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Chapter 11 – Chromosome Structure & DNA Sequence Organization

Lecture Overview

  • Lecture by: Cindy Malone from CSU, Northridge

  • Slide Modifications by: Dr. Richard Quintana Feliciano

  • Primary Text: Essentials of Genetics, 10e, Klug et al., 2020

  • Reference Texts: Genetic Analysis (Sanders & Bowman); Genetics (Brooker)

  • Copyright Notice: © 2020, 2016, 2012 Pearson Education, Inc. All rights reserved

Chapter Contents

  • 11.1 Viral and Bacterial Chromosomes Are Relatively Simple DNA Molecules

  • 11.2 Mitochondria and Chloroplasts Contain DNA Similar to Bacteria and Viruses

  • 11.3 Specialized Chromosomes Reveal Variations in the Organization of DNA

  • 11.4 DNA Is Organized into Chromatin in Eukaryotes

  • 11.5 Eukaryotic Genomes Demonstrate Complex Sequence Organization Characterized by Repetitive DNA

  • 11.6 The Vast Majority of a Eukaryotic Genome Does Not Encode Functional Genes

Chapter Concepts

  • Genetic Information and Organization:

    • In viruses and bacteria, genetic information is contained in short, circular DNA molecules that are free of associated proteins, resulting in relatively simpler DNA structures.

    • Eukaryotic Cells:

    • Contain large amounts of DNA organized into nucleosomes.

    • DNA present during most of the cell cycle as chromatin fibers.

    • During cell division, uncoiled chromatin fibers condense into visible chromosomes.

    • Eukaryotic genomes contain unique and repetitive DNA sequences, with a significant portion devoted to noncoding DNA.

Introduction to Chromosome Organization

  • DNA Composition:

    • DNA is organized into genes which are organized into chromosomes.

  • Technological Insights:

    • Molecular analyses using light and electron microscopy have shed light on chromosome organization.

    • Includes eukaryotic structures like polytene chromosomes and lampbrush chromosomes.

DNA Organization in Eukaryotes

Chromatin

  • Interphase Chromatin Structure:

    • During interphase, chromosomes unwind and form chromatin, which is dispersed throughout the nucleus.

    • Chromatin is replicated in this state.

  • Cell Division:

    • Chromatin condenses back into visible chromosomes during cell division.

Histones

  • Histone Composition:

    • Eukaryotic chromatin consists of histones (positively charged proteins) that bind chromosomal DNA.

    • Histones are essential for DNA organization and gene expression.

    • Types of Histones:

    • There are five main types: H2A, H2B, H3, H4, and H1.

    • All contain positively charged lysines and arginines, facilitating electrostatic bonding to DNA phosphates.

Chromatin Structure and Nucleosomes

  • Nucleosomes:

    • Composed of DNA wrapped twice around a histone octamer (two histone tetramers).

    • Each nucleosome contains:

    • Two H3-H4 dimers and two H2A-H2B dimers.

    • Length ≈ 11 nm and contains 147 base pairs (bp) of DNA.

    • Histone H1:

    • Binds to the spacer DNA between nucleosomes.

Higher Order Structure of Chromatin

  • Chromatin Fiber Composition:

    • Nucleosomes coil into a 10 nm fiber ("beads on a string"), further organized into 30 nm fibers (solenoid), and then into larger structures of 300 nm and 700 nm chromatid.

  • Histone Tail Modifications:

    • Histone tails can be modified (methylated, acetylated, phosphorylated) to regulate DNA organization and gene expression.

Chromatin Remodeling and Gene Expression

Chromatin Remodeling Mechanism

  • Importance in Epigenetics:

    • Chromatin remodeling is crucial for epigenetic mechanisms, allowing heritable changes in gene expression without altering the DNA sequence.

  • Accessibility of DNA:

    • Chromatin must relax to enable DNA-protein interactions and promote gene expression.

Observations from Studies

  • X-ray Diffraction:

    • Revealed the structural complexity of the DNA superhelix encircled by histones.

  • Histone Tail Structures:

    • Unstructured histone tails interact with adjacent nucleosomes, allowing dynamic modifications impacting their function.

Histone Code and Modifications

  • Histone Code Concept:

    • The pattern of chemical modifications of histones influences gene expression and overall genetic function.

  • Types of Modifications:

    • Enzyme-specific modifications include:

    • Acetylation: Histone Acetyltransferase (HAT) adds acetyl groups to histones, neutralizing positive charges and relaxing their grip on DNA, thereby facilitating gene activity.

    • Methylation: Primarily done by histone methyltransferases, affecting transcription levels.

    • Phosphorylation: Introduced by kinases, which add phosphate groups, influencing cell cycle and DNA replication by imparting a negative charge.

