Satellite DNA 

Mr. Arvind Kumar

Introduction

  • Satellite DNA refers to repetitive, non-coding DNA sequences that form distinct “satellite bands” when genomic DNA is separated by density-gradient ultracentrifugation.

  • First described by Yasmineo and colleagues (1960s) when studying mouse DNA.

  • Called “satellite” because they appear as lighter or heavier bands separate from the main DNA in cesium chloride (CsCl) gradients.

  • Present in eukaryotic genomes, often in heterochromatin, especially centromeric and pericentromeric regions.

  • Does not code for proteins but has structural, regulatory, and evolutionary roles.

General Features

  • Made of tandemly repeated sequences (identical or nearly identical motifs).

  • Repeat length may range from 1 bp → several hundred bp.

  • Total length can extend up to megabases of DNA.

  • Found mostly in non-coding heterochromatic DNA.

  • Highly species-specific (useful in evolutionary studies).

  • Shows high polymorphism in length and sequence (basis of DNA profiling).

 

Classification

Satellite DNA is classified based on repeat unit size:

A. Classical (Major) Satellite DNA

  • Long repeats, >100 bp per unit.

  • Found in centromeres, pericentromeres.

  • Example: Human α-satellite DNA (171 bp repeat unit, organized in higher-order arrays).

B. Minisatellite DNA

  • Repeat size: 10–60 bp.

  • Length: up to 20 kb.

  • Found in subtelomeric regions, telomeres.

  • Example: Telomeric repeat (TTAGGG)n.

  • Applications: DNA fingerprinting, population genetics, identity testing.

C. Microsatellite DNA 

  • Repeat size: 1–6 bp.

  • Widely distributed throughout the genome.

  • Highly polymorphic (vary between individuals).

  • Example: (CA)n, (CAG)n repeats.

  • Applications: Forensics, paternity testing, disease diagnostics.

D. Satellite-like DNA (Intermediate Repeats)

  • Interspersed repeats that resemble satellites but not strictly tandem.

  • Example: Variable Number Tandem Repeats (VNTRs).

 

Location in Genome

  • Centromeres → α-satellite DNA in humans stabilizes kinetochore assembly.

  • Telomeres → Minisatellite repeats protect chromosome ends.

  • Pericentromeric heterochromatin → structural stability.

  • Y chromosome → contains specific satellite repeats.

 

Molecular Organization

  • Arranged as tandem head-to-tail repeats.

  • Organized into higher-order repeats (HORs) in centromeres.

  • Shows variation in copy number (basis of genetic polymorphism).

 

Functions

Structural Roles

  • Centromere function: essential for kinetochore assembly & chromosome segregation.

  • Telomere stability: prevents chromosome shortening and fusion.

  • Maintains nuclear architecture (heterochromatin organization).

Regulatory Roles

  • Influences epigenetic modifications (DNA methylation, histone modification).

  • Regulates gene expression near repeat-rich regions.

Evolutionary Roles

  • Satellite DNA evolves rapidly → used as phylogenetic markers.

  • Explains genome size variability (C-value paradox).

Practical Roles

  • Used in DNA fingerprinting, forensic science, population genetics, paternity testing.

  • Helps in marker-assisted selection in plants and animals.

 

Techniques

  • CsCl density gradient centrifugation → classical method (separate satellite bands).

  • Restriction enzyme digestion & gel electrophoresis → reveals repeat motifs.

  • Southern blotting → detects repeat patterns.

  • FISH (Fluorescence In Situ Hybridization) → chromosomal mapping of repeats.

  • PCR amplification → microsatellite/minisatellite analysis.

  • Next-generation sequencing (NGS) → detailed repeat characterization.

 

Satellite DNA and Human Disease

  • Though mostly non-coding, expansions or instability of repeats can cause disease.

  • Trinucleotide Repeat Disorders (microsatellite expansions):

    • Huntington’s disease → (CAG)n repeat expansion.

    • Fragile X syndrome → (CGG)n expansion in FMR1 gene.

    • Myotonic dystrophy → (CTG)n expansion.

  • Genomic instability in cancer → microsatellite instability (MSI).

  • Epigenetic misregulation of satellite DNA linked to autoimmune diseases.

 

Applications

  • DNA fingerprinting (minisatellites, microsatellites).

  • Forensic analysis (STR profiling in crime cases).

  • Paternity testing (high polymorphism).

  • Genetic linkage studies (microsatellite markers).

  • Evolutionary biology (species-specific satellites as phylogenetic tools).

  • Medical diagnostics (detecting repeat expansion disorders).