Regulation of Translation In Eukaryotes

One of the ways that translation can be regulated in eukaryotes is by altering the genes that encode the proteins. Genes can undergo various changes that affect their expression and function, such as:

• Gene loss or deletion: Some genes can be lost or partially lost from cells, either by mutations or by chromosomal rearrangements. This can result in the absence of functional proteins that are normally produced from those genes. For example, during the differentiation of red blood cells, some genes are deleted from the genome, such as those encoding ribosomal RNA and histones.
• Gene amplification: Some genes can be duplicated or multiplied in the genome, leading to an increased number of copies of those genes. This can result in higher levels of protein production from those genes. For example, some cancer cells become resistant to the drug methotrexate by amplifying the gene for the enzyme dihydrofolate reductase, which is inhibited by the drug.
• Gene rearrangement: Some genes can be moved or rearranged in the genome, either by translocation, inversion, or transposition. This can result in different combinations of gene segments or different associations of genes with regulatory elements. For example, in B cells that produce antibodies, various segments of DNA encoding different parts of the antibody molecule are rearranged to generate diverse antibodies.
• Gene modification: Some genes can be modified at the level of DNA, such as by methylation or demethylation of cytosine bases. This can affect the accessibility and activity of those genes by influencing their interaction with transcription factors and chromatin modifiers. For example, cytosine methylation often occurs in CpG islands within promoter regions of genes, and the greater the extent of methylation, the less readily a gene is transcribed .

These changes in genes can have profound effects on the translation of proteins and the phenotypes of cells and organisms. They can also provide a source of genetic variation and evolution.

Sometimes, the number of copies of a gene in a cell can change due to various mechanisms. This can affect the amount and function of the protein encoded by that gene.

One way that genes can be lost is by deletion, which is the removal of a segment of DNA from a chromosome. Deletion can occur spontaneously during DNA replication or repair, or it can be induced by environmental factors such as radiation or chemicals. Deletion can result in the loss of one or more genes, depending on the size and location of the deleted segment. For example, during the differentiation of red blood cells, a large portion of the DNA in the nucleus is deleted, leaving behind only the genes that are essential for hemoglobin synthesis.

Another way that genes can be lost is by silencing, which is the suppression of gene expression without altering the DNA sequence. Silencing can occur by various epigenetic modifications, such as DNA methylation, histone modification, or RNA interference. These modifications can prevent the binding of transcription factors or RNA polymerase to the gene promoter, or degrade the mRNA transcript before it can be translated. Silencing can be reversible or irreversible, depending on the type and extent of the modification. For example, some genes are silenced during embryonic development and remain inactive throughout life, while others are silenced in response to environmental stimuli and can be reactivated later.

On the other hand, genes can also be amplified, which is the increase in the number of copies of a gene in a cell. Amplification can occur by various mechanisms, such as duplication, transposition, or extrachromosomal replication. Duplication is the production of an extra copy of a gene within a chromosome, which can occur during DNA replication or repair. Transposition is the movement of a gene from one location to another on the same or different chromosome, which can occur by cut-and-paste or copy-and-paste mechanisms mediated by transposable elements. Extrachromosomal replication is the formation of circular DNA molecules that contain one or more genes and replicate independently of the chromosomes. These molecules are called plasmids in bacteria and episomes in eukaryotes.

Amplification can have various effects on gene expression and function, depending on the type and location of the amplified gene. For instance, amplification can increase the amount of protein produced by a gene, which can confer an advantage or disadvantage to the cell depending on the protein`s role. For example, some cancer cells amplify genes that encode growth factors or their receptors, which stimulate cell proliferation and survival. Alternatively, amplification can alter the regulation or interaction of a gene with other genes, which can affect its function and activity. For example, some antibiotic-resistant bacteria amplify genes that encode enzymes that degrade or modify antibiotics, which reduce their effectiveness.

As you can see, genes can be lost or amplified by various mechanisms that affect their expression and function. These changes can have significant consequences for cellular processes and phenotypes.

