Gene Amplification as a Developmental Strategy

Abstract

Gene amplification is known to be critical for upregulating gene expression in a few cases, but the extent to which amplification is utilized in the development of diverse organisms remains unknown. By quantifying genomic DNA hybridization to microarrays to assay gene copy number, we identified two additional developmental amplicons in the follicle cells of the Drosophila ovary. Both amplicons contain genes which, following their amplification, are expressed in the follicle cells, and the expression of three of these genes becomes restricted to specialized follicle cells late in differentiation. Genetic analysis establishes that at least one of these genes, yellow-g, is critical for follicle cell function, because mutations in yellow-g disrupt eggshell integrity. Thus, during follicle cell differentiation the entire genome is overreplicated as the cells become polyploid, and subsequently specific genomic intervals are overreplicated to facilitate gene expression.

A portrait of copy-number polymorphism in Drosophila melanogaster

“…A contiguous set of seven probes on chromosome arm 3L representing six genes (CG32022, CG6511, Chorion Protein 18, Chorion Protein 15, Chorion Protein 16, and Paramyosin) show beyond-threshold negative ratios. Chorion protein and adjacent genes (e.g., CG32022 and Paramyosin) are known to be amplified in the follicle cells of D. melanogaster females, where amplification of chorion genes is required for normal eggshell development and female fertility (8,9). From these results we conclude that the false-positive rate predicted from male-female hybridizations is an upper limit.…”

Extending the dynamic range of transcription factor action by translational regulation

“…This scenario can be realized as a consequence of gene amplification, which is commonplace in bacteria, but the number of gene duplications (i.e., M) typically stays below 10 [81]. While gene amplification also occurs in some strongly specialized eukaryotic cells, it is generally seen as a strategy to massively increase the protein production rate [82][83][84], or as a hallmark of cancer [85,86]. Alternatively, a high multiplicity of M regulatory sites could occur in a single promotor or enhancer region.…”

Drosophila follicle cell amplicons as models for metazoan DNA replication: A cyclinE mutant exhibits increased replication fork elongation

“…Because follicle cells are terminally differentiated and do not undergo divisions or rearrangement of the amplified DNA, the amplification profile is reflective of the number of replication forks that have passed through and replicated a given site. Despite the fact that for some DAFCs the peak of amplification is 60-to 80-fold, whereas for others it is only 4-fold, the gradient extends over 100 kb in each DAFC (1,2). Thus the extent of the gradient reflects the progression of the replication forks during amplification.…”

“…The gradient of amplified DNA for all four DAFCs extends Ϸ50 kb to either side of the maximally amplified DNA at the origin. The extent of the gradient is the same for all of the DAFCs despite the difference in the number of rounds of replication initiation, with DAFC-30B only 4-fold amplified and DAFC-66D amplifying 60-to 80-fold (1,2,37,38). It is not clear whether replication fork barriers (RFBs) limit the size of the gradients and block fork elongation.…”

“…Replication forks progress bidirectionally from these origins to produce gradients of amplified DNA in an onion-skin structure. There are at least four Drosophila amplicons in follicle cells (DAFCs) (DAFC-7F, DAFC-30B, DAFC-62D, and DAFC-66D) containing genes encoding eggshell constituents (2). Because the increased gene copy number produced by amplification is needed for adequate production of these proteins, mutants affecting gene amplification are female sterile and exhibit egg shell defects (1).…”