Chapter 11 Genetics

GENETIC
AN I NTE G RATE D APPR OAC H
A N A LY S I S
Chapter 11
Chromosome Structure
Lectures by Kathleen Fitzpatrick Erin Kelleher Simon Fraser University
2/25/14
Mark F. Sanders
John L. Bowman
Copyright 2012 Pearson Education Inc.
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
Genetics Analysis: An Integrated Approach
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Genetics Analysis: An Integrated Approach Copyright 2012 Pearson Education Inc.
Bacterial and Archaeal chromosomes are compacted into the nucleoid
How does this process occur? 1) Proteins help package the DNA 2) 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
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 20,0001000,000 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
Centromeric nucleosomes facilitate attachment of the kinetochore
Centromeric nucleosome
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
Banding and Chromosome Structure

Prior 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

Fluorescent In-Situ Hybridization (FISH), chromosome painting
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Chromosome painting an alternative strategy to identification by G-band
Structural Rearrangements in Human Cancers
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
- 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
Acetyl groups
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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
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
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
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Chapter 11 Genetics

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GENETIC

AN I NTE G RATE D APPR OAC H

Lectures by Kathleen Fitzpatrick Erin Kelleher Simon Fraser University

Copyright 2012 Pearson Education Inc.

11.1 Bacterial and Archaeal Chromosomes Are Simple in Organization

Genetics Analysis: An Integrated Approach

Bacterial and Archaeal chromosomes are compacted into the nucleoid

Proteins Associated with Chromosomes

11.2 Eukaryotic Genomes

Eukaryotic Chromosome Shapes

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

Chromatime that is only packaged by nucleosomes resembles beads on a string

Higher Levels of Chromatin Compaction

Highest order packaging, interphase and metaphase

Higher-Order Chromatin Condensation

The Radial-Loop Scaffold Model

Roles of Higher-Order Chromatin Condensation

Heterochromatin and Euchromatin

Centromeres exhibit unique packaging

Centromeric nucleosomes facilitate attachment of the kinetochore

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

Budding yeast are weird

Variable Chromatin Condensation and Chromosomal Banding

Banding and Chromosome Structure

XXX, XO, XXY

Fluorescent In-Situ Hybridization (FISH), chromosome painting

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

Chromosome painting an alternative strategy to identification by G-band

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

Structural Rearrangements in Human Cancers

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

Nucleosome Distribution and Synthesis During Replication

Nucleosomes and Gene Expression

Epigenetics and Histone Modification

Important Features of Epigenetic Modification

2. Transmissible during cell division

Drosophila as a model for chromatin modification

Su(var) and E(var) Mutations

Su(var) genes, HP-1 and HMT

Su(var) Mutant Cell

Chromatin remodeling and X-chromosome inactivation

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

XIST- X inactivation specific transcript

Eukaryotic Interphase Chromosome Territories

Genetics Analysis: An Integrated Approach

Copyright 2012 Pearson Education Inc.

Copyright 2012 Pearson Education Inc.

Centromeric clustering in yeast

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