Gene Expression Regulation

• Gene expression, which leads to a functional protein, can be regulated at multiple stages.
• These stages include:
  • Transcription
  • Processing of the primary transcript
  • mRNA stability
  • mRNA translation
  • Polypeptide processing and assembly, including necessary cofactors
  • Enzyme or protein activity control
  • Protein degradation

Positive and Negative Regulation

• Gene expression is controlled through both positive and negative regulation mechanisms.
• In positive regulation, a gene requires a positive signal, such as a hormone, to be expressed.
• In negative regulation, a gene is inherently active but needs the removal of inhibitory factors to express itself.
• Negative regulation is relatively uncommon in higher organisms but more prevalent in bacteria.

Transcription Regulation

• At the level of transcription, regulation involves several steps:
  • Access to coding DNA via acetylation to open histones.
  • RNA polymerase must recognize the promoter using general transcription factors.
  • Initiation and RNA synthesis are controlled by activator proteins and repressors, that can inhibit RNA polymerase.
  • Elongation regulation is rare.
  • Usually, RNA polymerase stops at terminator sites.

Gene Expression in Eukaryotes

• Eukaryotes possess more genes than bacteria and regulate gene expression differently.
• These regulations can vary according to tissues and stages of development.
• Eukaryotic genes are sequestered in the nucleus.
• Eukaryotic DNA is condensed in nucleosomes and covered with histones.
• Transcriptional control in eukaryotes is orchestrated by transcription factors (TFs).
• General TFs bind at core promoter sites with RNA polymerase.
• Sequence-specific TFs bind to various regulatory sites of specific genes.
• General transcription factors are required for transcription initiation and proper RNA polymerase binding to DNA.
• Specific transcription factors increase transcription in certain cells or in response to signals.
• General transcription factors bind to the promoter region of a gene to facilitate subsequent transcription.
• RNA polymerase II binds to the promoter to begin the transcription at the start site (+1).
• Transcription factor binding sites exist within the DNA's cis-regulatory elements, known as promoters and cis-regulatory modules (enhancers).
• Genes' promoters help RNA polymerase and the general transcription factors bind, and is the DNA sequence surrounding the transcription start site.

Specific Transcription Factors

• They regulate protein-encoding genes.
• Typically, they share four general properties:
  • Responding to a stimulus that signals gene activation.
  • Capability of entering the nucleus unlike most proteins.
  • Recognizing and binding to a specific DNA sequence.
  • Making contact with the transcription apparatus either directly or indirectly.
• Transcription factors usually feature at least two domains: one for DNA binding and another for interacting with the transcription apparatus.
• Coactivators and mediators aid the function of transcription factors.
• They bind to transcription factors and parts of the transcription apparatus, and transmit signals from activator proteins to general TFs.

Enhancers and Insulator Sequences

• Cis-regulatory Modulators
• They can be thousands of bases away, either before or after the promoters they control.
• DNA looping allows activator proteins at the enhancer to contact the transcription apparatus via the mediator complex (or coactivators).
• A single enhancer can control several genes in its vicinity.

Chromatin Changes

• Difficulty in access to DNA
• Densely packaged DNA is heterochromatin, which is not transcribed.
• Histone H1 tails contain lysine residues, that can be acetylated or deacetylated..
• All four core histones, namely H2A, H2B, H3, and H4, can be acetylated.
• Heterochromatin is highly condensed, restricting the access of transcriptional enzymes to the DNA.
• Acetylation/deacetylation of histones and methylation of cytosine form inactive DNA.
• DNA methylation and histone deacetylation repress transcription.
• The degree of acetylation affects nucleosome aggregation and gene expression.
• Non-acetylated histones form more condensed heterochromatin, whereas acetylated histones form less condensed chromatin.
• Histone acetyltransferases (HATs) add acetyl groups, and histone deacetylases (HDACs) remove them.
• A generalized sequence of events for activation of a eukaryotic gene:
  • A transcription factor binds to the DNA.
  • Histone acetyl transferase binds to this trancription factor.
  • HAT acetylates histones, loosening nucleosome association.
  • Chromatin remodeling complex rearranges nucleosomes, which then allows binding access to the DNA
  • Further transcription factors binding
  • RNA polymerase binds to the DNA
  • Initiation requiring a positive signal transmitted via the mediator complex.
• Transcription regulators work together.

DNA Methylation

• In eukaryotes, it controls gene expression.
• DNA methylation is essential for long-term inactivation of genes during cell differentiation and gene imprinting in mammals.
• Methylation constantly silences the maternal or paternal allele of a gene in early development.
• Certain genes are expressed in a parent-of-origin-specific way, known as epigenetic inheritance.
• A small percentage of newly synthesized DNAs (around 3% in mammals) are chemically modified by methylation.
• Methylation mainly occurs in symmetrical CG sequences.
• Transcriptionally active genes show lower levels of methylated DNA than inactive genes.
• A gene for methylation is essential for development in mice.
• Methylation results in fragile X syndrome, caused by FMR-1 gene silencing.
• DNA methylation is a marker for genes involved in tissue differentiation, usually CG for animals.

Methylases

• Maintenance : They add methyl groups to locations during chromosome division.
• De novo: They add/remove methyl groups.
• There are two normal methylation processes in eukaryotic cells:
  • De novo methylation is involved embryogenesis or differentiation processes in adult cells.
  • Maintenance methylation maintains the established methylation pattern.
• Two mechanisms alter the pattern of methylation:
  • Passive demethylation when DNMT1 fails.
  • Active demethylation is performed by a recently described demethylase.
• Methylation in eukaryotes silences gene expression.
• Housekeeping genes, expressed in all tissues, have nonmethylated CG-islands.
• CG-islands of genes are nonmethylated in tissues where the genes are expressed.
• Most DNA methylation patterns are erased after fertilization, and newly modified patterns are made.

Genetic Imprinting

• In eukaryotes, its basis lies in DNA methylation patterns.
• It occurs when methylation patterns from the gametes survive the formation of the zygote and affect gene expression.
• It ensures that only one of a pair of some alleles in a diploid cell is expressed.
• The other copy is silenced by methylation, where the choice is based on its parental origin.

X-Chromosome Inactivation

• In female XX animals
• It is a specific form of imprinting in animals.
• Females have two X chromosomes, while males have one.
• Evolution has created varied mechanisms for gene dosage compensation to balance gene expression in males and females.
• In mammals, one of the X-chromosomes in each female cell is silenced through methylation of the Xist gene on the chromosome.
• The Xist gene causes the inactivation of the X-chromosome that carries it.
• X-inactivation involves the Xist gene and Xist RNA.

Gene Regulation Summary

• Regulation of gene expression involves complex interactions between transcription factors, DNA sequences, chromatin structure, and epigenetic factors.
• Transcriptional regulation features involves transcription and DNA sequences like enhancers and suppressors, modulating gene expression.
• Chromatin changes control DNA accessibility via chromatin remodeling, including modifications that regulate chromatin structure and gene accessibility.
• DNA methylation controls gene expression through chromatin structure.
• DNA methylation is heritable and is altered by environmental factors.
• X-chromosome inactivation equalizes gene expression between sexes in female XX individuals.