R (2013) Overview of DNA microarrays: types, applications, and their future. Curr
Protoc Mol Biol Chapter 22: Unit 22 1
Buttitta L, Tanaka TS, Chen AE, Ko MS, Fan CM (2003) Microarray analysis of somitogenesis
reveals novel targets of different WNT signaling pathways in the somitic mesoderm. Dev Biol
258:91–104
Chambon P (1996) A decade of molecular biology of retinoic acid receptors. Faseb J 10:940–954
Chatagnon A, Veber P, Morin V, Bedo J, Triqueneaux G, Semon M, Laudet V, d’Alche-Buc F, Benoit
G (2015) RAR/RXR binding dynamics distinguish pluripotency from differentiation associated
cis-regulatory elements. Nucleic Acids Res 43:4833–4854
Chazaud C, Bouillet P, Oulad-Abdelghani M, Dolle P (1996) Restricted expression of a novel retinoic
acid responsive gene during limb bud dorsoventral patterning and endochondral ossification. Dev
Genet 19:66–73
Chen A, Chen D, Chen Y (2018) Advances of DNase-seq for mapping active gene regulatory
elements across the genome in animals. Gene 667:83–94
Chen F, Desai TJ, Qian J, Niederreither K, Lu J, Cardoso WV (2007) Inhibition of Tgf beta signaling
by endogenous retinoic acid is essential for primary lung bud induction. Development 134:2969–
2979
81
Bakken TE, Hodge RD, Miller JA, Yao Z, Nguyen TN, Aevermann B, Barkan E, Bertagnolli D,
Casper T, Dee N, Garren E, Goldy J, Graybuck LT, Kroll M, Lasken RS, Lathia K, Parry S, Rimorin
C, Scheuermann RH, Schork NJ et al (2018) Single-nucleus and single-cell transcriptomes
compared in matched cortical cell types. PLoS ONE 13:e0209648
Balmer JE, Blomhoff R (2002) Gene expression regulation by retinoic acid. J Lipid Res 43:1773–
1808
Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J (2012) Hi-C: a comprehensive
technique to capture the conformation of genomes. Methods 58:268–276
Benbrook DM, Chambon P, Rochette-Egly C, Asson-Batres MA (2014) History of retinoic acid
receptors. Subcell Biochem 70:1–20
Bibel M, Richter J, Schrenk K, Tucker KL, Staiger V, Korte M, Goetz M, Barde YA (2004)
Differentiation of mouse embryonic stem cells into a defined neuronal lineage. Nat Neurosci
7:1003–1009
Blat Y, Kleckner N (1999) Cohesins bind to preferential sites along yeast chromosome III, with
differential regulation along arms versus the centric region. Cell 98:249–259
Bouillet P, Chazaud C, Oulad-Abdelghani M, Dolle P, Chambon P (1995a) Sequence and expression
pattern of the Stra7 (Gbx-2) homeobox-containing gene induced by retinoic acid in P19 embryonal
carcinoma cells. Dev Dyn 204: 372-82
Bouillet P, Oulad-Abdelghani M, Vicaire S, Garnier JM, Schuhbaur B, Dolle P, Chambon P (1995b)
Efficient cloning of cDNAs of retinoic acid-responsive genes in P19 embryonal carcinoma cells
and characterization of a novel mouse gene, Stra1 (mouse LERK-2/Eplg2). Dev Biol 170: 420-33
Bouillet P, Oulad-Abdelghani M, Ward SJ, Bronner S, Chambon P, Dolle P (1996) A new mouse
member of the Wnt gene family, mWnt-8, is expressed during early embryogenesis and is
ectopically induced by retinoic acid. Mech Dev 58:141–152
Bouillet P, Sapin V, Chazaud C, Messaddeq N, Decimo D, Dolle P, Chambon P (1997) Developmental expression pattern of Stra6, a retinoic acid-responsive gene encoding a new type of membrane
protein. Mech Dev 63:173–186
Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L, Kirschner MW, Klein AM (2018) The
dynamics of gene expression in vertebrate embryogenesis at single-cell resolution. Science 360
Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ (2013) Transposition of native
chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins
and nucleosome position. Nat Methods 10:1213–1218
Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf
WJ (2015) Single-cell chromatin accessibility reveals principles of regulatory variation. Nature
523:486–490
Bumgarner R (2013) Overview of DNA microarrays: types, applications, and their future. Curr
Protoc Mol Biol Chapter 22: Unit 22 1
Buttitta L, Tanaka TS, Chen AE, Ko MS, Fan CM (2003) Microarray analysis of somitogenesis
reveals novel targets of different WNT signaling pathways in the somitic mesoderm. Dev Biol
258:91–104
Chambon P (1996) A decade of molecular biology of retinoic acid receptors. Faseb J 10:940–954
Chatagnon A, Veber P, Morin V, Bedo J, Triqueneaux G, Semon M, Laudet V, d’Alche-Buc F, Benoit
G (2015) RAR/RXR binding dynamics distinguish pluripotency from differentiation associated
cis-regulatory elements. Nucleic Acids Res 43:4833–4854
Chazaud C, Bouillet P, Oulad-Abdelghani M, Dolle P (1996) Restricted expression of a novel retinoic
acid responsive gene during limb bud dorsoventral patterning and endochondral ossification. Dev
Genet 19:66–73
Chen A, Chen D, Chen Y (2018) Advances of DNase-seq for mapping active gene regulatory
elements across the genome in animals. Gene 667:83–94
Chen F, Desai TJ, Qian J, Niederreither K, Lu J, Cardoso WV (2007) Inhibition of Tgf beta signaling
by endogenous retinoic acid is essential for primary lung bud induction. Development 134:2969–
2979