The Nopp140 gene in Drosophila melanogaster displays length polymorphisms in its large repetitive second exon

Abstract

Nopp140, often called the nucleolar and Cajal body phosphoprotein (NOLC1), is a predicted chaperone for the transcription and processing of rRNA as it assembles into small and large ribosomal subunits. Nopp140 is conserved among the metazoans with an amino terminal LisH dimerization domain followed by a large central domain consisting of alternating acidic and basic motifs of low sequence complexity, and then a carboxyl terminus that can be variable due to alternative splicing. Treacle is another nucleolar chaperon in vertebrates that is structurally and functionally related to Nopp140. While the large central domains of vertebrate Nopp140 and treacle are encoded by several exons, the similar domain in Drosophila Nopp140 is encoded by a single exon. We define three overlapping repeat sequence patterns (P, P, and P) within the central domain of D. melanogaster Nopp140. These repeat patterns are poorly conserved in other Drosophila species. A length polymorphism for the P pattern in D. melanogaster displays either two or three 96 base pair repeats, respectively referred to as Nopp140-Short and Nopp140-Long. PCR characterization of the long and short alleles shows a poorly-defined, artefactual bias toward amplifying the long allele over the short allele. Fly lines homozygous for one or the other allele, or heterozygous for both alleles, show no discernible phenotypes. The significance of this polymorphism lies in discerning the properties of the Nopp140s large central domain in assemblage and phase separations in nucleoli and Cajal bodies.