Alternative Splicing : There are five basic modes of alternative splicing. Alternative splicing is a process that occurs during gene expression and allows for the production of multiple proteins protein isoforms from a single gene coding. Alternative splicing can occur due to the different ways in which an exon can be excluded from or included in the messenger RNA. This results in what is called alternative splicing. The pattern of splicing and production of alternatively-spliced messenger RNA is controlled by the binding of regulatory proteins trans-acting proteins that contain the genes to cis-acting sites that are found on the pre-RNA.
Some of these regulatory proteins include splicing activators proteins that promote certain splicing sites and splicing repressors proteins that reduce the use of certain sites. Some common splicing repressors include: heterogeneous nuclear ribonucleoprotein hnRNP and polypyrimidine tract binding protein PTB.
Proteins that are translated from alternatively-spliced messenger RNAs differ in the sequence of their amino acids which results in altered function of the protein. This is one reason why the human genome can encode a wide diversity of proteins. Alternative splicing is a common process that occurs in eukaryotes; most of the multi-exonic genes in humans are spliced alternatively. Unfortunately, abnormal variations in splicing are also the reason why there are many genetic diseases and disorders.
Mechanism of Splicing : Alternative splicing can result in protein isoforms. The splicing of messenger RNA is accomplished and catalyzed by a macro-molecule complex known as the spliceosome.
Interactions between these sub-units and the small nuclear ribonucleoproteins snRNP found in the spliceosome create a spliceosome A complex which helps determine which introns to leave out and which exons to keep and bind together. Once the introns are cleaved and removed, the exons are joined together by a phosphodiester bond.
As noted above, splicing is regulated by repressor proteins and activator proteins, which are are also known as trans-acting proteins. Equally as important are the silencers and enhancers that are found on the messenger RNAs, also known as cis-acting sites. These regulatory functions work together in order to create splicing code that determines alternative splicing.
Like transcription, translation is controlled by proteins that bind and initiate the process. In translation, before protein synthesis can begin, ribosome assembly has to be completed. This is a multi-step process. In ribosome assembly, the large and small ribosomal subunits and an initiator tRNA tRNA i containing the first amino acid of the final polypeptide chain all come together at the translation start codon on an mRNA to allow translation to begin.
First, the small ribosomal subunit binds to the tRNA i which carries methionine in eukaryotes and archaea and carries N-formyl-methionine in bacteria. Because the tRNA i is carrying an amino acid, it is said to be charged. Next, the small ribosomal subunit with the charged tRNA i still bound scans along the mRNA strand until it reaches the start codon AUG, which indicates where translation will begin. The start codon also establishes the reading frame for the mRNA strand, which is crucial to synthesizing the correct sequence of amino acids.
A shift in the reading frame results in mistranslation of the mRNA. The anticodon on the tRNA i then binds to the start codon via basepairing. The complex consisting of mRNA, charged tRNA i , and the small ribosomal subunit attaches to the large ribosomal subunit, which completes ribosome assembly.
These components are brought together by the help of proteins called initiation factors which bind to the small ribosomal subunit during initiation and are found in all three domains of life. In addition, the cell spends GTP energy to help form the initiation complex. Once ribosome assembly is complete, the charged tRNA i is positioned in the P site of the ribosome and the empty A site is ready for the next aminoacyl-tRNA. The polypeptide synthesis begins and always proceeds from the N-terminus to the C-terminus, called the N-to-C direction.
In eukaryotes, several eukaryotic initiation factor proteins eIFs assist in ribosome assembly. Translation is ready to begin. The binding of eIF-2 to the 40S ribosomal subunit is controlled by phosphorylation. Therefore, the 43S complex cannot form properly and translation is impeded. When eIF-2 remains unphosphorylated, it binds the 40S ribosomal subunit and actively translates the protein.
Translation Initiation Complex : Gene expression can be controlled by factors that bind the translation initiation complex. The ability to fully assemble the ribosome directly affects the rate at which translation occurs. But protein synthesis is regulated at various other levels as well, including mRNA synthesis, tRNA synthesis, rRNA synthesis, and eukaryotic initiation factor synthesis.
