Differential gene expression
Believe it or not, all of the cells within a multicellular organism (excluding red blood cells and gametes) contain exactly the same DNA. In which case, why is a heart composed of cardiomyocytes? Or the liver hepatocytes? How can cells containing the same DNA be so physiologically different?
The answer lies in differential gene expression – the combination of genes that are turned on (expressed) or turned off (repressed) in particular cells – this is what makes each cell unique.
Gene expression is regulated by both internal and external factors – a perfect interplay between the genome and the environment.1
The journey from gene to protein is complex and tightly controlled within each cell. It consists of two major steps: transcription and translation. These steps differ in prokaryotic and eukaryotic cells. Here, we will focus on eukaryotic cells.
DNA vs RNA
To understand fully the different processes involved in gene expression, it is key that you can know the differences between DNA and RNA.
Need to recap?
What is transcription?
Transcription is the synthesis of any type of complimentary RNA from a DNA template: note, several types of RNA can be encoded by a DNA strand [see DNA vs. RNA list]. Here, we focus specifically on transcription that leads to pre-mRNA, mRNA and eventually proteins.
In the process of gene expression, transcription involves the production of messenger RNA (mRNA) from a DNA template. It takes place in the nucleus of a cell and is catalyzed by the enzyme RNA polymerase II.
RNA polymerase
All eukaryotes have three different types of RNA polymerase:
All eukaryotes have three different types of RNA polymerase:
- RNA polymerase I transcribes rRNA genes
- RNA polymerase II transcribes mRNA, miRNA, snRNA, and snRNA genes
- RNA polymerase III transcribes an array of RNA genes, including but not limited to tRNA and 5S rRNA genes.2
The steps of transcription
The process of transcription entails several steps:
1. Initiation
The first step of transcription to form mRNA involves RNA polymerase II binding to a promoter region just upstream of the gene that is to be transcribed. Promoters are often classified as strong or weak based on their effects on transcription rates and thus gene expression. Transcription factors are proteins that help to position RNA polymerase II and assist in the breaking of the hydrogen bonds in the DNA helix. 3
2. Elongation
RNA polymerase II breaks the hydrogen bonds connecting two strands of DNA in the double helix. The enzyme then uses the single DNA strand as a template to build an RNA strand in the 5' to 3' direction, adding each complementary nucleotide to the 3' end of the strand. In RNA, the nucleotide thymine is replaced by the nucleotide uracil.3
What do we mean by 5' and 3'?
This refers to the carbon numbers in DNA and RNA's backbone. The 5' carbon ribose ring frequently has a phosphate group attached, and the 3' carbon end has a hydroxyl (-OH) group attached. The asymmetry gives the DNA and RNA strands a "direction".
Schematic detailing a template DNA strand moving through the RNA polymerase enzyme.
The DNA strand moves through the RNA polymerase II enzyme. In the region behind where the nucleotides are being added to form the pre-mRNA strand, the DNA helix re-forms. This means that the pre-mRNA produced is eventually released from the DNA template a single strand.
3. Termination
Termination marks the end of RNA polymerase II adding nucleotides to the pre-mRNA strand and the release of the pre-mRNA. Despite extensive research, there is still ambiguity surrounding the precise physiological cause of termination - several mechanisms are outlined in this review paper.
From pre-mRNA to mRNA
Eukaryotic pre-mRNAs must go through several additional processing steps before translation can occur. Firstly, they have a 5' cap added and a 3' poly-A-tail added to protect against transcript degradation.4
Many eukaryotic pre-mRNAs are subject to splicing. Here, the non-coding sections of the pre-mRNA (introns) are cut out, and the coding sections (the exons) are effectively glued back together.
Schematic showing pre-mRNA undergoing splicing to form mature mRNA.
Alternative splicing may also take place, whereby exons or noncoding regions within the pre-Mrna transcript are joined or skipped, resulting in multiple mRNAs being encoded by a single gene.
After these modifications have taken place, the resulting strand is known as mature mRNA. This mature mRNA is then able to leave the nucleus and enter the cell cytoplasm where translation takes place.
