10.2: Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.

Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a protein. This happens through mRNA splicing, which involves the removal of non-coding regions and merging of the coding ones. mRNA processing can also be used as a regulatory mechanism through variation in splicing patterns such as skipping of certain exons, alternative splicing, and inclusion of introns.

The addition of a poly-A tail at the 3’ end and a 5’ cap to produce the mature mRNA are also regulatory points during RNA processing. Regulation occurs through variation in the polyadenylation signal, which determines where the poly-A tail will be added onto the mRNA. In some cases, more than one poly-A signal is present at the 3’ end which will change the length of the 3’ untranslated region, but the final protein product will be the same. However, the stability and the translation potential the variants mRNA may differ, which can alter the amount of protein produced. In other cases, an additional poly-A signal is present on the intron or exon within the gene sequence which may lead to variation in splicing sites for polyadenylation and result in different proteins from the same strand of pre-mRNA.The addition of the 5’ cap, which is made up of methylated guanosine, is regulated by two mechanisms. One involves the regulation of the methyltransferases that add the methyl group to the guanosine, and the other is through regulation of the cellular signaling pathways that lead to methylation.

Next, the mature mRNA needs to be transported from the nucleus to the cytoplasm through nuclear pore complexes (NPCs) to be translated. This is regulated by the mRNA to forming a complex, known as the ribonucleoparticle, with RNA binding proteins. NPCs only allow mRNAs that are in the complex to pass into the cytoplasm. Once an mRNA enters the cytoplasm for translation, it can either be targetted individually or as a part of a group through specific regulations, or it can undergo a common regulation with all other mRNAs in the cytoplasm. In specific regulation, particular trans-acting elements, like proteins and different types of RNAs, regulate transcription. In general regulation, the proteins involved in the translation machinery are activated or inhibited, which in turn affects the translation of all transcripts. The most common translational regulatory mechanism is the modification of the translation initiation factor.

Gene expression can also be regulated through post-translational modifications, where an enzyme-catalyzed reversible modification can alter the function of a protein. A common post-translational modification is phosphorylation, which is carried out by enzymes known as kinases. Dephosphorylation of proteins, on the other hand, is carried out by proteins known as phosphatases. Phosphorylation of a protein can result in its activation or deactivation and alter its function.

Cells can precisely regulate gene expression at every step, from DNA to protein. This regulation occurs during transcription; during RNA processing, localization, and degradation; and during and after translation. 

Transcriptional regulation is mediated by proteins that bind to regulatory sequences on DNA. These transcription factors are one of the most common ways to control gene expression and can either initiate transcription or prevent it.

Transcription generates pre mRNA that must be processed to mature mRNA through several regulated processes. 

mRNA splicing, which removes the non-coding regions in precursor mRNA and joins the coding ones, controls gene expression through differential splicing patterns and RNA binding proteins.  The addition of a poly-A tail and a 5’ cap to produce the mature mRNA is also controlled.

Next, the mRNA must associate with RNA binding proteins to form a complex known as a ribonucleoparticle. This process is highly regulated, and only an mRNA that exists in a ribonucleoparticle can be transported from the nucleus to the cytoplasm to be translated.

Translational control is another crucial point for the regulation of gene expression. Regulation can be specific, where an individual or a subset mRNAs are involved, or general, where most mRNA transcripts are affected. 

In specific regulation, inhibition of translation is controlled through interactions with trans-acting elements, such as proteins and certain types of RNA, including microRNAs and short interfering RNAs.

In general regulation, the various proteins involved in the translation machinery are activated or inhibited, which affects all transcripts.

Finally, post-translational modifications, such as phosphorylation, can either activate or deactivate proteins, while others, like ubiquitination, can lead to their degradation.