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Gene Conversion

Gene Conversion

Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...

Conservative Site-specific Recombination and Phase Variation

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...

Exon Recombination

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon...

Crossing Over

Crossing Over

Crossing over is the exchange of genetic information between homologous chromosomes during prophase I of meiosis I. Genetic recombination gives rise to allelic diversity in the newly formed daughter cells. In humans, crossing over produces genetically distinct haploid egg and sperm cells that undergo fertilization to produce unique offspring. Before cell division starts, the germ cell’s chromosome(s) undergo duplication in the S phase of the cell cycle. As the cells enter prophase I,...

Viral Recombination

Viral Recombination

Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.

Homologous Recombination

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...

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Related Experiment Video

Updated: Sep 3, 2025

Author Spotlight: Characterizing DNA Replication of Pathogenic Repeats to Uncover Mechanisms of Replication Fork Stalling and Expansion

Author Spotlight: Characterizing DNA Replication of Pathogenic Repeats to Uncover Mechanisms of Replication Fork Stalling and Expansion

Published on: September 13, 2024

Recombination of repeat elements generates somatic complexity in human genomes.

Giovanni Pascarella¹, Chung Chau Hon¹, Kosuke Hashimoto²

¹RIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, Japan.

|July 26, 2022

Summary

This summary is machine-generated.

Somatic recombination of repetitive DNA elements like Alu and L1 is common in the human genome, varying by tissue and cell type. This process is linked to genomic instability in neurodegenerative diseases.

Keywords:

Alu L1 NAHR non-allelic homologous recombination recombination repeat elements somatic mosaicism structural variants

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Recombineering Homologous Recombination Constructs in Drosophila

Recombineering Homologous Recombination Constructs in Drosophila

Published on: July 13, 2013

Area of Science:

Genomics and Molecular Biology
Human Genetics
Neuroscience

Background:

Non-allelic homologous recombination between repetitive elements is a known driver of evolution and genetic disorders.
The extent and implications of somatic recombination of these elements in the healthy and diseased human genome remain incompletely understood.

Purpose of the Study:

To investigate the prevalence and characteristics of somatic recombination of Alu and L1 elements in the human genome.
To explore the tissue-specific patterns and potential roles of retroelement-mediated recombination in health and disease, particularly neurodegeneration.

Main Methods:

Combined short- and long-DNA read sequencing of repetitive elements.
Development and application of a novel bioinformatics pipeline for analyzing recombination events.
Comparative analysis of recombination profiles in human-induced pluripotent stem cells and differentiated neurons, and in neurodegenerative disease states.

Main Results:

Somatic recombination of Alu and L1 elements is widespread across the human genome.
Distinct tissue-specific recombination patterns were identified, with enrichment of retroelements at centromeres and cancer-associated genes.
Neuron-specific recombination correlated with chromatin changes during cell differentiation, and altered profiles were observed in Parkinson's and Alzheimer's disease.

Conclusions:

Somatic recombination of repetitive elements significantly contributes to genomic diversity in humans.
Retroelement recombination may serve as a marker for genomic instability in neurodegenerative conditions.
This study provides new insights into the role of somatic recombination in both normal human biology and disease pathogenesis.