Fig. 1

CPATs identification, validation and functional investigation strategy

(A) Sequence alignment of promoter regions (200 bp upstream of TSS) of hspa5 and herpud1from human, mouse and zebrafish genomes. Highlighted regions indicate ERSE I in green, Atf6 RE in pink and TATA in red. (B) Strategy for identification of CPATs included an exact match to: (i) the first half of the ERSE I and II consensus sequence required for NFY binding (CCAAT/ATTGG), (ii) the second half of the ERSE I and II shown to have Atf6 binding activity (CCACG) and (iii) the Atf6 RE shown to have Atf6 binding activity (TGACGTG). Sequences pertaining to each criteria was identified in the proximal promoters (acquired from BioMart, designated as −500 bp from the TSS) of orthologous genes in zebrafish, mouse, and human. All genes were converted to the zebrafish ortholog and Venn diagram indicates the zebrafish genes that overlap between each criteria. Cumulative set of genes either having a complete ERSEI/II site (635 genes), the Atf6 RE (15 genes) or both (2) were designated as constitutive putative Atf6 target genes or CPATS (=652 genes). Canonical Atf6 target genes are indicated. (C) CPATs were validated against other in-silico methods of finding transcription factor targets such as public databases (tftargets and Harmonize), ENCODE for tagged ATF6-genome occupancy in human cells and functional datasets in human cells and mouse livers. Finally, CPATs were assessed in different functional contexts known for Atf6 activity in zebrafish and mouse livers generated in our group: stress-independent nAtf6 overexpression; exposure toxicants (EtOH or iAs) and physiological stress during mouse liver regeneration after partial hepatectomy (PH). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)