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1. Identification and characterization of homeobox transcription factor genes in Strongylocentrotus purpuratus, and their expression in embryonic development

Author

Howard-Ashby, Meredith, Materna, Stefan C., Brown, C. Titus, Chen, Lili, Cameron, R. Andrew, and Davidson, Eric H.

Subjects
DNA binding proteins -- Chemical properties, DNA binding proteins -- Genetic aspects, Embryonic development -- Chemical properties, Embryonic development -- Genetic aspects, Biological sciences
Abstract

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2006.08.039 Byline: Meredith Howard-Ashby, Stefan C. Materna, C. Titus Brown, Lili Chen, R. Andrew Cameron, Eric H. Davidson Keywords: Transcription factor; Sea urchin; Homeobox; Development Abstract: A set of 96 homeobox transcription factors was identified in the Strongylocentrotus purpuratus genome using permissive blast searches with a large collection of authentic homeodomain sequences from mouse, human and fly. A phylogenetic tree was constructed to compare the sea urchin homeobox gene family to those of vertebrates, with the result that with the only a few exceptions, orthologs of all vertebrate homeodomain genes were uncovered by our search. QPCR time course measurements revealed that 65% of these genes are expressed within the first 48 h of development (late gastrula). For genes displaying sufficiently high levels of transcript during the first 24 h of development (late blastula), whole mount in situ hybridization was carried out up to 48 h to determine spatial patterns of expression. The results demonstrate that homeodomain transcription factors participate in multiple and diverse developmental functions, in that they are used at a range of time points and in every territory of the developing embryo. Author Affiliation: Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA Article History: Received 18 April 2006; Revised 4 August 2006; Accepted 16 August 2006

Published
2006

2. Gene families encoding transcription factors expressed in early development of Strongylocentrotus purpuratus

Author

Howard-Ashby, Meredith, Materna, Stefan C., Brown, C. Titus, Chen, Lili, Cameron, R. Andrew, and Davidson, Eric H.

Subjects
DNA binding proteins -- Genetic aspects, Biological sciences
Abstract

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2006.08.033 Byline: Meredith Howard-Ashby, Stefan C. Materna, C. Titus Brown, Lili Chen, R. Andrew Cameron, Eric H. Davidson Keywords: Transcription factor; Sea urchin; Development; bHLH; Sox; Nuclear receptor; Basic zipper; smad Abstract: All genes encoding transcription factors of the bHLH, Nuclear Receptor, Basic Leucine Zipper, T-box, Smad, Sox, and other smaller families were identified in the Strongylocentrotus purpuratus genome by means of a permissive blast search of the genome using a database of known transcription factors. Phylogenetic trees were constructed for the major families, permitting a comparison of the regulatory protein repertoire of the sea urchin and other species. QPCR and whole mount in situ hybridization experiments revealed the temporal and spatial expression patterns of these genes during early development. These regulatory genes are initially expressed at a broad range of time points, and the large majority of genes of all families are expressed within the first 48 h of development. The observations suggest assignment of many regulatory genes to specific developmental sub-networks, including endomesodermal, oral, aboral, and apical. Author Affiliation: Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA Article History: Received 1 June 2006; Revised 5 August 2006; Accepted 16 August 2006

Published
2006

3. High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution

Author

Howard-Ashby, Meredith, Materna, Stefan C., Brown, C. Titus, Tu, Qiang, Oliveri, Paola, Cameron, R. Andrew, and Davidson, Eric H.

