Lecture 4

• Genome Size Variation

  Genome sizes vary significantly among different life forms, from small bacterial genomes to much larger eukaryotic genomes
• Non-Coding DNA Proportion

  As genome sizes increase, the proportion of non-coding DNA also rises
• In simpler organisms like bacteria, the majority of DNA is coding, while in more complex organisms, such as humans, a large part of the genome consists of non-coding sequences
• Factors Contributing to Large Genome Sizes

  • Gene Duplication
  • Large Introns
  • Transposons
  • Repetitive DNA
  • Non-repetitive DNA
• Gene Duplication

  Families of genes and pseudogenes may share regulatory sequences, resulting in coordinated control of gene expression
• Large Introns

  Introns can be substantial in size and often contain sequences like retrotransposons
• Transposons

  Includes elements such as Long Interspersed Nuclear Elements (LINEs), Short Interspersed Nuclear Elements (SINEs), retroviruses, and retrotransposons
• Repetitive DNA

  Consists of simple sequence repeats and segmental duplications
• Non-repetitive DNA


  The part of the genome that does not include repetitive sequences
• Gene Duplication in Eukaryotes

  • Leads to families and super-families of genes within the genome
  • Genes in families can be dispersed or clustered, and the maintenance of clusters suggests functional coordination
• Multiple Hemoglobin Genes

  • Human hemoglobin is made of different subunits, whose genes are located on different chromosomes
  • The expression of these genes changes developmentally, enabling the transition from fetal to adult forms of hemoglobin
• Gene Size Variation in Eukaryotes

  • Gene sizes in eukaryotes can vary significantly; for instance, the human Huntingtin gene is much larger than its counterpart in the Fugu fish
  • This size variation is often due to the presence of large introns containing retrotransposons
• The human haploid genome is approximately 3.2 x 10^9 bp in length
• The human genome contains around 22,000 protein-coding genes and a large number of pseudogenes
• The largest human gene is the dystrophin gene, with over 2.4 million bp
• Highly Repetitive Elements

  Nearly half of the human genome is made up of repetitive elements, including transposons and retrotransposons
• Functional Implications of Repetitive Elements

  Retrotransposons play a significant role in gene expression regulation, affecting chromatin structure, gene transcription, and pre-mRNA processing
• Euchromatin

  • Euchromatin appears as a loosely packed form of DNA, which is transcriptionally active, allowing genes to be transcribed into RNA
  • When observed under electron micrographs, euchromatin isolated from an interphase nucleus appears as a quasi-regular thread, approximately 30 nm thick
  • Upon partial unpacking in low salt conditions, the chromatin's "beads on a string" structure becomes evident, a phenomenon first observed in 1974. This refers to nucleosomes connected by linker DNA
• Nucleosome

  Each nucleosome, resembling a bead, consists of DNA wrapped around histone proteins and contains about 200 bp of DNA
• Nucleosome Core Particle

  • Each nucleosome core particle comprises eight histone subunits: two each of H2A, H2B, H3, and H4
  • The nucleosome core particle can be dissociated to release individual histones, and high salt conditions can cause disassociation
• Histone Characteristics

  Histones are basic proteins rich in arginine (R) and lysine (K), carrying a positive charge
• Histone Expression and Purification

  Histones can be expressed and purified individually, for example in bacteria such as Escherichia coli, which naturally do not have histones
• Interactions Between Histones

  Histones H3 and H4 can interact to form a dimer, and two H3-H4 dimers interact to form a tetramer. H2A-H2B dimers can then bind to this tetramer to form the full nucleosome
• DNA and Nucleosome Formation

  A specific sequence of DNA is used to bind the histone octamer and form the nucleosome, facilitating the study of nucleosome structure and dynamics
• In vitro Nucleosome and Chromatin Structure Analysis

