GENETIC ANALYSIS OF NEMATODE DEVELOPMENT

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
305	3130	1040	40%
305	3130	1120	30%
305	3130	1080	30%

Progress 05/01/97 to 08/31/11

Outputs
OUTPUTS: We have continued to analyze regulators of germline proliferation, survival and differentiation. We found that the FBF RNA-binding protein is a broad-spectrum regulator of differentation mRNAs and published its targets and their initial analysis in PNAS. We found that GLD-2/RNP-8 is a broad spectrum regulator of oogenesis mRNAs and published its targets in PNAS. We discovered a chemical method to reprogram germ cell fates and identified a stem cell pool and published this finding in Nature Chemical Biology. We also discovered that germline stem cells are sexually dimorphic in adults and published this finding in Developmental Biology. We also have disseminated this information via presentations at international meetings and in seminars. PARTICIPANTS: Individuals: Judith Kimble, PI; 8 postdoctoral associates; 9 graduate students; 4 technicians/specialists/scientists; 1 sabbatical visitor; 1 administrative assistant. Partner organization: Howard Hughes Medical Institute. Collaborators: Marvin Wickens, Jeff Hardin, Jose Perez-Martin. TARGET AUDIENCES: Biomedical and basic scientific research communities with the intent of increasing knowledge. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Our research has uncovered regulatory proteins and pathways that control a variety of conserved biological processes, including stem cell maintenance, the mitosis/meiosis decision and the sperm/oocyte decision. Our findings have provided insight into controls of proliferation and differentiation that function in virtually all animals, including humans. Many of our regulators have been implicated in the control of human disease, including cancer, stroke and arthritis.

Publications

Morgan, C.T., Lee, M.-H., and J. Kimble (2010) Chemical reprogramming of Caenorhabditis elegans germ cell fate. Nature Chemical Biology 6, 102-104.
Cinquin, O., Crittenden, S.L., Morgan, D.E. and J. Kimble (2010) Progression from a stem cell-like state to early differentiation in the C. elegans germ line. PNAS 107, 2048-2053.
Kershner, A. and J. Kimble (2010) Genome-wide analysis of mRNA targets for Caenorhabditis elegans FBF, a conserved stem cell regulator. PNAS 107, 3936-3941.
Morgan, D. Crittenden, S.L. and J. Kimble (2010) The C. elegans adult male germline: stem cells and sexual dimorphism. Developmental Biology 346, 204-214.
Kim, K.W, Wilson, T.L. and J. Kimble (2010) The GLD-2/RNP-8 cytoplasmic poly(A) polymerase is a broad-spectrum regulator of the oogenesis program. PNAS 107(40), 17445-17450.

Progress 01/01/09 to 12/31/09

Outputs
OUTPUTS: (1) Germline fate decisions. We have continued to analyze regulators of germline proliferation, survival and differentiation. We found that the FBF RNA-binding protein can act as an activator and that the GLD-2 cytoplasmic poly(A) polymerase can partner with different proteins to control distinct fates. We also discovered a chemical method to reprogram germ cell fates and identified a stem cell pool. (2) Gonadogenesis. We continued to analyze regulators of early gonadogenesis. We found that HLH-2/E/daughterless controls the specification of regulatory cells that control organogenesis. PARTICIPANTS: Individuals: Judith Kimble, PI; 8 postdoctoral associates; 7 graduate students; 5 technicians/specialists/scientists; 3 undergraduate researchers; 1 administrative assistant. Partner organization: Howard Hughes Medical Institute. Collaborators: Marvin Wickens, Jeff Hardin. TARGET AUDIENCES: Biomedical and basic scientific research communities with the intent of increasing knowledge. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Our research has uncovered regulatory proteins and pathways that control a variety of conserved biological processes, including stem cell maintenance, the mitosis/meiosis decision and the sperm/oocyte decision. Our findings have provided insight into controls of proliferation and differentiation that function in virtually all animals, including humans. Many of our regulators have been implicated in human disease, including cancer, stroke and arthritis.

Publications

Chesney, M.A., Lam, N., Morgan, D.E., Phillips, B.T. and J. Kimble (2009) C. elegans HLH-2/E/Daughterless controls key regulatory cells during gonadogenesis. Developmental Biology 331, 14-25.
Phillips, B and J. Kimble (2009) A new look at TCF and β-catenin through the lens of a divergent C. elegans Wnt pathway. Developmental Cell 17, 27-34.
Byrd, D.T. and J. Kimble (2009) Scratching the niche that controls Caenorhabditis elegans germline stem cells. Seminars in Cell & Developmental Biology 20, 1107-1113.
King, R.S., Maiden, S.L., Hawkins, N.C., Kidd, A.R., Kimble, J., Hardin J., and T.D. Walston (2009) The N- or C-terminal domains of DSH-2 can activate the C. elegans Wnt/β-catenin asymmetry pathway. Developmental Biology 328(2), 234-244.
Suh, N., Crittenden, S.L., Goldstrohm, A., Hook, B., Thompson, B., Wickens, M. and J. Kimble (2009) FBF and its dual control of gld-1 expression in the Caenorhabditis elegans germline. Genetics 181, 1249-1260.
Kim, K.W., Nykamp, K., Suh, N., Bachorik, J.L., Wang, L. and J. Kimble (2009) Antagonism between GLD-2 binding partners controls gamete sex. Developmental Cell 16, 723-733.

