Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites

Abstract

The gibbon genome exhibits extensive karyotypic diversity with an increased rate of chromosomal rearrangements during evolution. In an effort to understand the mechanistic origin and implications of these rearrangement events, we sequenced 24 synteny breakpoint regions in the white-cheeked gibbon (Nomascus leucogenys, NLE) in the form of highquality BAC insert sequences (4.2 Mbp). While there is a significant deficit of breakpoints in genes, we identified seven human gene structures involved in signaling pathways (DEPDC4, GNG10), phospholipid metabolism (ENPP5, PLSCR2), boxidation (ECH1), cellular structure and transport (HEATR4), and transcription (ZNF461), that have been disrupted in the NLE gibbon lineage. Notably, only three of these genes show the expected evolutionary signatures of pseudogenization. Sequence analysis of the breakpoints suggested both nonclassical nonhomologous end-joining (NHEJ) and replicationbased mechanisms of rearrangement. A substantial number (11/24) of human-NLE gibbon breakpoints showed new insertions of gibbon-specific repeats and mosaic structures formed from disparate sequences including segmental duplications, LINE, SINE, and LTR elements. Analysis of these sites provides a model for a replication-dependent repair mechanism for double-strand breaks (DSBs) at rearrangement sites and insights into the structure and formation of primate segmental duplications at sites of genomic rearrangements during evolution.

A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons

“…The results for HLE and SSY are summarized in Figures 1 and 2 and below. Data on HLA and NLE have been already reported (Carbone et al 2006;Roberto et al 2007;Misceo et al 2008;Girirajan et al 2009). …”

“…In particular, we took into consideration the Hylobatidae ancestral karyotype proposed by Misceo et al (2008) and the FISH data already published on other gibbon species (Muller et al 2003;Roberto et al 2007;Misceo et al 2008;Girirajan et al 2009). …”

“…Molecular cytogenetic techniques now allow a significantly higher resolution than chromosome painting through the use of hybridization of precisely mapped BAC clones, microarrays, and selective sequencing. Using these approaches we recently defined the chromosomal changes and synteny block organization of Hylobates lar (HLA, lar gibbon) and Nomascus leucogenys (NLE, white-cheeked gibbon) (Carbone et al 2006;Roberto et al 2007;Misceo et al 2008;Girirajan et al 2009). Yet, the reconstruction of the evolutionary history of rearrangements is only as complete as the taxonomic array of relevant species.…”

Hominoid fission of chromosome 14/15 and the role of segmental duplications

“…It raises the possibility that not only duplication triggers chromosomal rearrangement through NAHR but also that chromosomal breakage gives rise to duplication events (Kehrer-Sawatzki and Cooper 2008;Girirajan et al 2009). We propose a possible additional role of SDs in genome evolution where the occurrence of duplication events in response to chromosomal breakage might represent a possible ''feedback mechanism'' that produces additional DNA material to recover the damage caused by the breakage.…”

Nomascus leucogenys (Primates: Hylobatidae)

“…In contrast to other apes, which show limited chromosomal variation, chromosomes of Hylobatidae evolved rapidly, resulting in a diverse karyotypic pattern among different species and subspecies (reviewed by Girirajan et al 2009). The rates of rearrangements in gibbons are 10-20 times higher than the mammalian default rate.…”