Thomas Cline

Thomas Cline

Professor Emeritus of Genetics, Genomics and Development

Env Full Directory Information

Research Interests

We have been studying how sexual dimorphism in the fruit fly, Drosophila melanogaster, is genetically programmed and how that programming may have evolved.  All our work over nearly four decades has been related in one way or another to the remarkable master regulatory switch gene Sex-lethal (Sxl), which is at the heart of the fruit fly sex determination system.  We have taken advantage of Sxl's unique features to explore a variety of different research questions, with an increasing emphasis on evolution as understanding of insect sex-determination mechanisms has progressed.  In anticipation of retirement,  I am currently winding down my lab and hence am no longer accepting advisees.  Currently my highest research priority is getting into print the results of a number of completed studies, four of which are described below. 

Current Projects

Background: Sxl is the direct target of the Drosophila sex-determination signal, X-chromosome dose.  In one of the first events directed by the zygotic genome, the double dose of "X-chromosome signal element" (XSEs) gene products in chromosomal females (XX) activates the "establishment" promoter of Sxl in the soma.  The single dose of XSE products in males (XY) is not sufficient to do so.  The pulse of SXL protein thereby generated only in diplo-X animals engages a positive feedback loop for the productive splicing of transcripts originating from the Sxl "maintenance" promoter, which becomes active in both sexes as the establishment promoter shuts down.  This promoter remains active thereafter.  The full-length SXL proteins thereby generated elicit all aspects of female development, including X-chromosome dosage compensation, by interacting with the RNA products of downstream regulatory gene targets such as transformer (tra).  Because males lack that initiating pulse of SXL protein, they never engage the splicing feedback loop, hence never make feminizing SXL proteins, and thus develop male by default.  In germ cells, Sxl is required both for oogenesis and meiotic recombination (a female-specific process in Drosophila), but little is known about its regulation and functioning in that cell type beyond the fact that cell-cell communication between somatic and germ cells in the gonad is important.


Functional evolution of Sxl:  Sxl would seem to be a quintessentially female-specific gene, since its job is to feminize the fruit fly, and males without it develop normally.  Nevertheless, in other insects, Sxl is neither a master sex switch nor female-specific, and there is certainly no indication that it epigenetically maintains its activity through a positive autoregulatory feedback loop on pre-mRNA splicing, as it does in Drosophila.  Instead transformer, a downstream target of Sxl in Drosophila, has that role -- including the epigenetic splicing feedback aspect.  We asked how, when, and even whether the ancestor of Sxl in Drosophila shed its non-female-specific functions.  We reached the rather surprising conclusion that they were never lost, but are simply non-essential under laboratory conditions.  This study included (1) knocking out Sxl's closest paralog; (2) knocking out Sxl in Drosophila virilis, a species distant from melanogaster and notable for the large amount of nearly full length SXL protein that its males produce; and (3) discovering non-sex-specific Drosophila Sxl mRNAs that contain a previously unknown, evolutionarily ancient, alternatively spliced exon whose duplication we suggest was an important step in the evolution of Sxl's sex-determination role.


An unanticipated branch in the regulatory pathway controlling female nervous system development:  It had been thought that Sxl directed all aspect of female somatic differentiation through its effects on tra.  However, we discovered that some aspects of nervous system development required for ovulation are controlled by Sxl, but not by its working solely through tra.  This "tra-insufficient feminization" pathway is exciting both because it involves an aspect of fly behavior that is comparatively simple and because this aspect of behavior is particularly amenable to genetic analysis.  We speculate that this aspect of Sxl function may represent an ancestral, female-specific role that Sxl had when it was regulated by tra, before it became a regulator of tra.


A new member of the "Sxl autoregulation facilitator" (SAF) gene group:  Simply by simultaneously increasing the dose of Sxl and the SAF gene sans-fille, we could induce female expression of Sxl in the male germline and thereby disrupt spermatogenesis without killing the males.  Using a genetic selection for suppressors of this sterilizing effect, we identified a new SAF gene we named helper-of-Sex-lethal (hsx).  A striking feature of the SAF group that hsx shares is its property of facilitating Sxl positive autoregulation in both the germline and soma (most genes with which Sxl interacts are different in these two cell types).  Although we failed in our goal of identifying Sxl regulators that are germline-specific, our recent generation of a new class of Sxl+ duplication has allowed us to design a more powerful suppressor screen with a better chance of achieving this goal.


Structure-function studies of SXL in the germline: We have exploited a variety of mutant Sxl alleles to compare and contrast the roles of various aspects of SXL structure in the germline vs. soma.  Among the more informative findings are (1) that the N-terminus unique to SXL proteins controlling somatic sex determination is not required for SXL germline activities; and (2) that the germline functioning of a mutant Sxl allele that is only defective with respect to its functioning in germ cells can be restored by a single SXL amino acid substitution, but that suppression of the germline defect comes at the expense of somatic functionality.


Selected Publications

Grainyhead and Zelda compete for binding to the promoters of the earliest-expressed Drosophila genes. [Harrison, M.M., Botchan, M.R., and T.W. Cline (2010) Dev. Biol. In Press -- Epub ahead of print PMID#20599892] 

Effects of Wolbachia infection and ovarian tumor mutations on Sex-lethal germline functioning in Drosophila. [S. Sun and T.W. Cline (2009) Genetics 181, 1291-1301]

Sexual back talk with evolutionary implications: stimulation of the Drosophila sex-determination gene Sex-lethal by its target transformer. [S.G. Siera and T.W. Cline (2008) Genetics 180, 1963-1981]

Drosophila melanogaster male somatic cells feminized solely by Tra(F) can collaborate with female germ cells to make functional eggs. [D.S. Evans and T.W. Cline (2007) Genetics 175,631-642] 

The TAGteam DNA motif controls the timing of Drosophila pre-blastoderm transcription. [J.R. ten Bosch, J.A. Benavides and T.W. Cline (2006) Development 133, 1967-1977] 

Recruitment of the proneural gene scute to the Drosophila sex-determination pathway. [L.A. Wrischnik, J.R. Timmer, L.A. Megna, and T.W. Cline (2003) Genetics 165, 2007-2027]

A host-parasite interaction suppresses oogenesis defects of Drosophila sex-determination gene mutants. [D. J. Starr and T.W. Cline (2002) Nature 418, 76-79]

An extracellular activator of the Drosophila JAK/STAT pathway is a sex-determination signal element. [L. Sefton, J. R. Timmer, Y. Zhang, F. Beranger, and T. W. Cline (2000) Nature 405, 970-973]

Functioning of the Drosophila integral U1/U2 protein independent of U1 and U2 small nuclear ribonucleoprotein particles is revealed by snf+ gene dose effects. [Cline, T.W., Rudner, D.Z., Barbash, D.A., Bell, M., and R. Vutien (1999) Proc. Nat. Acad. Sci. U.S. 96, 14451-14458]

Key aspects of the primary sex determination mechanism are conserved across the genus Drosophila. [J. W. Erickson and T. W. Cline (1998) Development 125, 3259-3268]

Vive la difference: males vs. females in flies vs. worms. [T.W. Cline and B.J. Meyer (1996) Annual Review of Genetics 30, 637-701]

Last Updated 2010-08-05