Jun Ma

Summary

Affiliation: Cincinnati Children's Hospital Medical Center
Country: USA

Publications

  1. ncbi request reprint The activity of the Drosophila morphogenetic protein Bicoid is inhibited by a domain located outside its homeodomain
    Chen Zhao
    Division of Developmental Biology, Children s Hospital Research Foundation, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
    Development 129:1669-80. 2002
  2. ncbi request reprint Actively seeking activating sequences
    Jun Ma
    Division of Developmental Biology, Cincinnati Children s Hospital Research Foundation, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, Ohio 45229, USA
    Cell 116:S75-6, 2 p following S76. 2004
  3. pmc A two-dimensional simulation model of the bicoid gradient in Drosophila
    Jingyuan Deng
    Division of Biomedical Informatics, Cincinnati Children s Hospital Research Foundation, Cincinnati, Ohio, United States of America
    PLoS ONE 5:e10275. 2010
  4. pmc Uncovering a dynamic feature of the transcriptional regulatory network for anterior-posterior patterning in the Drosophila embryo
    Junbo Liu
    Division of Biomedical Informatics, Cincinnati Children s Research Foundation, Cincinnati, Ohio, United States of America
    PLoS ONE 8:e62641. 2013
  5. pmc A spatial point pattern analysis in Drosophila blastoderm embryos evaluating the potential inheritance of transcriptional states
    Feng He
    Division of Biomedical Informatics, Cincinnati Children s Research Foundation, Cincinnati, Ohio, United States of America
    PLoS ONE 8:e60876. 2013
  6. pmc Fates-shifted is an F-box protein that targets Bicoid for degradation and regulates developmental fate determination in Drosophila embryos
    Junbo Liu
    Division of Biomedical Informatics, Cincinnati Children s Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
    Nat Cell Biol 13:22-9. 2011
  7. pmc A multiscale investigation of bicoid-dependent transcriptional events in Drosophila embryos
    Feng He
    Division of Biomedical Informatics, Cincinnati Children s Research Foundation, Cincinnati, Ohio, United States of America
    PLoS ONE 6:e19122. 2011
  8. pmc Distance measurements via the morphogen gradient of Bicoid in Drosophila embryos
    Feng He
    State Key Laboratory of Brain and Cognitive Science Institute of Biophysics Chinese Academy of Sciences 15 Datun Road Beijing 100101, China
    BMC Dev Biol 10:80. 2010
  9. ncbi request reprint Crossing the line between activation and repression
    Jun Ma
    Division of Developmental Biology, Cincinnati Children s Hospital Research Foundation, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
    Trends Genet 21:54-9. 2005
  10. doi request reprint Transcriptional activators and activation mechanisms
    Jun Ma
    Division of Biomedical Informatics, Division of Developmental Biology, Cincinnati Children s Research Foundation, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
    Protein Cell 2:879-88. 2011

Collaborators

  • Hung Tseng
  • Feng He
  • Vrushank Dave
  • Wei Wang
  • Chen Zhao
  • Martin Howard
  • Xiaodong Lin
  • Jie Ren
  • Fan Yang
  • Junbo Liu
  • David Cheung
  • Dechen Fu
  • Hongjuan Cui
  • CECELIA MILES
  • Martin Kreitman
  • Jingyuan Deng
  • Yanjun Song
  • Han Fei Ding
  • Tai Li
  • Goleeta Alam
  • Jamie M Baird-Titus
  • Choong Chin Liew
  • Kimber Clark-Baldwin
  • Mark Rance
  • Beth A Chaney
  • Xiao Zeng
  • Naseruddin Hoti
  • Tinchung Leung
  • Dongyi Zhang
  • Dong Yi Zhang
  • Long Jason Lu
  • Dieter Egli
  • Gengqiang Xie
  • Bo Hu
  • William T Gunning
  • Yanjuan Xu
  • Xuehong Liang
  • Igor Stagljar
  • Yixu Chen
  • Xiaoyan Guo
  • Renjie Jiao
  • Jane Ding
  • Adam A Dempsey
  • Hong Chang Tang
  • Carol A Caperelli
  • Run Zheng
  • Ying Wen
  • Michael Dorsey
  • Johannes Bischof
  • Yi Wang
  • Herbert Jackle
  • Wolfgang Driever
  • Sartaj Tabassum
  • Dierk Niessing
  • Mian Wu
  • Iris Söll
  • Daniel J Carson

