51
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Zhang M, Skirkanich J, Lampson MA, Klein PS. Cell Cycle Remodeling and Zygotic Gene Activation at the Midblastula Transition. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 953:441-487. [DOI: 10.1007/978-3-319-46095-6_9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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52
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Svoboda P, Fulka H, Malik R. Clearance of Parental Products. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 953:489-535. [DOI: 10.1007/978-3-319-46095-6_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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53
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Gaiti F, Calcino AD, Tanurdžić M, Degnan BM. Origin and evolution of the metazoan non-coding regulatory genome. Dev Biol 2016; 427:193-202. [PMID: 27880868 DOI: 10.1016/j.ydbio.2016.11.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 11/14/2016] [Accepted: 11/18/2016] [Indexed: 02/09/2023]
Abstract
Animals rely on genomic regulatory systems to direct the dynamic spatiotemporal and cell-type specific gene expression that is essential for the development and maintenance of a multicellular lifestyle. Although it is widely appreciated that these systems ultimately evolved from genomic regulatory mechanisms present in single-celled stem metazoans, it remains unclear how this occurred. Here, we focus on the contribution of the non-coding portion of the genome to the evolution of animal gene regulation, specifically on recent insights from non-bilaterian metazoan lineages, and unicellular and colonial holozoan sister taxa. High-throughput next-generation sequencing, largely in bilaterian model species, has led to the discovery of tens of thousands of non-coding RNA genes (ncRNAs), including short, long and circular forms, and uncovered the central roles they play in development. Based on the analysis of non-bilaterian metazoan, unicellular holozoan and fungal genomes, the evolution of some ncRNAs, such as Piwi-interacting RNAs, correlates with the emergence of metazoan multicellularity, while others, including microRNAs, long non-coding RNAs and circular RNAs, appear to be more ancient. Analysis of non-coding regulatory DNA and histone post-translational modifications have revealed that some cis-regulatory mechanisms, such as those associated with proximal promoters, are present in non-animal holozoans, while others appear to be metazoan innovations, most notably distal enhancers. In contrast, the cohesin-CTCF system for regulating higher-order chromatin structure and enhancer-promoter long-range interactions appears to be restricted to bilaterians. Taken together, most bilaterian non-coding regulatory mechanisms appear to have originated before the divergence of crown metazoans. However, differential expansion of non-coding RNA and cis-regulatory DNA repertoires in bilaterians may account for their increased regulatory and morphological complexity relative to non-bilaterians.
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Affiliation(s)
- Federico Gaiti
- School of Biological Sciences, University of Queensland, Brisbane, Australia.
| | - Andrew D Calcino
- Department of Integrative Zoology, University of Vienna, Vienna, Austria.
| | - Miloš Tanurdžić
- School of Biological Sciences, University of Queensland, Brisbane, Australia.
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, Australia.
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54
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Suzuki KIT, Suzuki M, Shigeta M, Fortriede JD, Takahashi S, Mawaribuchi S, Yamamoto T, Taira M, Fukui A. Clustered Xenopus keratin genes: A genomic, transcriptomic, and proteomic analysis. Dev Biol 2016; 426:384-392. [PMID: 27842699 DOI: 10.1016/j.ydbio.2016.10.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 10/21/2016] [Accepted: 10/26/2016] [Indexed: 01/21/2023]
Abstract
Keratin genes belong to the intermediate filament superfamily and their expression is altered following morphological and physiological changes in vertebrate epithelial cells. Keratin genes are divided into two groups, type I and II, and are clustered on vertebrate genomes, including those of Xenopus species. Various keratin genes have been identified and characterized by their unique expression patterns throughout ontogeny in Xenopus laevis; however, compilation of previously reported and newly identified keratin genes in two Xenopus species is required for our further understanding of keratin gene evolution, not only in amphibians but also in all terrestrial vertebrates. In this study, 120 putative type I and II keratin genes in total were identified based on the genome data from two Xenopus species. We revealed that most of these genes are highly clustered on two homeologous chromosomes, XLA9_10 and XLA2 in X. laevis, and XTR10 and XTR2 in X. tropicalis, which are orthologous to those of human, showing conserved synteny among tetrapods. RNA-Seq data from various embryonic stages and adult tissues highlighted the unique expression profiles of orthologous and homeologous keratin genes in developmental stage- and tissue-specific manners. Moreover, we identified dozens of epidermal keratin proteins from the whole embryo, larval skin, tail, and adult skin using shotgun proteomics. In light of our results, we discuss the radiation, diversification, and unique expression of the clustered keratin genes, which are closely related to epidermal development and terrestrial adaptation during amphibian evolution, including Xenopus speciation.
