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  1. Article ; Online: Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species.

    Hezroni, Hadas / Koppstein, David / Schwartz, Matthew G / Avrutin, Alexandra / Bartel, David P / Ulitsky, Igor

    Cell reports

    2015  Volume 11, Issue 7, Page(s) 1110–1122

    Abstract: The inability to predict long noncoding RNAs from genomic sequence has impeded the use of comparative genomics for studying their biology. Here, we develop methods that use RNA sequencing (RNA-seq) data to annotate the transcriptomes of 16 vertebrates ... ...

    Abstract The inability to predict long noncoding RNAs from genomic sequence has impeded the use of comparative genomics for studying their biology. Here, we develop methods that use RNA sequencing (RNA-seq) data to annotate the transcriptomes of 16 vertebrates and the echinoid sea urchin, uncovering thousands of previously unannotated genes, most of which produce long intervening noncoding RNAs (lincRNAs). Although in each species, >70% of lincRNAs cannot be traced to homologs in species that diverged >50 million years ago, thousands of human lincRNAs have homologs with similar expression patterns in other species. These homologs share short, 5'-biased patches of sequence conservation nested in exonic architectures that have been extensively rewired, in part by transposable element exonization. Thus, over a thousand human lincRNAs are likely to have conserved functions in mammals, and hundreds beyond mammals, but those functions require only short patches of specific sequences and can tolerate major changes in gene architecture.
    MeSH term(s) Base Sequence ; Conserved Sequence/genetics ; Evolution, Molecular ; Humans ; RNA, Long Noncoding/genetics ; Sequence Analysis, RNA ; Transcriptome/genetics
    Chemical Substances RNA, Long Noncoding
    Language English
    Publishing date 2015-05-19
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2015.04.023
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Mutation of a nucleosome compaction region disrupts Polycomb-mediated axial patterning.

    Lau, Mei Sheng / Schwartz, Matthew G / Kundu, Sharmistha / Savol, Andrej J / Wang, Peggy I / Marr, Sharon K / Grau, Daniel J / Schorderet, Patrick / Sadreyev, Ruslan I / Tabin, Clifford J / Kingston, Robert E

    Science (New York, N.Y.)

    2017  Volume 355, Issue 6329, Page(s) 1081–1084

    Abstract: Nucleosomes play important structural and regulatory roles by tightly wrapping the DNA that constitutes the metazoan genome. The Polycomb group (PcG) proteins modulate nucleosomes to maintain repression of key developmental genes, ... ...

    Abstract Nucleosomes play important structural and regulatory roles by tightly wrapping the DNA that constitutes the metazoan genome. The Polycomb group (PcG) proteins modulate nucleosomes to maintain repression of key developmental genes, including
    MeSH term(s) Animals ; Body Patterning/genetics ; Cell Line ; Gene Expression Regulation, Developmental ; Gene Silencing ; Genes, Homeobox ; Mice ; Mice, Mutant Strains ; Mutation ; Nucleosomes/genetics ; Nucleosomes/metabolism ; Polycomb Repressive Complex 1/genetics ; Polycomb Repressive Complex 1/metabolism ; Protein Binding ; Skeleton/growth & development
    Chemical Substances Cbx2 protein, mouse ; Nucleosomes ; Polycomb Repressive Complex 1 (EC 2.3.2.27)
    Language English
    Publishing date 2017-03-09
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.aah5403
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Independent regulation of vertebral number and vertebral identity by microRNA-196 paralogs.

    Wong, Siew Fen Lisa / Agarwal, Vikram / Mansfield, Jennifer H / Denans, Nicolas / Schwartz, Matthew G / Prosser, Haydn M / Pourquié, Olivier / Bartel, David P / Tabin, Clifford J / McGlinn, Edwina

    Proceedings of the National Academy of Sciences of the United States of America

    2015  Volume 112, Issue 35, Page(s) E4884–93

    Abstract: The Hox genes play a central role in patterning the embryonic anterior-to-posterior axis. An important function of Hox activity in vertebrates is the specification of different vertebral morphologies, with an additional role in axis elongation emerging. ... ...

