Research Article

In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites

Table 2

Pigmentation gene expression network components organized by reference and component type.

ReferenceTranscription factors Promoter/target geneRegulatory elementsTranscription factor binding sequencesEvolutionary conservationYear

Bentley et al., 1994 [42]USF, MITF, SP1Tyrosinase, 115 bp fragment M-box, CR1, CR2CATGTG, GGTGGA, GTGATAATTurtle, quail, human1994

Besch and Berking, 2014 [43]POU domain TFs, POU3F2 (Brn2)MITF promoterATGCAAAT2014

Fuse et al., 1996 [44]MITFMITF promoter, melanocyte GATA, CRE, TATA-likeCATGTG1996

Gorkin et al., 2012 [45]SOX10, MITF, TEAD1, JUND, FOS, JUN6-mers and 7-mers are more informative in these analyses than k-mers of other lengths2489 putative melanocyte enhancersACA[AGC]AG SOX102012
CAC[AG][TG]G MITF
GGAAT[GT][TC] TEAD1
[AG]TGA[CG]TCA JUND,FOS,JUN

Loftus et al., 2009 [46] MITF, SOX10GpnmbE-box motifCACGTG,
CACATGT,
CACATGA
(variant in other species), TCACATGA
Mouse, rat, dog, cat, horse, platypus, chicken2009

Moro et al., 1999 [47] MITF, AP-1, AP-2, SP-1MC1RE-box, TATA box, AP-1, AP-2, SP-1GCCTGCGG AP-21999
GCCCGGGG AP-2
TGACTCAG AP-1
CAAGTG (E-box)
CAGAGT (E-box)
CACCTG (E-box)
CAGGTG (E-box)
CAGGTG (E-box)
CAGCTG (E-box)

Murisier et al., 2006 [48] SOX10, SP-1Tyrp1 melanocytesE-box, SP-1 sites AACAAA,2006
CANNTG E-box consensus
[AT][AT]CAA[TA] SP-1

Murisier et al., 2007 [49] Tyrosinase, retinal pigmented epitheliumDRE located at −15 kb acts as a strong transcriptional enhancer in melanocytesConserved noncoding sequences (CNS) that might represent putative novel regulatory elements of the Tyr gene2007

Murisier et al., [50] MITF, SOX10, Brn2, Mitf, Otx2, Pax2, Pax3, Pax6, Sox10, Tbx2, USF-1Tyrosinase, core enhancer requires the E-boxes and Sox10 motifsDRE: distal reg. Elem, E-box, M-boxCANNTG E-box2007
AGTCANNTGCT M-box
[AT] [AT]CAA[TA] potential SOX binding

Schwahn et al., 2005 [51] LEF-1MITF, tyrosinase, DCT, TRP-1, PMEL17, Moel for DCT expression in proliferating and senescent normal human melanocytesM-box that includes the MITF CATGTG, which overlaps with (ER-a), USF-1, TFE-3, Isl-1 and AP-1 binding elementsCTTTGGGTCATGTG LEF-1 & M-box 2005
GGTCATGTGCT estrogen RE

Vachtenheim and Borovanský, 2010 [11]MITF, PAX3, LEF-1, SOX10, CREB, POU3F2, USF-1, p53, Tbx2Mc1R, EDNRB, RAB27A, OA1, PMEL17, MLANA, Gpnmb, melanostatin I, Aim1TYR, TRP-1, TRP-2 (DCT),M-box, E-box, MITF binding motifsMITF binding sites: AGTCATGTGCT, ACATGTGA, AATCATGTGCT,
GGTCATGTGCT, GCACATGAGT, GCTCACATGCT, TCACGTGTG,
TCACATGAA, GGCACATGATG, ACAGCTGA, CCATATGA
2010

Vance and Goding, 2004 [52]MITF, SOX10, LEF1, CREB, PAX3MITF promoterM-box (T) CATGTG (A)–268 CATTGTC –262 (SOX10),
-260 TTAATACTACTGGAACT –244 (PAX3),
–228 AATTGGCCTTGATCTGAC –211 (SOX10A/B),
–199 CTTTGAT –193 (LEF1),
–147 TGACGTCA –140 (CREB),
–127 AATTGATATCAACATT –112 (OC)
2004

Wan et al., 2011 [53] MITF, SOX10, PAX3, STAT3, CREB, LEF-1, ITF2, FOXD3, BRN2 (POU3F2)MITF promoter, tyrosinase promoter2011

Watanabe et al., 2002 [54] MITF, SOX10, PAX3 MITF M promoterDistal enhancer[AT][AT]CAA[AT]G SOX102002
CATTGAA SOX10-s1
AACAAA SOX10-s2
TTTTGTT SOX10-s3
AACAAAA SOX10-s4

Relevant information extracted from references is presented in the table. References are ordered alphabetically by the first author.