Subjects
Genetic research, DNA binding proteins, Zinc finger proteins, Embryonic development, Biological sciences
Abstract

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2006.10.016 Byline: Meredith Howard-Ashby, Stefan C. Materna, C. Titus Brown, Qiang Tu, Paola Oliveri, R. Andrew Cameron, Eric H. Davidson Keywords: Regulome; Transcription factor usage; Indirect development Abstract: A global scan of transcription factor usage in the sea urchin embryo was carried out in the context of the Strongylocentrotus purpuratus genome sequencing project, and results from six individual studies are here considered. Transcript prevalence data were obtained for over 280 regulatory genes encoding sequence-specific transcription factors of every known family, but excluding genes encoding zinc finger proteins. This is a statistically inclusive proxy for the total 'regulome' of the sea urchin genome. Close to 80% of the regulome is expressed at significant levels by the late gastrula stage. Most regulatory genes must be used repeatedly for different functions as development progresses. An evolutionary implication is that animal complexity at the stage when the regulome first evolved was far simpler than even the last common bilaterian ancestor, and is thus of deep antiquity. Author Affiliation: Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA Article History: Received 5 October 2006; Revised 13 October 2006; Accepted 13 October 2006

Published
2006

4. The C.sub.2H.sub.2 zinc finger genes of Strongylocentrotus purpuratus and their expression in embryonic development

Author

Materna, Stefan C., Howard-Ashby, Meredith, Gray, Rachel F., and Davidson, Eric H.

Subjects
Genetic research, DNA binding proteins, Embryonic development, Biological sciences
Abstract

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2006.08.032 Byline: Stefan C. Materna, Meredith Howard-Ashby, Rachel F. Gray, Eric H. Davidson Keywords: Zinc finger; Zf-c2h2; Transcription factor; Genome; Sea urchin; Development Abstract: The C.sub.2H.sub.2 zinc finger is one of the most abundant protein domains and is thought to have been extensively replicated in diverse animal clades. Some well-studied proteins that contain this domain are transcriptional regulators. As part of an attempt to delineate all transcription factors encoded in the Strongylocentrotus purpuratus genome, we identified the C.sub.2H.sub.2 zinc finger genes indicated in the sequence, and examined their involvement in embryonic development. We found 377 zinc finger genes in the sea urchin genome, about half the number found in mice or humans. Their expression was measured by quantitative PCR. Up to the end of gastrulation less than a third of these genes is expressed, and about 75% of the expressed genes are maternal; both parameters distinguish these from all other classes of regulatory genes as measured in other studies. Spatial expression pattern was determined by whole mount in situ hybridization for 43 genes transcribed at a sufficient level, and localized expression was observed in diverse embryonic tissues. These genes may execute important regulatory functions in development. However, the functional meaning of the majority of this large gene family remains undefined. Author Affiliation: Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA Article History: Received 25 May 2006; Revised 4 August 2006; Accepted 16 August 2006