These segments of DNA are called transposable elements (TEs), also known as transposons or mobile DNA. They are DNA sequences that can move or duplicate themselves from one location in the genome to another in a process called transposition. Eukaryotic TEs are traditionally divided into two classes: Class I and Class II.

Class I TEs, also known as retrotransposons, move through an RNA intermediate. They use a reverse transcriptase enzyme to copy their RNA into DNA, which is then inserted into a new location in the genome. Class I TEs can be further subdivided into long terminal repeat (LTR) retrotransposons, which have direct repeats at their ends, and non-LTR retrotransposons, which do not.

Class II TEs, also known as DNA transposons, move through a DNA intermediate. They use a transposase enzyme to cut and paste themselves from one location to another. Class II TEs can be further subdivided into three subclasses: cut-and-paste transposons, which excise as double-stranded DNA and reinsert elsewhere in the genome; Helitrons, which utilize a mechanism probably related to rolling-circle replication; and Mavericks, whose mechanism of transposition is not yet well understood, but that likely replicate using a self-encoded DNA polymerase.

Transposition can have various effects on gene expression and genome evolution. For instance, TEs can insert into or near genes and alter their transcription, splicing, translation or function. They can also cause chromosomal rearrangements such as deletions, duplications, inversions or translocations by recombining with each other or with homologous sequences. Moreover, they can carry genes or regulatory elements with them and spread them across the genome or between different species.

TEs are ubiquitous and abundant in eukaryotic genomes. For example, they make up about 45% of the human genome and 85% of the maize genome. However, most of them are inactive or silenced by various mechanisms such as DNA methylation or RNA interference. Only a small fraction of them are still capable of transposition and contribute to genetic variation and adaptation.

One of the ways that eukaryotic cells can regulate gene expression is by modifying the bases in DNA. This can affect the transcriptional activity of a gene, either by changing its sequence or by altering its accessibility to transcription factors.

One common type of DNA modification is cytosine methylation. Cytosine is one of the four nucleotides that make up DNA, and it can be methylated at its 5 position by enzymes called DNA methyltransferases (DNMTs). This often occurs in regions of DNA that contain many CpG dinucleotides, where a cytosine is followed by a guanine. These regions are called CpG islands, and they are usually found in the promoter regions of genes, which are the sequences that initiate transcription.

The extent of cytosine methylation in CpG islands can influence the expression of the associated genes. The greater the degree of methylation, the less likely a gene is to be transcribed. This is because methylated cytosines can repress transcription in two ways:

• They can recruit methyl-binding proteins (MBPs), which can block the binding of transcription factors or recruit other proteins that modify histones and make the chromatin more compact and inaccessible.
• They can inhibit the binding of transcription factors directly, especially those that recognize CpG-rich motifs.

Cytosine methylation is a stable and heritable modification that can be maintained through cell division by the action of maintenance DNMTs, which copy the methylation pattern from the parent strand to the daughter strand during DNA replication. However, cytosine methylation can also be reversed by enzymes called DNA demethylases, which remove the methyl group from cytosine and restore its original state. This process is called active demethylation, and it can occur in response to various signals and stimuli, such as development, differentiation, or environmental factors.

Another type of DNA modification is hydroxymethylation, which involves the addition of a hydroxyl group to the 5 position of cytosine by enzymes called ten-eleven translocation (TET) proteins. This modification can be an intermediate step in active demethylation, as hydroxymethylated cytosines can be further processed by DNA demethylases or base excision repair enzymes to generate unmethylated cytosines. Alternatively, hydroxymethylation can have its own regulatory effects on gene expression, as hydroxymethylated cytosines can have different interactions with MBPs and transcription factors than methylated or unmethylated cytosines.

Other types of DNA modifications include formylation, carboxylation, and glucosylation of cytosine, as well as adenine methylation at the 6 position. These modifications are less common and less understood than cytosine methylation and hydroxymethylation, but they may also play roles in gene regulation in eukaryotic cells.

In summary, modification of the bases in DNA is a way of regulating gene expression in eukaryotes by affecting the transcriptional activity of genes. The most prevalent and studied modification is cytosine methylation, which can repress transcription by recruiting MBPs or inhibiting transcription factors. Cytosine methylation can be reversed by active demethylation, which involves hydroxymethylation and other steps. Other types of DNA modifications also exist and may have regulatory functions.

