Characterization of Somatically-Eliminated Genes During Development of the Sea Lamprey (Petromyzon marinus)

Abstract

The sea lamprey (Petromyzon marinus) is a basal vertebrate that undergoes developmentally programmed genome rearrangements (PGRs) during early development. These events facilitate the elimination of ∼20% of the genome from the somatic cell lineage, resulting in distinct somatic and germline genomes. Thus far only a handful of germline-specific genes have been definitively identified within the estimated 500 Mb of DNA that is deleted during PGR, although a few thousand germline-specific genes are thought to exist. To improve our understanding of the evolutionary/developmental logic of PGR, we generated computational predictions to identify candidate germline-specific genes within a new transcriptomic dataset derived from adult germline and the early embryonic stages during which PGR occurs. Follow-up validation studies identified 44 germline-specific genes and further characterized patterns of transcription and DNA loss during early embryogenesis. Expression analyses reveal that many of these genes are differentially expressed during early embryogenesis and presumably function in the early development of the germline. Ontology analyses indicate that many of these germline-specific genes play known roles in germline development, pluripotency, and oncogenesis (when misexpressed). These studies provide support for the theory that PGR serves to segregate molecular functions related to germline development/pluripotency in order to prevent their potential misexpression in somatic cells. This larger set of eliminated genes also allows us to extend the evolutionary/developmental breadth of this theory, as some deleted genes (or their gnathostome homologs) appear to be associated with the early development of somatic lineages, perhaps through the evolution of novel functions within gnathostome lineages.

Keywords: development; genome; lamprey; rearrangement; vertebrate..

Fig. 1

Examples of secondary validation of somatically depleted genes. Validated sequences show amplification in testes DNA but no or reduced amplification in DNA from a panel of somatic tissues (liver, kidney, fin, muscle, blood) from two animals (males 12 and 13). T = Testes, L = Liver, K = Kidney, F = Fin, M = Muscle, B = Blood, m = 100 bp DNA ladder. The lowest band under “m” corresponds to the 100-bp band of the DNA ladder in all panels except for that of HMF1, which corresponds to the 200-bp band. Amplified loci are labeled with their corresponding human homolog.

Fig. 2

Relative abundance of a subset (n = 23) of somatically depleted genes based on qPCR in genomic DNA. Relative abundance estimates were calculated using the ΔΔct method of relative quantification using two sequences that amplify consistently in germline, somatic, and embryonic tissues as controls (supplementary table S1, Supplementary Material online, comp4257946_c0_seq1 and comp4249214_c0_seq1). The ΔΔct values for each gene are standardized to ΔΔct values from testes. D1, D2, D2.5, D3, D4, and D5 correspond to days 1–5 post-fertilization.

Fig. 3

Transcription and differential expression of somatically depleted genes based on Nanostring estimates. (Left) Transcript abundance as estimated by Nanostring count values. Data are presented using a spectral color theme to highlight the broad range of expression values across genes, tissues, and embryonic time points. Purple indicates low expression and red indicates high expression. Transcripts are labeled with their corresponding human homolog. (Center) Log₂-fold changes in expression relative to D1. (Right) Red asterisks indicate genes that are differentially expressed between testes and any embryonic time point (D1–5), blue asterisks indicate genes that are differentially expressed between D1 and any subsequent time point (D1 vs. D2, D1 vs. D2.5, etc.), and green asterisks indicate genes that are differentially expressed between adjacent time points (D1 vs. D2, D2 vs. D2.5, etc.). D1, D2, D2.5, D3, D4, and D5 correspond to days 1–5 post-fertilization.