Replication of heterochromatin and structure of polytene chromosomes

Heterochromatin is characteristically the last portion of the genome to be replicated. In polytene cells, heterochromatic sequences are underreplicate d because S phase ends before replication of heterochromatin is completed. Truncated heterochromatic DNAs have been identified in polytene cells of Dr osophila and may be the discontinuous molecules that form between fully rep licated euchromatic and underreplicated heterochromatic regions of the chro mosome. In this report, we characterize the temporal pattern of heterochrom atic DNA truncation during development of polytene cells. Underreplication occurred during the first polytene S phase, yet DNA truncation, which was f ound within heterochromatic sequences of all four Drosophila chromosomes, d id not occur until the second polytene S phase, DNA truncation was correlat ed with underreplication, since increasing the replication of satellite seq uences with the cycE(1672) mutation caused decreased production of truncate d DNAs. Finally, truncation of heterochromatic DNAs was neither quantitativ ely nor qualitatively affected by modifiers of position effect variegation including the Y chromosome, Su(var)205(2), parental origin, or temperature. We propose that heterochromatic satellite sequences present a barrier to D NA replication and that replication forks that transiently stall at such ba rriers in late S phase of diploid cells are left unresolved in the shortene d S phase of polytene cells. DNA truncation then occurs in the second polyt ene S phase, when new replication forks extend to the position of forks lef t unresolved in the first polytene S phase.