Download - Chapter 11 Genetics
Lectures by Kathleen FitzpatrickSimon Fraser University
Copyright © 2012 Pearson Education Inc. Mark F. Sanders John L. Bowman
G E N E T I CA N I N T E G R A T E D A P P R O A C H
A N A LY S I S Chapter 11Chromosome Structure
Erin Kelleher2/25/14
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11.1 Bacterial and Archaeal Chromosomes Are Simple in Organization
• Bacteria have single chromosomes that are almost always circular. However, some species have linear chromosomes, and some species have more than one chromosome
• When there are multiple chromosomes, the largest chromosome generally harbors the essential genes
• Plasmids – extrachromosomal circular DNAs that exist in more than one copy and carry non-essential genes (antibiotic resistance genes are common 2
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Bacterial and Archaeal chromosomes are compacted into the nucleoid
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How does this process occur?1) Proteins help package the DNA2) Supercoiling – DNA becomes tightly wound
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Proteins Associated with Chromosomes
• Small nucleoid-associated proteins participate in the DNA bending that contributes to folding and condensation of chromosomes
• Structural maintenance of chromosome (SMC) proteins: these attach directly to the DNA, holding it in coils or V-shapes to form large nucleoprotein complexes
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Supercoiling
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11.2 Eukaryotic Genomes
• Multiple chromosomes, always linear
• Proteins are involved in organizing, condensing and segregating chromosomes
• The DNA and associated proteins of a chromosome are called chromatin - each chromosome is approximately half DNA and half protein
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Eukaryotic Chromosome Shapes
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Chromatin Composition
• Each chromosome is approximately half DNA and half protein
• About half of the proteins are histone proteins, small basic proteins that tightly bind DNA
• The remaining proteins, the nonhistone proteins, are very diverse and perform a variety of tasks in the nucleus
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Histones
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Nucleosome Assembly
• Histones H2A and H2B assemble into dimers; H3 and H4 also form dimers
• Two H3-H4 dimers form a tetramer, after which two H2A-H2B dimers associate with it to form the octamer
• The wrapping of DNA around the nucleosome is the first level of DNA condensation, and compacts the DNA about sevenfold
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Chromatime that is only packaged by nucleosomes resembles beads on a string
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Higher Levels of Chromatin Compaction
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Highest order packaging, interphase and metaphase
interphase
metaphase
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Higher-Order Chromatin Condensation
• Chromatin loops of 20 to 100 kb are anchored to the chromosome scaffold by nonhistone proteins at sites called MARs (matrix attachment regions)
• The radial loop-scaffold model suggests that the loops gather into “rosettes” and are further compressed by nonhistone proteins
• Metaphase chromatin is compacted 250-fold compared to the 300-nm fiber
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The Radial-Loop Scaffold Model
• Chromatin loops in 20,000- 1000,000 bp
• Chromatin is packaged into loops by non-histone scaffold proteins that attach to Matrix Attachment Regions (MARs)
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Roles of Higher-Order Chromatin Condensation
• Chromosome compaction allows for efficient separation of chromosomes at anaphase
• The chromatin loops formed during condensation play a role in the regulation of gene expression
• Active transcription takes place in segments of loops distant from MARs; thus larger loops have more active transcription than small loops
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Heterochromatin and Euchromatin
• Chromosome condensation varies from one part of a chromosome to another
• Regions that contain actively expressed genes and are less condensed during interphase are called euchromatin
• Regions that remain condensed in interphase and contain many fewer expressed genes are called heterochromatin
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Types of Heterochromatin
• Facultative heterochromatin exhibits variable levels of condensation, related to levels of transcription of resident genes
• Constitutive heterochromatin is permanently condensed, found prominently in centromeres and telomeres, and composed primarily of repetitive DNA sequences
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Centromeres exhibit unique packaging
Normal nucleosome Centromeric nucleosome
The N-terminal tail of CENP-A allows the binding of kinetochore proteins to the centromere
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Centromeric nucleosomes facilitate attachment of the kinetochore
Centromeric nucleosome
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Budding yeast centromeres have consensus sequences that recruit centromeric nucleosomes
CDE I CDE II CDE III
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Budding yeast are weird
• Centromeric DNA sequences of all other eukaryotes are highly repetitive and constitutively heterochromatic
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Variable Chromatin Condensation and Chromosomal Banding
• Densely packed heterochromatin absorbs more stain and creates dark bands.
