Positive Selection Drives the Evolution of rhino, a Member of the Heterochromatin Protein 1 Family in Drosophila

Abstract

Heterochromatin comprises a significant component of many eukaryotic genomes. In comparison to euchromatin, heterochromatin is gene poor, transposon rich, and late replicating. It serves many important biological roles, from gene silencing to accurate chromosome segregation, yet little is known about the evolutionary constraints that shape heterochromatin. A complementary approach to the traditional one of directly studying heterochromatic DNA sequence is to study the evolution of proteins that bind and define heterochromatin. One of the best markers for heterochromatin is the heterochromatin protein 1 (HP1), which is an essential, nonhistone chromosomal protein. Here we investigate the molecular evolution of five HP1 paralogs present in Drosophila melanogaster. Three of these paralogs have ubiquitous expression patterns in adult Drosophila tissues, whereas HP1D/rhino and HP1E are expressed predominantly in ovaries and testes respectively. The HP1 paralogs also have distinct localization preferences in Drosophila cells. Thus, Rhino localizes to the heterochromatic compartment in Drosophila tissue culture cells, but in a pattern distinct from HP1A and lysine-9 dimethylated H3. Using molecular evolution and population genetic analyses, we find that rhino has been subject to positive selection in all three domains of the protein: the N-terminal chromo domain, the C-terminal chromo-shadow domain, and the hinge region that connects these two modules. Maximum likelihood analysis of rhino sequences from 20 species of Drosophila reveals that a small number of residues of the chromo and shadow domains have been subject to repeated positive selection. The rapid and positive selection of rhino is highly unusual for a gene encoding a chromosomal protein and suggests that rhino is involved in a genetic conflict that affects the germline, belying the notion that heterochromatin is simply a passive recipient of “junk DNA” in eukaryotic genomes.

dDsk2 regulates H2Bub1 and RNA polymerase II pausing at dHP1c complex target genes

“…Co-purified proteins identified with high confidence are listed in Table 1. In addition to dHP1c, WOC and ROW, these experiments detected the dHP1b isoform 34 ; the boundary protein BEAF- 32 (ref. 35); the chromosomal proteins Chromator and Z4, which are known to form a complex 36,37 ; the RNA-binding protein Blanks 38 ; the ubiquitin receptor protein dDsk2; and coilin, a factor that marks Cajal bodies and associates to the histone locus 39 .…”

Structural insights into Rhino-mediated germline piRNA cluster formation

“…Recent studies have shown that a Heterochromatin Protein 1 (HP1) homolog Rhino (Rhi), also known as HP1D, is anchored at the dual-strand piRNA clusters to trigger the piRNA production [3,4]. Rhi is a germline-specific protein that is under rapid and positive selection during evolution [5]. Like other HP1 family proteins, Rhi exists in all Drosophila species and shares the similar domain architecture, which contains a chromodomain (CD) at the N-terminus, a chromoshadow domain (CSD) at the C-terminal region, and a hinged region between CD and CSD domains [5].…”

“…Rhi is a germline-specific protein that is under rapid and positive selection during evolution [5]. Like other HP1 family proteins, Rhi exists in all Drosophila species and shares the similar domain architecture, which contains a chromodomain (CD) at the N-terminus, a chromoshadow domain (CSD) at the C-terminal region, and a hinged region between CD and CSD domains [5].…”

“…As a "royal family" member, the CD has been predominantly characterized as a methylated lysine-binding module [5]. To understand the mechanism by which Rhi specifically recognizes piRNA clusters, we solved a 1.8-Å resolution crystal structure of Rhi-CD in complex with the H3K9me3 peptide by molecular replacement (Supplementary information, Table S1).…”

Drosophila HP1c isoform interacts with the zinc-finger proteins WOC and Relative-of-WOC to regulate gene expression

“…The existence of multiple isoforms suggests functional specialization, with different isoforms playing different functions. For instance, in Drosophila, three of the five HP1 isoforms (HP1a, HP1b, and HP1c) are ubiquitously expressed, while the other two (HP1d/Rhino and HP1e) are predominantly expressed in the germline (Vermaak et al 2005). Moreover, ubiquitously expressed HP1 isoforms show differential chromosomal distributions, as HP1a is mainly associated to heterochromatin, while HP1c is excluded from centromeric heterochromatin and HP1b is found both at euchromatic and heterochromatic domains (Smothers and Henikoff 2001).…”