Published
2006

6. The genome of the sea urchin Strongylocentrotus purpuratus

Author

Sodergren, Erica, Weinstock, George M., Davidson, Eric H., Cameron, R. Andrew, Gibbs, Richard A., Angerer, Robert C., Angerer, Lynne M., Arnone, Maria Ina, Burgess, David R., Burke, Robert D., Coffman, James A., Dean, Michael, Elphick, Maurice R., Ettensohn, Charles A., Foltz, Kathy R., Hamdoun, Amro, Hynes, Richard O., Klein, William H., Marzluff, William, McClay, David R., Morris, Robert L., Mushegian, Arcady, Rast, Jonathan P., Smith, L. Courtney, Thorndyke, Michael C., Vacquier, Victor D., Wessel, Gary M., Wray, Greg, Zhang, Lan, Elsik, Christine G., Ermolaeva, Olga, Hlavina, Wratko, Hofmann, Gretchen, Kitts, Paul, Landrum, Melissa J., Mackey, Aaron J., Maglott, Donna, Panopoulou, Georgia, Poustka, Albert J., Pruitt, Kim, Sapojnikov, Victor, Song, Xingzhi, Souvorov, Alexandre, Solovyev, Victor, Wei, Zheng, Whittaker, Charles A., Worley, Kim, Durbin, K. James, Shen, Yufeng, Fedrigo, Olivier, Garfield, David, Haygood, Ralph, Primus, Alexander, Satija, Rahul, Severson, Tonya, Gonzalez-Garay, Manuel L., Jackson, Andrew R., Milosavljevic, Aleksandar, Tong, Mark, Killian, Christopher E., Livingston, Brian T., Wilt, Fred H., Adams, Nikki, Belle, Robert, Carbonneau, Seth, Cheung, Rocky, Cormier, Patrick, Cosson, Bertrand, Croce, Jenifer, Fernandez-Guerra, Antonio, Geneviere, Anne-Marie, Goel, Manisha, Kelkar, Hemant, Morales, Julia, Mulner-Lorillon, Odile, Robertson, Anthony J., Goldstone, Jared V., Cole, Bryan, Epel, David, Gold, Bert, Hahn, Mark E., Howard-Ashby, Meredith, Scally, Mark, Stegeman, John J., Allgood, Erin L., Cool, Jonah, Judkins, Kyle M., McCafferty, Shawn S., Musante, Ashlan M., Obar, Robert A., Rawson, Amanda P., Rossetti, Blair J., Gibbons, Ian R., Hoffman, Matthew P., Leone, Andrew, Istrail, Sorin, Materna, Stefan C., Samanta, Manoj P., Stolc, Viktor, Tongprasit, Waraporn, Tu, Qiang, Bergeron, Karl-Frederik, Brandhorst, Bruce P., Whittle, James, Berney, Kevin, Bottjer, David J., Calestani, Cristina, Peterson, Kevin, Chow, Elly, Yuan, Qiu Autumn, Elhaik, Eran, Graur, Dan, Reese, Justin T., Bosdet, Ian, Heesun, Shin, Marra, Marco A., Schein, Jacqueline, Anderson, Michele K., Brockton, Virginia, Buckley, Katherine M., Cohen, Avis H., Fugmann, Sebastian D., Hibino, Taku, Loza-Coll, Mariano, Majeske, Audrey J., Messier, Cynthia, Nair, Sham V., Pancer, Zeev, Terwilliger, David P., Agca, Cavit, Arboleda, Enrique, Chen, Nansheng, Churcher, Allison M., Hallböök, Finn, Humphrey, Glen W., Idris, Mohammed M., Kiyama, Takae, Liang, Shuguang, Mellott, Dan, Mu, Xiuqian, Murray, Greg, Olinski, Robert P., Raible, Florian, Rowe, Matthew, Taylor, John S., Tessmar-Raible, Kristin, Wang, D., Wilson, Karen