Progress 01/01/08 to 12/31/08

Outputs
OUTPUTS: (1) Germline fate decisions. We have continued to analyze regulators of germline proliferation, survival and differentiation. In this area, we identified LARP-1 as a key regulator of ERK/MAP kinase expression. (2) Gonadogenesis. We have continued to analyze regulators of early gonadogenesis. In this area, we found by X-ray crystallography, in collaboration with Dr. Wenqing Xu in Seattle, that the SYS-1 protein has an architecture very similar to that of beta-catenins. We conclude that functional beta-catenins exist that cannot be recognized by sequence similarity. PARTICIPANTS: Individuals: Judith Kimble, PI; 7 postdoctoral associates; 7 graduate students; 4 technicians/specialists/scientists; 3 undergraduate researchers; 1 administrative assistant. Partner organization: Howard Hughes Medical Institute. Collaborators: Marvin Wickens, Wenqing Xu, Jeff Hardin. TARGET AUDIENCES: Biomedical and basic scientific research communities with the intent of increasing knowledge. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Our research has uncovered regulatory proteins and pathways that control a variety of conserved biological processes, including the decisions between mitosis and meiosis and spermatogenesis and oogenesis. Our findings have provided insight into controls of proliferation and differentiation that function in virtually all animals, including humans. Many of our regulators have been implicated in human disease, including cancer, stroke and arthritis.

Publications

Crittenden, S.L. and J. Kimble (2008) Analysis of the C. elegans germline stem cell region. In Germline Stem Cells, edited by Steven X. Hou and Shree Ram Singh. Methods in Molecular Biology 450, 27-44.
Liu, J., Phillips, B.T., Amaya, M.F., Kimble, J. and W. Xu (2008) The C. elegans SYS-1 protein is a bona-fide β−catenin. Developmental Cell 14, 751-761.
Nykamp, K., Lee, M.-H. and J. Kimble (2008) C. elegans La-related protein, LARP-1, localizes to germline P bodies and attenuates Ras-MAPK signaling during oogenesis. RNA 14, 1378-1389.
Stumpf, C.R., Kimble, J. and M. Wickens (2008) A Caenorhabditis elegans PUF protein family with distinct RNA binding specificity. RNA 14, 1550-1557.

Progress 01/01/07 to 12/31/07

Outputs
OUTPUTS: (1) Germline fate decisions. We have continued to analyze regulators of germline proliferation, survival and differentiation. In this area, we have made several key advances during the past year. Specifically, we found that mRNAs encoding MAP kinase enzmes are controlled by the PUF RNA-binding proteins in both nematodes and human ES cells. In addition, we analyzed the control of fog-1 expression and found that FOG-1 distribution corresponds to sperm number. (2) Gonadogenesis. We have continued to analyze regulators of early gonadogenesis. In this area, we found that the SYS-1 functional beta-catenin is localized to one daughter of asymmetric cell divisions, that this SYS-1 asymmetry is widespread throughout the C. elegans lineage, that SYS-1 controls many asymmetric cell divisions, including the EMS division in the early embryo, and that SYS-1 asymmetry is controlled by the Wnt signaling pathway. We proposed a model by which Wnt signaling controls the ratio of SYS-1/beta-catenin and POP-1/TCF to drive cell fate asymmetrically after an asymmetric cell division. PARTICIPANTS: Individuals: Judith Kimble, PI; 6 postdoctoral associates; 8 graduate students; 4 technicians/specialists/scientists; 3 undergraduate researchers; 1 administrative assistant

Partner organization: Howard Hughes Medical Institute (HHMI)

Collaborators: Marvin Wickens; James A. Thomson; Jeff Hardin; Geraldine Seydoux TARGET AUDIENCES: Biomedical and basic scientific research communities with the intent of increasing knowledge.

Impacts
Our research has uncovered regulatory proteins and pathways that control a variety of conserved biological processes, including the decisions between mitosis and meiosis and spermatogenesis and oogenesis. Our findings have provided insight into controls of proliferation and differentiation that function in virtually all animals, including humans. Many of our regulators have been implicated in human disease, including cancer, stroke and arthritis.