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Affiliation(s)
- Ken-Ichi T Suzuki
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
| | - Miyuki Suzuki
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Mitsuki Shigeta
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Joshua D Fortriede
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Shuji Takahashi
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Shuuji Mawaribuchi
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Takashi Yamamoto
- Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akimasa Fukui
- Laboratory of Tissue and Polymer Sciences, Faculty of Advanced Life Science, Hokkaido University, N10W8, Sapporo 060-0810, Japan.
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55
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Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C, Kitzman J, Nakayama T, Izutsu Y, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJC, Fujiyama A, Harland RM, Taira M, Rokhsar DS. Genome evolution in the allotetraploid frog Xenopus laevis. Nature 2016; 538:336-343. [PMID: 27762356 PMCID: PMC5313049 DOI: 10.1038/nature19840] [Citation(s) in RCA: 649] [Impact Index Per Article: 81.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 09/09/2016] [Indexed: 02/07/2023]
Abstract
To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We demonstrate the allotetraploid origin of X. laevis by partitioning its genome into two homeologous subgenomes, marked by distinct families of “fossil” transposable elements. Based on the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged ~34 million years ago (Mya) and combined to form an allotetraploid ~17–18 Mya. 56% of all genes are retained in two homeologous copies. Protein function, gene expression, and the amount of flanking conserved sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.
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Affiliation(s)
- Adam M Session
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA.,US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Yoshinobu Uno
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Taejoon Kwon
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, USA.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea
| | - Jarrod A Chapman
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Atsushi Toyoda
- Center for Information Biology, and Advanced Genomics Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Shuji Takahashi
- Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Akimasa Fukui
- Laboratory of Tissue and Polymer Sciences, Faculty of Advanced Life Science, Hokkaido University, N10W8, Kita-ku, Sapporo 060-0810, Japan
| | - Akira Hikosaka
- Division of Human Sciences, Graduate School of Integrated Arts and Sciences, Hiroshima University, 1-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8521, Japan
| | - Atsushi Suzuki
- Amphibian Research Center, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Mariko Kondo
- Misaki Marine Biological Station (MMBS), Graduate School of Science, The University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa 238-0225, Japan
| | - Simon J van Heeringen
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, 259 RIMLS, M850/2.97, Geert Grooteplein 28, Nijmegen 6525 GA, the Netherlands
| | - Ian Quigley
- Salk Institute, Molecular Neurobiology Laboratory, La Jolla, San Diego, California 92037, USA
| | - Sven Heinz
- Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, San Diego, California 92037, USA
| | - Hajime Ogino
- Department of Animal Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Haruki Ochi
- Institute for Promotion of Medical Science Research, Yamagata University Faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata, Yamagata 990-9585, Japan
| | - Uffe Hellsten
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jessica B Lyons
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA
| | - Oleg Simakov
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | | | | | - Yoko Kuroki
- Department of Genome Medicine, National Research Institute for Child Health and Development, NCCHD, 2-10-1, Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Toshiaki Tanaka
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Tatsuo Michiue
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Minoru Watanabe
- Institute of Institution of Liberal Arts and Fundamental Education, Tokushima University, 1-1 Minamijosanjima-cho, Tokushima 770-8502, Japan
| | - Ozren Bogdanovic
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Ryan Lister
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Georgios Georgiou
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, 259 RIMLS, M850/2.97, Geert Grooteplein 28, Nijmegen 6525 GA, the Netherlands
| | - Sarita S Paranjpe
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, 259 RIMLS, M850/2.97, Geert Grooteplein 28, Nijmegen 6525 GA, the Netherlands
| | - Ila van Kruijsbergen
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, 259 RIMLS, M850/2.97, Geert Grooteplein 28, Nijmegen 6525 GA, the Netherlands
| | - Shengquiang Shu
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Joseph Carlson
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Tsutomu Kinoshita
- Department of Life Science, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland, 655 W Baltimore St, Baltimore, Maryland 21201, USA