  • Through in vitro reconstitution, crystal structures of nucleosomes have been obtained, providing detailed insights into the organization of DNA and histones
  • The addition of the H1 histone, or linker histone, to the "beads on a string" form of chromatin, can lead to the formation of a more compact 30 nm fiber, a step in further DNA compaction
• Chromatin Packaging and Organization

  • DNA compaction increases from the "beads on a string" structure (11 nm fiber) to a 30 nm fiber, and further to higher-order structures like extended chromatin (300 nm), compacted chromatin (700 nm), and ultimately metaphase chromosomes (1400 nm)
  • During mitosis, DNA is highly compacted into chromosomes, which are much shorter than the extended length of DNA
  • Sperm DNA is even more densely packed than typical chromatin, primarily using protamines instead of histones
• Chromosome Territory

  • Chromosomes occupy distinct domains within the interphase nucleus, allowing for regulated access to DNA for transcription and replication
  • The presence of nucleosomes and histones poses questions about how transcription can occur without obstruction and whether histones interfere with DNA replication
• Histone 'Tails'


  Extend from the nucleosome and can undergo post-translational modifications
• Histone Modifications and the 'Histone Code'

  • Acetylation of lysine residues is common and generally associated with transcriptional activation by loosening chromatin structure
  • A term describing the hypothesis that the pattern of histone modifications acts like a code in regulating gene expression
• Chromatin Remodeling

  1. Histone-modifying complexes are recruited to chromatin by gene activator proteins

  2. Nucleosomes can be removed, repositioned, replaced, or covalently modified, affecting DNA accessibility for transcription machinery
• Gene Silencing

  • Methylation can lead to chromatin compaction or relaxation, affecting gene expression
  • Involve histone modifications that create a more compact chromatin state, hindering transcription factor access
• Complexity of the Histone Code

  • Histones can be modified in various ways, not only by acetylation or methylation but also by phosphorylation, ubiquitination, and other chemical modifications
  • Each modification can influence different outcomes in DNA-related processes, such as transcription, replication, and repair
• Maintenance of Histone Modifications During Transcription

  • Histone modifications are part of epigenetic regulation, which can be maintained across cellular generations
  • The maintenance of histone marks during and after transcription is complex, as RNA polymerase II must navigate through nucleosomes
• Transcription Through Nucleosomes

  1. As RNA polymerase II transcribes DNA, it encounters nucleosomes which may be temporarily removed or repositioned

  2. Post-translational histone marks are generally maintained or re-established after transcription to preserve the regulatory state
• Origins of Replication

  • Controlled to ensure precise DNA replication. In yeast, these origins are known as Autonomous Replication Sequences (Ars)
• Histone Management During Replication

  • During replication, parental histones are distributed to new strands, and new histones are incorporated
  • Histone modifications and DNA methylation are copied to maintain gene expression patterns
• Replication Process

  1. Initiation involves the formation of a pre-replicative complex (pre-RC) at origins, which includes ORC (Origin Recognition Complex), Cdc6, Cdt1, and Mcm helicases

  2. In S phase, the pre-RC is activated, allowing the recruitment of DNA polymerases and other replication factors

  3. As DNA unwinds, parental histones are partially retained while new histones are added. NAP-1 and CAF-1 chaperone new histones to ensure proper nucleosome assembly
• Histone Management During Replication

  • H3-H4 tetramers are likely retained and reassembled onto new DNA, while H2A-H2B dimers are displaced and replaced
  • New histones are synthesized, acetylated to maintain an open chromatin structure, and then incorporated into nucleosomes
  • After replication, new histones undergo modifications to replicate the epigenetic state of the parental chromatin, ensuring that daughter cells maintain the same gene expression patterns
• Epigenetic Regulation

  • DNA Methylation and Histone Modification interplay to regulate gene expression, typically silencing genes through chromatin condensation
  • Both histone modifications and DNA methylation are crucial for passing on epigenetic information to daughter cells, influencing traits and susceptibility to conditions
• Studies indicate environmental conditions (like diet and stress) experienced by parents can influence gene expression patterns in offspring through epigenetic mechanisms