Detail Information

Publications38

  1. ncbi request reprint The activity of the Drosophila morphogenetic protein Bicoid is inhibited by a domain located outside its homeodomain
    Chen Zhao
    Division of Developmental Biology, Children s Hospital Research Foundation, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
    Development 129:1669-80. 2002
    ....
  2. ncbi request reprint Actively seeking activating sequences
    Jun Ma
    Division of Developmental Biology, Cincinnati Children s Hospital Research Foundation, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, Ohio 45229, USA
    Cell 116:S75-6, 2 p following S76. 2004
  3. pmc A two-dimensional simulation model of the bicoid gradient in Drosophila
    Jingyuan Deng
    Division of Biomedical Informatics, Cincinnati Children s Hospital Research Foundation, Cincinnati, Ohio, United States of America
    PLoS ONE 5:e10275. 2010
    ....
  4. pmc Uncovering a dynamic feature of the transcriptional regulatory network for anterior-posterior patterning in the Drosophila embryo
    Junbo Liu
    Division of Biomedical Informatics, Cincinnati Children s Research Foundation, Cincinnati, Ohio, United States of America
    PLoS ONE 8:e62641. 2013
    ..We suggest that this dynamic feature offers a window of opportunity for hb to faithfully interpret, and directly benefit from, Bcd gradient properties, including its scaling properties, to help craft a robust AP patterning outcome...
  5. pmc A spatial point pattern analysis in Drosophila blastoderm embryos evaluating the potential inheritance of transcriptional states
    Feng He
    Division of Biomedical Informatics, Cincinnati Children s Research Foundation, Cincinnati, Ohio, United States of America
    PLoS ONE 8:e60876. 2013
    ..Our results are consistent with the possibility where the positional information encoded by the Bcd morphogen gradient may not need to be decoded de novo at all mitotic cycles in the Drosophila blastoderm embryo...
  6. pmc Fates-shifted is an F-box protein that targets Bicoid for degradation and regulates developmental fate determination in Drosophila embryos
    Junbo Liu
    Division of Biomedical Informatics, Cincinnati Children s Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
    Nat Cell Biol 13:22-9. 2011
    ..Our study is an experimental demonstration that, contrary to an alternative hypothesis, Bcd protein degradation is required for normal gradient formation and developmental fate determination...
  7. pmc A multiscale investigation of bicoid-dependent transcriptional events in Drosophila embryos
    Feng He
    Division of Biomedical Informatics, Cincinnati Children s Research Foundation, Cincinnati, Ohio, United States of America
    PLoS ONE 6:e19122. 2011
    ..For example, it remains controversial whether the Drosophila morphogenetic protein Bicoid (Bcd) plays a transient or sustained role in activating its target genes to establish sharp expression boundaries during development...
  8. pmc Distance measurements via the morphogen gradient of Bicoid in Drosophila embryos
    Feng He
    State Key Laboratory of Brain and Cognitive Science Institute of Biophysics Chinese Academy of Sciences 15 Datun Road Beijing 100101, China
    BMC Dev Biol 10:80. 2010
    ..Despite extensive studies of this morphogen, how embryo geometry may affect gradient formation and target responses has not been investigated experimentally...
  9. ncbi request reprint Crossing the line between activation and repression
    Jun Ma
    Division of Developmental Biology, Cincinnati Children s Hospital Research Foundation, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
    Trends Genet 21:54-9. 2005
    ..This article discusses selected examples to illustrate the dynamic nature of the transcriptional regulation process and highlights the important roles of not only the individual proteins but also their communication system...
  10. doi request reprint Transcriptional activators and activation mechanisms
    Jun Ma
    Division of Biomedical Informatics, Division of Developmental Biology, Cincinnati Children s Research Foundation, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
    Protein Cell 2:879-88. 2011
    ..Activators bound to the enhancer can facilitate either the recruitment of RNA polymerase II to the promoter or its elongation. This article examines a few selected issues in understanding activator functions and activation mechanisms...
