Classification of human genomic DNA according to repetitiveness and function, pseudogenes, transposons.

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The human genome is a complex and diverse structure composed of different classes of DNA sequences, which vary significantly in terms of *function, **repetitiveness, and **evolutionary origin*. While only a small fraction of genomic DNA directly encodes proteins, the rest contributes to regulation, structural organization, and evolutionary potential. Some sequences, like pseudogenes and transposons, are remnants of evolutionary history with varying degrees of functionality.

Classification by function

1. Coding DNA

•⁠ ⁠*Protein-coding genes* (~1.5% of the genome)

• • Transcribed into mRNA, translated into proteins.
  • Includes exons and introns.
  • Organized into ~20,000–25,000 genes.

2. Non-coding functional DNA

•⁠ ⁠*Regulatory sequences*

• • Promoters, enhancers, silencers, and insulators.
  • Control gene expression spatially and temporally.

•⁠ ⁠*Non-coding RNAs*

• • Includes tRNA, rRNA, snRNA, snoRNA, miRNA, and lncRNA.
  • Functions range from translation and splicing to gene silencing.

•⁠ ⁠*Origins of replication*

• • Specific sites where DNA replication begins.

3. Non-functional or semi-functional DNA

•⁠ ⁠*Pseudogenes* – non-functional gene copies. •⁠ ⁠*Repetitive DNA* – often involved in genome structure or evolution.

Classification by repetitiveness

1. Unique (single-copy) sequences

•⁠ ⁠~50–60% of the genome. •⁠ ⁠Includes most protein-coding genes and many regulatory elements.

2. Moderately repetitive sequences

•⁠ ⁠20–40% of the genome. •⁠ ⁠Includes:

• • Gene families (e.g., histones, rRNA genes).
  • Dispersed repeats – mainly transposable elements.

3. Highly repetitive sequences

•⁠ ⁠Often in heterochromatic regions (e.g., centromeres and telomeres). •⁠ ⁠Typically not transcribed. •⁠ ⁠Examples:

• • Satellite DNA – short sequences repeated thousands of times.
  • Minisatellites (VNTRs) and microsatellites (STRs) – useful in DNA fingerprinting.

Pseudogenes

Pseudogenes are genomic sequences similar to known genes but are non-functional due to accumulated mutations. They may arise through:

•⁠ ⁠Processed pseudogenes

• • Derived from reverse transcription of mRNA and reintegration into the genome.
  • Lack introns and regulatory sequences.

•⁠ ⁠Non-processed (duplicated) pseudogenes

• • Created by duplication followed by inactivation via mutations.

•⁠ ⁠Unitary pseudogenes

• • Functional gene loses its function without duplication.

Though traditionally seen as “junk DNA,” some pseudogenes may regulate gene expression (e.g., as competing endogenous RNAs or antisense transcripts).

Transposable elements

Transposons (also called *mobile genetic elements*) are DNA sequences that can change their position within the genome, affecting genomic stability and evolution.

They make up over *45%* of the human genome and fall into two major classes:

1. Retrotransposons

Move via an RNA intermediate (copy-and-paste mechanism).

•⁠ ⁠*LINEs* (Long Interspersed Nuclear Elements)

• • ~20% of the genome.
  • Autonomous (can encode reverse transcriptase).

•⁠ ⁠*SINEs* (Short Interspersed Nuclear Elements)

• • ~13% of the genome.
  • Non-autonomous; rely on LINEs for movement (e.g., Alu elements).

•⁠ ⁠*LTR elements*

• • Related to endogenous retroviruses.

2. DNA transposons

Move via a DNA intermediate (cut-and-paste mechanism).

•⁠ ⁠Inactive in humans, but evidence of ancient activity. •⁠ ⁠Contain transposase gene flanked by terminal inverted repeats.

Functional significance of repetitive and mobile DNA

•⁠ ⁠Can influence gene expression by insertion near regulatory regions. •⁠ ⁠Provide raw material for evolution (gene duplication, exon shuffling). •⁠ ⁠Involved in genome organization (e.g., centromere formation). •⁠ ⁠Can cause mutations and genomic instability (insertions, recombination).

Summary table

Classification	Examples	Notes
Coding DNA	Protein-coding genes	~1.5% of genome
Regulatory DNA	Promoters, enhancers	Controls gene activity
Repetitive DNA	Satellite DNA, LINEs, SINEs	Structural and regulatory roles
Pseudogenes	Processed, unprocessed	Non-functional gene copies
Transposons	LINEs, Alu elements	Mobile genetic elements

References

Related articles

•⁠ ⁠DNA •⁠ ⁠Gene expression •⁠ ⁠Repetitive DNA •⁠ ⁠Pseudogene •⁠ ⁠Transposon •⁠ ⁠Genome evolution •⁠ ⁠Non-coding RNA

Literature

• ALBERTS, Bruce. Molecular Biology of the Cell. 6. edition. New York : Garland Science, 2015. 428–452 pp. ISBN 978-0-8153-3218-3.