Structure and Basal Transcription Complex of RNA Polymerase II Core Promoters in the Mammalian Genome: An Overview

Abstract

The mammalian core promoter is a sophisticated and crucial component for the regulation of transcription mediated by the RNA polymerase II. It is generally defined as the minimal region of contiguous DNA sequence that is sufficient to accurately initiate a basal level of gene expression. The core promoter represents the ultimate target for nucleation of a functional pre-initiation complex composed of the RNA polymerase II and associated general transcription factors. Among the more than 40 distinct proteins assembling the basal transcription complex, TFIID plays a central role in recognizing and binding specific core promoter elements to support creating an environment that facilitates transcription initiation. Several common DNA motifs, like the TATA box, initiator region, or the downstream promoter element, are found in a subset of core promoters present in various combinations. Another class of promoters that is usually absent of a TATA box is constituted by the so-called CpG islands, which are associated with the majority of protein-coding genes within the mammalian genome.

Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis

“…In both C. intestinalis and human, most TATA-containing promoters showed a sharp TSS distribution, and almost all broad-type promoters were TATA-less promoters. These results were consistent with the fact that TATA-binding protein is responsible for specifying the exact position of transcription initiation (Baumann et al 2010). However, in spite of the absence of TATA boxes, TATAless promoters did not always show a broad TSS distribution; there were many TATA-less promoters with a sharp TSS distribution.…”

Functional diversity of melanopsins and their global expression in the teleost retina

“…Proximal core transcription elements within 200 bp upstream of the major TSS, such as TATA boxes, were determined (http://zeus2.itb.cnr.it/ *webgene/wwwHC_tata.html) and manually compared with the TATA box consensus sequence (TATAWAWN [37]). Other factors involved in general transcription [38,39] were also determined within the flanking 200 bp upstream of the TSS and the downstream 5 0 -untranslated region (5 0 -UTR): CAAT/CCAAT-box (consensus sequence GGNCAATCT [40]); Downstream Promoter Element (DPE) (consensus sequence RGWCGTG [41]); Motif Ten Element (MTE) (consensus sequence CSARCSSAACG [42]); B Recognition Element (BRE) (consensus sequence SSRCGCC [43]); and GC box (consensus sequence KRGGCGKRRY [44]). Analyses to determine the presence of putative binding sites (cis-elements) for known vertebrate transcription factors [(e.g.…”

Silencing of the Nuclear RPS10 Gene Encoding Mitochondrial Ribosomal Protein Alters Translation in Arabidopsis Mitochondria

“…The role of mitochondrial S10 protein in plants is unknown, but in bacteria its homolog, called as NusE, is a multifunctional protein (Kaczanowska and Rydén-Aulin, 2007). NusE is one of the proteins that complete the ribosomal assembly and is involved in transcriptional antitermination and in tethering the ribosome to the RNA polymerase (Baumann et al, 2010).…”