Transcription is the process by which a cell converts DNA to RNA, allowing it to respond to intra- and extracellular signals. Transcription regulation is mainly achieved by the interaction of transcription factors with specific DNA sequences and chromatin structure. Transcription factors are proteins that bind to DNA and promote or repress transcription. Transcription factors can be classified into two types: general and specific.

General transcription factors are required for the assembly of the basic transcription machinery at the core promoter, which is a short sequence near the transcription start site that contains elements such as the TATA box and the initiator. General transcription factors include TFIID, which binds to the TATA box and recruits other factors such as TFIIB, TFIIF, TFIIE, TFIIH, and RNA polymerase II. The formation of this complex initiates transcription.

Specific transcription factors are responsible for regulating the expression of specific genes in response to various signals, such as hormones, nutrients, stress, and development. Specific transcription factors can act as activators or repressors. Activators bind to enhancer sequences, which are distant regions of DNA that can enhance transcription of a target gene. Activators recruit coactivators, such as histone acetyltransferases (HATs) and chromatin remodeling complexes, which modify histones and DNA to make the chromatin more accessible for transcription. Repressors bind to silencer sequences, which are regions of DNA that can inhibit transcription of a target gene. Repressors recruit corepressors, such as histone deacetylases (HDACs) and DNA methyltransferases (DNMTs), which modify histones and DNA to make the chromatin more compact and repressive for transcription.

The regulation of transcription by specific transcription factors is often combinatorial, meaning that it requires the coordinated interactions of multiple proteins. Different combinations of transcription factors can result in different patterns of gene expression in different cell types, tissues, or developmental stages. For example, the expression of globin genes in red blood cells is regulated by a combination of erythroid-specific factors (such as GATA1 and EKLF) and ubiquitous factors (such as NF-Y and SP1) that bind to regulatory elements in the globin gene locus.

The regulation of transcription by specific transcription factors is also often dynamic, meaning that it can change rapidly in response to changing conditions. For example, the expression of genes involved in stress response is regulated by a transcription factor called nuclear factor kappa B (NF-κB), which is normally sequestered in the cytoplasm by an inhibitor protein called IκB. When cells are exposed to stress signals, such as cytokines or pathogens, IκB is phosphorylated and degraded by a kinase complex called IKK, allowing NF-κB to translocate to the nucleus and activate the expression of genes that mediate inflammation and immunity.

The regulation of transcription by specific transcription factors is a key mechanism by which eukaryotic cells control their gene expression and adapt to various stimuli. Transcription deregulation can lead to serious diseases, such as cancers.

6. Histones act as non-specific repressors

Histones are proteins that provide structural support for chromosomes by forming complexes with DNA called nucleosomes. Histones also play a role in the regulation of gene expression by affecting the accessibility of DNA to transcription factors and other proteins. Histones can be modified by enzymes that add or remove chemical groups to specific amino acids in their tails. These modifications can alter the charge and shape of histones, and influence their interactions with DNA and other proteins.

One of the most common histone modifications is acetylation, which involves the addition of an acetyl group to a lysine residue. Acetylation reduces the positive charge of histones, which weakens their attraction to the negatively charged DNA. This results in a more relaxed chromatin structure, which allows transcription factors and other proteins to access the DNA and activate gene expression .

Another common histone modification is methylation, which involves the addition of a methyl group to a lysine or arginine residue. Methylation can have different effects on gene expression depending on the specific residue and the number of methyl groups added. For example, methylation of lysine 4 on histone H3 (H3K4me) is associated with active transcription, while methylation of lysine 9 on histone H3 (H3K9me) is associated with gene silencing .

Histone modifications can also recruit or repel other proteins that recognize specific marks on histones. These proteins are called readers, and they can further modulate chromatin structure and gene expression. For example, bromodomain-containing proteins can bind to acetylated histones and promote transcription, while chromodomain-containing proteins can bind to methylated histones and repress transcription.

