Question

how do non protein coding sequences affect gene expression and protein activity

Answer 1

Non-coding DNA

When people refer to coding DNA, they are specifically referring to DNA that encodes proteins. However, much of DNA does not encode proteins. This portion of DNA is what has been commonly called junk DNA, and it is anything but. Part of the non-coding DNA is made (or transcribed) into functional RNA molecules. These RNA molecules are used to make proteins. Some examples include transfer RNA, ribosomal RNA, and translation-controlling RNA.

Another function of non-coding DNA is to regulate gene transcription. These sections of DNA provide binding sites for proteins that can affect transcription. These are called regulatory sites. An important regulatory site common to all genes is a promoter region. This is a section of non-coding DNA where transcriptional proteins can bind. In addition, many genes can have additional regulatory sites. These sites bind proteins that enhance or inhibit transcription. In some cases of highly regulated genes, there can be both types of regulatory sites.

Because these sequences are found in many different organisms and have a high degree of homology (the order of bases in the DNA sequence is very similar). These sequences are also highly conserved. This means that they are found in the DNA generation after generation. The thought is that if they were not present in the DNA then the organism would likely not survive to reproduce.

Protein production can be controlled at several steps. Two of these can be affected by non-coding DNA. As mentioned, some of the noncoding DNA sequences are regulatory sites that bind proteins and thereby control transcription. Others are transcribed into RNA and can control translation. One of these, microRNA, is predicted to control the translational activity of approximately 30% of all protein-coding genes in mammals. microRNA binds to transcripts (the product of transcription) and blocks their translation into proteins.

Only about 1 percent of DNA is made up of protein-coding genes; the other 99 percent is noncoding. Noncoding DNA does not provide instructions for making proteins. Scientists once thought noncoding DNA was “junk,” with no known purpose. However, it is becoming clear that at least some of it is integral to the function of cells, particularly the control of gene activity. For example, noncoding DNA contains sequences that act as regulatory elements, determining when and where genes are turned on and off. Such elements provide sites for specialized proteins (called transcription factors) to attach (bind) and either activate or repress the process by which the information from genes is turned into proteins (transcription). Noncoding DNA contains many types of regulatory elements:

Promoters provide binding sites for the protein machinery that carries out transcription. Promoters are typically found just ahead of the gene on the DNA strand.

Enhancers provide binding sites for proteins that help activate transcription. Enhancers can be found on the DNA strand before or after the gene they control, sometimes far away.

Silencers provide binding sites for proteins that repress transcription. Like enhancers, silencers can be found before or after the gene they control and can be some distance away on the DNA strand.

Insulators provide binding sites for proteins that control transcription in a number of ways. Some prevent enhancers from aiding in transcription (enhancer-blocker insulators). Others prevent structural changes in the DNA that repress gene activity (barrier insulators). Some insulators can function as both an enhancer blocker and a barrier.

Other regions of noncoding DNA provide instructions for the formation of certain kinds of RNA molecules. RNA is a chemical cousin of DNA. Examples of specialized RNA molecules produced from noncoding DNA include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), which help assemble protein building blocks (amino acids) into a chain that forms a protein; microRNAs (miRNAs), which are short lengths of RNA that block the process of protein production; and long noncoding RNAs (lncRNAs), which are longer lengths of RNA that have diverse roles in regulating gene activity.

Some structural elements of chromosomes are also part of noncoding DNA. For example, repeated noncoding DNA sequences at the ends of chromosomes form telomeres. Telomeres protect the ends of chromosomes from being degraded during the copying of genetic material. Repetitive noncoding DNA sequences also form satellite DNA, which is a part of other structural elements. Satellite DNA is the basis of the centromere, which is the constriction point of the X-shaped chromosome pair. Satellite DNA also forms heterochromatin, which is densely packed DNA that is important for controlling gene activity and maintaining the structure of chromosomes.

Some noncoding DNA regions, called introns, are located within protein-coding genes but are removed before a protein is made. Regulatory elements, such as enhancers, can be located in introns. Other noncoding regions are found between genes and are known as intergenic regions.

The identity of regulatory elements and other functional regions in noncoding DNA is not completely understood. Researchers are working to understand the location and role of these genetic components.