Saturday, February 11, 2012

New #openaccess paper in G3 from my lab w/ many others on 'Programmed DNA elimination in Tetrahymena' #CiliatesRule

A new paper in which the lab was involved has been published recently (just found it though it is not in Pubmed yet): Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophila.  It was a collaboration between Kathy Collins, multiple Tetrahymena researchers, the Eisen lab, and the UC Davis Genome Center Bioinformatics core (Joseph Fass and Dawei Lin).  The paper is in G3, an open access journal from the Genetics Society. 

This stems from the project I coordinated on the sequencing and analysis of the macronuclear genome of the single-celled ciliate Tetrahymena thermophila.  This organism, like other ciliates, has two nuclei - one called the micronucleus and one called the micronucleus macronucleus.  In essence you can view the micronucleus as the germ line for this single-celled creature and the micronucleus macronucleus is akin to somatic cells.  The micronucleus is reserved mostly for reproduction.  And the micronucleus macronucleus is used for gene expression.  In sexual reproduction, haploid versions of the micronuclear genomes from two lineages merge together just like in sexual reproduction for other eukaryotes.  After sex the offspring then create a macronuclear genome by taking the micronuclear genome and processing it in a variety of ways - going from 5 chromosomes for example to hundreds.  Plus many regions of the micronuclear genome are "spliced" out and never make it into the macronuclear genome.  Our new paper focuses on trying to better characterize which regions of the micronuclear genome get eliminated.

For more on our past work on Tetrhymena genomics see here which includes links to much more information including to my 2006 blog post about our first paper on the project. 

Note - the work in my lab on the sequencing was supported by grants from NSF and NIH-NIGMS.

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