  11. pmc Shaping a morphogen gradient for positional precision
    Feng He
    Division of Biomedical Informatics, Cincinnati Children s Hospital Research Foundation, Cincinnati, Ohio, USA
    Biophys J 99:697-707. 2010
    ..Our results demonstrate that the positional information provided by the wt Bcd gradient profile is highly precise and necessary for patterning precision...
  12. pmc Interplay between positive and negative activities that influence the role of Bicoid in transcription
    Dechen Fu
    Division of Developmental Biology, Cincinnati Children s Hospital Research Foundation, Graduate Program in Molecular and Developmental Biology, University of Cincinnati College of Medicine 3333 Burnet Avenue Cincinnati, OH 45229, USA
    Nucleic Acids Res 33:3985-93. 2005
    ..These and other results suggest that an activator can undergo switches between its active and inactive states through sensing the opposing actions of positive and negative co-factors...
  13. ncbi request reprint A composite motif of the Drosophila morphogenetic protein bicoid critical to transcription control
    Chen Zhao
    Division of Developmental Biology, Children s Hospital Research Foundation, Cincinnati, Ohio 45229, USA
    J Biol Chem 278:43901-9. 2003
    ..Our study suggests that the activity of Bcd is intricately controlled by multiple mechanisms involving the actions of co-repressor proteins...
  14. ncbi request reprint The co-activator CREB-binding protein participates in enhancer-dependent activities of bicoid
    Dechen Fu
    Division of Developmental Biology, Cincinnati Children s Hospital Research Foundation, Graduate Program in Molecular and Developmental Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
    J Biol Chem 279:48725-33. 2004
    ..Together, these experiments suggest that dCBP is an enhancer-dependent co-activator of Bcd, facilitating its activation through multiple mechanisms...
  15. pmc Enhancer sequences influence the role of the amino-terminal domain of bicoid in transcription
    Dechen Fu
    Graduate Program in Molecular and Developmental Biology, Division of Developmental Biology, Children s Hospital Research Foundation, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
    Mol Cell Biol 23:4439-48. 2003
    ..We propose that the amino-terminal domain of Bcd is an enhancer-specific switch that contributes to the protein's ability to activate different target genes in distinct manners...
  16. ncbi request reprint The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site
    Jamie M Baird-Titus
    Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, 231 Albert Sabin Way, Medical Sciences Building, Cincinnati, OH 45267 0524, USA
    J Mol Biol 356:1137-51. 2006
    ..This finding is supportive of the adaptive-recognition theory of protein-DNA interactions...
  17. pmc Probing intrinsic properties of a robust morphogen gradient in Drosophila
    Feng He
    Division of Biomedical Informatics, Cincinnati Children s Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
    Dev Cell 15:558-67. 2008
    ..The robustness of this gradient is conferred by its intrinsic properties of "self-correcting" the inevitable input variations to achieve a precise and reproducible output...
  18. pmc Dampened regulates the activating potency of Bicoid and the embryonic patterning outcome in Drosophila
    Junbo Liu
    Division of Biomedical Informatics, Cincinnati Children s Research Foundation, 3333 Burnet Avenue, Cincinnati, Ohio 45229, USA
    Nat Commun 4:2968. 2013
    ..Thus, unlike another Bcd-interacting F-box protein Fate-shifted (Fsd), which controls AP patterning through regulating the Bcd gradient profile, Dmpd achieves its patterning role through regulating the activating potency of Bcd. ..
  19. pmc Adaptation of the length scale and amplitude of the Bicoid gradient profile to achieve robust patterning in abnormally large Drosophila melanogaster embryos
    David Cheung
    Division of Biomedical Informatics, Cincinnati Children s Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
    Development 141:124-35. 2014
    ....
  20. ncbi request reprint Hypomutable regions of yeast TFIIB in a unigenic evolution test represent structural domains
    Xiao Zeng
    Division of Developmental Biology, Children s Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
    Gene 309:49-56. 2003
    ....