Histone modifications are dynamic and reversible, and they can be influenced by various factors such as cell cycle, development, differentiation, stress, and disease. Histone modifications are part of the epigenetic mechanisms that regulate gene expression without changing the DNA sequence .

Positive regulation of gene expression occurs when the presence of an active regulator protein, such as an activator, enhances the transcription of a gene or a set of genes. Unlike negative regulation, which involves repressors that block transcription, positive regulation requires the binding of activators to specific DNA sequences, called enhancers, that are often located far away from the promoter. The activators can interact with the transcription machinery and recruit other co-activators or chromatin modifiers that facilitate the access of RNA polymerase to the promoter.

Some examples of positive regulation in eukaryotes are:

• Steroid hormones, such as estrogen and testosterone, can enter the cell and bind to their specific receptors in the cytoplasm or the nucleus. The hormone-receptor complex then acts as an activator that binds to enhancers on target genes and stimulates their transcription.
• Some genes have multiple promoters that can be used under different conditions or in different cell types. For instance, the gene encoding calcitonin, a hormone that regulates calcium levels in the blood, has two promoters: one in the thyroid gland and one in the brain. The use of different promoters allows the expression of calcitonin in both tissues, but with different splicing patterns and functions.
• Some genes are regulated by alternative splicing, which can generate different mRNA variants from the same gene. For example, the gene encoding tropomyosin, a protein involved in muscle contraction, has 12 exons and can produce more than 40 different mRNA isoforms by alternative splicing. The splicing pattern is controlled by various splicing factors that bind to enhancers or silencers on the pre-mRNA and influence the selection of splice sites.

Positive regulation of gene expression is important for cellular differentiation, development, adaptation and response to stimuli. It allows cells to express specific genes only when they are needed or when they receive a signal from another molecule. However, positive regulation also needs to be balanced by negative regulation to prevent excessive or inappropriate gene expression that could lead to diseases.

Chromatin remodeling is the process of altering the structure and accessibility of chromatin, the complex of DNA and histone proteins that forms the eukaryotic genome. Chromatin remodeling can affect gene expression by changing the interaction between DNA and the transcription machinery. There are two main types of chromatin remodeling: covalent histone modifications and ATP-dependent nucleosome sliding.

Covalent histone modifications

Histones are proteins that wrap around DNA to form nucleosomes, the basic units of chromatin. Histones have long tails that protrude from the nucleosome core and can be modified by various enzymes. These modifications include acetylation, methylation, phosphorylation, ubiquitination, and sumoylation. Each modification can have different effects on chromatin structure and function, depending on the type, location, and combination of modifications.

One of the most common and well-studied histone modifications is acetylation, which involves the addition of an acetyl group to a lysine residue on the histone tail. Acetylation generally reduces the positive charge of the histone tail, weakening its interaction with the negatively charged DNA backbone. This makes the chromatin more open and accessible to transcription factors and other regulatory proteins. Acetylation is catalyzed by histone acetyltransferases (HATs) and reversed by histone deacetylases (HDACs).

Another important histone modification is methylation, which involves the addition of one, two, or three methyl groups to a lysine or arginine residue on the histone tail. Methylation can have different effects on chromatin structure and function, depending on the specific residue and degree of methylation. For example, methylation of lysine 4 on histone H3 (H3K4me) is associated with active transcription, while methylation of lysine 9 on histone H3 (H3K9me) is associated with gene silencing. Methylation is catalyzed by histone methyltransferases (HMTs) and reversed by histone demethylases (HDMs).

Covalent histone modifications can act as signals for the recruitment or exclusion of other chromatin-associated proteins that can further modulate gene expression. For instance, bromodomains are protein domains that recognize and bind to acetylated lysines on histones, while chromodomains are protein domains that recognize and bind to methylated lysines on histones. These domains are often found in transcription factors, chromatin remodelers, and histone modifiers that can either activate or repress gene expression.

