ChIP-seq analysis reveals genes regulated by TFIIE and association of TFIIE with various pathways

Previous studies on transcription factor II E(TFIIE) showed that TFIIE was a general transcription factor and that was involved in the transcription of genes to be transcribed. It is supposed that TFIIE is recruited to promoter sites of genes to be transcribed and plays a role in transcription initiation. The aim of this study was to investigate and identify the disease-specific role of TFIIE rather than its general transcription factor role, and characterize the cellular pathways and genes occupied by TFIIE. In this regards, ChIP-seq analysis was performed. For ChIP-seq data, POLR2A ChIP-seq and eGFP-GTF2E2 ChIP-seq were used on human K562 cell line data obtanined from the ENCODE (Encyclopedia of DNA Elements) Project Consortium database.Six significantly enriched KEGG pathways were identified. These pathways involved splicesomes, alcoholism, ATP-dependent chromatin remodeling, necroptosis, neutrophil extracellular trap formation and systemic lupus erythematosus. Also, sixteen significantly enriched GO terms were identifed, six related to molecular functions, three related to biological processes and seven related to cellular components. The molecular function category contains nucleosomal DNA binding, nucleosome binding, pre-mRNA 5’-splice site binding, pre-mRNA binding, protein heterodimerization activity, and structural constitute of chromatin. The biological process category contains RNA splicing, ribonucleoprotein complex biogenesis, and mRNA 5’-splice site recognition. The cellular component category contains U1-snRNP, nucleosome, spliceosomal snRNP complex, protein-DNA complex, DNA packaging complex, Sm-like protein family complex, and small-nuclear ribonucleoprotein complex. A significant enrichment of 3 motifs was also discovered.The current study revealed TFIIE-associated genes and association of TFIIE with certain groups of cellular pathways.This might shed light on disease specific role of TFIIE and help future studies characterize TFIIE-related human diseases.