Identification of Genes That Promote or Antagonize Somatic Homolog Pairing Using a High-Throughput FISH–Based Screen

Abstract

The pairing of homologous chromosomes is a fundamental feature of the meiotic cell. In addition, a number of species exhibit homolog pairing in nonmeiotic, somatic cells as well, with evidence for its impact on both gene regulation and double-strand break (DSB) repair. An extreme example of somatic pairing can be observed in Drosophila melanogaster, where homologous chromosomes remain aligned throughout most of development. However, our understanding of the mechanism of somatic homolog pairing remains unclear, as only a few genes have been implicated in this process. In this study, we introduce a novel high-throughput fluorescent in situ hybridization (FISH) technology that enabled us to conduct a genome-wide RNAi screen for factors involved in the robust somatic pairing observed in Drosophila. We identified both candidate “pairing promoting genes” and candidate “anti-pairing genes,” providing evidence that pairing is a dynamic process that can be both enhanced and antagonized. Many of the genes found to be important for promoting pairing are highly enriched for functions associated with mitotic cell division, suggesting a genetic framework for a long-standing link between chromosome dynamics during mitosis and nuclear organization during interphase. In contrast, several of the candidate anti-pairing genes have known interphase functions associated with S-phase progression, DNA replication, and chromatin compaction, including several components of the condensin II complex. In combination with a variety of secondary assays, these results provide insights into the mechanism and dynamics of somatic pairing. In addition to their number and structure, the position and spatial dynamics of chromosomes are under tight control, as direct interactions between chromosomes can contribute to the activation or repression of genes. Here, we focus on a particular type of interaction, known as somatic homolog pairing, which occurs between the maternal and paternal copies of chromosomes. While the role of somatic pairing on downstream homology-driven processes is well-established, there is much to be learned about how homologous chromosome segments find each other, physically align, and form stable pairing interactions within somatic cells. Taking advantage of a novel high-throughput FISH technology and the fact that homologous chromosomes are intimately paired along their lengths in the somatic cells of Drosophila, we have conducted a screen for factors that are important for the fidelity of somatic pairing. Ultimately, the characterization of these pairing genes will shed light on the mechanism of pairing, as well as pairing-mediated processes that have implications for development and disease. Finally, the efficacy of our screen for pairing genes suggests that the high-throughput FISH technology described here will prove useful for studying forms of nuclear organization and chromosome positioning beyond pairing.