ATP-dependent nucleosome sliding

Nucleosome sliding is the process of moving nucleosomes along the DNA strand, changing the position and spacing of nucleosomes relative to each other and to the underlying DNA sequence. Nucleosome sliding can affect gene expression by exposing or occluding regulatory elements such as promoters, enhancers, or silencers. Nucleosome sliding is catalyzed by ATP-dependent chromatin remodeling complexes that use energy from ATP hydrolysis to alter the interaction between DNA and histones.

There are four major families of ATP-dependent chromatin remodeling complexes in eukaryotes: SWI/SNF, ISWI, CHD, and INO80. Each family has distinct subunits, targets, and functions in chromatin remodeling. For example, SWI/SNF complexes are involved in gene activation by sliding nucleosomes away from promoters or enhancers, while ISWI complexes are involved in gene repression by sliding nucleosomes closer together to form compact chromatin. CHD complexes are involved in both gene activation and repression by sliding nucleosomes in either direction depending on the context. INO80 complexes are involved in DNA repair and replication by sliding nucleosomes to facilitate access to damaged DNA.

ATP-dependent chromatin remodeling complexes can be recruited to specific genomic regions by interacting with transcription factors or covalent histone modifications. For instance, SWI/SNF complexes can be recruited by acetylated histones or activator proteins that bind to acetylated histones. ISWI complexes can be recruited by methylated histones or repressor proteins that bind to methylated histones.

Regulation by chromatin remodeling is essential for many biological processes in eukaryotes, such as development, differentiation, cell cycle, response to stress, and genome stability. Dysregulation of chromatin remodeling can lead to various diseases such as cancer, neurodegeneration, and developmental disorders.

After transcription, mRNA undergoes several modifications before it can be translated into proteins. These modifications include capping, polyadenylation, and splicing. Each of these steps can be regulated to affect the quantity or quality of the final protein product.

Capping

Capping is the addition of a 7-methylguanosine (m7G) cap to the 5` end of the mRNA. This cap protects the mRNA from degradation by exonucleases and facilitates its export from the nucleus to the cytoplasm. It also enhances the binding of the mRNA to the ribosome and promotes translation initiation.

The capping process is catalyzed by three enzymes: RNA triphosphatase, guanylyltransferase, and methyltransferase. The activity of these enzymes can be regulated by various factors, such as phosphorylation, protein-protein interactions, and RNA-binding proteins. For example, some viral proteins can inhibit capping enzymes to suppress host gene expression and favor viral replication.

Polyadenylation

Polyadenylation is the addition of a poly(A) tail to the 3` end of the mRNA. This tail also protects the mRNA from degradation and enhances its translation efficiency. It also influences the stability and localization of the mRNA in the cytoplasm.

The polyadenylation process involves two steps: cleavage and polyadenylation. The cleavage step requires a polyadenylation signal (PAS) in the mRNA, which is usually a hexanucleotide sequence (AAUAAA or a variant) followed by a GU-rich or U-rich region. The PAS is recognized by a complex of proteins called cleavage and polyadenylation specificity factor (CPSF), which recruits other factors to form the cleavage complex. The cleavage complex then cuts the mRNA at a specific site downstream of the PAS.

The polyadenylation step requires a poly(A) polymerase (PAP), which adds adenine nucleotides to the 3` end of the cleaved mRNA. The PAP is activated by another protein complex called cleavage stimulation factor (CstF), which binds to the GU-rich or U-rich region downstream of the PAS. The length of the poly(A) tail is determined by the balance between PAP and deadenylases, which are enzymes that remove adenine nucleotides from the tail.

The polyadenylation process can be regulated by alternative PAS usage, which can generate different mRNAs from the same gene. For example, some genes have multiple PAS in their 3` untranslated regions (UTRs), and different PAS can be selected depending on the cell type or condition. This can result in different lengths of 3` UTRs, which can affect the stability, localization, or interactions of the mRNAs with other molecules.

Splicing

Splicing is the removal of introns and joining of exons in the mRNA. This process increases the diversity of proteins that can be produced from a single gene, as different combinations of exons can be spliced together to form different mRNAs. This phenomenon is called alternative splicing.