Alteration in any of these components affects the rate at which translation can occur. A cell can rapidly change the levels of proteins in response to the environment by adding specific chemical groups to alter gene regulation. Proteins can be chemically modified with the addition of methyl, phosphate, acetyl, and ubiquitin groups. The addition or removal of these groups from proteins regulates their activity or the length of time they exist in the cell.
Sometimes these modifications can regulate where a protein is found in the cell; for example, in the nucleus, the cytoplasm, or attached to the plasma membrane. Chemical modifications occur in response to external stimuli such as stress, the lack of nutrients, heat, or ultraviolet light exposure.
These changes can alter protein function, epigenetic accessibility, transcription, mRNA stability, or translation; all resulting in changes in expression of various genes. This is an efficient way for the cell to rapidly change the abundance levels of specific proteins in response to the environment.
Because proteins are involved in every stage of gene regulation, the phosphorylation of a protein depending on the protein that is modified can alter accessibility to the chromosome, can alter translation by altering transcription factor binding or function , can change nuclear shuttling by influencing modifications to the nuclear pore complex , can alter RNA stability by binding or not binding to the RNA to regulate its stability , can modify translation increase or decrease , or can change post-translational modifications add or remove phosphates or other chemical modifications.
All of these protein activities are affected by the phosphorylation process. The enzymes which are responsible for phosphorylation are known as protein kinases. The addition of a phosphate group to a protein can result in either activation or deactivation; it is protein dependent. Another example of chemical modifications affecting protein activity include the addition or removal of methyl groups. Methyl groups are added to proteins via the process of methylation; this is the most common form of post-translational modification.
The addition of methyl groups to a protein can result in protein-protein interactions that allows for transcriptional regulation, response to stress, protein repair, nuclear transport, and even differentiation processes. Methylation on side chain nitrogens is considered largely irreversible while methylation of the carboxyl groups is potentially reversible. Methylation in the proteins negates the negative charge on it and increases the hydrophobicity of the protein.
Methylation on carboxylate side chains covers up a negative charge and adds hydrophobicity. The addition of this chemical group changes the property of the protein and, thus, affects it activity. The addition of an ubiquitin group to a protein marks that protein for degradation. Ubiquitin acts like a flag indicating that the protein lifespan is complete.
These proteins are moved to the proteasome, an organelle that functions to remove proteins to be degraded. Ubiquitin Tags : Proteins with ubiquitin tags are marked for degradation within the proteasome.
Altogether, Henriques et al. Profound challenges in the field remain to be resolved to further clarify enhancer mechanisms. A major challenge is to rigorously assign functional enhancer—promoter connections and quantify enhancer strength with regard to each target gene in its endogenous context. Another challenge is identifying enhancers genome-wide. These results indicate that enhancers are difficult to distinguish from promoters by histone modification patterns alone and highlight the utility of using unstable bidirectional transcription for enhancer identification.
The features and mechanisms that specify rapid Pol II termination and eRNA instability at these sites remain to be fully identified. Enhancers and promoters share many features, including similar sequence motifs, transcription machinery, chromatin environment, and changes in activity upon binding of activators or repressors Core et al.
However, the functional role of transcription from enhancers remains elusive. It is tempting to speculate that transcription itself helps mediate enhancer—promoter colocalization, perhaps through Pol II's affinity for common coactivators such as Mediator, CBP, Integrator, remodeling complexes, and histone modifiers.
Alternatively, transcription may simply maintain open and active chromatin architecture for example, Scruggs et al. Either model of transcription-driven enhancer and promoter connectivity helps to explain their extreme similarities in initiation and pausing behaviors.
We apologize to authors whose work could not be cited in this brief communication. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of Health. View all Enhancer transcription: what, where, when, and why? Nathaniel D. Tippens 1 , 2 , Anniina Vihervaara 1 and John T. Previous Section Next Section. Previous Section. Science : — Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.
Nat Genet 46 : — CrossRef Medline Google Scholar. Genome-wide characterization of mammalian promoters with distal enhancer functions. Nat Genet 49 : — Google Scholar. Widespread transcriptional pausing and elongation control at enhancers. Genes Dev this issue. Further Exploration Concept Links for further exploration cis-regulatory element transcription transcription factor DNA promoter. Related Concepts 5. You have authorized LearnCasting of your reading list in Scitable.
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