title: Underreplicated regions in Drosophila melanogaster are enriched with fast-evolving genes and highly conserved noncoding sequences.
abstract: Many late replicating regions are underreplicated in polytene chromosomes of Drosophila melanogaster. These regions contain silenced chromatin and overlap long syntenic blocks of conserved gene order in drosophilids. In this report we show that in D. melanogaster the underreplicated regions are enriched with fast-evolving genes lacking homologs in distant species such as mosquito or human, indicating that the phylogenetic conservation of genes correlates with replication timing and chromatin status. Drosophila genes without human homologs located in the underreplicated regions have higher nonsynonymous substitution rate and tend to encode shorter proteins when compared with those in the adjacent regions. At the same time, the underreplicated regions are enriched with ultraconserved elements and highly conserved noncoding sequences, especially in introns of very long genes indicating the presence of an extensive regulatory network that may be responsible for the conservation of gene order in these regions. The regions have a modest preference for long noncoding RNAs but are depleted for small nucleolar RNAs, microRNAs, and transfer RNAs. Our results demonstrate that the underreplicated regions have a specific genic composition and distinct pattern of evolution.
authors: Research Computing Centre, The University of Queensland, St Lucia, Queensland, AustraliaInstitute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia makunin@hotmail.com.
authors: Igor V
authors: IV
authors: Makunin
authors: Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaNovosibirsk State University, Russia.
authors: Tatyana D
authors: TD
authors: Kolesnikova
authors: Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
authors: Natalya G
authors: NG
authors: Andreyenkova
mesh_terms: D000818:Animals; D042522:DNA Replication Timing; D029721:Drosophila Proteins / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics*; D019143:Evolution, Molecular; D006801:Humans; D019476:Insect Proteins / Q000235:genetics*; D010802:Phylogeny; D022661:RNA, Untranslated / Q000235:genetics
chemical_list: D029721:Drosophila Proteins; D019476:Insect Proteins; D022661:RNA, Untranslated
keywords: Drosophila melanogaster; fast-evolving genes; replication timing