The splicing process is catalyzed by a large complex of proteins and small nuclear RNAs (snRNAs) called spliceosome. The spliceosome recognizes specific sequences at the boundaries of introns and exons, called splice sites, and cuts and ligates them accordingly. The splice sites are usually composed of short conserved sequences: GU at the 5` end and AG at the 3` end of introns, and pyrimidine-rich regions near these ends.

The splicing process can be regulated by various factors that influence splice site selection or spliceosome assembly. These factors include splicing enhancers or silencers, which are sequences in introns or exons that bind to splicing regulators such as SR proteins or hnRNPs. These regulators can either promote or inhibit splicing of certain exons or introns by interacting with spliceosomal components or modifying nearby RNA structures.

Another way to regulate splicing is by alternative promoters or polyadenylation sites, which can affect the inclusion or exclusion of certain exons or introns in the mRNA. For example, some genes have multiple promoters that can initiate transcription at different sites, resulting in different lengths of 5` UTRs that may contain or lack splice sites.

Editing

Editing is the alteration (“editing”) of bases in mRNA after transcription. This process can change the coding sequence or structure of the mRNA, affecting its translation or interactions with other molecules.

One type of editing is adenosine-to-inosine (A-to-I) editing, which is catalyzed by enzymes called adenosine deaminases acting on RNA (ADARs). Inosine is recognized as guanosine by most cellular machineries, so A-to-I editing can alter base pairing and hydrogen bonding in RNA duplexes. This can affect splicing, stability, localization, or translation of mRNAs.

Another type of editing is cytidine-to-uridine (C-to-U) editing, which is catalyzed by enzymes called apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC) proteins. C-to-U editing can change amino acids or create stop codons in mRNAs, affecting their translation or stability.

Editing can be regulated by various factors that modulate the expression or activity of editing enzymes or their substrates. For example, some editing enzymes require cofactors such as metal ions or RNA-binding proteins to function properly. Some editing substrates have specific structures or sequences that are recognized by editing enzymes.

Degradation

Degradation is the breakdown of mRNA into smaller fragments that are eventually recycled into nucleotides. This process controls the amount and lifespan of mRNAs in cells.

The degradation process involves two main pathways: deadenylation-dependent and deadenylation-independent pathways. Both pathways start with shortening or removal of the poly(A) tail by deadenylases, which makes mRNAs more susceptible to degradation by exonucleases.

In deadenylation-dependent pathway, after deadenylation, mRNAs are degraded either from their 5` end by decapping enzymes followed by 5`-to-3` exonucleases, or from their 3` end by 3`-to-5` exonucleases such as exosome.

In deadenylation-independent pathway, mRNAs are degraded without prior deadenylation by endonucleases that cleave them internally at specific sites. These sites are usually AU-rich elements (AREs) in 3` UTRs that are recognized by ARE-binding proteins such as tristetraprolin (TTP). The cleaved fragments are then degraded further by exonucleases.

The degradation process can be regulated by various factors that affect deadenylation, decapping, endonucleolytic cleavage, or exonucleolytic digestion of mRNAs. These factors include RNA-binding proteins that either stabilize or destabilize mRNAs by binding to their UTRs or coding regions; microRNAs (miRNAs) that either block translation or induce degradation of target mRNAs; small interfering RNAs (siRNAs) that induce degradation of target mRNAs through RNA interference (RNAi); and environmental stimuli such as stress or hormones that modulate gene expression through post-transcriptional mechanisms.

Alternative splicing and alternative polyadenylation are two post-transcriptional processes that can generate different mRNA isoforms from a single gene. Both have the potential to alter the identity, abundance, localization or interaction of the encoded protein. In this section, we will briefly describe how these two processes work and how they are coordinated in eukaryotes.

Alternative splicing

Alternative splicing is the process of selecting different combinations of exons and introns to form mature mRNA. It is regulated by various cis-elements (such as splice sites, branch points, enhancers and silencers) and trans-factors (such as splicing factors, RNA-binding proteins and chromatin modifiers) that interact with the pre-mRNA. Alternative splicing can produce different mRNA isoforms that may encode different protein variants with distinct functions or interactions, or that may be subjected to different regulatory mechanisms such as degradation or translation.