    Abstract The Hox genes play a central role in patterning the embryonic anterior-to-posterior axis. An important function of Hox activity in vertebrates is the specification of different vertebral morphologies, with an additional role in axis elongation emerging. The miR-196 family of microRNAs (miRNAs) are predicted to extensively target Hox 3' UTRs, although the full extent to which miR-196 regulates Hox expression dynamics and influences mammalian development remains to be elucidated. Here we used an extensive allelic series of mouse knockouts to show that the miR-196 family of miRNAs is essential both for properly patterning vertebral identity at different axial levels and for modulating the total number of vertebrae. All three miR-196 paralogs, 196a1, 196a2, and 196b, act redundantly to pattern the midthoracic region, whereas 196a2 and 196b have an additive role in controlling the number of rib-bearing vertebra and positioning of the sacrum. Independent of this, 196a1, 196a2, and 196b act redundantly to constrain total vertebral number. Loss of miR-196 leads to a collective up-regulation of numerous trunk Hox target genes with a concomitant delay in activation of caudal Hox genes, which are proposed to signal the end of axis extension. Additionally, we identified altered molecular signatures associated with the Wnt, Fgf, and Notch/segmentation pathways and demonstrate that miR-196 has the potential to regulate Wnt activity by multiple mechanisms. By feeding into, and thereby integrating, multiple genetic networks controlling vertebral number and identity, miR-196 is a critical player defining axial formulae.
    MeSH term(s) Animals ; Gene Deletion ; Mice ; Mice, Knockout ; MicroRNAs/genetics ; MicroRNAs/physiology ; Spine/anatomy & histology ; Transcription, Genetic ; Transcriptome
    Chemical Substances MIRN196 microRNA, mouse ; MicroRNAs
    Language English
    Publishing date 2015-09-01
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1512655112
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Gremlin 1 identifies a skeletal stem cell with bone, cartilage, and reticular stromal potential.

    Worthley, Daniel L / Churchill, Michael / Compton, Jocelyn T / Tailor, Yagnesh / Rao, Meenakshi / Si, Yiling / Levin, Daniel / Schwartz, Matthew G / Uygur, Aysu / Hayakawa, Yoku / Gross, Stefanie / Renz, Bernhard W / Setlik, Wanda / Martinez, Ashley N / Chen, Xiaowei / Nizami, Saqib / Lee, Heon Goo / Kang, H Paco / Caldwell, Jon-Michael /
    Asfaha, Samuel / Westphalen, C Benedikt / Graham, Trevor / Jin, Guangchun / Nagar, Karan / Wang, Hongshan / Kheirbek, Mazen A / Kolhe, Alka / Carpenter, Jared / Glaire, Mark / Nair, Abhinav / Renders, Simon / Manieri, Nicholas / Muthupalani, Sureshkumar / Fox, James G / Reichert, Maximilian / Giraud, Andrew S / Schwabe, Robert F / Pradere, Jean-Phillipe / Walton, Katherine / Prakash, Ajay / Gumucio, Deborah / Rustgi, Anil K / Stappenbeck, Thaddeus S / Friedman, Richard A / Gershon, Michael D / Sims, Peter / Grikscheit, Tracy / Lee, Francis Y / Karsenty, Gerard / Mukherjee, Siddhartha / Wang, Timothy C

    Cell

    2015  Volume 160, Issue 1-2, Page(s) 269–284

    Abstract: The stem cells that maintain and repair the postnatal skeleton remain undefined. One model suggests that perisinusoidal mesenchymal stem cells (MSCs) give rise to osteoblasts, chondrocytes, marrow stromal cells, and adipocytes, although the existence of ... ...

