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  • 1
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    Germline stem cells anchored by adherens junctions in the Drosophila ovary niches (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-06-08
    Description: How stem cells are recruited to and maintained in their niches is crucial to understanding their regulation and use in regenerative medicine. Here, we demonstrate that DE-cadherin-mediated cell adhesion is required for anchoring germline stem cells (GSCs) in their niches in the Drosophila ovary. Two major components of this adhesion process, DE-cadherin and Armadillo/beta-catenin, accumulate at high levels in the junctions between GSCs and cap cells, one of the niche components. Removal of these proteins from GSCs results in stem cell loss. Furthermore, DE-cadherin is required for recruiting GSCs to their niche. Our study demonstrates that anchorage of GSCs in their niche by DE-cadherin-mediated adhesion is important for stem cell maintenance and function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Song, Xiaoqing -- Zhu, Chun-Hong -- Doan, Chuong -- Xie, Ting -- 1R01 GM64428-01/GM/NIGMS NIH HHS/ -- HD 17608/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2002 Jun 7;296(5574):1855-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12052957" target="_blank"〉PubMed〈/a〉
    Keywords: Adherens Junctions/*physiology ; Alleles ; Animals ; Armadillo Domain Proteins ; Cadherins/genetics/*physiology ; Cell Adhesion ; Cell Differentiation ; Drosophila/cytology/genetics/growth & development/*physiology ; *Drosophila Proteins ; Female ; Insect Proteins/genetics/physiology ; Larva/physiology ; Mutation ; Oocytes/*cytology/physiology/ultrastructure ; Ovary/cytology/growth & development/physiology ; Proto-Oncogene Proteins/genetics/physiology ; Signal Transduction ; Stem Cells/cytology/*physiology/ultrastructure ; *Trans-Activators ; Transcription Factors ; Wnt1 Protein
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Protein competition switches the function of COP9 from self-renewal to differentiation (2014)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2014-08-15
    Description: The balance between stem cell self-renewal and differentiation is controlled by intrinsic factors and niche signals. In the Drosophila melanogaster ovary, some intrinsic factors promote germline stem cell (GSC) self-renewal, whereas others stimulate differentiation. However, it remains poorly understood how the balance between self-renewal and differentiation is controlled. Here we use D. melanogaster ovarian GSCs to demonstrate that the differentiation factor Bam controls the functional switch of the COP9 complex from self-renewal to differentiation via protein competition. The COP9 complex is composed of eight Csn subunits, Csn1-8, and removes Nedd8 modifications from target proteins. Genetic results indicated that the COP9 complex is required intrinsically for GSC self-renewal, whereas other Csn proteins, with the exception of Csn4, were also required for GSC progeny differentiation. Bam-mediated Csn4 sequestration from the COP9 complex via protein competition inactivated the self-renewing function of COP9 and allowed other Csn proteins to promote GSC differentiation. Therefore, this study reveals a protein-competition-based mechanism for controlling the balance between stem cell self-renewal and differentiation. Because numerous self-renewal factors are ubiquitously expressed throughout the stem cell lineage in various systems, protein competition may function as an important mechanism for controlling the self-renewal-to-differentiation switch.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pan, Lei -- Wang, Su -- Lu, Tinglin -- Weng, Changjiang -- Song, Xiaoqing -- Park, Joseph K -- Sun, Jin -- Yang, Zhi-Hao -- Yu, Junjing -- Tang, Hong -- McKearin, Dennis M -- Chamovitz, Daniel A -- Ni, Jianquan -- Xie, Ting -- GM64428/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2014 Oct 9;514(7521):233-6. doi: 10.1038/nature13562.