THE GERMLINE GENE ENCODING DNA-POLYMERASE-ALPHA IN THE HYPOTRICHOUS CILIATE OXYTRICHA-NOVA IS EXTREMELY SCRAMBLED

We report the structure of the micronuclear (germline) gene encoding t he large catalytic subunit of DNA polymerase alpha (DNA pol alpha) in the ciliate Oxytricha nova. It contains 44 internal eliminated segment s (IESs) that divide the gene into 45 macronuclear-destined segments ( MDSs) that are in a non-randomly scrambled order with an inversion nea r the gene center. Odd numbered MDSs 29-43, containing 230 bp out of a total of 4938 bp of macronuclear sequence, are missing from the 14 kb cloned gene. The missing MDSs have not been located but are at least several kilobases from the main body of the gene. The remarkably scram bled DNA pol alpha gene must be extensively cut, re-ordered and splice d and an inversion must occur to produce an unscrambled, functional ve rsion of the gene during development of a new macronucleus. Unscrambli ng is hypothesized to occur by a homologous recombination mechanism gu ided by repeat sequences at MDS ends.