H., Yaguchi, Shunsuke, Gaasterland, Terry, Galindo, Blanca E., Gunaratne, Herath J., Juliano, Celina, Kinukawa, Masashi, Moy, Gary W., Neill, Anna T., Nomura, Mamoru, Raisch, Michael, Reade, Anna, Roux, Michelle M., Song, Jia L., Su, Yi-Hsien, Townley, Ian K., Voronina, Ekaterina, Wong, Julian L., Amore, Gabriele, Branno, Margherita, Brown, Euan R., Cavalieri, Vincenzo, Duboc, Veronique, Duloquin, Louise, Flytzanis, Constantin, Gache, Christian, Lapraz, Francois, Lepage, Thierry, Locascio, Annamaria, Martinez, Pedro, Matassi, Giorgio, Matranga, Valeria, Range, Ryan, Rizzo, Francesca, Roettinger, Eric, Wilson, Karen, Beane, Wendy, Bradham, Cynthia, Byrum, Christine, Glenn, Tom, Hussain, Sofia, Loza, Mariano, Manning, Gerard, Miranda, Esther, Thomason, Rebecca, Walton, Katherine, Wikramanayke, Athula, Whittaker, Charles, Wu, Shu-Yu, Xu, Ronghui, Brown, C. Titus, Chen, Lili, Gray, Rachel F., Lee, Pei Yun, Nam, Jongmin, Oliveri, Paola, Smith, Joel, Muzny, Donna, Bell, Stephanie, Chacko, Joseph, Cree, Andrew, Curry, Stacey, Davis, Clay, Dinh, Huyen, Dugan-Rocha, Shannon, Fowler, Jerry, Gill, Rachel, Hamilton, Cerrissa, Hernandez, Judith, Hines, Sandra, Hume, Jennifer, Jackson, LaRonda, Jolivet, Angela, Kovar, Christie, Lee, Sandra, Lewis, Lora, Miner, George, Morgan, Margaret, Nazareth, Lynne V., Okwuonu, Geoffrey, Parker, David, Pu, Ling-Ling, Thom, Rachel, Wright, Rita, Sodergren, Erica, Weinstock, George M., Davidson, Eric H., Cameron, R. Andrew, Gibbs, Richard A., Angerer, Robert C., Angerer, Lynne M., Arnone, Maria Ina, Burgess, David R., Burke, Robert D., Coffman, James A., Dean, Michael, Elphick, Maurice R., Ettensohn, Charles A., Foltz, Kathy R., Hamdoun, Amro, Hynes, Richard O., Klein, William H., Marzluff, William, McClay, David R., Morris, Robert L., Mushegian, Arcady, Rast, Jonathan P., Smith, L. Courtney, Thorndyke, Michael C., Vacquier, Victor D., Wessel, Gary M., Wray, Greg, Zhang, Lan, Elsik, Christine G., Ermolaeva, Olga, Hlavina, Wratko, Hofmann, Gretchen, Kitts, Paul, Landrum, Melissa J., Mackey, Aaron J., Maglott, Donna, Panopoulou, Georgia, Poustka, Albert J., Pruitt, Kim, Sapojnikov, Victor, Song, Xingzhi, Souvorov, Alexandre, Solovyev, Victor, Wei, Zheng, Whittaker, Charles A., Worley, Kim, Durbin, K. James, Shen, Yufeng, Fedrigo, Olivier, Garfield, David, Haygood, Ralph, Primus, Alexander, Satija, Rahul, Severson, Tonya, Gonzalez-Garay, Manuel L., Jackson, Andrew R., Milosavljevic, Aleksandar, Tong, Mark, Killian, Christopher E., Livingston, Brian T., Wilt, Fred H., Adams, Nikki, Belle, Robert, Carbonneau, Seth, Cheung, Rocky, Cormier, Patrick, Cosson, Bertrand, Croce, Jenifer, Fernandez-Guerra, Antonio, Geneviere, Anne-Marie, Goel, Manisha, Kelkar, Hemant, Morales, Julia, Mulner-Lorillon, Odile, Robertson, Anthony