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA [2] Chinese Academy of Sciences Key Laboratory of Infection and Immunity, Institute of Biophysics, 15 Da Tun Road, Beijing 100101, China [3]. ; 1] Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA [2] Department of Cell Biology and Anatomy, University of Kansas School of Medicine, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, USA [3]. ; 1] Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China [2]. ; Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA. ; 1] Department of Molecular Biology and Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9148, USA [2] Howard Hughes Medical Institute, Chevy Chase, Maryland 20815-6789, USA. ; Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China. ; 1] Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA [2] Chinese Academy of Sciences Key Laboratory of Infection and Immunity, Institute of Biophysics, 15 Da Tun Road, Beijing 100101, China. ; Chinese Academy of Sciences Key Laboratory of Infection and Immunity, Institute of Biophysics, 15 Da Tun Road, Beijing 100101, China. ; Department of Plant Sciences, Tel Aviv University, Tel Aviv 69978, Israel. ; 1] Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA [2] Department of Cell Biology and Anatomy, University of Kansas School of Medicine, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25119050" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Binding, Competitive ; *Cell Differentiation ; Cell Proliferation ; DNA Helicases/metabolism ; Drosophila Proteins/metabolism ; Drosophila melanogaster/*cytology/*metabolism ; Female ; Intracellular Signaling Peptides and Proteins/metabolism ; Male ; Multiprotein Complexes/*chemistry/*metabolism ; Ovary/cytology ; Peptide Hydrolases/*chemistry/*metabolism ; Protein Binding ; Stem Cells/*cytology/*metabolism ; Ubiquitins/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Evolutionary and biomedical insights from the rhesus macaque genome (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-04-14
    Description: The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rhesus Macaque Genome Sequencing and Analysis Consortium -- Gibbs, Richard A -- Rogers, Jeffrey -- Katze, Michael G -- Bumgarner, Roger -- Weinstock, George M -- Mardis, Elaine R -- Remington, Karin A -- Strausberg, Robert L -- Venter, J Craig -- Wilson, Richard K -- Batzer, Mark A -- Bustamante, Carlos D -- Eichler, Evan E -- Hahn, Matthew W -- Hardison, Ross C -- Makova, Kateryna D -- Miller, Webb -- Milosavljevic, Aleksandar -- Palermo, Robert E -- Siepel, Adam -- Sikela, James M -- Attaway, Tony -- Bell, Stephanie -- Bernard, Kelly E -- Buhay, Christian J -- Chandrabose, Mimi N -- Dao, Marvin -- Davis, Clay -- Delehaunty, Kimberly D -- Ding, Yan -- Dinh, Huyen H -- Dugan-Rocha, Shannon -- Fulton, Lucinda A -- Gabisi, Ramatu Ayiesha -- Garner, Toni T -- Godfrey, Jennifer -- Hawes, Alicia C -- Hernandez, Judith -- Hines, Sandra -- Holder, Michael -- Hume, Jennifer -- Jhangiani, Shalini N -- Joshi, Vandita -- Khan, Ziad Mohid -- Kirkness, Ewen F -- Cree, Andrew -- Fowler, R Gerald -- Lee, Sandra -- Lewis, Lora R -- Li, Zhangwan -- Liu, Yih-Shin -- Moore, Stephanie M -- Muzny, Donna -- Nazareth, Lynne V -- Ngo, Dinh Ngoc -- Okwuonu, Geoffrey O -- Pai, Grace -- Parker, David -- Paul, Heidie A -- Pfannkoch, Cynthia -- Pohl, Craig S -- Rogers, Yu-Hui -- Ruiz, San Juana -- Sabo, Aniko -- Santibanez, Jireh -- Schneider, Brian W -- Smith, Scott M -- Sodergren, Erica -- Svatek, Amanda F -- Utterback, Teresa R -- Vattathil, Selina -- Warren, Wesley -- White, Courtney Sherell -- Chinwalla, Asif T -- Feng, Yucheng -- Halpern, Aaron L -- Hillier, Ladeana W -- Huang, Xiaoqiu -- Minx, Pat -- Nelson, Joanne O -- Pepin, Kymberlie H -- Qin, Xiang -- Sutton, Granger G -- Venter, Eli -- Walenz, Brian P -- Wallis, John W -- Worley, Kim C -- Yang, Shiaw-Pyng -- Jones, Steven M -- Marra, Marco A -- Rocchi, Mariano -- Schein, Jacqueline E -- Baertsch, Robert -- Clarke, Laura -- Csuros, Miklos -- Glasscock, Jarret -- Harris, R Alan -- Havlak, Paul -- Jackson, Andrew R -- Jiang, Huaiyang -- Liu, Yue -- Messina, David N -- Shen, Yufeng -- Song, Henry Xing-Zhi -- Wylie, Todd -- Zhang, Lan -- Birney, Ewan -- Han, Kyudong -- Konkel, Miriam K -- Lee, Jungnam -- Smit, Arian F A -- Ullmer, Brygg -- Wang, Hui -- Xing, Jinchuan -- Burhans, Richard -- Cheng, Ze -- Karro, John E -- Ma, Jian -- Raney, Brian -- She, Xinwei -- Cox, Michael