Publications

Thompson, B., M. Wickens and J. Kimble (2007) Translational control in development. In Translational Control in Biology and Medicine (M.B. Mathews, N. Sonenberg, J.W.B. Hershey, eds). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, pp.507-544.
Phillips, B.T., Kidd III, A.R., King, R. Hardin, J. and J. Kimble (2007) Reciprocal asymmetry of SYS-1/B-catenin and POP-1/TCF controls asymmetric divisions in Caenorhabditis elegans. PNAS 104(9), 3231-3236.
Lamont, L.B. and J. Kimble (2007) Developmental expression of FOG-1/CPEB protein and its control in the Caenorhabditis elegans hermaphrodite germ line. Developmental Dynamics 236(3), 871-879.
Kimble, J. and D.C. Page (2007) The mysteries of sexual identity: the germ cell's perspective. Science 316, 400-401.
Kimble, J. and S. Crittenden (2007) Controls of germline stem cells, entry into meiosis, and the sperm/oocyte decision in Caenorhabditis elegans. Ann. Rev. Cell Dev. Biol. 23, 405-433.
Lee, M-H., Hook, B., Pan, G., Kershner, A.M., Merritt, C., Seydoux, G., Thomson, J.A., Wickens, M. and J. Kimble (2007) Conserved regulation of MAP kinase expression by PUF RNA-binding proteins. PLoS Genetics 3(12), e233.

Progress 01/01/06 to 12/31/06

Outputs
(1) Germline fate decisions. We have continued to analyze regulators of germline proliferation, survival and differentiation. In this area, we have made several key advances during the past year. We found a regulator of MAPK signaling to be a direct target of Notch signaling that controls germline proliferation; we analyzed the cell cycle of germ cells mitotic region; and we identified the gld-1 mRNA as a direct target of GLD-2 poly(A) polymerase activity. (2) Gonadogenesis. We have continued to analyze regulators of early gonadogenesis. In this area, we learned that the specification of the distal tip cell is dependent on a conserved protein called CEH-22 and that the ceh-22b promoter is a direct target of Wnt/MAPK signaling.

Impacts
Our research has uncovered regulatory proteins and pathways that control a variety of conserved biological processes, including the decisions between mitosis and meiosis and spermatogenesis and oogenesis. Our findings have provided insight into controls of proliferation and differentiation that function in virtually all animals, including humans. Many of our regulators have been implicated in human disease, including cancer, stroke and arthritis.

Publications

Crittenden, S. and J. Kimble (2006) Immunofluorescence methods for Caenorhabditis elegans. In Basic Methods in Microscopy: Protocols and Concepts from Cells: A Laboratory Manual (D.L. Spector and R.D. Goldman, eds). pp. 193-200.
Lee, M.H., Hook, B., Lamont, L.B., M. Wickens and J. Kimble (2006) LIP-1 phosphatase controls the extent of germline proliferation in C. elegans. The EMBO Journal 25(1), 88-96.
Thompson, B.E., Lamont, L.B. and J. Kimble (2006) Germ-line induction of the Caenorhabditis elegans vulva. PNAS 103(3), 620-625.
Chesney, M.A., Kidd III, A.R. and J. Kimble (2006) gon-14 functions with class B and class C synthetic multivulva genes to control larval growth in Caenorhabditis elegans. Genetics 172, 915-928.
Lam, N., Chesney, M.A. and J. Kimble (2006) Wnt signaling and CEH-22/tinman/Nkx2.5 specify a stem cell niche in C. elegans. Current Biology 16, 287-295.
Crittenden, S.L., Leonhard, K.A., Byrd, D.T. and J. Kimble (2006) Cellular analyses of the mitotic region in the Caenorhabditis elegans adult germ line. Molecular Biology of the Cell 17(7), 3051-3061.
Morrison, S.J. and J. Kimble (2006) Asymmetric and symmetric stem-cell divisions in development and cancer. Nature 441, 1068-1074.
Suh, N., Eckmann, C.R., Wickens, M. and J. Kimble (2006) The GLD-2 poly(A) polymerase activates gld-1 mRNA in the C. elegans germ line. PNAS 103(41), 15208-15112.
Hesselson, D. and J. Kimble (2006) Growth control by EGF-repeats of the C. elegans Fibulin-1C isoform. J. Cell Biol. 175(2), 217-223.

Progress 01/01/05 to 12/31/05

Outputs
(1) Germline fate decisions. We have continued to analyze regulators of germline proliferation, survival and differentiation. Specifically, we have learned that the FOG-1/CPEB RNA regulatory protein controls germline proliferation when present at low levels, but sperm specification at high levels. We have also learned that FBF functions redundantly with another Puf protein, called PUF-8, to control the sperm/oocyte decision. (2) Gonadogenesis. We are analyzing controls of early gonadogenesis. We have identified SYS-1, a novel protein with the activity of beta-catenin genes, and shown that Wnt signaling regulates the ratio of the POP-1/TCF DNA binding protein and the SYS-1/beta-catenin. We have also found that cyclin D integrates Wnt signaling with sex determination and cell cycle progression in the early gonad.

