Let us make an in-depth study of the gene regulation in eukaryotes. After reading this article you will learn about: 1. Chromatin Modification 2. Control of Transcription by Hormones 3. Regulation of Processing of mRNA 4. Control of Life Span of mRNA 5. Gene Amplification 6. Post Translation Regulation and 7. Post Transcription Gene Silencing.
Introduction to Gene Regulation:
The expression of genes can be regulated in eukaryotes by all the principles as those of prokaryotes. But there are many additional mechanisms of control of gene expression in eukaryotes as genome is much bigger. The genes are present in the nucleus where mRNA is synthesized. The mRNA is then exported to cytoplasm where translation takes place.
In eukaryotes, the organization is multicellular and specialized into tissues and organs. The cells are differentiated and cells of a tissue generally produce a specific protein involving a particular set of genes. All other genes become permanently shut off and are never transcribed.
Structural features of eukaryotes that influence the gene expression are the presence of nucleosomes in chromatin, heterochromatin and the presence of the split genes in chromosomes.
As compared to prokaryotic genes, the eukaryotic genes have many more regulatory binding sites and they are controlled by many more regulatory proteins. Regulatory sequences can be present thousands of nucleotides away from the promoter, may lie upstream and downstream. These regulatory sequences act from a distance. The intervening DNA loops out, so that the regulatory sequence and promoter come to lie near each other.
Most of the regulation of gene control occurs at the initiation of transcription level. Initiation of translation also influences gene regulation immensely.
Chromatin Modification:
The genome of eukaryotes is wrapped in histone proteins to form nucleosomes. This condition leads to partial concealment of genes and reduces the expression of genes.
The packing of DNA with histone octomers is not permanent. Any portion of DNA can be released from the octomer whenever DNA binding proteins have to act on it. These DNA binding proteins or enzymes recognize their binding sites on DNA only when it is released from histone octomer or when present on linker DNA. The DNA is unwrapped from nucleosomes.
This unwrapping of DNA from nucleosomes is performed by nucleosome modifier enzymes or nucleosome remodelling complex. They act in various ways. They may remodel the structure of octomer or slide the octomer along DNA, thus uncover the DNA binding sites for the action of regulatory proteins. Thus the genes are activated.
Some of these nucleosome modifiers add acetyl groups (acetylation) to the tails of histones, thus loosen the DNA wrapping and in the process exposes the DNA binding sites. All these lead to the expression of genes. Similarly, deacetylation by deacetylases causes inactivation of DNA.
Nucleosomes are entirely absent in the regions that are active in transcription like rRNA genes.
Dense form of chromatin is called heterochromatin in eukaryotes. It leads to gene inhibition or gene silencing. Heterochromatin is densely packaged part of chromatin which does not allow gene expression. Densely packaged chromatin cannot be easily transcribed. Some enzymes make the chromatin more dense. Telomeres and contromeres are in the form of heterochromatin.
In higher animals about 50% of the genome is in the form of heterochromatin. Enzymes are capable of changing the density of chromatin by chemically modifying the tails of histones. This affects transcription.
In this way, both activation and repression of transcription is performed by modification of chromatin into heterochromatin and euchromatin.
Methylation:
Methylation of certain sequences of DNA prevents the transcription of genes in mammals. It has been observed that genes, which are heavily methylated are not transcribed, therefore not expressed. DNA methylase enzymes cause methylation of certain DNA sequences thereby silencing of genes.
Control of Transcription by Hormones:
Various intercellular and intracellular signals regulate the gene expression.
Hormones exercise considerable control over transcription. Hormones are extracellular substances synthesized by endocrine glands. They are carried to the distant target cells. Various hormones like insulin, estrogen, progesterone, testosterone etc. often act by “switching on” transcription of DNA.
The hormone on entering a target cell forms a complex with the receptor present in the cytoplasm. This hormone-receptor complex enters the nucleus and binds to a particular chromosome by means of specific proteins. This initiates the transcription. Hormone-receptor complex can enhance or suppress the expression of genes.
It has been observed in chickens that when hormone estrogen is injected, the oviduct responds by synthesizing mRNA, which is responsible for synthesis of albumen. The hormone directly binds to DNA and acts as an inducer.
Regulation of Processing of mRNA:
Genes of eukaryotes have non-coding regions (introns) in between coding regions (exons). Such genes are called split genes. The entire gene is transcribed to produce mRNA which is called precursor mRNA or primary transcript (pre-mRNA). Before translation takes place, the introns are spliced out by excision and discarded. This is known as processing of mRNA and the processed mRNA is called mature mRNA. This takes part in protein synthesis. Mature mRNA is considerably smaller than precursor mRNA.
Higher eukaryotes have various mechanisms by which pre-mRNA is processed in alternate or differential ways to produce different mRNAs which encode different proteins. Multiple proteins are produced from one gene by alternate mRNA processing. Many cells take advantage of different splicing pathways to alter the expression of genes and synthesize different polypeptides. Alternate mRNA splicing increases the number of proteins expressed by a single eukaryotic gene.
Alternate processing of pre-mRNA is accomplished by exon skipping, by retaining certain introns etc.
These alternate processing pathways are highly regulated.
Example:
In drosophilla mRNA is processed in four different ways, therefore produces four different kinds of muscle protein myosin. Different kind of myosin is produced in larva, pupa and late embryonic stages.
Control of Life Span of mRNA:
In prokaryotes the life span of an mRNA molecule is very brief, lasting only for a minute or less. The mRNA immediately degenerates after the protein synthesis.
But as the mRNA in eukaryotes is transported to cytoplasm through the nucleopores, this mRNA is repeatedly translated. This repeated translation of mRNA is achieved by increasing the life span of mRNA. In a highly differentiated cell, single mRNA molecule having long life span is able to produce large amount of single protein. Life span of a eukaryotic mRNA varies from a few hours to several days.
Examples:
Chicken oviduct cells have a single copy of ovalbumen gene but produce large amount of albumen.
Silk gland of silkworm produces a very long thread made of protein fibroin, which forms cocoon. Silk gland is a single polyploid cell. It produces large number of mRNA molecules, which have long life span of several days.
Gene Amplification:
A mechanism exists in various organisms whereby the number of genes is increased many fold without mitosis division. This is called gene amplification.
During amplification DNA repeatedly undergoes replication without mitotic separation into daughter DNA molecules or chromatids. This enables the cell to produce large amount of protein in a short time.
Post Translation Regulation:
In prokaryotes, a single polycistronic mRNA molecule codes for many different proteins. But in eukaryotes having mono-cistronic mRNA, synthesis of different proteins is achieved in a different way. A single mRNA yields a large polypeptide called polyprotein. This polyprotein is then cleaved in alternate ways to produce different proteins. Each protein is regarded as the product of a single gene. In this system, there are many cleaving sites on the polyprotien.
Post Transcription Gene Silencing:
Many small RNAs exist in eukaryotes that play their role in silencing of genes. These small RNAs act on mRNA resulting in disruption of translation. These small RNAs are micro RNAs (miRNAs), small interfering RNAs (siRNAs) and many others.