Chromosome Type Polytene and Lambrush | Zoology Optional Notes for UPSC PDF Download

Discovery and Early Observations

Polytene chromosomes, initially termed a 'permanent spireme' by Balbiani in 1881, were first identified in various tissues of Chironomus plumosus larvae. These tissues include salivary glands, Malpighian tubules, intestine, hypoderm, and muscles. The chromosomes were described as a cylindrical cord that repeatedly unraveled and filled the nucleus.

Subsequent Research and Revelation

1. Confirmation of Non-Continuity:

   • In 1933–1934, researchers (Painter, 1933; Heitz and Bauer, 1933; King and Beams, 1934) demonstrated through squashed preparations that the 'spireme' is not continuous but consists of separate elements.
   • The number of these elements closely aligns with the haploid number of mitotic chromosomes.
   • Elements result from tight synapsis of homologous chromosomes, each with a distinct and constant morphology, displaying transverse-banding patterns.

2. Giant Size Explanation:

   • Koltzoff (1934) proposed that the giant size of salivary gland chromosomes is due to multistrandedness.

3. Terminology Adoption:

   • The term 'polytene' was suggested by Koller (1935) and later adopted by Darlington (1937).

Peculiarities of Polytene Chromosomes

1. Mitosis Elimination:

   • Polytene chromosome formation is associated with the elimination of mitosis after each DNA doubling.
   • The cell cycle comprises only two periods: synthetic (S) and intersynthetic (G).

2. DNA Strand Behavior:

   • DNA strands do not segregate at the end of each replication period; instead, they remain paired to varying degrees.

3. Inability for Mitosis:

   • Polytene chromosomes formed are incapable of participating in mitosis.

4. Intact Nuclear Structure:

   • The nuclear membrane and nucleolus remain intact during consecutive DNA replication cycles.

5. Developmental Context:

   • Polytene chromosomes arise and reach high levels in tissues and organs when rapid development is required while maintaining a high level of function.
   • Organs with polytene chromosomes are often associated with intense secretory functions and rapid growth.

Morphology of Polytene Chromosomes

1. Varied Morphology:

   • Morphology varies due to different degrees of synapsis of DNA strands.

2. Development from Diploid Nuclei:

   • Polytene chromosomes develop from diploid nuclei through successive duplication of each chromatid.

3. Types of Polyteny: 
   Classic Polytene Chromosomes:

   • Develop when homologous chromatid conjugation is maximal.
   • Form cylindrical cables with a distinct banding pattern.
     

4. Cryptic Polyteny (Reticular Structure):

   • Occurs when the degree of chromatid conjugation is minimal.
   • Forms a polyploid nucleus with a reticular structure.
     

5. Pompon-like Chromosome:

   • Results when conjugation of chromatids is disturbed in only one chromosome of the set.
   • Loses its banding pattern and appears diffuse, resembling a pompon.

Morphological Disparities in Polytenes between Females and Males

1. General Morphology:

   • Broadly, the morphology of polytene chromosomes is similar in females and males.

2. Distinct X-Chromosome in Males:

   • The polytene X-chromosome in Drosophila males exhibits differences.
   • Contains half as much DNA as the female counterpart but occupies a similar area.
   • Loosely packed structure, synthesizing twice as much RNA as a single female chromosome.
   • Enriched with nonhistone proteins compared to the female X-chromosome.

3. Role of Y Chromosome in Males:

   • In males, the Y chromosome remains part of the chromocentre along with centromeres and pericentromeric heterochromatin.

Chromocentres and Heterochromatin in Polytene Nuclei

1. Chromocentre Formation:

   • Nonhomologous chromosomes are often joined by their centromeric regions to form a common chromocentre in polytene nuclei.
   • Chromocentres correspond to heterochromatin in mitotic chromosomes.

