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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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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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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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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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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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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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Enhanced Genome Editing with Cas9 Ribonucleoprotein in Diverse Cells and Organisms
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RNA editing generates cellular subsets with diverse sequence within populations.

Dewi Harjanto1, Theodore Papamarkou2, Chris J Oates3

  • 1Laboratory of Lymphocyte Biology, The Rockefeller University, New York, New York 10065, USA.

Nature Communications
|July 16, 2016
PubMed
Summary
This summary is machine-generated.

RNA editing creates diversity within cell populations. A new Bayesian model reveals significant variations in RNA editing rates among individual cells, distinguishing cell-to-cell variability from population averages.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Immunology

Background:

  • RNA editing is a post-transcriptional mechanism altering RNA sequences.
  • Editing rates can be uniform across cells or vary, leading to population heterogeneity.

Purpose of the Study:

  • To develop a statistical model to differentiate uniform RNA editing from cell-specific variations.
  • To investigate the variance of RNA editing rates in murine immune cells.

Main Methods:

  • A hierarchical Bayesian model was employed using single-cell and bulk RNA sequencing data.
  • Experimental validation involved targeted amplification of specific RNA transcripts from single cells.
  • The model's predictions were assessed during lipopolysaccharide (LPS) stimulation in dendritic cells.

Main Results:

  • The model successfully quantified RNA editing rate variance at specific sites.
  • High editing rate variance was predicted and experimentally confirmed in murine macrophages and dendritic cells.
  • Dynamic changes in editing rate variance were observed in dendritic cells upon LPS stimulation.

Conclusions:

  • RNA editing contributes to cellular diversity through significant site-specific variations among individual cells.
  • The developed Bayesian model provides a robust method for analyzing RNA editing heterogeneity.
  • Understanding RNA editing variance is crucial for interpreting cellular responses and functions.