J -- Demuth, Jeffery P -- Dumas, Laura J -- Han, Sang-Gook -- Hopkins, Janet -- Karimpour-Fard, Anis -- Kim, Young H -- Pollack, Jonathan R -- Vinar, Tomas -- Addo-Quaye, Charles -- Degenhardt, Jeremiah -- Denby, Alexandra -- Hubisz, Melissa J -- Indap, Amit -- Kosiol, Carolin -- Lahn, Bruce T -- Lawson, Heather A -- Marklein, Alison -- Nielsen, Rasmus -- Vallender, Eric J -- Clark, Andrew G -- Ferguson, Betsy -- Hernandez, Ryan D -- Hirani, Kashif -- Kehrer-Sawatzki, Hildegard -- Kolb, Jessica -- Patil, Shobha -- Pu, Ling-Ling -- Ren, Yanru -- Smith, David Glenn -- Wheeler, David A -- Schenck, Ian -- Ball, Edward V -- Chen, Rui -- Cooper, David N -- Giardine, Belinda -- Hsu, Fan -- Kent, W James -- Lesk, Arthur -- Nelson, David L -- O'brien, William E -- Prufer, Kay -- Stenson, Peter D -- Wallace, James C -- Ke, Hui -- Liu, Xiao-Ming -- Wang, Peng -- Xiang, Andy Peng -- Yang, Fan -- Barber, Galt P -- Haussler, David -- Karolchik, Donna -- Kern, Andy D -- Kuhn, Robert M -- Smith, Kayla E -- Zwieg, Ann S -- 062023/Wellcome Trust/United Kingdom -- R01 HG002939/HG/NHGRI NIH HHS/ -- U54 HG003068/HG/NHGRI NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2007 Apr 13;316(5822):222-34.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA. agibbs@bcm.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17431167" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biomedical Research ; *Evolution, Molecular ; Female ; Gene Duplication ; Gene Rearrangement ; Genetic Diseases, Inborn ; Genetic Variation ; *Genome ; Humans ; Macaca mulatta/*genetics ; Male ; Multigene Family ; Mutation ; Pan troglodytes/genetics ; Sequence Analysis, DNA ; Species Specificity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Cofilin promotes actin polymerization and defines the direction of cell motility (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-05-01
    Description: A general caging method for proteins that are regulated by phosphorylation was used to study the in vivo biochemical action of cofilin and the subsequent cellular response. By acute and local activation of a chemically engineered, light-sensitive phosphocofilin mimic, we demonstrate that cofilin polymerizes actin, generates protrusions, and determines the direction of cell migration. We propose a role for cofilin that is distinct from its role as an actin-depolymerizing factor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ghosh, Mousumi -- Song, Xiaoyan -- Mouneimne, Ghassan -- Sidani, Mazen -- Lawrence, David S -- Condeelis, John S -- GM38511/GM/NIGMS NIH HHS/ -- GM61034/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2004 Apr 30;304(5671):743-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15118165" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Depolymerizing Factors ; Actins/*metabolism ; Animals ; Biopolymers ; Cell Line, Tumor ; *Cell Movement ; Light ; Lim Kinases ; Microfilament Proteins/genetics/*physiology ; Microinjections ; Mutation ; Phenylacetates/chemistry ; Phosphorylation ; Protein Binding ; Protein Kinases/metabolism ; Pseudopodia/physiology/ultrastructure ; RNA, Small Interfering ; Rats
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    NMDA receptor structures reveal subunit arrangement and pore architecture (2014)
    Nature Publishing Group (NPG)
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    Publication Date: 2014-07-11
    Description: N-methyl-d-aspartate (NMDA) receptors are Hebbian-like coincidence detectors, requiring binding of glycine and glutamate in combination with the relief of voltage-dependent magnesium block to open an ion conductive pore across the membrane bilayer. Despite the importance of the NMDA receptor in the development and function of the brain, a molecular structure of an intact receptor has remained elusive. Here we present X-ray crystal structures of the Xenopus laevis GluN1-GluN2B NMDA receptor with the allosteric inhibitor, Ro25-6981, partial agonists and the ion channel blocker, MK-801. Receptor subunits are arranged in a 1-2-1-2 fashion, demonstrating extensive interactions between the amino-terminal and ligand-binding domains. The transmembrane domains harbour a closed-blocked ion channel, a pyramidal central vestibule lined by residues implicated in binding ion channel blockers and magnesium, and a approximately twofold symmetric arrangement of ion channel pore loops. These structures provide new insights into the architecture, allosteric coupling and ion channel function of NMDA receptors.