Impacts
Our research has uncovered regulatory proteins and pathways that control a variety of conserved biological processes, including the decisions between mitosis and meiosis and spermatogenesis and oogenesis. Our findings have provided insight into controls of proliferation and differentiation that function in virtually all animals, including humans. Many of our regulators have been implicated in human disease, including cancer, stroke and arthritis.

Publications

Kidd III, A.R., Miskowski, J.A., Siegfried, K.R., Sawa, H. and J. Kimble (2005) A beta-catenin identified by functional rather than sequence criteria and its role in Wnt/MAPK signaling. Cell 121, 761-772.
Thompson, B.E., Bernstein, D.S., Bachorik, J.L., Petcherski, A.G., Wickens, M. and J. Kimble (2005) Dose-dependent control of proliferation and sperm specification by FOG-1/CPEB. Development 132, 3471-3481.
Bachorik, J. L. and J. Kimble (2005) Redundant control of the Caenorhabditis elegans sperm/oocyte switch by PUF-8 and FBF-1, two distinct PUF RNA-binding proteins. PNAS 102(31), 10893-10897.
Kimble, J. and S.L. Crittenden (2005) Germline proliferation and its control (August 15, 2005). WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.13.1, http://www.wormbook.org.
Tilmann, C. and J. Kimble (2005) Cyclin D regulation of a sexually dimorphic asymmetric cell division. Developmental Cell 9, 489-499.

Progress 01/01/04 to 12/31/04

Outputs
(1) Germline fate decisions. We have continued to analyze regulators of germline proliferation, survival and differentiation. Specifically, we have learned that FBF controls two branches of regulatory proteins that in turn control entry into meiosis. One branch is composed of GLD-1 and NOS-3 and the other branch is composed of GLD-2 and GLD-3. (2) Gonadogenesis. We are analyzing several distinct controls of early gonadogenesis. We have found three regulatory genes that control formation of the four-celled gonadal primordium, including the single C. elegans Hand gene. We have also found five genes that control organ polarity (sys-1, sys-3, gon-14, gon-15, and gon-16). Finally, we have found one gene which encodes a forkhead transcription factor that controls sexual dimorphism of early gonadogenesis.

Impacts
Our research has uncovered regulatory proteins and pathways that control a variety of conserved biological processes, including the decisions between mitosis and meiosis and spermatogenesis and oogenesis. Our findings have provided insight into controls of proliferation and differentiation that function in virtually all animals, including humans. Many of our regulators have been implicated in human disease, including cancer, stroke and arthritis.

Publications

Siegfried, K.R., Kidd, A.R., Chesney, M.A. and J. Kimble (2004) The sys-1 and sys-3 genes cooperate with Wnt signaling to establish the proximal-distal axis of the C. elegans gonad. Genetics 166(1), 171-186.
Chang, W., Tilmann, C., Thoemke, K., Markussen, F.-H., Mathies, L.D., Kimble, J. and D. Zarkower (2004) A forkhead protein controls sexual identity of the C. elegans male somatic gonad. Development, 131(6), 1425-1436.
Kwak, J.E., Wang, L., Ballantyne, S., Kimble, J. and M. Wickens (2004) Mammalian GLD-2 homologs are poly(A) polymerases. PNAS 101(13), 4407-4412.
Mathies, L.D., Schvarzstein, M., Morphy, K.M., Blelloch, R., Spence, A.M. and J. Kimble (2004) tra-1/GLI controls development of somatic gonadal precursors in C. elegans. Development, 131, 4333-4343.
Wang L., Kimble, J. and M. Wickens (2004) Tissue-specific modification of gld-2 mRNA in C. elegans: Likely C-to-U editing. RNA 10, 1444-1448.
Eckmann, C.R., Crittenden, S.L., Suh, N. and J. Kimble (2004) GLD-3 and control of the mitosis/meiosis decision in the C. elegans germ line. Genetics 168(1), 147-160.
Lamont, L.B., Crittenden, S.L., Bernstein, D., Wickens, M. and J. Kimble (2004) FBF-1 and FBF-2 regulate the size of the mitotic region in the C. elegans germ line. Developmental Cell 7(5), 697-707.
Hesselson, D., Newman, C., Kim, K.W. and J. Kimble (2004) GON-1 and fibulin have antagonistic roles in control of organ shape. Current Biology 14(22), 2005-2010.

Progress 01/01/03 to 12/31/03

Outputs
(1) Germline fate decisions. We have continued to analyze regulators of germline proliferation, survival and differentiation. Specifically, we have learned that FBF controls two branches of regulatory proteins that in turn control entry into meiosis. One branch is composed of GLD-1 and NOS-3 and the other branch is composed of GLD-2 and GLD-3. (2) Gonadogenesis. We are analyzing several distinct controls of early gonadogenesis. We have found three regulatory genes that control formation of the four-celled gonadal primordium, including the single C. elegans Hand gene. We have also found five genes that control organ polarity (sys-1, sys-3, gon-14, gon-15, and gon-16). Finally, we have found one gene which encodes a forkhead transcription factor, that controls sexual dimorphism of early gonadogenesis.