  21. pmc Drosophila Bicoid is a substrate of sumoylation and its activator function is subject to inhibition by this post-translational modification
    Junbo Liu
    Division of Biomedical Informatics, Cincinnati Children s Research Foundation, 3333 Burnet Avenue, Cincinnati, OH, United States
    FEBS Lett 586:1719-23. 2012
    ..We provide evidence suggesting that the SUMO moiety has an intrinsic inhibitory activity for the activator function of Bcd...
  22. pmc Evaluating the Drosophila Bicoid morphogen gradient system through dissecting the noise in transcriptional bursts
    Feng He
    Division of Biomedical Informatics, Cincinnati Children s Research Foundation, Cincinnati, OH 45229, USA
    Bioinformatics 28:970-5. 2012
    ..We describe a statistical model to dissect the noise in transcriptional bursts in a developmental system...
  23. pmc Scaling of the Bicoid morphogen gradient by a volume-dependent production rate
    David Cheung
    Division of Biomedical Informatics, Cincinnati Children s Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
    Development 138:2741-9. 2011
    ..In this model, the Bcd production rate, which is dependent on the total number of bcd mRNA molecules in the anterior, is scaled with embryo volume...
  24. ncbi request reprint Solution structure of the K50 class homeodomain PITX2 bound to DNA and implications for mutations that cause Rieger syndrome
    Beth A Chaney
    Department of Molecular Genetics, Biochemistry, and Microbiology, College of Medicine, University of Cincinnati, 231 Albert Sabin Way, Medical Sciences Building, Cincinnati, Ohio 45267 0524, USA
    Biochemistry 44:7497-511. 2005
    ..Overall, the role of K50 in homeodomain recognition is further clarified, and the results indicate that native K50 homeodomains may exhibit differences from altered specificity mutants...
  25. pmc Morphogen gradient formation and action: insights from studying Bicoid protein degradation
    Junbo Liu
    Division of Biomedical Informatics, Cincinnati Children s Research Foundation, Cincinnati, OH, USA
    Fly (Austin) 5:242-6. 2011
    ..Finally, we discuss the role of Bcd-encoded positional information in controlling the positioning and precision of developmental decisions...
  26. pmc The role of TFIIB-RNA polymerase II interaction in start site selection in yeast cells
    Dong Yi Zhang
    Division of Developmental Biology, Children s Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
    Nucleic Acids Res 30:3078-85. 2002
    ..We discuss a model in which the TFIIB-RNAPII interaction controls the start site selection process by influencing the conformation of PIC prior to or during PIC assembly, as opposed to PIC stability...
  27. ncbi request reprint bozozok directly represses bmp2b transcription and mediates the earliest dorsoventral asymmetry of bmp2b expression in zebrafish
    Tinchung Leung
    Developmental Biology, Institute Biology 1, University of Freiburg, Hauptstrasse 1, D 79104 Freiburg, Germany
    Development 130:3639-49. 2003
    ..Thus, similar to Drosophila Dpp, asymmetry of Bmp expression in zebrafish is initiated at the transcriptional level, and the shape of the gradient and its function as a morphogen are later modulated by post-transcriptional mechanisms...
  28. ncbi request reprint Triphenyl tin benzimidazolethiol, a novel antitumor agent, induces mitochondrial-mediated apoptosis in human cervical cancer cells via suppression of HPV-18 encoded E6
    Naseruddin Hoti
    Department of Molecular and Cell Biology, Key Laboratory of Structural Biology, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, People s Republic of China
    J Biochem 134:521-8. 2003
    ..Taken together, we propose that TPT-benzimidazolethiol could has the potential to be developed into a new therapeutic agent for treating HPV-associated cervical neoplasia...
  29. ncbi request reprint Overexpression of autophagy-related genes inhibits yeast filamentous growth
    Jun Ma
    Department of Molecular, Cellular and Developmental Biology and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109 2216, USA
    Autophagy 3:604-9. 2007
    ..Rather, these results highlight an additional undefined regulatory mechanism linking autophagy and filamentous growth, possibly independent of the upstream nitrogen-sensing machinery feeding into both processes...
  30. ncbi request reprint The peripheral blood transcriptome dynamically reflects system wide biology: a potential diagnostic tool