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263351/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263351/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Chia-Hsueh -- Lu, Wei -- Michel, Jennifer Carlisle -- Goehring, April -- Du, Juan -- Song, Xianqiang -- Gouaux, Eric -- R37 NS038631/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2014 Jul 10;511(7508):191-7. doi: 10.1038/nature13548. Epub 2014 Jun 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Vollum Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA [2]. ; 1] Vollum Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA [2] Howard Hughes Medical Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA. ; Vollum Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25008524" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Dizocilpine Maleate/chemistry ; Ion Channels/chemistry ; Ligands ; *Models, Molecular ; Phenols ; Piperidines/chemistry ; Protein Binding ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Receptors, N-Methyl-D-Aspartate/*chemistry ; Xenopus laevis/*physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
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    The oyster genome reveals stress adaptation and complexity of shell formation (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-09-21
    Description: The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Guofan -- Fang, Xiaodong -- Guo, Ximing -- Li, Li -- Luo, Ruibang -- Xu, Fei -- Yang, Pengcheng -- Zhang, Linlin -- Wang, Xiaotong -- Qi, Haigang -- Xiong, Zhiqiang -- Que, Huayong -- Xie, Yinlong -- Holland, Peter W H -- Paps, Jordi -- Zhu, Yabing -- Wu, Fucun -- Chen, Yuanxin -- Wang, Jiafeng -- Peng, Chunfang -- Meng, Jie -- Yang, Lan -- Liu, Jun -- Wen, Bo -- Zhang, Na -- Huang, Zhiyong -- Zhu, Qihui -- Feng, Yue -- Mount, Andrew -- Hedgecock, Dennis -- Xu, Zhe -- Liu, Yunjie -- Domazet-Loso, Tomislav -- Du, Yishuai -- Sun, Xiaoqing -- Zhang, Shoudu -- Liu, Binghang -- Cheng, Peizhou -- Jiang, Xuanting -- Li, Juan -- Fan, Dingding -- Wang, Wei -- Fu, Wenjing -- Wang, Tong -- Wang, Bo -- Zhang, Jibiao -- Peng, Zhiyu -- Li, Yingxiang -- Li, Na -- Wang, Jinpeng -- Chen, Maoshan -- He, Yan -- Tan, Fengji -- Song, Xiaorui -- Zheng, Qiumei -- Huang, Ronglian -- Yang, Hailong -- Du, Xuedi -- Chen, Li -- Yang, Mei -- Gaffney, Patrick M -- Wang, Shan -- Luo, Longhai -- She, Zhicai -- Ming, Yao -- Huang, Wen -- Zhang, Shu -- Huang, Baoyu -- Zhang, Yong -- Qu, Tao -- Ni, Peixiang -- Miao, Guoying -- Wang, Junyi -- Wang, Qiang -- Steinberg, Christian E W -- Wang, Haiyan -- Li, Ning -- Qian, Lumin -- Zhang, Guojie -- Li, Yingrui -- Yang, Huanming -- Liu, Xiao -- Wang, Jian -- Yin, Ye -- Wang, Jun -- 268513/European Research Council/International -- England -- Nature. 2012 Oct 4;490(7418):49-54. doi: 10.1038/nature11413. Epub 2012 Sep 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22992520" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics ; Animal Shells/chemistry/*growth & development ; Animals ; Apoptosis Regulatory Proteins/genetics ; Crassostrea/*genetics ; DNA Transposable Elements/genetics ; Evolution, Molecular ; Female ; Gene Expression Regulation, Developmental/genetics ; Genes, Homeobox/genetics ; Genome/*genetics ; Genomics ; HSP70 Heat-Shock Proteins/genetics ; Humans ; Larva/genetics/growth & development ; Mass Spectrometry ; Molecular Sequence Annotation ; Molecular Sequence Data ; Polymorphism, Genetic/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Analysis, DNA ; Stress, Physiological/genetics/*physiology ; Transcriptome/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
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    The genome of the sea urchin Strongylocentrotus purpuratus (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-11
