Lecture 16: Chromosomes
Aims
To provide an overview of the main structural features of chromosomes and to consider how the genome is packaged into chromatin.
Learning Objectives
● Understand how DNA is packaged into chromatin and describe the structure and function of histones.
● Understand that chromosome structure changes at different phases of the cell cycle.
● Understand the structure-function relationships of telomeres, centromeres, replication origins and kinetochores.
● Understand that non-protein-coding DNA exists in the genome and be able to describe characteristics of repeated DNA elements.
● Describe the different types of eukaryotic transposable elements and their replication and transposition mechanisms.
Overview of Chromosome Structure and Genome Packaging
The primary structural features of chromosomes involve complex packaging of the genome into chromatin fibers.
Diploid eukaryotic cells contain two copies of each chromosome; each pair is distinct in size and DNA sequence.
Individual chromosomes are most easily distinguished during the metaphase of mitosis.
A karyotype is the organized representation of all the chromosomes in a eukaryotic cell at the metaphase stage.
Even during interphase, individual chromosomes are not randomly distributed; they occupy distinct subnuclear territories within the nucleus.
The Hierarchy of DNA Packaging into Chromatin
A chromosome is composed of a highly coiled fiber of chromatin.
Under an electron microscope, interphase chromatin appears as "beads on a string."
The "beads" are nucleosomes, which represent the initial level of DNA compaction.
The fiber consists of DNA wrapped around nucleosome cores.
The fiber is a supercoiled version of the beads-on-a-string array, providing further compaction.
DNA is packaged by histone octamers into a compact yet flexible chromatin scaffold.
This scaffold must be flexible enough to be re-modelled to accommodate large protein complexes required for gene transcription and DNA replication, provided the appropriate recruiting proteins are present.
Chromatin is engineered to allow flexible responses to changes in signaling pathways and cell differentiation status, which alter transcription factor activity.
Detailed Structure and Function of Histones
Biochemical analysis shows that nucleosomes consist of a protein core around which DNA is wound, similar to cotton on a bobbin.
The protein subunits of the nucleosome are known as core histones.
Subunit structure and interactions:
The nucleosome core contains a histone octamer made of eight subunits.
The N-terminal tails of these eight core histone subunits project outward from the nucleosome core.
These tails are free to interact with other proteins, facilitating the regulation of chromatin structure and function.
Linker Histones (e.g., H1):
Linker histones like H1 strap the DNA onto the histone octamer.
They limit the movement of DNA relative to the histone octamer.
This stabilization is crucial for the formation of the fiber.
H1 facilitates the establishment of heterochromatin, which is transcriptionally silent.
Dynamic Organization of Interphase Chromatin
Interphase chromatin comprises a set of dynamic "fractal globules."
Fractal globules are described as "globules within globules" that can reversibly condense and decondense without becoming knotted.
Subnuclear localization:
The nuclear periphery in interphase cells is primarily composed of transcriptionally inactive DNA.
Active RNA transcripts are excluded from the nuclear periphery.
Specialized DNA Sequences: Telomeres
Telomeres are specialized repetitive DNA sequences located at the ends of chromosomes.
They define the physical ends of the chromosome and are essential for maintaining chromosome integrity and preventing DNA loss.
The human telomeric repeat sequence is .
Telomeres are replicated by a specialized DNA Polymerase known as Telomerase.
Telomerase synthesizes single-stranded overhanging arrays of the repeat, which can reach several hundred nucleotides in length.
Specialized DNA Sequences: Centromeres and Kinetochores
Centromeres contain specialized proteins and DNA sequences that facilitate the segregation of duplicated chromosomes during cell division.
Chromosome segregation requires the attachment of chromosomes to the mitotic or meiotic spindle.
Centromeric Composition:
Centromeres contain alpha-satellite DNA repeats.
These repeats readily form condensed chromatin with histone octamers that contain unusual subunits.