    Abstract The stem cells that maintain and repair the postnatal skeleton remain undefined. One model suggests that perisinusoidal mesenchymal stem cells (MSCs) give rise to osteoblasts, chondrocytes, marrow stromal cells, and adipocytes, although the existence of these cells has not been proven through fate-mapping experiments. We demonstrate here that expression of the bone morphogenetic protein (BMP) antagonist gremlin 1 defines a population of osteochondroreticular (OCR) stem cells in the bone marrow. OCR stem cells self-renew and generate osteoblasts, chondrocytes, and reticular marrow stromal cells, but not adipocytes. OCR stem cells are concentrated within the metaphysis of long bones not in the perisinusoidal space and are needed for bone development, bone remodeling, and fracture repair. Grem1 expression also identifies intestinal reticular stem cells (iRSCs) that are cells of origin for the periepithelial intestinal mesenchymal sheath. Grem1 expression identifies distinct connective tissue stem cells in both the bone (OCR stem cells) and the intestine (iRSCs).
    MeSH term(s) Animals ; Bone and Bones/cytology ; Cartilage/metabolism ; Intercellular Signaling Peptides and Proteins/metabolism ; Intestine, Small/cytology ; Intestine, Small/metabolism ; Mesenchymal Stem Cells/cytology ; Mesenchymal Stem Cells/metabolism ; Mice ; Mice, Inbred C57BL
    Chemical Substances Grem1 protein, mouse ; Intercellular Signaling Peptides and Proteins
    Language English
    Publishing date 2015-02-15
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2014.11.042
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Third Report on Chicken Genes and Chromosomes 2015.

    Schmid, Michael / Smith, Jacqueline / Burt, David W / Aken, Bronwen L / Antin, Parker B / Archibald, Alan L / Ashwell, Chris / Blackshear, Perry J / Boschiero, Clarissa / Brown, C Titus / Burgess, Shane C / Cheng, Hans H / Chow, William / Coble, Derrick J / Cooksey, Amanda / Crooijmans, Richard P M A / Damas, Joana / Davis, Richard V N / de Koning, Dirk-Jan /
    Delany, Mary E / Derrien, Thomas / Desta, Takele T / Dunn, Ian C / Dunn, Matthew / Ellegren, Hans / Eöry, Lél / Erb, Ionas / Farré, Marta / Fasold, Mario / Fleming, Damarius / Flicek, Paul / Fowler, Katie E / Frésard, Laure / Froman, David P / Garceau, Valerie / Gardner, Paul P / Gheyas, Almas A / Griffin, Darren K / Groenen, Martien A M / Haaf, Thomas / Hanotte, Olivier / Hart, Alan / Häsler, Julien / Hedges, S Blair / Hertel, Jana / Howe, Kerstin / Hubbard, Allen / Hume, David A / Kaiser, Pete / Kedra, Darek / Kemp, Stephen J / Klopp, Christophe / Kniel, Kalmia E / Kuo, Richard / Lagarrigue, Sandrine / Lamont, Susan J / Larkin, Denis M / Lawal, Raman A / Markland, Sarah M / McCarthy, Fiona / McCormack, Heather A / McPherson, Marla C / Motegi, Akira / Muljo, Stefan A / Münsterberg, Andrea / Nag, Rishi / Nanda, Indrajit / Neuberger, Michael / Nitsche, Anne / Notredame, Cedric / Noyes, Harry / O'Connor, Rebecca / O'Hare, Elizabeth A / Oler, Andrew J / Ommeh, Sheila C / Pais, Helio / Persia, Michael / Pitel, Frédérique / Preeyanon, Likit / Prieto Barja, Pablo / Pritchett, Elizabeth M / Rhoads, Douglas D / Robinson, Charmaine M / Romanov, Michael N / Rothschild, Max / Roux, Pierre-François / Schmidt, Carl J / Schneider, Alisa-Sophia / Schwartz, Matthew G / Searle, Steve M / Skinner, Michael A / Smith, Craig A / Stadler, Peter F / Steeves, Tammy E / Steinlein, Claus / Sun, Liang / Takata, Minoru / Ulitsky, Igor / Wang, Qing / Wang, Ying / Warren, Wesley C / Wood, Jonathan M D / Wragg, David / Zhou, Huaijun