2. Types of Heterochromatin in Drosophila:

   • Two types: a and b heterochromatin.
   • a heterochromatin primarily consists of satellite DNA, with short nucleotide sequences repeated extensively.
   • b heterochromatin comprises mainly middle-repeated mobile elements.

3. Variability in Chromocentre Formation:

   • Chromocentre formation is not universal; in many species, a common chromocentre does not form.

Intercalary Heterochromatin and its Characteristics

1. Distribution and Characteristics:

   • Approximately 240 regions of intercalary heterochromatin scattered throughout the genome.
   • Share characteristics with centromeric heterochromatin:
     • Late DNA replication.
     • Underreplication during polytenization cycles.
     • Ectopic pairing.

2. Functional Distinction:

   • In contrast to centromeric heterochromatin, intercalary heterochromatin contains genes necessary only during specific developmental stages.
   • Genes in intercalary heterochromatin are repressed after their developmental role is fulfilled.

Occurrence of Polytene Chromosomes in Various Organisms

Insects (Diptera)

• Larvae:
  • Classic type polyteny observed in salivary glands, gut, midgut, hindgut, gastric caeca, Malpighian tubules, fat bodies, epidermal cells, hypoderm, and ring gland.
• Pupae:
  • Classic type polyteny in Malpighian tubules, cardiac wall, fat body, rectum, foot pad cells, bristle-forming cells.
• Adults:
  • Classic type polyteny in Malpighian tubules, hindgut, midgut, and fat body.

Other Organisms

• Collembola (Insects), Protozoa, Infusoria:
  • Classic type polyteny.
• Mammals:
  • Cryptic or cryptic-classic types. Cryptic types can transform to classic through mutations or inbreeding.
• Plants:
  • Classic type polyteny in salivary glands, macronuclear anlage.
  • Cryptic and semicryptic types in trophoblast cells, tumor cells.
  • Cryptic type polyteny in antipocis, suspensors, endosperm, synergids, endosperm haustorium, tissue culture, callus culture.
  • Cryptic types can transform to classic, especially at low temperatures.

Multistrandedness of Polytene Chromosomes

Cellular Growth Phenomenon

• Cell Growth vs. Division:

  • Growth characterized by an increase in the size of relatively few cells rather than an increase in cell number through division.
  • Common in Insecta, accompanied by parallel increases in nuclear size and DNA content.

• Chromosome Structure:

  • Chromosomes of this type are observed as a bundle of individual chromatids.

• Polyteny Levels (C):

  • Vary considerably within an organ, between organs, and among organisms and species.
  • Not all DNA fragments polytenize to the same extent.
  • Local underreplication during polytenization, especially in pericentric heterochromatin and intercalary/telomeric heterochromatin.

Polytene Chromosome Levels in Different Organisms

Banding Pattern in Polytene Chromosomes

• Chromomeres and Banding:

  • Variation in DNA coiling and associated proteins along the linear axis leads to chromomeres.
  • Chromomeres are regions of high concentration.
  • Specific pattern: homologous chromomeres align and fuse as a band across the polytene element.

• Stability and Specificity:

  • Banding is a stable and specific feature.
  • Individual bands can be recognized, mapped, and assigned reference numbers.

• Dynamic Structure:

  • Chromomere structure is flexible.
  • Banding pattern highly variable with intra- and/or extracellular condition changes.

Somatic Synapsis of Homologous Chromosomes

• Definition:

  • Somatic synapsis occurs when two homologous polytene chromosomes fuse.

• Precision in Synapsis:

  • Chromosomes synapse band to band with high precision.
  • Gives the impression of a single chromosome.

• Occurrence:

  • Not obligatory; varies in dipteran insects, absent in plants or Collembolan insects.

• Frequency in Drosophila melanogaster:

  • Varies between 6.5% and 45% during normal development.

• Influence of Factors:

  • Asynapsis enhanced in hybrids from various crosses.
  • Modifiers like temperature and quantity of Y-chromosome heterochromatin influence asynapsis degree.

