Programmed loss of millions of base pairs from a vertebrate genome

2009/06/26 by Jeramiah J. Smith, Francesca Antonacci, Evan E. Eichler +1 · 1 voice · 26 citations
Biochemistry, Genetics and Molecular Biology · Agricultural and Biological Sciences · #Genomics and Phylogenetic Studies #Animal Genetics and Reproduction #Chromosomal and Genetic Variations

paper · doi:10.1073/pnas.0902358106

Abstract

In general, the strict preservation of broad-scale structure is thought to be critical for maintaining the precisely tuned functionality of vertebrate genomes, although nearly all vertebrate species undergo a small number of programmed local rearrangements during development (e.g., remodeling of adaptive immune receptor loci). However, a limited number of metazoan species undergo much more extensive reorganizations as a normal feature of their development. Here, we show that the sea lamprey (Petromyzon marinus), a jawless vertebrate, undergoes a dramatic remodeling of its genome, resulting in the elimination of hundreds of millions of base pairs (and at least one transcribed locus) from many somatic cell lineages during embryonic development. These studies reveal the highly dynamic nature of the lamprey genome and provide the first example of broad-scale programmed rearrangement of a definitively vertebrate genome. Understanding the mechanisms by which this vertebrate species regulates such extensive remodeling of its genome will provide invaluable insight into factors that can promote stability and change in vertebrate genomes.

Citations

• Basic local alignment search tool

Cited by

• First Report of a Mitochondrial Pseudogene in Agnathan Vertebrates (Cyclostomata: Petromyzontidae)
• Development and analysis of a germline BAC resource for the sea lamprey, a vertebrate that undergoes substantial chromatin diminution. [europepmc]
• The origins of vertebrate adaptive immunity. [europepmc]
• Explosive expansion of betagamma-crystallin genes in the ancestral vertebrate. [europepmc]
• RNA-Mediated Epigenetic Programming of Genome Rearrangements. [europepmc]
• Programmed DNA elimination in Tetrahymena: a small RNA-mediated genome surveillance mechanism. [europepmc]
• C. elegans piRNAs mediate the genome-wide surveillance of germline transcripts. [europepmc]
• Genetic consequences of programmed genome rearrangement. [europepmc]
• Silencing of germline-expressed genes by DNA elimination in somatic cells. [europepmc]
• Genomes on the edge: programmed genome instability in ciliates. [europepmc]
• Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. [europepmc]
• Insular Dysfunction Reflects Altered Between-Network Connectivity and Severity of Negative Symptoms in Schizophrenia during Psychotic Remission. [europepmc]
• Insight from the lamprey genome: glimpsing early vertebrate development via neuroendocrine-associated genes and shared synteny of gonadotropin-releasing hormone (GnRH). [europepmc]
• PGBD5: a neural-specific intron-containing piggyBac transposase domesticated over 500 million years ago and conserved from cephalochordates to humans. [europepmc]
• The lamprey: a jawless vertebrate model system for examining origin of the neural crest and other vertebrate traits. [europepmc]
• Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development. [europepmc]
• Programmed DNA elimination in multicellular organisms. [europepmc]
• The evolution of tenascins and fibronectin. [europepmc]
• Evolution of the CNS myelin gene regulatory program. [europepmc]
• Evolution and expression of the phosphodiesterase 6 genes unveils vertebrate novelty to control photosensitivity. [europepmc]
• The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. [europepmc]
• Intron and gene size expansion during nervous system evolution. [europepmc]
• Programmed DNA Elimination in Vertebrates. [europepmc]
• Delete and survive: strategies of programmed genetic material elimination in eukaryotes. [europepmc]
• An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes. [europepmc]
• The hagfish genome and the evolution of vertebrates. [europepmc]

Discussions

• Imagine deliberately deleting 20% of your genome at birth. That's what sea lamprey embryos do! Smith et al. found ~500 million base pairs are permanently removed from body cells, kept secret only in s [bsky, 17 points, 3 comments]

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