    Cytogenetic and genome research

    2015  Volume 145, Issue 2, Page(s) 78–179

    MeSH term(s) Animals ; Chickens/classification ; Chickens/genetics ; Chickens/physiology ; Chromosome Mapping ; Chromosomes/genetics ; DNA Methylation ; Evolution, Molecular ; Female ; Gene Expression Profiling ; Genetic Variation ; Genomics/methods ; In Situ Hybridization, Fluorescence/methods ; Male ; Molecular Sequence Annotation ; Phylogeny
    Language English
    Publishing date 2015-07-14
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2087824-2
    ISSN 1424-859X ; 1424-8581
    ISSN (online) 1424-859X
    ISSN 1424-8581
    DOI 10.1159/000430927
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Third Report on Chicken Genes and Chromosomes 2015

    Schmid, Michael / Smith, Jacqueline / Burt, David W. / Aken, Bronwen L. / Antin, Parker B. / Archibald, Alan L. / Ashwell, Chris / Blackshear, Perry J. / Boschiero, Clarissa / Brown, C. Titus / Burgess, Shane C. / Cheng, Hans H. / Chow, William / Coble, Derrick J. / Cooksey, Amanda / Crooijmans, Richard P.M.A. / Damas, Joana / Davis, Richard V.N. / de Koning, Dirk-Jan /
    Delany, Mary E. / Derrien, Thomas / Desta, Takele T. / Dunn, Ian C. / Dunn, Matthew / Ellegren, Hans / Eöry, Lél / Erb, Ionas / Farré, Marta / Fasold, Mario / Fleming, Damarius / Flicek, Paul / Fowler, Katie E. / Frésard, Laure / Froman, David P. / Garceau, Valerie / Gardner, Paul P. / Gheyas, Almas A. / Griffin, Darren K. / Groenen, Martien A.M. / Haaf, Thomas / Hanotte, Olivier / Hart, Alan / Häsler, Julien / Hedges, S. Blair / Hertel, Jana / Howe, Kerstin / Hubbard, Allen / Hume, David A. / Kaiser, Pete / Kedra, Darek / Kemp, Stephen J. / Klopp, Christophe / Kniel, Kalmia E. / Kuo, Richard / Lagarrigue, Sandrine / Lamont, Susan J. / Larkin, Denis M. / Lawal, Raman A. / Markland, Sarah M. / McCarthy, Fiona / McCormack, Heather A. / McPherson, Marla C. / Motegi, Akira / Muljo, Stefan A. / Münsterberg, Andrea / Nag, Rishi / Nanda, Indrajit / Neuberger, Michael / Nitsche, Anne / Notredame, Cedric / Noyes, Harry / O'Connor, Rebecca / O'Hare, Elizabeth A. / Oler, Andrew J. / Ommeh, Sheila C. / Pais, Helio / Persia, Michael / Pitel, Frédérique / Preeyanon, Likit / Prieto Barja, Pablo / Pritchett, Elizabeth M. / Rhoads, Douglas D. / Robinson, Charmaine M. / Romanov, Michael N. / Rothschild, Max / Roux, Pierre-François / Schmidt, Carl J. / Schneider, Alisa-Sophia / Schwartz, Matthew G. / Searle, Steve M. / Skinner, Michael A. / Smith, Craig A. / Stadler, Peter F. / Steeves, Tammy E. / Steinlein, Claus / Sun, Liang / Takata, Minoru / Ulitsky, Igor / Wang, Qing / Wang, Ying / Warren, Wesley C. / Wood, Jonathan M.D. / Wragg, David / Zhou, Huaijun