Molecular Organization of Bands and Interbands

• Genome Band Estimate:

  • D. melanogaster genome: 3500–5000 bands.

• Euchromatin Characteristics:

  • Euchromatin contains approximately 120 megabase pairs of DNA and about 14 thousand genes.
  • A medium-sized band contains 30 kilobase (kb) pairs of DNA, containing between 3 and 5 genes.

• Interbands Definition and Characteristics:

  • Regions between two bands are interbands or interchromomeres.
  • Difficult to identify precisely due to small size (0.05–0.38 mm).
  • Molecular size: 0.3–3.8 kb.

• Proteins in Interbands:

  • Various nonhistone proteins located in interbands.
  • Include RNA polymerase II, proteins binding RNA in ribonucleoprotein particles, and proteins in heterogeneous RNA complexes.

• Genetic Organization:

  • Two types of interbands:
    • Type I corresponds to regulatory regions of genes inactive in salivary glands.
    • Type II corresponds to genes constantly active in this tissue, containing housekeeping genes.

Puffs in Polytene Chromosomes

Discovery and Nomenclature

• Painter's Description (1935):
  • Achromatic swollen segments as salient features of the third chromosome of D. melanogaster.
• Bridges' Term 'Puffs' (1935):
  • Some swellings, especially in the X-chromosomal 2B region, referred to as 'puffs.'
  • Absence of thickenings in other larvae regions with usual bands.

Specificity and Timetable

• Tissue-Specific Spectrum:
  • Spectrum of puffs and Balbiani rings specific to each tissue at a given development stage.
• Timetable by Ashburner (1970):
  • Detailed timetable of changes in puff activity tabulated for Drosophila.

Transcription Activity

• Active Transcription Sites:
  • Puffs are sites of very active transcription.
• DNA Amplification in Sciarids:
  • Certain puffs in Sciarids species involved in DNA amplification.
  • Differ from majority of puffs, termed 'DNA puffs.'
  • Accumulation of extra DNA in 'DNA puffs,' arising in late stages of larval development for coding salivary gland secretion proteins.

Common Features of Polytene Chromosomes

Utility in Genetic Analysis

• Accurate Gene Mapping:

  • Small deletions aid precise gene mapping.
  • First genes in D. melanogaster polytene chromosomes mapped in 1930s with accuracy to bands.
  • Hundreds of genes precisely located on polytene chromosomes maps today.

• Visualization of Heterozygous Inversions:

  • Heterozygous inversions clearly visible in polytene chromosomes.
  • Crucial for genetic analysis in populations.

Lampbrush Chromosomes

Discovery and Introduction

• Flemming's Discovery (1882):
  • Lampbrush chromosomes discovered in salamander egg cells (Ambystoma mexicanum).
• Rückert's Term 'Lampbrush Chromosome' (1892):
  • Rückert introduces the term "lampbrush chromosome" into biological nomenclature.

Structure and Characteristics

• First Meiotic Division:

  • Present during the first meiotic division.
  • Decondensation during prolonged diplotene stage produces large chromosomal structures.

• Size Comparison:

  • Length ranges from 400 to 800 mm, up to 30 times larger than mitotic chromosomes.

Chromosome Structure in Early Prophase

• Bivalent Structure:
  • In early prophase, a LBC is a bivalent with two pairs of conjugating homologues forming a tetrad.
    
• Chromatid Composition:
  • Chromatid composed of regions of condensed inactive chromatin (chromomeres) and side loops of decondensed chromatin.
    
• Contractibility of Loops:
  • Side loops are extensible and contractible, leading to the contraction and dilation of chromomeres.

Visual Structures in Goose Lampbrush Chromosome

• Distinctive Structures:
  • Magnification of distinctive structures in the second goose lampbrush chromosome.
  • Telomeres, centromere, chiasm, and sister chromatids observed.