The Kinetochore:
The kinetochore is the protein structure that facilitates attachment to the spindle.
Inner Plate proteins: These bind to the chromatin containing the alpha-satellite DNA.
Outer Plate proteins: These bind to the protein components of the mitotic spindle (microtubules).
This mechanism ensures the faithful segregation of sister chromatids during cell division.
In yeast, the kinetochore is characterized as a "basket" structure that links a single nucleosome of centromeric chromatin to a single microtubule.
Genome Composition and Protein-Coding Capacity
Total Genes: Account for roughly of the human genome.
Protein-Coding DNA: Only of the human genome actually encodes the information necessary to make cellular proteins.
Complexity Trends:
Increasing biological complexity is accompanied by an increasing number of protein-coding genes.
Complexity also correlates with increasing amounts of non-protein-coding DNA.
Role of Non-protein-coding DNA:
Used for regulating transcription and organizing access to protein-coding genes.
Contains cis-regulatory information which determines precisely when and where adjacent protein-coding genes are transcribed in the body.
Repeated DNA: Approximately of the human genome is composed of repeated DNA sequence elements.
Transposable Elements (Mobile Genetic Elements)
Transposable elements, or transposons, are mobile sequences that move within the genome. They make up nearly half of the DNA in the human genome.
There are three primary types of transposable elements:
1. DNA Transposons:
Move by a "cut-and-paste" mechanism without self-duplication.
Require the enzyme Transposase, which is encoded by the transposon itself.
Highly powerful mutagens.
Examples: P-element (found in flies), Tn3/Tn10 (found in E. coli), and the Activator-Dissociator system (Ac-Ds) in maize.
The Ac-Ds system was discovered by Barbara McClintock in 1952 through gene crossover experiments in maize, where dark pigments did not follow normal genetic patterns.
2. Retroviral Retrotransposons:
Behave similarly to retroviruses (e.g., HIV).
Replicate via RNA intermediates.
Produce new DNA copies that integrate at new genomic locations using self-encoded Reverse Transcriptase.
3. Non-retroviral PolyA Retrotransposons:
Abundant in vertebrate genomes.
Replicate via an RNA intermediate using self-encoded Reverse Transcriptase (copy-and-paste mechanism).
Examples: Long Interspersed Elements (LINEs, such as human L1) and Short Interspersed Elements (SINEs, such as human Alu and mouse B1).
L1 elements integrate directly into the genome at new locations without needing to be packaged into a virus-like particle.
L1 insertions can cause human disease by disrupting genes, such as in cases of Haemophilia.
Most copies of these elements in the genome are defective, ancient relics containing many mutations that prevent them from expressing functional proteins.
Evolutionary and Biological Significance of Genomic Expansion
Non-retroviral retrotransposons have expanded dramatically during the evolution of higher mammal genomes.
The human Alu and mouse B1 elements evolved from a single-copy RNA gene in a common ancestor.
Potential advantages of transposable element expansion include:
Genomic Expansion and Diversity: Increases total genome size, providing raw material for evolutionary processes.
Adaptation to New Environments: Insertions can create novel phenotypes, accelerating the rate of adaptation and speciation.
Gene Regulation: Some transposable elements have evolved into regulatory elements that control the expression of other genes.
Chromosomal Rearrangements: They can facilitate rearrangements that lead to the formation of new genes and gene families.
Genomic Stability: Certain elements contribute to the stabilization of chromosomal structures.
Vocabulary and Discussion
The following terms are central to understanding chromosome structure: cell, nucleosomes, Lax, base pairs, histones, chromosome, nucleus, chromatids, centromere, double stranded, and DNA.
Questions and Discussion items:
Composition of our genome: Highlights the disparity between total DNA and the that is protein-coding.
The nature of repeated DNA: Explored as "parasitic DNA" consisting of various retrotransposons.
Evolutionary impacts: Considering why organisms retain so many transposable elements given their mutagenic potential.