Control of Gene Expression in Eukaryotes
Introduction to Control of Gene Expression in Eukaryotes
Regulation of gene expression is significantly more complex and finely tuned in eukaryotes compared to prokaryotes.
Multicellular eukaryotes face unique demands that necessitate intricate control mechanisms:
Cell Differentiation: Creating various specialized cell types (e.g., muscle cells, neurons, skin cells) from a single genome, each expressing a distinct set of genes.
Development: Orchestrating the precise timing and location of gene expression during embryonic development and throughout the organism's life.
Differential gene expression: This fundamental process is responsible for:
Forming specialized cell types with unique structures and functions.
Arranging these diverse cells into complex tissues and organs.
Coordinating cell activity across the entire organism to maintain homeostasis and respond to environmental changes.
Ultimately, forming and maintaining the structure and function of multicellular organisms.
Levels of Gene Expression Control in Eukaryotes
Gene expression in eukaryotes can be controlled at multiple, distinct levels, providing numerous checkpoints for regulation. These levels include:
Chromatin Remodeling: Regulating access to DNA by altering chromatin structure (unique to eukaryotes).
Transcriptional Control: Regulating when and how often a gene is transcribed into mRNA.
RNA Processing: Regulating splicing, capping, and polyadenylation of pre-mRNA (unique to eukaryotes).
mRNA Transport: Controlling the movement of mRNA from the nucleus to the cytoplasm (unique to eukaryotes).
Translational Control: Regulating the rate at which mRNA is translated into protein.
Post-Translational Control: Regulating the modification, activation, or degradation of proteins after translation.
Chromatin Remodeling
Overview
Cells detect various internal and external molecular signals (e.g., hormones, growth factors) that induce or repress gene expression.
For a gene to be transcribed, the DNA containing that gene must be made physically accessible to the transcription machinery.
Chromatin remodeling is the dynamic process required to decondense specific regions of DNA, making them accessible for transcription factors and RNA polymerase.
Chromatin Structure
Eukaryotic DNA is highly organized and complexed with proteins to form chromatin:
Histones: Small, positively charged proteins (H2A, H2B, H3, H4, plus linker histone H1) that DNA wraps around. Their positive charge allows them to bind tightly to the negatively charged DNA phosphate backbone.
Nucleosomes: The fundamental repeating unit of chromatin, consisting of approximately 146 base pairs of DNA wrapped nearly twice around an octamer of histone proteins (two copies each of H2A, H2B, H3, and H4).
30nm Fiber: Nucleosomes are further coiled and folded into a 30nm diameter fiber, often stabilized by the H1 linker histone.
Higher-order structures: The 30nm fiber is then organized into even more complex, compact structures within the nucleus, especially during mitosis.
This extensive compaction restricts access for RNA polymerase and other transcription factors, therefore, for transcription to occur, chromatin must be remodeled to an 'open' state.
Accessing Genes through Remodeling
The stretch of DNA that contains the promoter and other regulatory sequences must be released from its condensed state to allow access for RNA polymerase and general transcription factors.
The DNA transitions from a highly condensed, inaccessible “closed” chromatin state (often referred to as heterochromatin) to a decondensed, accessible “open” chromatin state (known as euchromatin), facilitating transcription initiation.
Evidence of Chromatin Structure and Function
Research Example
Researchers Weintraub and Groudine provided early evidence for the dynamic nature of chromatin structure using DNase I, an enzyme that non-specifically cuts DNA.
Mechanism: DNase I cannot cut tightly condensed DNA (chromatin in the 'closed' state), as its active site is physically blocked.
Observation: However, actively transcribed genes (chromatin in the 'open' state) are preferentially cut by DNase I because their DNA is less tightly packed and thus more exposed. Conversely, inactive genes in the same cell show resistance to DNase I, akin to total DNA.
This differential sensitivity directly demonstrated that active genes reside in a more open and accessible chromatin configuration.
Mechanisms of Chromatin Remodeling
Key players involved in the dynamic processes of chromatin remodeling include:
DNA methylation.
Histone modification.
Chromatin-remodeling complexes.
DNA Methylation
Mechanism
DNA methyl transferases: These are a family of enzymes that catalyze the addition of a methyl group (CH_{3}) covalently to the 5'-carbon of cytosine bases in DNA.
In mammals, these enzymes preferentially target cytosine residues that are followed by a guanine base, forming CpG sites. Clustered CpG sites (CpG islands) are often found in gene promoters.
Effects of Methylation
Methylated CpG sequences have two primary effects on gene expression:
Blocking Transcription Factor Binding: The bulky methyl groups can physically impede the binding of general and regulatory transcription factors to the promoter region.
Recruiting Repressor Proteins: Methylated CpG sites are recognized by specific proteins (e.g., methyl-CpG-binding proteins - MeCPs) that, in turn, recruit other proteins which trigger chromatin condensation (e.g., histone deacetylases).
Actively transcribed genes typically have few or no methylated CpG sequences near their promoters (hypomethylated promoters), indicating an 'open' chromatin state conducive to transcription.
Histone Modification
Overview
Modifications to the N-terminal tails of histone proteins (which protrude from the nucleosome) can drastically alter the condensation state of DNA.
Various chemical groups can be enzymatically added or removed from specific amino acid residues (primarily lysines and arginines) on histone tails, including:
Acetyl groups: (CH_{3}CO)
Methyl groups: (CH_{3})
Phosphate groups: (PO_{4})
Longer peptide chains (e.g., ubiquitin).
These modifications can either promote chromatin decondensation (making DNA accessible) or chromatin condensation (making DNA inaccessible), contributing to a complex regulatory system known as the histone code. This code dictates which genes are expressed or silenced in a particular cell type.
Types of Enzymes Involved
Histone acetyltransferases (HATs): These enzymes add acetyl groups to positively charged lysine residues on histone tails.
Effect: Acetylation neutralizes the positive charge of lysine, which weakens the electrostatic interaction between histones and the negatively charged DNA. This leads to a looser nucleosome structure, promoting DNA decondensation and increased gene expression.
Histone deacetylases (HDACs): These enzymes remove acetyl groups from histone tails.
Effect: Deacetylation restores the positive charge to lysine residues, strengthening histone-DNA interactions and leading to chromatin condensation and gene repression.
Chromatin-Remodeling Complexes
Chromatin-remodeling complexes: These are large multi-protein molecular machines that play a significant, ATP-dependent role in gene regulation by directly altering nucleosome structure.
They utilize the energy from ATP hydrolysis to rearrange chromatin structure through several mechanisms:
Nucleosome Sliding: They can cause nucleosomes to slide along the DNA molecule, exposing previously hidden regulatory sequences or covering active ones.
Nucleosome Ejection: They can completely remove histones from a section of DNA, making it entirely accessible for transcription factors and RNA polymerase.
Histone Exchange: They can replace standard histones with variant histones that promote either more open or more closed chromatin states.
These actions enable the precise control of gene expression by dynamically opening or closing access to specific DNA regions.
Inheritance of Chromatin Modifications
Epigenetic inheritance: This refers to heritable mechanisms by which patterns of DNA methylation and histone modification are accurately passed from parent cells to daughter cells during cell division.
Unlike genetic inheritance, epigenetic inheritance does not involve changes to the underlying DNA sequence.
These modifications effectively act as a form of