MBB 347

Histone Proteins and Chromatin Structure

  • The structure of chromatin is a complex assembled from DNA, histone proteins, and non-histone proteins.

  • The combination of these three components is termed chromatin.

  • DNA is wrapped around histone proteins to facilitate compaction.

  • Chromatin allows specific sections of DNA to be read at different times, ensuring efficient space utilization.

Types of Functional RNA Products

  • Various functional RNA products exist which are classified as non-protein coding genes. These include:

    • tRNA (Transfer RNA): Functions in translation, bringing amino acids to ribosomes.

    • rRNA (Ribosomal RNA): A component of ribosomes.

    • microRNAs: Involved in gene regulation by binding to mRNAs.

    • Long Interfering RNAs: Regulates gene expression at the transcriptional level.

    • Long Non-coding RNAs: Play roles in regulating transcription and chromatin remodeling.

  • All these RNA types are still classified as genes because mutations in these sequences can lead to specific phenotypic changes.

Classification of DNA Sequences

  • DNA sequences are typically classified by:

    • Function

    • Copy number within the genome

  • Major classes of different genes:

    • Protein coding genes: Directly code for proteins.

    • Long non-coding RNA genes: Encode for RNA molecules that do not translate into proteins.

    • Tandem Repeats: DNA sequences that are repeated in direct succession.

    • Repetitive DNA: Includes sequences that can be copied multiple times across the genome.

    • Pseudogenes: Sequences that resemble genes but have lost their protein-coding ability.

    • Intragenic regions: Non-coding sections located within genes.

Gene Coding and the Human Genome

  • The human genome consists of approximately:

    • 21,000 protein-coding genes

    • 440,000 long non-coding RNA genes

    • 1.6 million repetitive DNA sequences

  • Less than 5% of the human genome actually codes for proteins, specifically about 1.9%.

RNA Expression Types

  • Monocystronic RNA: Most common in eukaryotes, where a single mRNA only directs the synthesis of one protein.

  • Polycistronic RNA: More commonly found in prokaryotes. A single mRNA can code for multiple proteins during translation without any editing.

  • Eukaryotic mRNAs typically encode only one protein each but may produce different protein variants through splicing.

Splicing and mRNA Variants

  • Introns and exons undergo processing during the formation of a primary transcript.

  • Primary Transcript: The initial form of RNA prior to processing which includes both introns and exons.

  • RNA Processing Stages:

    • Removal of introns.

    • Joining together of exons.

    • Addition of poly A tails.

  • Most human genes are about 50,000 base pairs long, with over 95% consisting of non-coding sequences (introns and regulatory elements).

  • Complex Transcription Units: These units often have multiple splice sites and alternative splicing options, allowing for different mRNA types derived from the same gene.

  • Alternative Splicing: A process where different combinations of exons are spliced together, resulting in diverse mRNAs.

Alternative Polyadenylation

  • Genes may have alternative poly A sites, affecting the resulting mRNA's length and sequence.

  • Alternative Promoters: Specific regions that can initiate transcription in different cell types, leading to different first exons in the resulting mRNA.

Exon Duplication and Gene Families

  • Exon Duplication: Can occur during recombination in meiosis, leading to copies of exons within a gene.

  • Gene Duplication: Involves entire genes being duplicated, potentially leading to gene families which consist of functionally related but genetically distinct genes. Examples include:

    • Immunoglobulins (antibodies with various functions).

    • Olfactory receptors (responsible for smell).

    • Cytoskeletal proteins (which provide cell shape).

Pseudogenes

  • A pseudogene is a non-functional copy of a gene that has accumulated mutations preventing it from producing a functional product.

  • The prevalence of pseudogenes is often higher in multicellular eukaryotes compared to single-cell eukaryotes.

The ENCODE Project

  • The ENCODE (Encyclopedia of DNA Elements) project aimed to identify all functional elements within the human genome, emphasizing that many previously considered "junk" regions may still have important regulatory or functional roles.

Chromosomal Organization of Genes and Non-coding DNA

  • Larger multicellular genomes contain many genes but also significant non-functional sequences.

  • Gene distribution can vary:

    • Gene-rich regions: High density of genes in a compact area.

    • Gene deserts: Areas where genes are few and separated by large distances.

Simple Sequence DNA

  • Simple Sequence DNA: Represents the main type of repetitive DNA in chromosomes, constituting approximately 6% of the human genome.

    • Microsatellites: Repeated sequences of 1-13 base pairs that can repeat extensively.

    • Minisatellites: Larger sequences ranging from 1-5 kilobase pairs.

  • Simple sequence DNA is typically found concentrated at centromeres and telomeres, protecting chromosomal integrity during replication.

Implications of DNA Slippage

  • DNA Slippage: Can introduce expansions or contractions of microsatellite regions during replication, which may lead to genetic disorders. For example:

    • Huntington's Disease: An example where specific triplet repeats are expanded.

Applications in DNA Fingerprinting

  • DNA fingerprinting exploits individual differences in DNA, particularly using microsatellites and polymorphisms between individuals to establish identity or family relationships in forensic analysis.

  • Techniques include PCR amplification and restriction enzyme analysis, helping differentiate between DNA samples in various applications, including paternity testing and crime scene analysis.