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Mitochondrial D-loop sequences are integrated in the rat nuclear genome.

S Zullo1, L C Sieu, J L Slightom

  • 1Department of Human Genetics, Yale School of Medicine, New Haven, CT 06510.

Journal of Molecular Biology
|October 20, 1991
PubMed
Summary

Researchers discovered mitochondrial DNA (mtDNA) control region sequences within rat nuclear DNA (nucDNA). This finding confirms the presence of non-coding mtDNA elements in the nuclear genome, suggesting ancient integration and amplification events.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Evolutionary Biology

Background:

  • Mitochondrial DNA (mtDNA) sequences have been previously identified in nuclear genomes, but these were primarily coding sequences.
  • The origin of replication (D-loop) and its associated regulatory elements in mtDNA are crucial for mtDNA maintenance and replication.
  • Understanding the integration and fate of mtDNA sequences in the nuclear genome provides insights into genome evolution.

Purpose of the Study:

  • To identify and characterize non-coding mtDNA sequences within the nuclear genome of rats.
  • To investigate the evolutionary history and potential mechanisms of integration and amplification of these sequences.
  • To determine if any functional elements of the mtDNA control region are present in the nuclear genome.

Main Methods:

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  • Cloning of rat nuclear DNA (nucDNA) fragments.
  • DNA sequence analysis to identify homology with mtDNA sequences.
  • Sequence identity comparisons between nucDNA and mtDNA D-loop regions.
  • Divergence time estimations for integration events.
  • Southern blot hybridization to assess copy number and integration patterns.

Main Results:

  • Two nucDNA fragments (3.3 and 9.1 kilobase pairs) were cloned, each containing a 0.5 kilobase pair sequence with high identity (80-88%) to the mtDNA heavy strand origin of replication (D-loop).
  • These mtDNA-like sequences are covalently linked to unique nucDNA sequences, indicating genuine integration into the nuclear genome.
  • Divergence calculations suggest mtDNA insertion occurred approximately 13.6 million years ago, with subsequent separation around 6.5 million years ago.
  • The 3.3 knp fragment is low copy, while the 9.1 knp fragment is moderately repeated, and neither appears to be tandemly repeated.
  • The nucDNA clones contain remnants of LINE sequences and, in one case, viral reverse transcriptase-like sequences.

Conclusions:

  • This study provides the first sequence confirmation of a portion of the mtDNA control region (D-loop) within the nuclear genome.
  • The findings support a model of initial mtDNA insertion into nucDNA followed by amplification of surrounding nuclear sequences.
  • The absence of promoter elements suggests these integrated sequences may not be functional replication origins in the nucleus.
  • The presence of non-coding mtDNA elements in the nuclear genome highlights complex evolutionary dynamics between organellar and nuclear DNA.