Alternative polyadenylation

Alternative polyadenylation is the process of selecting different cleavage and polyadenylation sites (pA sites) within the 3`-untranslated region (3`-UTR) or the last exon of a pre-mRNA. It is regulated by various cis-elements (such as poly(A) signals, upstream and downstream elements) and trans-factors (such as cleavage and polyadenylation factors, RNA-binding proteins and chromatin modifiers) that interact with the pre-mRNA. Alternative polyadenylation can produce different mRNA isoforms that may have different 3`-UTR lengths and sequences, which may affect their stability, localization, translation or interaction with microRNAs or other RNA-binding proteins.

Coordination of alternative splicing and polyadenylation

Alternative splicing and alternative polyadenylation are not independent processes, but rather they are coordinated by several mechanisms that ensure the proper expression of genes. Some of these mechanisms are:

• Coupling: The selection of a pA site can influence the selection of a splice site, or vice versa, by affecting the availability or accessibility of cis-elements or trans-factors for either process.
• Competition: The selection of a pA site can compete with the selection of a splice site, or vice versa, by creating mutually exclusive choices for either process.
• Communication: The selection of a pA site can communicate with the selection of a splice site, or vice versa, by sending signals or feedbacks that modulate either process.

These mechanisms can result in various outcomes such as exon skipping, intron retention, alternative 3`-end formation or alternative 5`-end formation. These outcomes can have significant effects on gene expression and function in various biological contexts such as development, differentiation, stress response and disease.


mRNA degradation and RNA editing

Another way to regulate gene expression in eukaryotes is to control the stability and modification of mRNA molecules after their synthesis in the nucleus and before their translation in the cytoplasm. mRNA degradation is a process that reduces the amount of mRNA available for protein synthesis by exposing it to nucleases that cleave it into smaller fragments. The rate of mRNA degradation depends on several factors, such as the length of the poly(A) tail, the presence of AU-rich elements (AREs) in the 3` untranslated region (UTR), and the binding of specific RBPs that either protect or target the mRNA for decay. Some mRNAs are more stable than others and can persist for hours or days, while others are rapidly degraded within minutes. This allows cells to adjust the protein levels according to their needs and environmental signals.

RNA editing is a process that alters the nucleotide sequence of mRNA after transcription, resulting in a different amino acid sequence or a different quantity of the protein produced from the mRNA. RNA editing can occur by various mechanisms, such as base substitution, insertion, deletion, or modification. One common type of RNA editing is the deamination of adenosine (A) to inosine (I) or cytidine (C) to uridine (U) by enzymes called ADARs (adenosine deaminases acting on RNA) or APOBECs (apolipoprotein B mRNA editing enzyme catalytic polypeptide-like), respectively. These changes can affect the splicing, translation, or stability of the mRNA. For example, RNA editing can create or destroy splice sites, alter codons or stop codons, or introduce mismatches with miRNAs that regulate mRNA stability. RNA editing can also generate diversity and complexity in the transcriptome and proteome of eukaryotic cells.

Therefore, mRNA degradation and RNA editing are important post-transcriptional mechanisms that modulate gene expression in eukaryotes by affecting the quality and quantity of mRNA molecules available for translation.

Small and interfering RNA (siRNA) are a class of double-stranded RNA molecules, typically 20-24 base pairs in length, that operate within the RNA interference (RNAi) pathway. They interfere with the expression of specific genes with complementary nucleotide sequences by degrading mRNA after transcription, preventing translation.

The mechanism by which siRNA causes gene silencing through repression of translation occurs as follows:

• siRNA molecules are either synthesized in the laboratory or produced from long dsRNAs or small hairpin RNAs by an enzyme called Dicer in the cell.
• siRNA molecules bind to a protein complex called RNA-induced silencing complex (RISC), which unwinds the siRNA duplex and discards one strand.
• The remaining strand, called the guide strand, guides RISC to the target mRNA by base pairing with a complementary sequence.
• RISC cleaves the target mRNA, resulting in its degradation and inhibition of translation.

siRNA has been recognized as a promising therapeutic tool for antiviral, anticancer, or other genetic diseases, as it can specifically and efficiently knock down disease-related genes. However, siRNA also faces some challenges, such as low cellular uptake, nuclease-mediated degradation, off-target effects, and immune stimulation. Therefore, siRNA requires a carrier for its protection and efficient delivery into target cells. Various types of nanocarriers have been developed for siRNA delivery, such as liposomes, polymers, dendrimers, nanoparticles, and exosomes.