Impacts
Our research has uncovered regulatory proteins and pathways that control a variety of conserved biological processes, including the decisions between mitosis and meiosis and spermatogenesis and oogenesis. Our findings have provided insight into controls of proliferation and differentiation that function in virtually all animals, including humans. Many of our regulators have been implicated in human disease, including cancer, stroke and arthritis.

Publications

Crittenden, S., Eckmann, C.R. Wang, L., Bernstein, D., Wickens, M. and J. Kimble (2003) Regulation of the mitosis/meiosis decision in the Caenorhabditis elegans germline. Philosophical Transactions of the Royal Society of London B. 358, 1359-1362.
Mathies, L.D., Henderson, S.T. and J. Kimble (2003) The C. elegans Hand gene controls embryogenesis and early gonadogenesis. Development 130, 2881-2892.

Progress 01/01/02 to 12/31/02

Outputs
(1) Germline fate decisions. We have continued to analyze RNA binding proteins that regulate germline proliferation, survival and differentiation. Specifically, we have learned that FBF is essential for maintenance of germline stem cells, that GLD-3 antagonizes FBF function, and that GLD-2 and GLD-3 together constitute a new class of enzyme, a regulatory cytoplasmic poly(A) polymerase. (2) Gonadogenesis. We are focusing on controls of early gonadogenesis. We are analyzing the genetics, cell biology and molecular basis of three genes that control formation of the gonadal primordium in both sexes, and three genes that control axis formation in the early gonad. One of those genes encodes the C. elegans Hand transcription factor.

Impacts
Understanding basic development of organisms could assist in avoiding developmental errors and problems in reproduction.

Publications

Siegfried, K. and J. Kimble (2002) POP-1 controls axis formation during early gonadogenesis in C. elegans. Development 129(2), 443-453.
Wickens, M., Bernstein, D.S., Kimble, J. and R. Parker (2002) A PUF family portrait: 3'UTR regulation as a way of life. Trends in Genetics 18(3), 150-157.
Belfiore, M., Mathies, L.D., Pugnale, P., Moulder, G., Barstead, R., Kimble, J., and A. Puoti (2002) The MEP-1 zinc-finger protein acts with MOG DEAH box proteins to control gene expression via the fem-3 3? untranslated region in Caenorhabditis elegans. RNA 8(6), 725-739.
Crittenden, S.L., Bernstein, D.S, Bachorik, J.L., Thompson, B.E., Gallegos, M., Petcherski, A.G., Moulder, G., Barstead, R., Wickens, M. and J. Kimble (2002) A conserved RNA-binding protein controls germline stem cells in Caenorhabditis elegans. Nature 417, 660-663.
Rudel, D. and J. Kimble (2002) Evolution of discrete Notch-like receptors from a distant gene duplication in Caenorhabditis. Evolution and Development 4(5), 319-333.
Wang, L., Eckmann, C.R., Kadyk, L.C., Wickens, M. and J. Kimble (2002) A novel cytoplasmic poly(A) polymerase in Caenorhabditis elegans. Nature 419, 312-316.
Eckmann, C.R., Kraemer, B., Wickens, M. and Kimble, J. (2002) GLD-3, a Bicaudal-C homolog that inhibits FBF to control germline sex determination in C. elegans. Developmental Cell 3(11), 697-710.
Haag, E.S., Wang, S., and Kimble, J. (2002) Rapid coevolution of the nematode sex-determining genes fem-3 and tra-2. Current Biology 12, 2035-2041.

Progress 01/01/01 to 12/31/01

Outputs
(1) Germline fate decisions. We have continued to analyze RNA binding proteins that regulate germline proliferation, survival and differentiation. Specifically, we have learned that FBF is essential for maintenance of germline stem cells and that GLD-3 antagonizes FBF function. We have obtained deletion mutants in numerous genes identified by yeast two-hybrid screens and started to analyze them. (2) Gonadogenesis. We are focusing on controls of sexual dimorphism in early gonadogenesis. By a series of mutagenesis screens, we have identified six genes that are preferentially used for hermaphrodite gonadal development, and two or three that are preferentially used for male gonadal development. We have also identified three genes required for formation of the gonadal primordium.