CpG Islands

  • Definition:

    • Cytosine can be methylated to form 5-methylcytosine, typically silencing gene expression.

  • Mechanism:

    • Most common when a cytosine nucleotide is adjacent to a guanine nucleotide, forming CpG islands.

Chromatin Types: Euchromatin vs. Heterochromatin

  • Chromosome Diversity:

    • Chromosomes are not uniform; some sections are euchromatin (active, uncoiled, unstained) and some are heterochromatin (condensed, mostly inactive, stained dark).

    • Examples of Heterochromatin Locations:

    • Centromeres, telomeres, Y chromosome, Barr bodies.

Chromosome Banding Patterns

  • Gene Expression and Chromatin:

    • The positional effect of heterochromatin can influence gene expression.

  • Mitotic Chromosome Staining:

    • Characteristic banding patterns can be observed through different staining techniques:

    • G-banding: Stains across the length of chromosomes.

    • C-banding: Stains only the centromeres (heterochromatin).

Specialized Chromosomes and Their Variants

Polytene Chromosomes

  • Characteristics:

    • Found in Drosophila and some plants, visible due to distinctive chromomeres (bands).

  • Replication:

    • DNA undergoes multiple rounds of replication without strand separation, resulting in large puffs reflecting gene expression regions.

Lampbrush Chromosomes

  • Discovery:

    • First identified in the oocytes of sharks.

    • Display extensive looping of DNA; loops contain one DNA helix and the axis may contain two helices.

  • Structural Features:

    • Numerous condensed regions (chromomeres) with homologs connected via chiasmata.

Genomic Complexity in Eukaryotes

Pseudogenes

  • Functional Role:

    • Noncoding DNA that results from mutations and represents remnants of functional genes.

    • Comprises approximately 2-10% of the eukaryotic genome.

Viral and Bacterial Chromosomes

Overview of Simplicity

  • General Structure:

    • Viral and bacterial chromosomes are mostly single molecules with limited associated proteins, making them smaller than eukaryotic chromosomes.

Viral Genetic Material

  • Composition:

    • Viral chromosomes can exist as either DNA or RNA, being single or double-stranded, and can be circular or linear.

    • Examples:

    • Phage lambda (linear dsDNA), ΦX174 (circular ssDNA).

Bacterial Chromosomes

  • Structure:

    • Primarily circular, double-stranded DNA compacted in the nucleoid, specifically in E. coli.

    • Associated Proteins:

    • Histone-like proteins (e.g., HU, H-NS) assist in compaction by creating coils.

Nucleoid Organization

  • Observation and Imaging:

    • Bacterial nucleoids display fluorescent regions within the cytoplasm, showcasing organizational complexity with core areas and extruding loops called microdomains.

Mitochondria and Chloroplasts: DNA Characteristics

Mitochondrial DNA (mtDNA)

  • Nature:

    • Exists as double-stranded, circular DNA, typically without chromosomal proteins.

    • Lacks introns and exhibits minimal gene repetition.

  • Inheritance:

    • Maternal inheritance allows tracing ancestry; sperm contributes negligibly to offspring mitochondria.

    • Example: MERRF syndrome (a mitochondrial disease).

Chloroplast DNA (cpDNA)

  • Characteristics:

    • Circular, double-stranded DNA without associated proteins.

    • Contains more genes and introns compared to mtDNA, serving critical roles in photosynthesis for plant life.

Eukaryotic DNA Sequence Organization

Repetitive DNA

  • Categories:

    • Includes various classes of repetitive DNA sequences; many functional genes exist in multiple copies.

  • Importance:

    • Majority of repetitive sequences do not encode proteins and are beneficial for genomic structure.

Satellite DNA

  • Density Variation:

    • Eukaryotic DNA analyzed for density variations, with satellite DNA representing highly repetitive DNA sections found at heterochromatic regions.

Centromeric DNA Sequences

  • Function:

    • Essential for homolog separation during cell division.

    • The CEN region is a crucial component that supports chromosomal segregation by binding to kinetochore proteins.

Moderate Repetitive Sequences

  • Variable Number Tandem Repeats (VNTRs):

    • Serve as a basis for DNA fingerprinting; found between genes.

  • Short Tandem Repeats (STRs):

    • Repeated sequences (e.g., (CA)n) characterized by variable repetition counts, important in genetic mapping.

Repetitive Transposable Sequences

  • SINEs and LINEs:

    • Examples of dispersed elements; SINEs are <500 bp (e.g., Alu family), and LINEs approximately 6 kb (e.g., L1 family).

    • LINEs considered retrotransposons due to their RNA-based replication mechanisms.