J., Goldstone, Jared V., Cole, Bryan, Epel, David, Gold, Bert, Hahn, Mark E., Howard-Ashby, Meredith, Scally, Mark, Stegeman, John J., Allgood, Erin L., Cool, Jonah, Judkins, Kyle M., McCafferty, Shawn S., Musante, Ashlan M., Obar, Robert A., Rawson, Amanda P., Rossetti, Blair J., Gibbons, Ian R., Hoffman, Matthew P., Leone, Andrew, Istrail, Sorin, Materna, Stefan C., Samanta, Manoj P., Stolc, Viktor, Tongprasit, Waraporn, Tu, Qiang, Bergeron, Karl-Frederik, Brandhorst, Bruce P., Whittle, James, Berney, Kevin, Bottjer, David J., Calestani, Cristina, Peterson, Kevin, Chow, Elly, Yuan, Qiu Autumn, Elhaik, Eran, Graur, Dan, Reese, Justin T., Bosdet, Ian, Heesun, Shin, Marra, Marco A., Schein, Jacqueline, Anderson, Michele K., Brockton, Virginia, Buckley, Katherine M., Cohen, Avis H., Fugmann, Sebastian D., Hibino, Taku, Loza-Coll, Mariano, Majeske, Audrey J., Messier, Cynthia, Nair, Sham V., Pancer, Zeev, Terwilliger, David P., Agca, Cavit, Arboleda, Enrique, Chen, Nansheng, Churcher, Allison M., Hallböök, Finn, Humphrey, Glen W., Idris, Mohammed M., Kiyama, Takae, Liang, Shuguang, Mellott, Dan, Mu, Xiuqian, Murray, Greg, Olinski, Robert P., Raible, Florian, Rowe, Matthew, Taylor, John S., Tessmar-Raible, Kristin, Wang, D., Wilson, Karen H., Yaguchi, Shunsuke, Gaasterland, Terry, Galindo, Blanca E., Gunaratne, Herath J., Juliano, Celina, Kinukawa, Masashi, Moy, Gary W., Neill, Anna T., Nomura, Mamoru, Raisch, Michael, Reade, Anna, Roux, Michelle M., Song, Jia L., Su, Yi-Hsien, Townley, Ian K., Voronina, Ekaterina, Wong, Julian L., Amore, Gabriele, Branno, Margherita, Brown, Euan R., Cavalieri, Vincenzo, Duboc, Veronique, Duloquin, Louise, Flytzanis, Constantin, Gache, Christian, Lapraz, Francois, Lepage, Thierry, Locascio, Annamaria, Martinez, Pedro, Matassi, Giorgio, Matranga, Valeria, Range, Ryan, Rizzo, Francesca, Roettinger, Eric, Wilson, Karen, Beane, Wendy, Bradham, Cynthia, Byrum, Christine, Glenn, Tom, Hussain, Sofia, Loza, Mariano, Manning, Gerard, Miranda, Esther, Thomason, Rebecca, Walton, Katherine, Wikramanayke, Athula, Whittaker, Charles, Wu, Shu-Yu, Xu, Ronghui, Brown, C. Titus, Chen, Lili, Gray, Rachel F., Lee, Pei Yun, Nam, Jongmin, Oliveri, Paola, Smith, Joel, Muzny, Donna, Bell, Stephanie, Chacko, Joseph, Cree, Andrew, Curry, Stacey, Davis, Clay, Dinh, Huyen, Dugan-Rocha, Shannon, Fowler, Jerry, Gill, Rachel, Hamilton, Cerrissa, Hernandez, Judith, Hines, Sandra, Hume, Jennifer, Jackson, LaRonda, Jolivet, Angela, Kovar, Christie, Lee, Sandra, Lewis, Lora, Miner, George, Morgan, Margaret, Nazareth, Lynne V., Okwuonu, Geoffrey, Parker, David, Pu, Ling-Ling, Thom, Rachel, and Wright, Rita

