Screen for Genetic Modifiers of stbm Reveals that Photoreceptor Fate and Rotation Can Be Genetically Uncoupled in the Drosophila Eye

BACKGROUND: Polarity of the Drosophila compound eye arises primarily as a consequence of two events that are tightly linked in time and space: fate specification of two photoreceptor cells, R3 and R4, and the subsequent directional movement of the unit eyes of the compound eye, or ommatidia. While it is thought that these fates dictate the direction of ommatidial rotation, the phenotype of mutants in the genes that set up this polarity led to the hypothesis that these two events could be uncoupled. METHODOLOGY/PRINCIPAL FINDINGS: To definitively demonstrate these events are genetically separable, we conducted a dominant modifier screen to determine if genes, when misexpressed, could selectively enhance subclasses of mutant ommatidia in which the direction of rotation does not follow the R3/R4 cell fates, yet not affect the number of ommatidia in which rotation follows the R3/R4 cell fates. We identified a subset of P element lines that exhibit this selective enhancement. We also identified lines that behave in the opposite manner: They enhance the number of ommatidia that rotate in the right direction, but do not alter the number of ommatidia that rotate incorrectly with respect to the R3/R4 fates. CONCLUSIONS/SIGNIFICANCE: These results indicate that fate and direction of rotation can be genetically separated, and that there are genes that act between R3/R4 fate specification and direction of ommatidial rotation. These data affirm what has been a long-standing assumption about the genetic control of ommatidial polarity

Zebrafish brd2a and brd2b are paralogous members of the bromodomain-ET (BET) family of transcriptional coregulators that show structural and expression divergence

<p>Abstract</p> <p>Background</p> <p>Brd2 belongs to the bromodomain-extraterminal domain (BET) family of transcriptional co-regulators, and functions as a pivotal histone-directed recruitment scaffold in chromatin modification complexes affecting signal-dependent transcription. Brd2 facilitates expression of genes promoting proliferation and is implicated in apoptosis and in egg maturation and meiotic competence in mammals; it is also a susceptibility gene for juvenile myoclonic epilepsy (JME) in humans. The <it>brd2 </it>ortholog in <it>Drosophila </it>is a maternal effect, embryonic lethal gene that regulates several homeotic loci, including Ultrabithorax. Despite its importance, there are few systematic studies of <it>Brd2 </it>developmental expression in any organism. To help elucidate both conserved and novel gene functions, we cloned and characterized expression of <it>brd2 </it>cDNAs in zebrafish, a vertebrate system useful for genetic analysis of development and disease, and for study of the evolution of gene families and functional diversity in chordates.</p> <p>Results</p> <p>We identify cDNAs representing two paralogous <it>brd2 </it>loci in zebrafish, <it>brd2a </it>on chromosome 19 and <it>brd2b </it>on chromosome 16. By sequence similarity, syntenic and phylogenetic analyses, we present evidence for structural divergence of <it>brd2 </it>after gene duplication in fishes. <it>brd2 </it>paralogs show potential for modular domain combinations, and exhibit distinct RNA expression patterns throughout development. RNA <it>in situ </it>hybridizations in oocytes and embryos implicate <it>brd2a </it>and <it>brd2b </it>as maternal effect genes involved in egg polarity and egg to embryo transition, and as zygotic genes important for development of the vertebrate nervous system and for morphogenesis and differentiation of the digestive tract. Patterns of <it>brd2 </it>developmental expression in zebrafish are consistent with its proposed role in <it>Homeobox </it>gene regulation.</p> <p>Conclusion</p> <p>Expression profiles of zebrafish <it>brd2 </it>paralogs support a role in vertebrate developmental patterning and morphogenesis. Our study uncovers both maternal and zygotic contributions of <it>brd2</it>, the analysis of which may provide insight into the earliest events in vertebrate development, and the etiology of some forms of epilepsy, for which zebrafish is an important model. Knockdowns of <it>brd2 </it>paralogs in zebrafish may now test proposed function and interaction with homeotic loci in vertebrates, and help reveal the extent to which functional novelty or partitioning has occurred after gene duplication.</p

GMREP modifiers of the <i>sev-stbm</i> phenotype

*<p>Three additional classes were scored (missing R, extra R, failure to rotate) but these data were omitted to simplify the data set. “Total errors” includes defects in these three classes.</p

Modification of <i>sev-stbm</i> phenotype by GMREP lines.

