Promoting Transcription

Sequences that bind RNA polymerases in combination with transcription factors drive and regulate the production of 1° RNA transcript (Table 1-5). Proteins and transcription factors bind to sequences located 5', or upstream, of the gene to be expressed and are collectively called the promoter region of a gene. Negative numbering denotes the location of these sequences upstream of the first protein-encoding base. The promoter sequence initiates (or promotes) transcription of the downstream gene and harbors conserved sequences that are recognized by the transcription complex of enzymes.

The complexity and organization of the transcription regulatory sequences of genes differ between prokaryotic and eukaryotic cells. Prokaryotes contain a simple gene structure with sequences for polymerase binding occurring at -35 and -10 for each gene. The -10 sequence contains a consensus sequence of TATAAT, while the -35 region consists of TTGACA. Variations of these sequences as well as the sequences located adjacent to the gene determine the strength of the promoter's transcriptional activity. For example, small differences such as having a TATATA sequence rather than the consensus sequence at the -10 position will decrease the promoter's ability to bind to the RNA polymerase and result in decreased production of mRNA for that gene. In bacteria, operons regulate expression of multiple genes with related functions from the same promoter.

Table 1-5. Examples of Nucleic Acid Motifs

Name

Sequence

AP1 binding site

TGASTCAG

AP2 binding site

CCCCAGGC

AP3 binding site

GGGTGGGAAAG

AP4 binding site

YCAGCTGYGG

C/EBP

TGTGGAAAG

CCAAT box

CCAAT

CP1 binding site

YN(6)RRCCAATCA

CP2 binding site

YAGYN(3)RRCCAATC

CREB

TGACGTCA

CTF/NF1 binding sites

GCCAAT

GCN4 target site

ATGASTCAT

Glucocorticoid receptor

GGTACAN(3)TGTTCT

Homeobox protein-binding site

TCAATTAAAT

HSTF

CNNGAANNTTCNNG

INF-stimulated response

RGGAANNGAAACT

Lariat consensus sequence

YNYTRAY

MALT box

GGAKGGA

NF-1

TTGGMN(5)GCCAAT

Octamer sequence

ATTTGCAT

Poly A signal

AATAAA

Splice acceptor

Y(11)NYAGG

Splice donor

MAGGTRAGT

TATA box

TATA

Translational initiation sequence

RNNMTGG

R = A/G;Y = C/T; M = C/A;W =

A/T; N = A/T/C/G.

In eukaryotic genes, various promoter sequences bind multiple proteins, which catalytically modify and activate other bound proteins. Enhancer sequences increase the production of mRNA but are far removed from the gene. One of the pivotal proximally located sequences comprises a TATA box (TATAAA) located at -25 (Figure 1-5). These bases initiate binding of a TATA-binding protein (TBP) within the transcription factor D complex. Following this binding, transcription factors B, H, and E bind to and open the DNA strands downstream from the promoter. Finally, transcription factor F and RNA polymerase II bind to the transcription complex. The close proximity of these proteins to RNA polymerase II permits phosphorylation of the polymerase and initiation of transcription. In eukaryotic cells, variations in the recognition sequences alter the efficiency of transcription. These variations may be base pair changes or base modifications. For example, promoter sequences that are highly methylated do not bind well to the transcription factors or polymerase. As a result, a gene

Promoter region

Initiation codon +

Promoter region

Initiation codon +

CCAAT

TATAAA

ATG

Splice acceptor Splice donor site site

Exon Intron

Termination codon t

Termination codon t

TAA TAG or TGA

Exon Intron

Protein-coding sequence

TAA TAG or TGA

Protein-coding sequence

Protein-coding sequence

Figure 1-5. Gene structure. Gene structure depicting coding and noncoding regions of the eukaryotic gene. (Reprinted from Leonard D. Diagnostic Molecular Pathology, copyright 2003, with permission from Elsevier.)

may appear to be unaltered or intact but may be transcriptionally silent due to methylated bases in the promoter region.

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