Abstract

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.

Published
2006
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7. The Genome of the Sea Urchin Strongylocentrotus purpuratus

Author

Sodergren, Erica, primary, Weinstock, George M., additional, Davidson, Eric H, additional, Cameron, R. Andrew, additional, Gibbs, Richard A., additional, Angerer, Robert C., additional, Angerer, Lynne M., additional, Arnone, Maria Ina, additional, Burgess, David R., additional, Burke, Robert D., additional, Coffman, James A., additional, Dean, Michael, additional, Elphick, Maurice R., additional, Ettensohn, Charles A., additional, Foltz, Kathy R., additional, Hamdoun, Amro, additional, Hynes, Richard O., additional, Klein, William H., additional, Marzluff, William, additional, McClay, David R., additional, Morris, Robert L., additional, Mushegian, Arcady, additional, Rast, Jonathan P., additional, Smith, L. Courtney, additional, Thorndyke, Michael C., additional, Vacquier, Victor D., additional, Wessel, Gary M., additional, Wray, Greg, additional, Zhang, Lan, additional, Elsik, Christine G., additional, Ermolaeva, Olga, additional, Hlavina, Wratko, additional, Hofmann, Gretchen, additional, Kitts, Paul, additional, Landrum, Melissa J., additional, Mackey, Aaron J., additional, Maglott, Donna, additional, Panopoulou, Georgia, additional, Poustka, Albert J., additional, Pruitt, Kim, additional, Sapojnikov, Victor, additional, Song, Xingzhi, additional, Souvorov, Alexandre, additional, Solovyev, Victor, additional, Wei, Zheng, additional, Whittaker, Charles A., additional, Worley, Kim, additional, Durbin, K. James, additional, Shen, Yufeng, additional, Fedrigo, Olivier, additional, Garfield, David, additional, Haygood, Ralph, additional, Primus, Alexander, additional, Satija, Rahul, additional, Severson, Tonya, additional, Gonzalez-Garay, Manuel L., additional, Jackson, Andrew R., additional, Milosavljevic, Aleksandar, additional, Tong, Mark, additional, Killian, Christopher E., additional, Livingston, Brian T., additional, Wilt, Fred H., additional, Adams, Nikki, additional, Bellé, Robert, additional, Carbonneau, Seth, additional, Cheung, Rocky, additional, Cormier, Patrick, additional, Cosson, Bertrand, additional, Croce, Jenifer, additional, Fernandez-Guerra, Antonio, additional, Genevière, Anne-Marie, additional, Goel, Manisha, additional, Kelkar, Hemant, additional, Morales, Julia, additional, Mulner-Lorillon, Odile, additional, Robertson, Anthony J., additional, Goldstone, Jared V., additional, Cole, Bryan, additional, Epel, David, additional, Gold, Bert, additional, Hahn, Mark E., additional, Howard-Ashby, Meredith, additional, Scally, Mark, additional, Stegeman, John J., additional, Allgood, Erin L., additional, Cool, Jonah, additional, Judkins, Kyle M., additional, McCafferty, Shawn S., additional, Musante, Ashlan M., additional, Obar, Robert A., additional, Rawson, Amanda P., additional, Rossetti, Blair J., additional, Gibbons, Ian R., additional, Hoffman, Matthew P., additional, Leone, Andrew, additional, Istrail, Sorin, additional, Materna, Stefan C., additional, Samanta, Manoj P., additional, Stolc, Viktor, additional, Tongprasit, Waraporn, additional, Tu, Qiang, additional, Bergeron, Karl-Frederik, additional, Brandhorst, Bruce P., additional, Whittle, James, additional, Berney, Kevin, additional, Bottjer, David J., additional, Calestani, Cristina, additional, Peterson, Kevin, additional, Chow, Elly, additional, Yuan, Qiu Autumn, additional, Elhaik, Eran, additional, Graur, Dan, additional, Reese, Justin T., additional, Bosdet, Ian, additional, Heesun, Shin, additional, Marra, Marco A., additional, Schein, Jacqueline, additional, Anderson, Michele K., additional, Brockton, Virginia, additional, Buckley, Katherine M., additional, Cohen, Avis H., additional, Fugmann, Sebastian D., additional, Hibino, Taku, additional, Loza-Coll, Mariano, additional, Majeske, Audrey J., additional, Messier, Cynthia, additional, Nair, Sham V., additional, Pancer, Zeev, additional, Terwilliger, David P., additional, Agca, Cavit, additional, Arboleda, Enrique, additional, Chen, Nansheng, additional, Churcher, Allison M., additional, Hallböök, F., additional, Humphrey, Glen W., additional, Idris, Mohammed M., additional, Kiyama, Takae, additional, Liang, Shuguang, additional, Mellott, Dan, additional, Mu, Xiuqian, additional, Murray, Greg, additional, Olinski, Robert P., additional, Raible, Florian, additional, Rowe, Matthew, additional, Taylor, John S., additional, Tessmar-Raible, Kristin, additional, Wang, D., additional, Wilson, Karen H., additional, Yaguchi, Shunsuke, additional, Gaasterland, Terry, additional, Galindo, Blanca E., additional, Gunaratne, Herath J., additional, Juliano, Celina, additional, Kinukawa, Masashi, additional, Moy, Gary W., additional, Neill, Anna T., additional, Nomura, Mamoru, additional, Raisch, Michael, additional, Reade, Anna, additional, Roux, Michelle M., additional, Song, Jia L., additional, Su, Yi-Hsien, additional, Townley, Ian K., additional, Voronina, Ekaterina, additional, Wong, Julian L., additional, Amore, Gabriele, additional, Branno, Margherita, additional, Brown, Euan R., additional, Cavalieri, Vincenzo, additional, Duboc, Véronique, additional, Duloquin, Louise, additional, Flytzanis, Constantin, additional, Gache, Christian, additional, Lapraz, François, additional, Lepage, Thierry, additional, Locascio, Annamaria, additional, Martinez, Pedro, additional, Matassi, Giorgio, additional, Matranga, Valeria, additional, Range, Ryan, additional, Rizzo, Francesca, additional, Röttinger, Eric, additional, Beane, Wendy, additional, Bradham, Cynthia, additional, Byrum, Christine, additional, Glenn, Tom, additional, Hussain, Sofia, additional, Manning, Gerard, additional, Miranda, Esther, additional, Thomason, Rebecca, additional, Walton, Katherine, additional, Wikramanayke, Athula, additional, Wu, Shu-Yu, additional, Xu, Ronghui, additional, Brown, C. Titus, additional, Chen, Lili, additional, Gray, Rachel F., additional, Lee, Pei Yun, additional, Nam, Jongmin, additional, Oliveri, Paola, additional, Smith, Joel, additional, Muzny, Donna, additional, Bell, Stephanie, additional, Chacko, Joseph, additional, Cree, Andrew, additional, Curry, Stacey, additional, Davis, Clay, additional, Dinh, Huyen, additional, Dugan-Rocha, Shannon, additional, Fowler, Jerry, additional, Gill, Rachel, additional, Hamilton, Cerrissa, additional, Hernandez, Judith, additional, Hines, Sandra, additional, Hume, Jennifer, additional, Jackson, LaRonda, additional, Jolivet, Angela, additional, Kovar, Christie, additional, Lee, Sandra, additional, Lewis, Lora, additional, Miner, George, additional, Morgan, Margaret, additional, Nazareth, Lynne V., additional, Okwuonu, Geoffrey, additional, Parker, David, additional, Pu, Ling-Ling, additional, Thorn, Rachel, additional, and Wright, Rita, additional

