Question

Explain why it is ‘logical’ that cis-acting sequences that help enhance gene transcription rates are located upstream of the promotor, while the cis-acting sequences for negative effectors or repressors are typically located downstream, or even within, the promoter region of the gene.

Answer 1

Cis-acting Elements

Cis-acting elements are the DNA sequences which are recognized and bound by the trans-acting elements that regulate transcription. There are two types of cis-acting elements: promoters and regulatory elements. The example of a cis-acting sequence is the operator in the lac operon. DNA sequence bound to the lac repressor and prevents transcription of the adjacent genes on the same DNA molecule. The lac operator is known to act in cis for the regulation of the nearby genes and operator does not code for any protein or RNA. Therefore, cis-regulatory elements are present on the same DNA molecule as the gene they regulate while trans-regulatory elements regulates genes distant from the gene from which they were transcribed. cis-element contains short consensus sequences and there location is not fixed but are present within 200 bp upstream of the transcription start site. A single element is usually sufficient to confer a regulatory response Are located in a promoter or an enhancer regions and the protein are binds to the elements and their presence is also regulated.

Promoters are the short sequences of DNA of about40 base pairs (bp) and are located upstream of a transcription start site. Enhancer are the regulatory DNA sequences which act upon genes on the same DNA molecule and is bound by specific proteins called transcription factors and it enhance the transcription of the gene that are associated with it. Transcription factors bind to the enhancer sequences which are located upstream or downstream from an associated gene resulting in stimulation or enhancement of transcription of the related gene. Enhancer sequences are present thousands of base pairs away from the transcription start site of the gene. Since DNA is folded and coiled in the nucleus therefore the enhancer may be found near the transcription start site in the folded state. Enhancer sequences are present in both forward and reversed sequence orientations and affect gene transcription. Promoters consist of four components: the TATA box, a TFIIB recognition site, an initiator, and the downstream core promoter element. Upstream and downstream are related to the 5' to 3' direction in which RNA transcription takes place. Upstream is toward the 5' end of the RNA molecule while downstream is toward the 3' end and due to the anti-parallel nature of DNA i.e., the 3' end of the template strand is upstream of the gene and the 5' end is downstream. Some genes on the same DNA molecule are transcribed in opposite direction and also the upstream and downstream areas may change depending on which gene is used as the reference gene.