    Description: 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.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sea Urchin Genome Sequencing Consortium -- 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 -- Hallbook, F -- 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 -- Rottinger, Eric -- Beane, Wendy -- Bradham, Cynthia -- Byrum, Christine -- Glenn, Tom -- Hussain, Sofia -- Manning, Gerard -- Miranda, Esther -- Thomason, Rebecca -- Walton, Katherine -- Wikramanayke, Athula -- 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 -- Thorn, Rachel -- Wright, Rita -- 2P42 ESO7381/PHS HHS/ -- 5 U54 HG003273/HG/NHGRI NIH HHS/ -- EY11930/EY/NEI NIH HHS/ -- F32 ESO12794/PHS HHS/ -- F32 HD047136/HD/NICHD NIH HHS/ -- F32 HD047136-02/HD/NICHD NIH HHS/ -- F32 HD047136-03/HD/NICHD NIH HHS/ -- F32-HD47136/HD/NICHD NIH HHS/ -- GM058231/GM/NIGMS NIH HHS/ -- GM070840/GM/NIGMS NIH HHS/ -- GM61005/GM/NIGMS NIH HHS/ -- GM61464/GM/NIGMS NIH HHS/ -- HD-37105/HD/NICHD NIH HHS/ -- HD039948/HD/NICHD NIH HHS/ -- HD14483/HD/NICHD NIH HHS/ -- HD66219/HD/NICHD NIH HHS/ -- P30-CA14051/CA/NCI NIH HHS/ -- R01 ES006272/ES/NIEHS NIH HHS/ -- R01 ES006272-13/ES/NIEHS NIH HHS/ -- R01 GM070840/GM/NIGMS NIH HHS/ -- R01 HD028152/HD/NICHD NIH HHS/ -- R01ES006272/ES/NIEHS NIH HHS/ -- R37-HD12896/HD/NICHD NIH HHS/ -- RR-15044/RR/NCRR NIH HHS/ -- S19916/Biotechnology and Biological Sciences Research Council/United Kingdom -- T32 GM007601/GM/NIGMS NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 10;314(5801):941-52.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17095691" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcification, Physiologic ; Cell Adhesion Molecules/genetics/physiology ; Complement Activation/genetics ; Computational Biology ; Embryonic Development/genetics ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; Genes ; *Genome ; Immunity, Innate/genetics ; Immunologic Factors/genetics/physiology ; Male ; Nervous System Physiological Phenomena ; Proteins/genetics/physiology ; *Sequence Analysis, DNA ; Signal Transduction ; Strongylocentrotus purpuratus/embryology/*genetics/immunology/physiology ; Transcription Factors/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-08-06
    Description: The prevalent DNA modification in higher organisms is the methylation of cytosine to 5-methylcytosine (5mC), which is partially converted to 5-hydroxymethylcytosine (5hmC) by the Tet (ten eleven translocation) family of dioxygenases. Despite their importance in epigenetic regulation, it is unclear how these cytosine modifications are reversed. Here, we demonstrate that 5mC and 5hmC in DNA are oxidized to 5-carboxylcytosine (5caC) by Tet dioxygenases in vitro and in cultured cells. 5caC is specifically recognized and excised by thymine-DNA glycosylase (TDG). Depletion of TDG in mouse embyronic stem cells leads to accumulation of 5caC to a readily detectable level. These data suggest that oxidation of 5mC by Tet proteins followed by TDG-mediated base excision of 5caC constitutes a pathway for active DNA demethylation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3462231/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3462231/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉He, Yu-Fei -- Li, Bin-Zhong -- Li, Zheng -- Liu, Peng -- Wang, Yang -- Tang, Qingyu -- Ding, Jianping -- Jia, Yingying -- Chen, Zhangcheng -- Li, Lin -- Sun, Yan -- Li, Xiuxue -- Dai, Qing -- Song, Chun-Xiao -- Zhang, Kangling -- He, Chuan -- Xu, Guo-Liang -- 1S10RR027643-01/RR/NCRR NIH HHS/ -- GM071440/GM/NIGMS NIH HHS/ -- R01 GM071440/GM/NIGMS NIH HHS/ -- S10 RR027643/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2011 Sep 2;333(6047):1303-7. doi: 10.1126/science.1210944. Epub 2011 Aug 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Group of DNA Metabolism, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21817016" target="_blank"〉PubMed〈/a〉
    Keywords: 5-Methylcytosine/metabolism ; Animals ; Cell Line ; Cytosine/*analogs & derivatives/metabolism ; DNA/*metabolism ; DNA Methylation ; DNA-Binding Proteins/genetics/*metabolism ; Embryonic Stem Cells ; HEK293 Cells ; Humans ; Induced Pluripotent Stem Cells/metabolism ; Mice ; Oxidation-Reduction ; Proto-Oncogene Proteins/genetics/*metabolism ; RNA, Small Interfering ; Thymine DNA Glycosylase/genetics/*metabolism ; Transfection
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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