Published
2006
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8. The C2H2 zinc finger genes of Strongylocentrotus purpuratus and their expression in embryonic development

Author

Materna, Stefan C., Howard-Ashby, Meredith, Gray, Rachel F., and Davidson, Eric H.

Subjects
*HEREDITY, *PROTEINS, *GENETIC transcription, *GENETICS
Abstract

Abstract: The C2H2 zinc finger is one of the most abundant protein domains and is thought to have been extensively replicated in diverse animal clades. Some well-studied proteins that contain this domain are transcriptional regulators. As part of an attempt to delineate all transcription factors encoded in the Strongylocentrotus purpuratus genome, we identified the C2H2 zinc finger genes indicated in the sequence, and examined their involvement in embryonic development. We found 377 zinc finger genes in the sea urchin genome, about half the number found in mice or humans. Their expression was measured by quantitative PCR. Up to the end of gastrulation less than a third of these genes is expressed, and about 75% of the expressed genes are maternal; both parameters distinguish these from all other classes of regulatory genes as measured in other studies. Spatial expression pattern was determined by whole mount in situ hybridization for 43 genes transcribed at a sufficient level, and localized expression was observed in diverse embryonic tissues. These genes may execute important regulatory functions in development. However, the functional meaning of the majority of this large gene family remains undefined. [Copyright &y& Elsevier]

Published
2006
Full Text
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