Saturday, March 16, 2013

Genomes are dynamic entities

Sometime ago, i was wondering about genomes that are impossible to assemble. Differences in the DNA content of Germline and somatic cells is one more oddity that can make genomes much more complex than they might appear. Roundworm genomes of the somatic and germline show a clear change from germline to somatic cells. The loss of genes expressed in the Germline suggests a role for adaptation which might have been taken over by other mechanisms such as methylation, non-coding rna and other silencers of gene expression.

The recently published genome of the lamprey is another species known to have a similar mechanism of genome change. Further studies into the mechanism of such changes, their functional role and evolutionary significance will probably provide some insight into the evolution of tissue specific expression.

The loss of genes expressed in the germline followed by addition of telomeres and location of lost genes near ends of chromosomes also introduces the possibility that loss of germline DNA could be mediated by a telomerase inhibitor such as PINX1. The idea is that PINX1 is expressed in the germline leading to DNA being chewed from the ends of the chromosome. Once, the sequence containing PINX1 is lost, it will lead to expression of telomerase and stop further loss of DNA. To test this hypothesis PINX1 should be available in germline DNA but lost in the somatic genome.

Having obtained the somatic and germline genomes from the ascaris genome website, the PINX1 gene is found to be located on scaffold "AS02549" in the somatic genome and "AG00021" in the germline genome. Hence, it seems unlikely to be the germline DNA loss mechanism. However, its still possible that a trans regulatory element might be lost or some other telomerase inhibitor might be involved. The availability of gene expression data allows one to test this hypothesis. The fact that neither telomerase nor PINX1 is seen in the list of differentialy expressed genes suggests that a different mechanism might be in action.