<p>(A) Wild-type eyes have two ommatidial forms, dorsal (blue) and ventral (red); each class falls exclusively on the dorsal or ventral side of the equator (yellow/black line). (B) <i>sev-stbm</i> eyes have polarity defects in 11% of ommatidia. Three DV (red trapezoid) and one AP (black trapezoid) inversions are shown here. (C) A GMREP line that primarily enhances the number of DV defects in the <i>sev-stbm</i>/+ phenotype. (D) The number AP/DV (green trapezoid) defects is enhanced by the GMREP line shown here in a <i>sev-stbm</i>/+ background. (E) An eye representative of GMREP lines that enhance the AP-type defects in a <i>sev-stbm</i> background. (F) The modified eye shown in this panel has a marked increase in the number of R3/R3 and R4/R4 symmetric defects (yellow open rectangles and horseshoe shapes). Key: examples shown are for ommatidia in dorsal half of eye. Blue: wild-type; red: D/V inversion; black: A/P inversion; green: AP/DV inversion; yellow rectangle: R3/R3 symmetric ommatidia; yellow horseshoe: R4/R4 symmetric ommatidia.</p

Derivation of wild-type and mutant ommatidial forms.

<div><p>(A) In wild-type imaginal discs, ommatidial precursors rotate 90° counterclockwise in the dorsal half of the eye and 90° clockwise in the ventral half (green arrows). Final adult forms, following rotation and additional morphological changes, are shown as trapezoids. (B) Corresponding mutant forms of ommatidial precursors and adult trapezoids from dorsal half of the eye are shown. D/V forms arise as a consequence of the wrong fate choice followed by the right direction of rotation with respect to those fates. A/P forms occur when the wrong fates are chosen but, unlike D/V inversions, ommatidial precursors subsequently rotate in the wrong direction with respect to the fates. AP/DV ommatidial result from the correct fate choice but wrong direction of rotation.</p><p>Legend: photoreceptor R3 is denoted by red fill and R4 by blue fill. Green arrows indicate correct direction of rotation with respect to R3/R4 fates. Purple arrows indicate wrong direction of rotation. Anterior is to the right.</p></div

Zebrafish and are paralogous members of the bromodomain-ET (BET) family of transcriptional coregulators that show structural and expression divergence-2

S (lower) added to branches. At least one duplication of the gene has occurred in teleosts. zf626/zf619 cDNAs group with in zebrafish, while zf69 cDNA groups with sequences from the paralogous locus. zf626, GenBank: ; zf619, GenBank: ; zf69, GenBank: ; , GenBank: ; , GenBank: .2; chr16.1, 16.2, 16.3, from Ensembl: ENSDARG00000046087; , GenBank: ; , GenBank: ; , GenBank: ; , GenBank: ; , GenBank: ; , GenBank: ; , GenBank: ; , Ensembl: SINFRUG00000151665; , EMBL: ; , Ensembl: SINFRUG00000141925; , Ensembl: SINFRUG00000145405; , Ensembl: SINFRUG00000148459; , Ensembl: SINFRUG00000151665; , EMBL: ; , EMBL: ; , EMBL: ; , EMBL: ; , EMBL: ; , EMBL: ; , GenBank: ; , Ensembl: ENSORLG00000016659; , Ensembl: ENSORLG00000006490; , Ensembl: ENSORLG00000010329; , Ensembl: ENSORLG00000013915; , Ensembl: ENSORLG00000012190; , Ensembl: ENSORLG00000016149; , GenBank ; , EMBL: ; , GenBank: ; , GenBank: ; , EMBL: ; , EMBL: GenBank: ; , GenBank: ; , GenBank: .1; , Ensembl: ENSGALG00000013295; , Ensembl: ENSGALG00000006031; , GenBank: ; , GenBank: ; , GenBank: ; , GenBank: ; , GenBank: ; , GenBank: ; , GenBank: ; , GenBank: ; , GenBank: ;, GenBank: ; , GenBank: ; , GenBank: ; , GenBank: ; , GenBank: .<p><b>Copyright information:</b></p><p>Taken from "Zebrafish and are paralogous members of the bromodomain-ET (BET) family of transcriptional coregulators that show structural and expression divergence"</p><p>http://www.biomedcentral.com/1471-213X/8/39</p><p>BMC Developmental Biology 2008;8():39-39.</p><p>Published online 10 Apr 2008</p><p>PMCID:PMC2373290.</p><p></p

Zebrafish and are paralogous members of the bromodomain-ET (BET) family of transcriptional coregulators that show structural and expression divergence-9

