Generally, all cells in an organism are considered to have the same genome; the differences between cells being determined by differential expression of genes. However, a growing list of species, including sciarid flies, and various copepods and nematodes, are known to undergo genomic rearrangements during the differentiation of cell lineages. Recent findings have shown that two species of jawless vertebrates (cyclostomes), the hagfish and the sea lamprey, undergo extensive genomic remodelling during development.
Hagfish and lampreys are the closest extant relatives of the jawed vertebrates (gnathostomes). Controversy has reigned over whether lampreys are more closely related to gnathostomes than they are to hagfish. This debate appears to have been resolved by molecular phylogenetics; the two branches of jawless vertebrates are united as a monophyletic clade, the cyclostomes. However the division of hagfish and lampreys occurred shortly after the division of gnathostomes and cyclostomes in the early stages of vertebrate evolution (~500mya). Two whole genome duplications occurred during the early evolution of the vertebrates (referred to as 1R and 2R). It is not yet resolved whether these duplications occurred before the divergence of cyclostomes and gnathostomes. Opinion appears to be split as to whether this divergence occurred after 1R or after 2R. The easiest way to resolve this question is whole genome sequencing. It has been known for some time that hagfish undergo genomic rearrangements during early development. Smith et al (2009) have now shown a similar phenomenon occurring in the Sea Lamprey (Petromyzon marinus), explaing some of the difficulty in constructing a finished version of the sea lamprey genome.
Smith et al. found that the total DNA content of nuclei from germline (sperm) and various somatic cell types (blood, liver, kidney) differed by >20%, equating to ≈500Mb. They then performed southern blots in which the restricted genomes of blood or sperm cells were probed with a repetitive sequence element. A number of bands differed in size or intensity between the germline and somatic cells, showing that genome rearrangement had occurred. One specific band was present in the germline samples and virtually absent from a range of somatic tissues. This band, termed Germ1 consisted of sequences for the 18s ribosomal DNA, a retrotransposon, and a section of the 28s rDNA. When aligned to Lamprey genomic sequence (somatic cell derived), these sequences were all commonly found, but one section of Germ1, from one end of the fragment to the 28s rDNA section, was dramatically underrepresented; a germline specific sequence. Smith et al. then performed FISH (fluorescent in situ hybridisation) using the Germ1 clone against metaphase germline and somatic cells. In the germline they found many Germ1-like sequences distributed across several chromosomes, often arrayed in tandem repeats. In contrast, in somatic cell nuclei, Germ1 hybridised to only one chromosome pair, most likely equating to the functional rDNAs. Using real-time PCR over the period of early embryogenesis, the authors found Germ1 abundance was drastically reduced 2 or 3 days after fertilisation. Smith et al. estimate that Germ1-like sequences make up ~7% of the germline genome, therefore suggesting that ~13% more of it is also lost. By comparing germline BAC clones with somatic genome sequence, they managed to identify more lost sequences including a gene known to be expressed during germline development, SPOPL.
Smith et al. have therefore shown that the sea lamprey genome undergoes a dramatic rearrangement during the early development of the somatic tissues. A large proportion of the excised content is accounted for by the elimination of Germ1-like sequences. However, it appears likely that a number of specific genes are also lost. In most cases of large scale somatic genomic rearrangement the main excised component is made up of transposable elements and other repetitive sequences. It seems likely that this could be the main basis for that seen in lampreys, as Germ1-like sequences appear to be a strange fusion of transposon and duplicated ribosomal DNA genes. However, the finding that an individual gene, SPOPL, is also selectively deleted in somatic lineages suggests that genomic deletions could be linked to the genetic regulation of development.
Interestingly, when the common apoptosis assay TUNEL – which detects DNA breaks – is used during the first few weeks of lamprey embryonic development, nearly every nucleus is labelled. It seems likely that this effect (that was considered an artifact) is explained by developmentally regulated deletions. The deletion of SPOPL appeared to occur more gradually than that of Germ1- like sequences. Together with the observation that the total nuclear DNA content differed slightly between various somatic tissues, these findings suggest that this program of somatic genomic deletions could be occurring in an intricate, and tissue specific, progression during early development.
All jawed-vertebrates undergo programmed genomic rearrangements during the diversification of the immune system. VDJ recombination, mediated by the transposase derived RAG recombinase, generates antigenic diversity, allowing adaptive immune responses. Cyclostomes have an alternate RAG-independent adaptive immune system, termed VLR. The recombinational system used in VLR is not yet clear. Is this system linked to that employed during the early developmentally regulated deletion process?
Smith et al (2010) link the presence of chromatin diminution (ie the somatic genomic rearrangements) in this basal vertebrate taxon to the whole genome duplications that occurred in the vertebrate stem group. If the genomic rearrangement mechanisms seen in cyclostomes were present in the last common ancestor of jawed and jawless vertebrates perhaps this system predisposed the stem group vertebrates to whole genome duplications by creating a permissive environment for polyploidisation and rediploidisation? Although this is a fascinating idea, currently it is perhaps a slightly idle speculation. It is of pressing importance to understand the mechanisms underlying cyclostome genomic rearrangements. Are they the same between hagfish and lampreys? Are similar systems present in gnathostomes? Finished genome sequences for both germline and various somatic cell lineages will answer many questions regarding the effects and purposes of chromatin diminution, however one can understand that this is easier said than done considering the potential complexity of the rearrangements. Lampreys and hagfish are also so far unculturable in the laboratory, adding to the difficulty in expanding their experimental use. Perhaps the biggest question left hanging, is whether other jawed vertebrates employ programmed genomic rearrangements for purposes other than antigenic diversification? This remains a possibility as the consistency of the genome has been generally assumed rather than tested.
See also a follow up on a new paper from the same group: Genomic Rearrangement in Lampreys 2
Smith JJ, Antonacci F, Eichler EE, & Amemiya CT (2009). Programmed loss of millions of base pairs from a vertebrate genome. Proceedings of the National Academy of Sciences of the United States of America, 106 (27), 11212-7 PMID: 19561299
Smith JJ, Saha NR, & Amemiya CT (2010). Genome biology of the cyclostomes and insights into the evolutionary biology of vertebrate genomes. Integrative and comparative biology, 50 (1), 130-7 PMID: 21558194
Shimeld SM, & Donoghue PC (2012). Evolutionary crossroads in developmental biology: cyclostomes (lamprey and hagfish). Development (Cambridge, England), 139 (12), 2091-9 PMID: 22619386
This article is good for vertebrate phylogeny and cyclostome development. A free version here