Lampbrush Chromosome Structure

Morphological Differentiation of Loops

• Protein-Dependent Differentiation:

  • Numerous morphological types of Lampbrush Chromosome (LBC) loops identified.
  • Differentiation determined by type and number of proteins bound to emergent transcripts.

• Transcriptional Activity Types:

  • Two basic loop types in terms of transcriptional activity:
    • "Complex" Loops:
      • Matrix with complicated morphological structure (loop-formed or fibriform).
      • Classified as marker loops or side loops.
        
    • "Plain" Loops:
      • Majority of chromosome loops.
      • Delicate fibrous matrix, always loop-shaped.

• Conformation of DNA Axis:

  • Complex matrix morphology includes a spiral path around sporadic bead-like condensates.
  • Large masses of matrix forming 'lumpy loops' with highly contorted paths.

Domains in Lampbrush Chromosomes

• Open and Locked Chromatin:

  • Lampbrush chromosomes have domains of open chromatin with potentially transcriptive genes.
  • Also, domains of locked chromatin without expression.

• Association with Protein Bodies (PBs):

  • Avian lampbrush chromosomes associated with Protein Bodies (PBs).
  • PBs have a regular connection with the chromosome axis, especially in the heterochromatin region.
  • PBs potentially involved in coordinating spatial layout of chromosomes.
  • Frequent association of PBs with repetitive sequences surrounding the centromere.

Lampbrush Chromosome Transcription

Transcriptional Regulation Studies

• Model for Transcriptional Regulation:

  • LBCs used as a model in studies of transcriptional regulation.
  • Changes in transcriptional activity result in different morphological structures of LBC loops.

• Microchromosome Transcription Activity:

  • Higher transcriptional activity observed in microchromosomes due to greater gene density.

• Analyses Based on Side Loops:

  • Transcriptional activity analyses based on the assumption that side loops of LBCs are transcriptionally active sites.
  • Decrease in transcriptional activity observed as a shrinking of side loops.
    

• Variability with Reproductive Cycle:

  • Morphology and transcriptional activity of LBCs vary depending on the reproductive cycle and seasonal changes.

Classification by Transcriptional Polymerase

• Polymerase-Based Classification:

  • Loops classified based on the type of transcriptional polymerase.
  • Largest loops transcribed by polymerase II, smallest loops by polymerase III.
  • Contain 5S RNA coding units, tRNA, or short replication sequences.

• Division Based on Transcriptional Units:

  • LBCs divided into those with one transcriptional unit and those with two or more.
  • Over 1 μm length, one transcriptional unit transcribed by a densely compacted package of 13-20 polymerase molecules.

Transcriptional Regulation Mechanisms

• Chromosome Structure Modification:

  • Regulation through modifications of chromosome structure and post-transcription factors.
  • Loosening of chromatin with LBC preservation in the initial stage.

• Role of "Constitutive" Nucleosomes:

  • Presence of "constitutive" nucleosomes in LBCs preserves structure during transcriptional activity.
  • Activation of oocyte-specific topoisomerase I variant during LBC structure formation.

Outcome of Transcription

• Active vs. Inactive Chromatin:

  • Transcriptionally active loops represent 5-10% of DNA, remainder is inactive chromatin in chromomeres.
  • Result of transcription visible as a ribonucleoproteinic mantle.

• Asymmetrical Mantle and Loop Length:

  • Mantle tends to be asymmetrical, corresponding with rising electron density from base towards the middle of the loop.
  • Average length of a typical lampbrush chromosome loop is 10-15 μm.

• Transcription Rate and Loop Length:

  • Transcription rate in lampbrush chromosome loops is 5 μm per hour.
  • One loop transcribed within two to a dozen or so hours.
  • Average loop contains about 30-40 thousand base pairs, corresponding with the average length of RNA transcribed in oocytes.
    

• Consistency in Chromosome Maps:

  • Chromosome maps of different oocytes at various ages remain identical.
  • Suggests a species-specific nature of sequences transcribed during oogenesis.