• Loosely packed euchromatin absords less stain and creates light bands
• Giemsa is the most commonly used stain so we call these “G-Bands”
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Banding and Chromosome StructurePrior to DNA sequencing, banding patterns allowed scientists to reliably identify chromosomes and define regions within those chromosomes
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Karyotyping• Reliable identification of
chromosomes also allows for us to identify aneuploid individuals – those with more or less than two copies of each chromosome
• Most common human aneuploidies• Down syndrome – trisomy 21• Trisomy 18 and 13• XXX, XO, XXY
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Fluorescent In-Situ Hybridization (FISH), chromosome painting
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Chromosome painting – an alternative strategy to identification by G-band
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Structural Rearrangements in Human Cancers
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Nucleosome Distribution and Synthesis During Replication• Nucleosomes interfere with DNA replication via DNA
polymerase.
• Therefore, nucleosomes must be removed from the DNA to allow for replication, then quickly replaced after DNA synthesis is complete
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Nucleosomes and Gene Expression
• Nucleosomes also interfere with the recruitment of RNA polymerase to initiate transcription.
• chromatin remodeling – nucleosomes are displaced to expose promoter and other regulatory sequences
• Chromatin remodeling relies on chemical modifications to histones in nucleosomes are epigenetic marks or epigenetic modifications
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Histone Modifications
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Acetyl groups
- histones are modified at their N-terminus
- methyl groups generally confer more compact chromatin that reduces gene expression
- acetyl groups generally confer more open chromatin that increases gene expression
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Epigenetics and Histone Modification
• Epigenetic – a heritable change in gene expression that is NOT caused by a change in DNA sequence
• Histone modifications are epigenetically heritable because they can be transmitted through cell division and across generations
• The retention of some old histones during DNA replication provides a mechanism for maintaining the modifications and passing them to daughter cells
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Important Features of Epigenetic Modification
1. Alters chromatin structure
2. Transmissible during cell division
3. Reversible
4. Directly associated with gene transcription
5. Does not alter DNA sequence
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Drosophila as a model for chromatin modification
• Position effect variegation – genes that are adjacent to heterochomatic regions exhibit variable expression due to variable spreading of heterochromatin
• To identify proteins involved in chromatin packaging, scientists look for genes that modify position effect variegation
• Mutations of these genes enhance or suppress the variegating phenotype, E(var) and Su(var)
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Su(var) and E(var) Mutations
• Several dozen E(var) and Su(var) mutations have been identified in Drosophila
• Genetic analysis supports the hypothesis that chromatin is dynamic and associated with gene expression
• Genes have been identified that encode proteins that make epigenetic marks on histone proteins (adding methyl, acetyl, and phosphoryl groups)
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Su(var) genes, HP-1 and HMT
• Methylated histone locations (e.g., H3K9me) are methylated by HMTs
• These act as sites of HP-1 binding, and help condense chromatin structure and silence gene expression
• Mutations in either gene lead to failure to remodel chromatin to a condensed state, and thus suppress variegation
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Wild-type Cell
Su(var) Mutant Cell
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Chromatin remodeling and X-chromosome inactivation
Random X-inactivation is a mechanism of dosage compensation, which equalized the expression of sex-linked genes between males and females
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XIST- X inactivation specific transcript
- XIST is expressed only from the X-chromosome that was randomly chosen for inactivation
- XIST coats the X and recruits HMTs
- Methylated histones recruit HP1 and forms a silenced X-chromsome (Barr body)
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Eukaryotic Interphase Chromosome Territories
Chromosome territory: a 3D space in the nucleus that is occupied by individual chromosomes
Interchromosome domain: channels for movement of proteins, enzymes, and RNA molecules
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Dynamic Chromosomes
• Chromosomes do not occupy the same territory in each nucleus, but once confined to a territory, a chromosome does not leave until the M phase is initiated
• However, chromosomes are active within their territories and move, twist, and turn during transcription and DNA replication
• Chromosomes appear to be anchored in their territories by their centromeres
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Centromeric clustering in yeast