Weighted Gene Correlation Network Analysis (WGCNA) of Arabidopsis Somatic Embryogenesis (SE) and Identification of Key Gene Modules to Uncover SE-Associated Hub Genes
Table 3
Functional roles of several important CREs detected in the functionally uncharacterized hub gene promoter sequences retrieved from the PLACE database [46].
Cis-acting regulatory element
Function
ABADESI1
“ACGT” motif; transacting factor: TAF-1; responsive to ABA and desiccation. Expressed in seeds late during embryogenesis. Induced by ABA and osmotic stress in vegetative tissues.
CACGTGMOTIF
“CACGTG motif”; essential for expression of beta-phaseolin gene during embryogenesis
CANBNNAPA
Core of “(CA)n element” in storage protein genes; embryo- and endosperm-specific transcription of napin (storage protein) gene
CARGNCAT
Noncanonical CArG motif (CC-Wx8-GG); A relevant cis-element for the response to AGL15 (AGAMOUS-like 15) in vivo
DPBFCOREDCDC3
DPBF-1 and 2 (Dc3 promoter-binding factor-1 and 2) binding core sequence; Dc3 expression is embryo-specific and induced by ABA
DRE1COREZMRAB17
“DRE1” core found in maize (Z.M.) rab17 gene promoter; “DRE1” was protected, in in vivo footprinting, by a protein in embryos specifically, but in leaves, was protected when was treated with ABA and drought; rab17 is expressed during late embryogenesis and is induced by ABA
DRE2COREZMRAB17
“DRE2”; core sequence in rab17 gene promoter. rab17 is expressed during late embryogenesis and is induced by ABA
EBOXBNNAPA
“E-box” of napA storage-protein gene
PYRIMIDINEBOXOSRAMY1A
Found in the promoter of alpha-amylase (Amy2/32b) gene which is induced in the aleurone layers in response to GA in embryo
RYREPEATVFLEB4
RY repeat motif; quantitative seed expression; binding site of Arabidopsis B3-domain-containing transcription factor FUS3, mediates abscisic acid-induced transcription
SEF1MOTIF
“SEF1 (soybean embryo factor 1)” binding motif; regulates the expression of genes encoding for the beta-conglycinin seed storage proteins
SEF3MOTIFGM
“SEF3 binding site”; regulates the expression of genes encoding for the beta-conglycinin seed storage proteins
SEF4MOTIFGM7S
“SEF4 (soybean embryo factor 4)” binding motif; regulates the expression of genes encoding for the beta-conglycinin seed storage proteins
TATABOX2
“TATA box”; TATA box found in beta-phaseolin promoter which is accurate transcription initiation in the embryo stage