Impacts
(N/A)

Publications

Jin, S, Kimble, J. and R.E. Ellis (2001) Regulation of germ cell fate by a CPEB-related protein in C. elegans. Developmental Biology 229, 537-553.
Miskowski, J., Li, Y. and J. Kimble (2001) The sys-1 gene and sexual dimorphism during gonadogenesis in Caenorhabditis elegans. Developmental Biology 230, 61-73.
Rudel, D. and J. Kimble (2001) Conservation of glp-1 regulation and function in nematodes. Genetics 157, 639-654.
Kimble, J. (2001) The 2000 George W. Beadle Medal. John Sulston and Robert Waterston. Genetics 157, 467-468.
Wang, S. and J. Kimble (2001) The TRA-1 transcription factor binds TRA-2 to regulate sexual fates in Caenorhabditis elegans. The EMBO Journal 20(6), 1363-1372.
Siegfried, K. and J. Kimble. (2002) POP-1 controls axis formation during early gonadogenesis in C. elegans. Development 129(2), in press.
Wickens, M., Bernstein, D. S., Kimble, J. and Parker, R. (2002) A PUF family portrait: 3'UTR regulation as a way of life. Trends in Genetics, in press.
Wickens, M., Bernstein, D., Crittenden, S., Luitjens, C. and J. Kimble. (2002) PUF proteins and 3'UTR regulation in the C. elegans germline. Cold Spring Harbor review, in press.

Progress 01/01/00 to 12/31/00

Outputs
Germline fate decisions: We have continued to analyze RNA binding proteins that regulate germline proliferation, survival and differentiation. Included are the GLD-2 protein, FBF and GLS-1 as well as interactors for these proteins. Gonadogenesis: We are focusing on controls of sexual dimorphism in early gonadogenesis. Genetic and molecular analyses define a pathway of regulation that establishes the hermaphrodite, but not male gonad polarity. One of these genes is a core component on the wingless pathway. Evolution of regulatory pathways: We are analyzing the evolution of reproductive strategies by cloning sex determination genes from closely related nematode species. Most recently we have obtained fem-3 from both C. briggsae and C. remanei.

Impacts
(N/A)

Publications

Chen, P-J., A. Singal, J. Kimble, and R. E. Ellis (2000). A novel member of the Tob family of proteins controls sexual fate in Caenorhabditis elegans germ cells. Developmental Biology 217, 77-90.
Puoti, A. and J. Kimble (2000). The hermaphrodite sperm/oocyte switch requires the Caenorhabditis elegans homologs of PRP2 and PRP22. PNAS 97(7), 3276-3281.
Friedman, L. C., J. J. Higgin, G. Moulder, R. Barstead, R. T. Raines, and J. Kimble (2000). Prolyl 4-hydroxylase is required for viability and morphogenesis in C. elegans. PNAS 97, 4736-4741.
Haag, E. and J. Kimble (2000). Regulatory elements required for development of Caenorhabditis elegans hermaphrodites are conserved in the tra-2 homologue of C. remanei, a male/female sister species. Genetics 155(1), 105-116.
Petchersi, A. and J. Kimble (2000). LAG-3 is a putative transcriptional activator in the C. elegans pathway. Nature 405, 364-368.
Petcherski, A. and J. Kimble (2000). Mastermind is a putative activator for Notch. Current Biology 10(13), R471-R473.
Huang, K., K. D. Johnson, A. G. Petcherski, T. Vandergon, E. A. Mosser, N. G. Copeland, N. A. Jenkins, J. Kimble, and E. H. Bresnick (2000). A HECT domain ubiquitin ligase closely related to the mammalian protein WWP1 is essential for Caenorhabditis elegans embryogenesis. Gene 252(1-2), 137-145.
Wickens, M., E. B. Goodwin, J. Kimble, S. Strickland, and M. W. Hentze (2000). Translational control of developmental decisions. In Translational Control of Gene Expression, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. pp. 295-370.
Luitjens, C., M. Gallegos, B. Kraemer, J. Kimble, and M. Wickens (2000). CPEB proteins control two key steps in spermatogenesis in C. elegans. Genes & Development 14, 2596-2609.
Friedman, L. C., S. Santa Anna-Arriola, J. Hodgkin, and J. Kimble (2000). gon-4, a cell lineage regulator required for gonadogenesis in Caenorhabditis elegans. Developmental Biology 228, 350-362.
Jin, S., J. Kimble, and R. E. Ellis (2001). Regulations of germ cell fate by a CPEB-related protein in C. elegans. Developmental Biology 229, 537-553.
Miskowski, J., Y. Li, and J. Kimble (2001). The sys-1 gene and sexual dimorphism during gonadogenesis in Caenorhabditis elegans. Developmental Biology, in press.
Rudel, D. and J. Kimble (2001). Conservation of glp-1 regulation and function in nematodes. Genetics, in press.
Wang, S. and J. Kimble (2001). The TRA-1 transcription factor binds the TRA-2 MX regulatory region to regulate sexual fates in Caenorhabditis elegans. EMBO J., in press.

