Lecture 17 - chromosome structure Flashcards
What are key topics in chromosome structure?
Packaging of DNA into chromatin fibres - a flexible substrate that enables:
- selective gene expression
- faithful replication and transmission of the genome to progeny
- Main structural elements of eukaryotic chromosomes
- Genome composition - genes, intergenic DNA & DNA repeats
- Transposable elements - repetitive DNA sequences that make up approximately half of the DNA in the human genome
How can individual chromosomes be easily distinguished at metaphase of mitosis?
- Diploid eukaryotic cells contain 2 copies of each chromosome
- Each chromosome pair differs in SIZE & DNA SEQUENCE
What is the karyotype?
The karyotype of the parent organism is the organized representation of all the chromosomes in a eukaryotic cell at metaphase (B)
Where do individual chromosomes reside?
Individual chromosomes occupy distinct subnuclear territories even in interphase nuclei
What is a chromosome?
A highly coiled fibre of chromatin
What does a chromosome look like under the electron microscope?
Interphase chromatin resembles ‘beads on a string’ - the beads are nucleosomes.
Describe the structure of the 30nm chromatin fibre - a supercoiled array of nucleosomes
Nucleosomes are the fundamental structural units of chromatin, which is the material that makes up chromosomes in the nucleus of eukaryotic cells. A nucleosome consists of a segment of DNA wrapped around a core of histone proteins. The structure of the nucleosomes helps package the long DNA molecule into a compact form, enabling it to fit within the cell nucleus
What does biochemical analysis of nucleosomes reveal?
Nucleosomes are made of a protein core around which DNA is wound
What are the protein subunits of the nucleosome called?
core histones
How many N terminal tails are seen on a histone?
The N-terminal tails of the 9 core histone subunit project out from the nucleosome core and are free to interact with other proteins, facilitating regulation of chromatin structure and function
How many projections are there and what do they facilitate?
8 (2x H3, H4, H2A, H2B)
They facilitate regulation of chromatin structure and function
What do linker histones do?
Linker histones such as H1 strap DNA onto histone octamers and limit movement of DNA relative to histone octamer
- stabilizes formation of 30nm fibre
- Facilitates the establishment of transcriptionally silent heterochromatin
What is DNA packaged into?
DNA is packaged by histone octamers into a COMPACT, FLEXIBLE 30NM chromatin scaffold that can be re-modelled to accommodate protein complexes involved in gene transcription & DNA replication - (if the appropriate proteins are recruited)
What are chromatin engineered to do?
Chromatin is engineered to permit flexible responses to altered transcription factor activity caused by changes in cell differentiation status & changes in signalling pathway activities
What is interphase chromatin made of?
Interphase chromatin comprises a set of dynamic “fractal globules” (globules within globules) that can reversibly condense & decondense without becoming knotted.
What is the nuclear periphery in interphase cells composed of?
- Composed of transcriptionally inactive DNA.
- RNA transcripts are excluded from the periphery
What is a summary of chromatin?
- chromosomes made up of tightly packed chromatin
- structure supported by nucleosomes
- these nucleosomes contain histones that package chromatin
- fractal globules allow condensing of chromatin in interphase cells
What do the specialised DNA sequences that chromosomes contain facilitate?
- Reliable and complete DNA replication
- Segregation of duplicated chromosomes during cell division
What are telomeres?
specialised repetitive DNA sequences at chromosome ends
What are telomeres replicated by?
Telomeres are replicated by specialized DNA polymerase called TELOMERASE
What do telomeres define?
Telomeres define chromosome ends and maintain chromosome integrity
What is the telomere nucleotide sequence?
Single-stranded 3’ overhanging TTAGGG repeats arrays are synthesized by the Telomerase enzyme and can be several hundred nucleotides long
What does chromosome segregation during cell division require?
It requires attachment of chromosomes to the mitotic/meiotic spindle
What do centromeres contain?
They contain specialised proteins and DNA sequences that facilitate chromosome segregation during cell division
Describe the make up of centromeres
They contain alpha-satellite DNA repeats - that readily form condensed chromatin with histone octamers containing unusual subunits
What does the kinetochore Inner plate proteins do?
They bind to chromatin containing alpha-satellite DNA
What does the kinetochore Outer plate proteins do?
They bind to protein components of mitotic spindle i.e. microtubules
What is part of the mechanism of kinetochores?
Part of the mechanism for ensuring faithful segregation of sister chromatids at cell division
What does kinetochores in yeast look like?
In yeast, the kinetochore is a basket that links a single nucleosome of centromeric chromatin to a single microtubule
How % of the genome is used to make genes?