Several siRNA-based therapies have been approved or are under clinical trials for various diseases, such as age-related macular degeneration, transthyretin amyloidosis, hepatitis B virus infection, solid tumors, and respiratory syncytial virus infection. These therapies demonstrate the potential and challenges of siRNA as a novel class of drugs for gene regulation.

It occurs during the initiation or elongation reactions of protein synthesis.

• Translational initiation factors are proteins that bind to the mRNA and help recruit the ribosome and the first tRNA. The activity and availability of these factors can affect the rate of translation initiation and thus the amount of protein produced from a given mRNA. For example:

  • Heme stimulates the synthesis of globin by preventing the phosphorylation and consequent inactivation of eIF-2, a factor involved in the initiation of protein synthesis.
  • Interferon stimulates the phosphorylation of eIF-2, causing inhibition of initiation.
  • Iron-response elements (IREs) in mRNA for ferritin (an iron storage protein) and the transferrin receptor regulate translation of the respective mRNAs. These elements either destabilize the mRNA (transferrin receptor) or allow translation of the mRNA (ferritin) when iron levels are high.

• Translational elongation factors are proteins that facilitate the movement of the ribosome along the mRNA and the formation of peptide bonds between amino acids. The activity and availability of these factors can also affect the rate of translation elongation and thus the amount of protein produced from a given mRNA. For example:

  • Rapamycin is a drug that inhibits a protein kinase called mTOR, which regulates cell growth and metabolism. mTOR phosphorylates and activates an elongation factor called eEF-2K, which in turn phosphorylates and inhibits another elongation factor called eEF-2. By inhibiting mTOR, rapamycin reduces the phosphorylation of eEF-2K and eEF-2, leading to increased translation elongation.
  • Erythromycin is an antibiotic that binds to the bacterial ribosome and blocks the exit tunnel for the growing polypeptide chain, thus inhibiting translation elongation.

Translational control refers to the regulation of gene expression at the level of protein synthesis. It occurs during the initiation or elongation reactions of translation, and involves various factors that modulate the availability, stability, and activity of mRNA, ribosomes, and translation factors. Translational control in eukaryotic cells is critical for gene regulation during nutrient deprivation and stress, development and differentiation, nervous system function, aging, and disease .

Some examples of translational control in eukaryotic cells are:

• Heme stimulates the synthesis of globin by preventing the phosphorylation and consequent inactivation of eIF-2, a factor involved in the initiation of protein synthesis.
• Interferon stimulates the phosphorylation of eIF-2, causing inhibition of initiation.
• Iron-response elements (IREs) in mRNA for ferritin (an iron storage protein) and the transferrin receptor regulate translation of the respective mRNAs. These elements either destabilize the mRNA (transferrin receptor) or allow translation of the mRNA (ferritin) when iron levels are high.
• Gene silencing can occur through the use of small RNA products (miRNA), which can either block the translation of a target mRNA or induce degradation of the target mRNA. miRNA molecules are the products of many genes scattered throughout the chromosome, some even located in the introns of the genes they regulate. miRNAs are synthesized in the nucleus and processed to form an active molecule that will bind to the target RNA and ablate its expression .

Translational control allows eukaryotic cells to rapidly and precisely adjust their protein levels in response to changing environmental and physiological conditions, without altering their transcriptional programs. It also enables cells to generate diversity and complexity from a limited number of genes, by producing different protein isoforms from alternative splicing, polyadenylation, or editing of mRNA. Furthermore, translational control plays a key role in maintaining cellular homeostasis and preventing diseases such as cancer, neurodegeneration, and viral infections .

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