Progress 01/01/99 to 12/31/99

Outputs
(1) Germline fate decisions. We have further explored the proteins required for regulating the switch from the mitotic cell cycle to the meiotic cell cycle in C. elegans. The C. elegans homolog of Pumilio, called FBF, is required, as is one of the C. elegans homologs of CPEB, called FOG-1. FBF and FOG-1 are both RNA binding proteins. To further address their roles in mitosis/meiosis decisions, we have continued our genetic analysis of these two genes, have begun to study them cytologically and have identified numerous proteins that interact by two-hybrid assays in yeast. We have uncovered a complex web of regulators that control several fate decisions in the early germ line, including germline survival. (2) Gonadogenesis. We have continued our genetic and phenotypic characterization of mutants that have defects in early gonadogenesis. One class of particular interest affects hermaphrodite gonadogenesis specifically, another class affects male gonadogenesis specifically, and a third class affects formation of the gonadal primordium. In the first class we have multiple mutants and in some cases several alleles in single genes; in the second class, there is only one mutant, and in the third class, we have three mutants. Cloning efforts are underway as are the development of molecular markers to analyze gonadogenesis in detail. (3) Evolution of regulatory pathways. We have begun to explore the evolution of the Notch signaling pathway and the sex determination pathway in nematodes that are closely related to C. elegans. Our purpose is to understand how the core components of these genes have changed during evolution to effect new functions and new forms of regulation. To this end, we have identified homologs of glp-1 and lin-12, the two Notch receptors in C. elegans, in both C. briggsae and C. remanei; we have also identified a homolog of tra-2, the receptor in the sex determination pathway in the male/female species C. remanei. One goal of our work on the evolution of sex determination is to learn how species that reproduce as self-fertilizing hermaphrodites evolved from male/female species.

Impacts
(N/A)

Publications

Crittenden, S.L. and J. Kimble (1999) Confocal methods for Caenorhabditis elegans. In Methods in Molecular Biology, vol. 122: Confocal Microscopy Methods and Protocols (S. Paddock, ed.) Totowa, NJ: Humana Press Inc. pp. 141-151.
Puoti, A. and J. Kimble (1999) The Caenorhabditis elegans sex determination gene mog-1 encodes a member of the DEAH-box protein family. Molecular and Cellular Biology 19(3), 2189-2197.
Blelloch, R. and J. Kimble (1999) Control of organ shape by a secreted metalloprotease in the nematode Caenorhabditis elegans. Nature 399, 586-590.
Kraemer, B., Crittenden, S., Gallegos, M., Moulder, G., Barstead, R., Kimble, J., and M. Wickens (1999) NANOS-3 and FBF proteins physically interact to control the sperm-oocyte switch in Caenorhabditis elegans. Current Biology 9(18), 1009-1018.
Blelloch, R., Newman, C. and J. Kimble (1999) Control of cell migration during Caenorhabditis elegans development. Current Opinion in Cell Biology 11, 608-613.
Blelloch, R., Santa Anna-Arriola, S., Gao, D., Li, Y., Hodgkin, J. and J. Kimble (1999) The gon-1 gene is required for gonadal morphogenesis in Caenorhabditis elegans. Developmental Biology 216, 382-393.
Chen, P-J., Singal, A., Kimble, J. and R.E. Ellis (2000) A novel member of the Tob family of proteins controls sexual fate in Caenorhabditis elegans germ cells. Developmental Biology 217, 77-90.
Haag, E. and J. Kimble (2000) Regulatory elements required for development of C. elegans hermaphrodites are conserved in the tra-2 homologue of C. remanei, a male/female sister species. Genetics, in press.
Puoti, A. and J. Kimble (2000) The hermaphrodite sperm/oocyte switch requires the C. elegans homologs of PRP22 and PRP2. PNAS, in press.
Friedman, L.C., Higgin, J.J., Moulder, G., Barstead, R., Raines, R.T. and J. Kimble (2000) Prolyl 4-hydroxylase is required for viability and morphogenesis in C. elegans. PNAS, in press.
Petcherski, A. and J. Kimble (2000) LAG-3 a putative transcriptional activator in the C. elegans Notch pathway. Nature, in press.

Progress 01/01/98 to 12/31/98

Outputs
(1) Mitosis/meiosis decision. During the past year, we have found that FBF, an RNA binding protein that regulates the sperm/oocyte decision by repressing fem-3 translation, is required for germline stem cells as well. (2) Sperm/oocyte decision and germline survival. During the past year, we have identified the NANOS-3 and GLS-1 proteins as binding partners for FBF. We have explored the biological functions of NANOS-3 as well as two other NANOS paralogs, and found that they are required for the sperm/oocyte switch and also for germline survival. We explored the biological function of GLS-1 and found that it is required for germline survival. (3) Gonadogenesis. During the past year, we have learned that a secreted metalloprotease is essential for extension of the gonadal epithelial tube. We view this as a model system for extension of epithelial tubes generally and hypothesize that it occurs by remodelling the extracellular matrix. We have also found that extension is essential generally for morphogenesis of the entire organs. We have identified about 100 mutants in early gonadogenssis and begun to classify them according to their defects.