    Cytogenetic and Genome Research

    2015  Volume 145, Issue 2, Page(s) 78–179

    Institution Department of Human Genetics, University of Würzburg, Würzburg, and Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, University of Leipzig, Leipzig, Germany Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, and Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh European Bioinformatics Institute, EMBL, and Wellcome Trust Sanger Institute, Hinxton Medical Research Council Laboratory of Molecular Biology, Cambridge Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, and Section of Virology, Department of Medicine, Imperial College London, London School of Life Sciences, University of Nottingham, Nottingham School of Human and Life Sciences, Canterbury Christ Church University, and School of Biosciences, University of Kent, Canterbury Biological Services, Royal Hallamshire Hospital, University of Sheffield, Sheffield Institute of Integrative Biology, University of Liverpool, Liverpool School of Biological Sciences, University of East Anglia, Norwich, and Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, and Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden Institut de Génétique et Développement de Rennes, Université de Rennes1, and Equipe Génétique et Génomique, PEGASE, INRA, Rennes GenPhySE, INRA, and Plateforme Bioinformatique Toulouse Midi-Pyrénées, INRA, Biométrie et Intelligence Artificielle, Castanet-Tolosan, France Comparative Bioinformatics Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona, Spain Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel Department of Cellular and Molecular Medicine College of Agriculture and Life Sciences, and Department of Veterinary Science and Microbiology, University of Arizona, Tucson, Ariz Department of Poultry Science, Raleigh, N.C Department of Biochemistry, Duke University School of Medicine, NIEHS, Durham, N.C Microbiology and Molecular Genetics, Michigan State University Computer Science and Engineering, Michigan State University, and Avian Disease and Oncology Laboratory, USDA, ARS, East Lansing, Mich Department of Biology, University of Delaware, and Department of Animal and Food Sciences, University of Delaware, Newark, Del Department of Animal Science, University of California, Davis, Calif Division of Science and Environmental Policy, California State University Monterey Bay, Seaside, Calif Department of Animal and Rangeland Sciences, Oregon State University, Corvallis, Oreg Center for Biodiversity, Temple University, Philadelphia, Pa Department of Animal Science, Iowa State University, Ames, Iowa National Institute of Allergy and Infectious Diseases, NIH, and Medical Science and Computing Inc., High-Throughput Sequencing Bioinformatics Specialist, Computational Biology Section, Bethesda, Md Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, Md Virginia Tech University, Department of Animal and Poultry Sciences, Blacksburg, Va Department of Biological Sciences, Science and Engineering, University of Arkansas, Fayetteville, Ark Department of Genetics, Harvard Medical School, Boston, Mass., and The Genome Institute, Washington University School of Medicine, St. Louis, Mo., USA Departamento de Zootecnia, University of São Paulo, Piracicaba, Brazil Animal Biotechnology Group, Institute of Biotechnology Research, Jomo-Kenyatta University of Agriculture and Technology, Nairobi, Kenya Department of Anatomy and Developmental Biology, Monash University, Clayton, Vic., Australia School of Biological Sciences, University of Canterbury, and Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand Department of Radiation Genetics, Graduate School of Medicine, Kyoto University Yoshida Konoe, and Department of Late Effects Studies, Radiation Biology Center, Kyoto University Yoshida Konoe, Kyoto, Japan
    Language English
    Publishing date 2015-07-14
    Publisher S. Karger AG
    Publishing place Basel, Switzerland
    Document type Article
    Note Report
    ZDB-ID 2087824-2
    ISBN 978-3-318-05568-9 ; 978-3-318-05569-6 ; 3-318-05568-9 ; 3-318-05569-7
    ISSN 1424-859X ; 1424-8581
    ISSN (online) 1424-859X
    ISSN 1424-8581
    DOI 10.1159/000430927
    Database Karger publisher's database

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