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In  Drosophila  salivary gland polytene chromosomes, a substantial portion of heterochromatin is underreplicated. The combination of mutations  SuUR ES   and  Su(var)3-9 06   results in the polytenization of a substantial fraction of unique and moderately repeated sequences but has almost no effect on satellite DNA replication. The Rap1 interacting factor 1 (Rif) protein is a conserved regulator of replication timing, and in  Drosophila , it affects underreplication in polytene chromosomes. We compared the morphology of pericentromeric regions and labeling patterns of in situ hybridization of heterochromatin-specific DNA probes between wild-type salivary gland polytene chromosomes and the chromosomes of  Rif1  mutants and  SuUR Su(var)3-9 06   double mutants. We show that, despite general similarities, heterochromatin zones exist that are polytenized only in the  Rif1  mutants, and that there are zones that are under specific control of  Su(var)3-9 . In the  Rif1  mutants, we found additional polytenization of the largest blocks of satellite DNA (in particular, satellite 1.688 of chromosome X and simple satellites in chromosomes X and 4) as well as partial polytenization of chromosome Y. Data on pulsed incorporation of 5-ethynyl-2′-deoxyuridine (EdU) into polytene chromosomes indicated that in the  Rif1  mutants, just as in the wild type, most of the heterochromatin becomes replicated during the late S phase. Nevertheless, a significantly increased number of heterochromatin replicons was noted. These results suggest that  Rif1  regulates the activation probability of heterochromatic origins in the satellite DNA region.

cells

Effects of Mutations in the Drosophila melanogaster Rif1 Gene on the Replication and Underreplication of Pericentromeric Heterochromatin in Salivary Gland Polytene Chromosomes