Impacts
(N/A)

Publications

S. L. Crittenden and J. Kimble. 1998. Immunofluorescence methods for C. elegans. IN Cells: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 108.1-108.9.
L. C. Kadyk and J. Kimble. 1998. Genetic regulation of entry into meiosis in Caenorhabditis elegans. Development 125:1803-1813.
M. A. Horner, S. Quintin, M. E. Domeier, J. Kimble, M. Labouesse and S. E. Mango. 1998. pha-4, an HNF-3 homolog, specifies pharyngeal organ identity in Caenorhabditis elegans. Genes & Dev. 12:1947-1952.
J. Kimble, S. Henderson and S. Crittenden. 1998. Notch/LIN-12 signaling: transduction by regulated protein slicing. TIBS 23(9):353-357.
P. E. Kuwabara, P. G. Okkema and J. Kimble. 1998. Germ-line regulation of Caenorhabditis elegans. EMBO J. 17(21):251-262.
M. Gallegos, J. Ahringer, S. Crittenden and J. Kimble. 1998. Repression by the 3' UTR of gem-3, a six-determining gene, relies on a ubiquitous mog-dependent control in Caenorhabditis elegans. EMBO J. 17(21):6337-6347.
J. Hodgkin, H. R. Horvitz, B. R. Jasny and J. Kimble. 1998. C. elegans: Sequence to biology. Science 282:2011.
A. Puoti and J. Kimble. 1999. The Caenorhabditis elegans sex determination gene mog-1 encodes a member of the DEAH-box protein family. Mol. Cell. Biol. 19(3), in press.

Progress 01/01/97 to 12/31/97

Outputs
Brief Statement of Research Accomplishments During the Past Year (1) Mitosis/meiosis decision. During the past year, we have identified two activities that are essential for entry into the meiotic cell cycle from the mitotic cell cycle: gld-1 and gld-2. These are the first such activities identified in any multicellular eukaryote. We have cloned gld-2, and found that it is a large, complex gene with a novel predicted amino acid sequence. (2) Sperm/oocyte decision. During the past year, we have identified the FBF protein, which regulates the fem-3 gene post-transcriptionally to achieve the sperm/oocyte switch. We have also examined the mog-1 and mog-5 genes at the molecular level, and found that they are both DEAH-box putative RNA helicases. Both of these mog genes are also required for the sperm/oocyte switch. (3) Gonadogenesis. During the past year, we have made progress in three areas: (1) migration and morphogenesis, (2) cell cycle regulation, and (3) epithelial/mesenchymal transitions. In each case, we have identified key genes and cloned them. We have also begun a large scale mutagenesis to identify new gonadogenesis mutants.

Impacts
(N/A)

Publications

Kadyk, L., Lambie, E., and J. Kimble. 1997. glp-3 is required for mitosis and meiosis in the C. elegans germ line. Genetics 145, 111-121.
Anderson, P. and J. Kimble. 1997. mRNA and translation. In: C. elegans II. Edited by D.L. Riddle, T. Blumenthal, B.J. Meyer, and J.R. Priess. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. pp. 185-208.
Goodwin, E.B., Hofstra, K, Hurney, C.A., Mango, S., and J. Kimble. 1997. A genetic pathway for regulation of tra-2 translation. Development 124, 749-758.
Panganiban, G, Irvine, S.M., Lowe, C., Roehl, H., Corely, L.S., Sherbon, B., Grenier, J., Fallon, J.F., Kimble, J., Walker, M., Wary, G.A., Swalla, B.J., Martindale, M.Q., and S.B. Carroll. 1997. The origin and evolution of animal appendages. Proc. Natl. Acad. Sci. USA 94, 5162-5166.
Henderson, S.T., Gao, D., Christensen, S. and J. Kimble. 1997. Functional domains of LAG-2, a putative signaling ligand for LIN-12 and GLP-1 receptors in Caenorhabditis elegans. Mol. Biol. Cell 8, 1751-1762.
Crittenden, S.L. and J. Kimble. 1997. Immunofluorescent methods for C. elegans. In: Cell Biology: A Laboratory Manual (David Spector, Robert Goldman and Leslie Leinwand, eds.). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. pp. __-__.
Kimble, J. and P. Simpson. 1997. The LIN-12/Notch signaling pathway and its regulation. Annu. Rev. Cell Dev. Biology 13, 333-361.
Puoti, A., Gallegos, M., Zhang, B., Wickens, M.P., and J. Kimble. 1997. Controls of cell fate and pattern by 3' untranslated regions: the Caenorhabditis elegans sperm/oocyte decision. In: Cold Spring Harbor Symposia on Quantitative Biology, Volume LXII, 19-24.
Zhang, B., Gallegos, M., Puoti, A., Durkin, E., Kimble, J. and M. Wickens. 1997. A conserved RNA binding protein that regulates sexual fates in the C. elegans hermaphrodite germ line. Nature 390, 477-484.
Kadyk, L. C. and Kimble, J. 1998. Genetic regulation of entry into meiosis in C. elegans. Development 125, 1803-1813.