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Related Concept Videos

Exon Recombination02:32

Exon Recombination

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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. 
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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.
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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
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RNA-seq03:21

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Conservative Site-specific Recombination and Phase Variation02:53

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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.
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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...
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Related Experiment Video

Updated: Feb 20, 2026

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
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RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level

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Comparative genomics reveals LINE-1 recombination with diverse RNAs.

Cheuk-Ting Law1, Kathleen H Burns1

  • 1Department of Pathology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

Cell Genomics
|February 19, 2026
PubMed
Summary

Long interspersed element-1 (LINE-1) retrotransposons can form chimeric insertions with various RNA types. A new computational tool, TiMEstamp, aids in discovering these chimeras and understanding their role in genome evolution.

Keywords:
5′ transductionAluLINE-1U6 snRNAchimeric insertionscomparative genomicsmultiple sequence alignmentreverse transcriptionsplicingtransposable elements

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Last Updated: Feb 20, 2026

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
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Area of Science:

  • Genomics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Long interspersed element-1 (LINE-1) retrotransposons are abundant in mammalian genomes.
  • LINE-1 elements influence genome evolution and mobilize other sequences like Alu elements.
  • Comprehensive catalogs of LINE-1 chimeras are lacking.

Purpose of the Study:

  • To develop a computational pipeline for identifying LINE-1 chimeric insertions.
  • To estimate the age of LINE-1 insertions.
  • To discover new LINE-1 chimeras and understand their formation.

Main Methods:

  • Developed TiMEstamp, a computational pipeline using multiple sequence alignments (MSAs).
  • TiMEstamp estimates LINE-1 insertion age and identifies contemporaneous adjacent sequences.
  • Analyzed LINE-1 insertions to discover chimeric events.

Main Results:

  • Discovered novel chimeric insertions involving small RNAs, Alu elements, and mRNA fragments.
  • Identified LINE-1 loci with defunct promoters acquiring regulatory elements to restore activity.
  • Provided evidence for LINE-1 RNA's recombinatory potential.

Conclusions:

  • TiMEstamp pipeline effectively identifies LINE-1 chimeras and insertion ages.
  • LINE-1 chimeras have significant implications for genome evolution and TE domestication.
  • LINE-1 elements can regain activity through acquisition of regulatory elements.