Theory

The process by which cells manage the expression and activity of genes is known as gene regulation. The gene regulation ensures that genes are expressed at the right times, in the right place and in the right amounts. It is necessary for healthy growth, cellular operation, and environmental change adaption. Gene expression are required to be carefully controlled so that they are correctly expressed. Gene expressions, can be controlled at many different level or stages.
These can be broadly classified as –

1. Chromatin Conformation
2. Gene Transcription
3. Nuclear RNA modification, splicing, turnover and transport
4. Cytoplasmic RNA turnover
5. Translation
6. Post- translational modification
7. Protein localization
8. Protein turnover

Chromatin Conformation

Regulation of gene expression depends upon the accessibility and structure of chromatin. Chromatin is basically complex of DNA and proteins that make up chromosomes. Regulation of gene expression depends upon the chromatin as it can be open or closed affecting the ability of RNA polymerase to transcribe genes. RNA polymerase is unable to access DNA when chromatin is densely packed, or condensed. Condensed chromatin usually has less accessible genes, which makes them less likely to be translated into RNA.

How to tackle this?

Chemical modifications to histones, such as acetylation of lysine residues, can alter chromatin structure. Acetylation typically relaxes chromatin, making it easier for RNA polymerase to access the DNA and transcribe genes. This modification thus promotes gene expression. And, on the other hand, methylation has opposite effect.
Example- Trimethylation of lysine (K)4 in histone H3 is associated with transcriptional activation, while di-methylation of K9 is associated with transcriptional silencing Illustration - Imagine a library where books (genes) are stored on shelves (chromatin). The arrangement of these shelves and the accessibility of books affect how easily librarians (RNA polymerase) can retrieve and read the books (transcribe genes into RNA).

Gene Transcription

The promoter contains many sequence elements like TATA box which functions to direct RNA polymerase II to the correct position on the gene to initiate transcription. Other sequence elements like CAAT and GC boxes are also found that enhances the activity of RNA polymerase. Thus, these sequence elements are often referred to as ‘core’ or ‘minimal’ promoter elements, as they help in binding of polymerase to the promoter and thus, initiates basal transcription.
These core promoters or sequencing elements play an important role in regulation of gene expression.

Illustration - Imagine a theater production where the goal is to stage a successful play (gene expression). The promoter elements in a gene function like key roles and signals in the theater to ensure the play starts on time and runs smoothly. RNA polymerase II is like a stage manager whose task is to ensure that everything runs smoothly. TATA box is like director’s cue in the script, that tells the manager exactly where to start the play. As the light technician ensures that play is more engaging, similar is the function of CAAT box to enhance the activity of RNA. The combined functions of these ensure that play runs smoothly similarly in biotechnology, the combined functions of promoter, sequence elements and RNA Polymerase II ensures that regulation of gene expression takes place effectively.

Example - Positive regulation of gene transcription occurs when a transcriptional factor (activator) turns on gene transcription. Negative regulation of gene transcription occurs when a transcription factor (repressor) turns off gene transcription. Transcription factors like NAC (no apical meristem (NAM), Arabidopsis transcription activation factor (ATAF), cup-shaped cotyledon (CUC)), MYB (myeloblastosis-related), WRKY (WRKY-domain containing proteins), bZIP (basic leucine zipper), AP2/ERF (Apetala2/ethylene-responsive factor), and zinc finger are vital for plant stress response.

RNA modification, splicing, turnover and transport

For functional mRNA to enter into cytoplasm for translation, a number of processes should take place. All these processes influence the gene expression in a way or other. Recognition of different splice sites may generate different transcripts from the same gene.
Example- the FCA gene, which encodes an RNA-binding protein, promotes photoperiod-independent flowering in Arabidopsis. The alternative splicing/processing of FCA protein regulates it’s spatial (The alternative splicing of the FCA transcript restricts the expression of the FCA protein to shoot and root apices and young flower buds) and temporal accumulation.

Translation

Translation regulation in response to various signals is an important step in regulating gene expression. The efficiency of translation initiation and elongation can be influenced by a variety of factors. The presence of 5’ cap and 3’ poly (A) tail in mRNA enhances translation. Further, specific nucleotide position is known for regulation of gene expression.
Thus, controlling these factors can effectively regulate the gene expression

Post translational modification

In order to be functional, proteins can be modified after translation as well. It is possible for the precursor protein to undergo proteolytic cleavage to produce signal peptides, which point proteins towards certain organelles or subcellular structures. Glycosylation, acetylation, or phosphorylation can all alter a particular residue. Many proteins' activities and locations are controlled by reversible changes in these modifications, including acetylation and phosphorylation.

Protein Localization

Cellular functions in plants are performed well, if proteins are delivered to the correct subcellular compartment to perform their specific roles. For proper regulation of gene expression, it is important that regulatory proteins reach to their target genes. Changes in cellular functions and responses can result from mislocalization of genes and disruption of cellular signalling networks and gene expression patterns.
Thus, protein localization is a tightly controlled mechanism that guarantees proteins are delivered to the appropriate subcellular compartments by targeted signals. The appropriate operation of cellular functions and overall cellular homeostasis depend on this precise localization.
Example- Protein localization signal for Nucleus is Nucleus localization signal (NLS).

Protein turnover

Protein turnover is an integral aspect of gene regulation because it controls the availability and activity of proteins, which are the final products of gene expression. The term "protein turnover" describes the continuous synthesis and breakdown of proteins in a cell. This equilibrium guarantees that misfolded, damaged, or unnecessary proteins are eliminated and replaced with fresh proteins.
Changes like acetylation control the stability of proteins. N-terminal amino acid acetylation has the potential to improve protein stability, which in turn may have an impact on the protein's effective concentration and subsequent consequences on gene regulation.