    Choong Chin Liew
    ChondroGene, Inc, Toronto, Ontario, Canada
    J Lab Clin Med 147:126-32. 2006
    ....
  31. ncbi request reprint Basonuclin: a novel mammalian maternal-effect gene
    Jun Ma
    Department of Dermatology, University of Pennsylvania, PA 19104, USA
    Development 133:2053-62. 2006
    ..These results suggest that basonuclin is a new member of the mammalian maternal-effect genes and, interestingly, differs from the previously reported mammalian maternal-effect genes in that it also apparently perturbs oogenesis...
  32. ncbi request reprint Identifying leukocyte gene expression patterns associated with plasma lipid levels in human subjects
    Jun Ma
    ChondroGene, Inc, 800 Petrolia Road, Unit 15, Toronto, Ont, Canada M3J 3K4
    Atherosclerosis 191:63-72. 2007
    ..Our findings suggest that leukocytes respond to changing plasma lipid levels by regulating a network of genes, including genes involved in immune response, and lipid and fatty acid metabolism...
  33. ncbi request reprint Bmi-1 regulates the differentiation and clonogenic self-renewal of I-type neuroblastoma cells in a concentration-dependent manner
    Hongjuan Cui
    Department of Biochemistry and Cancer Biology, Medical University of Ohio, Toledo, Ohio 43614, USA
    J Biol Chem 281:34696-704. 2006
    ..These observations suggest that graded activation of a master regulator within individual tumors could trigger divergent developmental programs responsible for both tumor growth and heterogeneity...
  34. ncbi request reprint Localization of autophagy-related proteins in yeast using a versatile plasmid-based resource of fluorescent protein fusions
    Jun Ma
    Department of Molecular, Cellular, and Developmental Biology and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109 2216, USA
    Autophagy 4:792-800. 2008
    ..Collectively, this plasmid-based resource of yeast gene-vYFP fusions provides an initial toolkit for a variety of systematic and large-scale localization studies exploring pathway biology in the budding yeast...
  35. pmc Unconventional genomic architecture in the budding yeast saccharomyces cerevisiae masks the nested antisense gene NAG1
    Jun Ma
    Department of Molecular, Cellular, and Developmental Biology, Life Sciences Institute, Room 6026, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109 2216, USA
    Eukaryot Cell 7:1289-98. 2008
    ..Thus, NAG1 is important for two reasons. First, it contributes to yeast cell wall biogenesis. Second, its genomic context is novel, raising the possibility that other nested protein-coding genes may exist in eukaryotic genomes...
  36. ncbi request reprint CAF-1 is essential for Drosophila development and involved in the maintenance of epigenetic memory
    Yanjun Song
    National Laboratory of Biomacromolecules and State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, The Chinese Academy of Sciences, Datun Road 15, Chaoyang District, Beijing 100101, China
    Dev Biol 311:213-22. 2007
    ..Together, our results establish that dCAF-1-p180 is an essential gene for Drosophila development and further underscore the importance of dCAF-1 in regulating gene expression and DNA repair in vivo...
  37. pmc Bmi-1 is essential for the tumorigenicity of neuroblastoma cells
    Hongjuan Cui
    Department of Biochemistry and Cancer Biology, Medical University of Ohio, 3035 Arlington Ave, Toledo, OH 43614, USA
    Am J Pathol 170:1370-8. 2007
    ..These findings suggest a crucial role for Bmi-1 in neuroblastoma pathogenesis and provide insights into the molecular basis of neuroblastoma heterogeneity...
  38. pmc An interrelationship between autophagy and filamentous growth in budding yeast
    Jun Ma
    Department of Molecular, Cellular, and Developmental Biology and Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109 2216, USA
    Genetics 177:205-14. 2007
    ..This physiological connection highlights the central role of autophagy in regulating the cell's nutritional state and the responsiveness of PHG to that state...

Research Grants4

  1. Activities of the Bicoid Gradient in Drosophila Embryos
    Jun Ma; Fiscal Year: 2005
    ..abstract_text> ..
  2. Activities of the Bicoid Gradient in Drosophila Embryos
    Jun Ma; Fiscal Year: 2006
    ..abstract_text> ..
  3. Activities of the Bicoid Gradient in Drosophila Embryos
    Jun Ma; Fiscal Year: 2007
    ..abstract_text> ..