Upported and predicted transcripts from chromosome 16 ENSDARG00000046087 locus from Ensembl and NCBI databases, and D) partial cDNA from NCBI database. Some schematics include 5'UTR and 3' UTR, with wider rectangles depicting protein-coding regions. Boxes show conserved domains: bromodomain (red box); nuclear localization signal (horizontal striped); ET domain (yellow box); in C, degenerate second bromodomain (orange box); in C, upstream TAP domain (light blue box); valine-, leucine-rich region (VL-rich box); arginine-, serine-rich region (RS-rich box); start and stop codons (thick vertical lines); in A, SNPs between zf626 and zf619 (thin vertical lines); in B, discontinuous region in zf69 cDNA with repetitive sequences at bases 921–1033 and 1259–1413 (gray box); conserved intron/exon junction for alternative splicing in -related transcripts (arrow). Two-exon region in cDNA found in scaf_NA1181 is underscored in D. Length of cDNAs in base pairs is given in parentheses.<p><b>Copyright information:</b></p><p>Taken from "Zebrafish and are paralogous members of the bromodomain-ET (BET) family of transcriptional coregulators that show structural and expression divergence"</p><p>http://www.biomedcentral.com/1471-213X/8/39</p><p>BMC Developmental Biology 2008;8():39-39.</p><p>Published online 10 Apr 2008</p><p>PMCID:PMC2373290.</p><p></p

Zebrafish and are paralogous members of the bromodomain-ET (BET) family of transcriptional coregulators that show structural and expression divergence-8

S through ovaries are shown in E-J. maternal RNAs are dispersed and abundant in stage I and II oocytes (A, E), and are sometimes found inside the germinal vesicle (gv), as in G (see small oocytes at far right). By stage III,transcripts accumulate around the outside of the germinal vesicle and rather unevenly around the periphery of the cortex just inside the vitelline envelope (C, E; G, arrowheads). RNAs then localize around the periphery of the cortex by late stage III, early stage IV (I, arrowheads). RNAs are also present in follicle cells of stage III/IV oocytes (C; G, I, arrowheads outside oocyte). Although maternal transcripts are also dispersed throughout stage I and II oocytes, and often found inside the germinal vesicle (B, F, H, J), in contrast to , they become strictly localized to the region surrounding the micropyle (D, mp; H, J, arrowheads), the future animal pole, sometime during stage III, and are not expressed in follicle cells. A,B: 40X; C-F: 80X; G-J, 100X.<p><b>Copyright information:</b></p><p>Taken from "Zebrafish and are paralogous members of the bromodomain-ET (BET) family of transcriptional coregulators that show structural and expression divergence"</p><p>http://www.biomedcentral.com/1471-213X/8/39</p><p>BMC Developmental Biology 2008;8():39-39.</p><p>Published online 10 Apr 2008</p><p>PMCID:PMC2373290.</p><p></p

Zebrafish and are paralogous members of the bromodomain-ET (BET) family of transcriptional coregulators that show structural and expression divergence-10

) from the Tubingen strain, zebrafish chromosome 19 from the AB strain (Dr chr 19/AB), and Onchorynchus chromosome 2 (Om chr 2). Gene order is derived from contig views in Vega (Dr chr 19, Dr chr 19/AB), Ensembl (Dr chr 16, Hs chr 6, NA1181), direct reading of annotated genomic clones (Dr chr 19, BX510994.6; Dr chr 19/AB, AL672176.10), and reference 28 (Om chr 2). Brd2-related genes are shown in bold. Genes that reside on the same genomic clone are shown in single-spaced groups; genomic clones within the same chromosome that physically overlap are connected by vertical lines. Related genes or groups of genes between chromosomes that show conserved synteny are also connected by lines. Human resides within the MHC II complex on chromosome 6, in a conserved syntenic block between and genes; zebrafish is found in the same gene block within the fish MHC I core on chromosome 19, and is the true ortholog of mammalian . Gene content on chromosome 19 from strains Tubingen and AB differs outside the and the gene blocks, and may indicate recent genomic rearrangement. The zebrafish paralogous locus on chromosome 16 (alias loc 569354, ) is linked to sequences and other MHC II and III related genes, as is trout on chromosome 2, presumably representing the ancestral vertebrate configuration. on unmapped scaffold NA1181 consists of two exons encoding the second bromodomain of partial cDNA (GenBank: ), and with further genome assembly will likely be shown to derive from the same locus on chromosome 16.<p><b>Copyright information:</b></p><p>Taken from "Zebrafish and are paralogous members of the bromodomain-ET (BET) family of transcriptional coregulators that show structural and expression divergence"</p><p>http://www.biomedcentral.com/1471-213X/8/39</p><p>BMC Developmental Biology 2008;8():39-39.</p><p>Published online 10 Apr 2008</p><p>PMCID:PMC2373290.</p><p></p