Translation is the process by which an mRNA molecule is used as a template to build a protein from a specific sequence of amino acids encoded by the mRNA. This takes place within a complex in the cytoplasm called a ribosome.
Schematic showing pre-mRNA undergoing splicing to form mature mRNA. Alternative splicing may also take place, whereby exons or noncoding regions within the pre-Mrna transcript are joined or skipped, resulting in multiple mRNAs being encoded by a single gene.
After these modifications have taken place, the resulting strand is known as mature mRNA. This mature mRNA is then able to leave the nucleus and enter the cell cytoplasm where translation takes place.
What is translation?
Translation is the process by which an mRNA molecule is used as a template to build a protein from a specific sequence of amino acids encoded by the mRNA. This takes place within a complex in the cytoplasm called a ribosome.
What is a ribosome?
Ribosomes are small factories where protein synthesis takes place. They are made of a large subunit and a small unit, comprising a binding site for mRNA and two binding sites for transfer RNA (tRNA) in the large ribosomal subunit
The process of translation occurs in three main stages:
1. Initiation
The small unit of the ribosome binds to the start of the mRNA sequence, at the location of the start codon. In all mRNA molecules, the start codon has a sequence of AUG, which codes for the amino acid methionine. The tRNA carrying the anticodon recognizes this sequence and caries the amino acid methionine to the mRNA. Then, the large subunit of the ribosome binds to form the initiation complex.
2. Elongation
In this stage of translation, the ribosome continues down the mRNA strand translating each codon in turn. The corresponding amino acids are added by tRNA in a growing chain, linked together by peptide bonds. This continues until the entire sequence of codons is read, and the ribosome reaches a "stop" codon.
3. Termination
Stop codons include UAA, UAG, UGA. There are no tRNA's that can read and recognize these codons to recruit an amino acid, and therefore the ribosome recognizes that at this point the translation process is finished. The protein is released, and the components of the translation complex disperse.
Schematic summarizing the processes of initation, elongation and termination in translation.
Schematic summarizing the processes of initation, elongation and termination in translation.DNA replication via DNA polymerase:
Note that transcription and translation are different to DNA replication. DNA replication is the process by which the genome is conserved for the next generation. It involves the replication of a single DNA strand into two daughter strands via the enzyme DNA polymerase. Each daughter strand containing half of the original DNA double helix.
Summary of comparisons chart
Transcription | Translation | |
Location | Nucleus. | Cytoplasm. |
Purpose and product | To use genes as a template to create several forms of RNA (such as mRNA as discussed in this article). | To synthesize proteins from an RNA template. |
Initiation | RNA polymerase protein binds to the promoter region in the DNA and forms the transcription initiation complex. | Takes place when ribosome recognizes AUG start codon and binds the mRNA. |
Elongation | RNA polymerase travels in the 5' to 3' direction and builds an RNA strand. | tRNA with complimentary anticodons to the codons within mRNA binds to mRNA and builds a chain of amino acids joined by peptide bonds. |
Termination | The RNA transcript is released. RNA polymerase detaches from DNA and the DNA rewinds back into a double helix. | Ribosome encounters stop codon. No tRNAs are able to recognize stop codons and the ribosome thus dissembles tRNA and releases the polypeptide that has been built. |
References:
1. Gilbert SF. Developmental Biology. 6th edition. Sunderland (MA): Sinauer Associates; 2000. Differential Gene Expression. Available from: https://www.ncbi.nlm.nih.gov/books/NBK10061/
2. Carter and Drouin. 2009. Structural differentiation of the three eukaryotic RNA polymerases. Genomics. DOI: https://doi.org/10.1016/j.ygeno.2009.08.011.
3. Alberts B, Johnson A, Lewis J, et al. From DNA to RNA. Molecular Biology of the Cell. https://www.ncbi.nlm.nih.gov/books/NBK26887/
4. Ramanathan, Brett Robb and Chan. 2016. mRNA capping: biological functions and applications. Nucleic Acids Research. DOI: 10.1093/nar/gkw551
