Characterization of SALL2 gene isoforms and its targets across cell types reveals highly conserved networks

ABSTRACT: The SALL2 transcription factor (TF), an evolutionarily conserved gene through vertebrates, is involved in normal development and neuronal differentiation and considered as a tumor suppressor in certain human cancers. Several transcriptional targets of SALL2 are identified, these include the p21CDKN1A and p16INK4A cyclin-dependent kinase inhibitors, and the PMAIP1 and Bax pro-apoptotic genes, among others in various cell types. The human and mouse SALL2 gene loci contain two promoters, each one controlling the expression of a different protein isoform (namely E1 and E1A). However, several improvements on the human genome assembly and gene annotation through next-generation sequencing technologies over time reveal correction and annotation of additional isoforms, obscuring dissection of SALL2 isoform-specific transcriptional targets. We here integrated current data of normal/tumor gene expression databases along with ChIP-seq binding profiles to analyze SALL2 isoforms expression distribution and infer isoform-specific SALL2 targets. We found that the canonical SALL2 isoform (E1) is one of the lowest expressed, while isoform E1A is highly predominant across cell types. To dissect SALL2 isoform-specific targets, we analyzed publicly available ChIP-seq data from glioblastoma multiforme (GBM) and in-house ChIP-seq datasets performed in SALL2 wild-type and isoform E1A knockout HEK293 cells. Another available ChIP-seq data in HEK293 cells (ENCODE Consortium Phase III) overexpressing a non-canonical SALL2 isoform (herein named short_E1A) was analyzed but not included in the final analysis because we demonstrated that short_E1A is mostly localized in the cytoplasm, making impractical to dissect its direct transcriptional targets in this cell model. Regardless of cell type, our analysis reveals a highly conserved network of brain-specific TFs (i.e., SALL3, POU3F2, and NPAS3) and PODXL as a gene that is likely regulated by SALL2 across cell types. Our data integration identified a conserved molecular network in which SALL2 regulates target genes and encourages validation of publicly available ChIP-seq datasets for assessing transcriptional targets of a specific gene/isoform. Financial support: This work was supported by Fondecyt Regular Grants #1151031, #1191172 to Roxana Pincheira Fondecyt Regular Grant #120 to Ariel Castro, Postdoctorate Fondecyt Grant #3160129 and Fondecyt de Iniciacion # 1119028 to Matias I.Hepp.

ORGANISM(S): Homo sapiens

PROVIDER: GSE145940 | GEO | 2020/08/28

REPOSITORIES: GEO