20
What % of our genome encodes information for making cellular proteins
1.5%
Describe the genome of more complex organisms
More complex organisms have more protein coding genes and more non-protein-coding DNA
What accompanies increasing biological complexity?
a - increasing numbers of protein-coding genes
b - increasing amount of non protein-coding DNA - for regulating transcription and organization access to protein-coding genes
What does some of the non-protein-coding DNA encode?
Some of the non-protein-coding DNA encodes cis-regulatory information which determines where and when in the body adjacent protein-coding genes are transcribed
What % of the genome is made up of repeated DNA sequence elements?
50%
Most of these elements are copies of retrotransposons known as “parasitic DNA”
What are the 3 different types of repeated DNA sequences that make up 50% of the genome?
- DNA Transposons
- Retroviral retrotransposons
- Non-retroviral polyA retrotransposons
What are transposons?
They are mobile genetic elements that jump around the genome - also called ‘transposable elements’
What do DNA transposons do?
move by a cut-and-paste mechanism without self-duplication, requiring transposon-encoded enzyme Transposase.
e.g. P-element in fly, Activator-dissociator (maize), Tn3/Tn10 (E.coli)
They are powerful mutagens
What are retroviral retrotransposons?
behave like retroviruses (e.g. HIV) , replicating via RNA intermediates, producing new DNA copies that integrate at new genomic locations, using SELF-ENCODED REVERSE TRANSCRIPTASE
What are non-retro-viral PolyA retrotransposons?
They are abundant in vertebrate genomes & replicates via an RNA intermediate using its own retrotransposons-encoded Reverse Transcriptase - copy and paste
What are differences between retroviral retrotransposons & Non-retroviral polyA transposons?
Retroviral Transposons (ERVs): These are like old viruses that got stuck in our DNA a long time ago. They can make copies of themselves and insert those copies into new places in our DNA.
Anti-Retroviral Poly(A) Transposons (SINEs): These are short DNA pieces that don’t have the tools to copy themselves. They use tools from other elements (like LINEs) to make copies of themselves and insert them into new spots in our DNA.
What are examples of transposons?
- Human L1 elements (LINE-1 elements)
- Human Alu elements
- Mouse B1 elements
- Long Interspersed Elements - “LINEs”
- Short Interspersed Elements - “SINEs”
What are LINEs?
Long Interspersed Elements
What are SINEs?
Short Interspersed Elements
What occurs to products of L1 reverse transcription?
They are integrated directly into the genome at new locations without the need to be packaged into a virus-like particle
Some L1 insertions are known to disrupt geens and cause human disease e.gg. Haemophilia
Describe what occurs with most copies of DNA Transposons, Retroviral retrotransposons & non-retroviral polyA retrotransposons
Most of the copies of these elements in the genome are defective, ancient relicts of formerly functional elements, with many mutations that prevent expression of functional proteins.
Non-retroviral retrotransposons have expanded hugely in numbers during evolution of higher mammal genomes - e.g. human Alu and mouse B1 originally evolving from the single copy 7SL RNA gene in the common ancestor
What gene from a common ancestor did human Alu & mouse B1 come from?
7SL RNA
- Alu & B1 are SINEs (short-interspersed elements)
What is genomic expansion & diversity?
- They can increase genome size, providing more raw material for evolution
- They can create new genetic variation through recombination and creating new regulatory elements
What is gene regulation?
- They can evolve into regulatory elements that control gene expression
- They can influence the timing, location and level of gene expression
What is adaption to new environments?
- insertions can create novel phenotypes that may be advantageous in certain environments, which can accelerate the rate of adaption and speciation
What are chromosomal rearrangements?
retrotransposons can facilitate chromosomal rearrangements, which can lead to the formation of new genes & gene families
What is genome stability?
in some cases, retrotransposons can contribute to genomic stability by stabilising chromosomal structures
Summarise retrotransposons
The building blocks of chromatin are nucleosomes, which permit the reversible unfolding and compaction of chromatin that is needed to:
- allow gene transcription & DNA replication
- package DNA into the small volume of the nucleus and allow faithful segregation of the genome into daughters of dividing cells
Each linear chromosomes has 2 telomeres, a centromere and origins of replication. Telomeres prevent the loss of DNA sequences from chromosomal ends. Centromeres mediate chromosome attachment to the mitotic spindle via the kinetochore.
Genomes of more complex organism also have huge numbers of repeated DNA sequences - DNA transposons, retroviral retrotransposons & non-viral polyA retrotransposons are mobile geentic transposable elements, which make up almost half of the human genome.