| | - Shuuji Mawaribuchi
- Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane Minato-ku, Tokyo 108-8641, Japan
| | - Jerry Jenkins
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.,HudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA
| | - Jane Grimwood
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.,HudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.,HudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA
| | - Therese Mitros
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA
| | - Sahar V Mozaffari
- Department of Human Genetics, University of Chicago, 920 E. 58th St, CLSC 431F, Chicago, Illinois 60637, USA
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8568, Japan
| | - Yoshikazu Haramoto
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Takamasa S Yamamoto
- Division of Morphogenesis, Department of Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Chiyo Takagi
- Division of Morphogenesis, Department of Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Rebecca Heald
- University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition #3200, Berkeley California 94720-3200, USA
| | - Kelly Miller
- University of California, Berkeley, Department of Molecular and Cell Biology, Life Sciences Addition #3200, Berkeley California 94720-3200, USA
| | | | - Jacob Kitzman
- Department of Genome Sciences, University of Washington, Foege Building S-250, Box 355065, 3720 15th Ave NE, Seattle Washington 98195-5065, USA
| | - Takuya Nakayama
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Yumi Izutsu
- Department of Biology, Faculty of Science, Niigata University, 8050, Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan
| | - Jacques Robert
- Department of Microbiology &Immunology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Joshua Fortriede
- Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, Ohio 45229-3039, USA
| | - Kevin Burns
- Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, Ohio 45229-3039, USA
| | - Vaneet Lotay
- Department of Biological Sciences, University of Calgary, Alberta T2N 1N4, Canada
| | - Kamran Karimi
- Department of Biological Sciences, University of Calgary, Alberta T2N 1N4, Canada
| | - Yuuri Yasuoka
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Darwin S Dichmann
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland, 655 W Baltimore St, Baltimore, Maryland 21201, USA
| | - Douglas W Houston
- The University of Iowa, Department of Biology, 257 Biology Building, Iowa City, Iowa 52242-1324, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Foege Building S-250, Box 355065, 3720 15th Ave NE, Seattle Washington 98195-5065, USA
| | - Louis DuPasquier
- Department of Zoology and Evolutionary Biology, University of Basel, Basel CH-4051, Switzerland
| | - Peter D Vize
- Department of Biological Sciences, University of Calgary, Alberta T2N 1N4, Canada
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, Ohio 45229-3039, USA
| | - Michihiko Ito
- Department of Biological Sciences, School of Science, Kitasato University, 1-15-1 Minamiku, Sagamihara, Kanagawa 252-0373, Japan
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - John B Wallingford
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Yuzuru Ito
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Makoto Asashima
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Naoto Ueno
- Division of Morphogenesis, Department of Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan.,Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Yoichi Matsuda
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Gert Jan C Veenstra
- Radboud University, Faculty of Science, Department of Molecular Developmental Biology, 259 RIMLS, M850/2.97, Geert Grooteplein 28, Nijmegen 6525 GA, the Netherlands
| | - Asao Fujiyama
- Center for Information Biology, and Advanced Genomics Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.,Principles of Informatics, National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan.,Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizoka 411-8540, Japan
| | - Richard M Harland
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Daniel S Rokhsar
- University of California, Berkeley, Department of Molecular and Cell Biology and Center for Integrative Genomics, Life Sciences Addition #3200, Berkeley, California 94720-3200, USA.,US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.,Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
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56
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Khomtchouk BB, Hennessy JR, Wahlestedt C. MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps. BMC Bioinformatics 2016; 17:390. [PMID: 27659774 PMCID: PMC5034416 DOI: 10.1186/s12859-016-1260-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 09/14/2016] [Indexed: 11/10/2022] Open
Abstract
Background Heatmaps are an indispensible visualization tool for examining large-scale snapshots of genomic activity across various types of next-generation sequencing datasets. However, traditional heatmap software do not typically offer multi-scale insight across multiple layers of genomic analysis (e.g., differential expression analysis, principal component analysis, gene ontology analysis, and network analysis) or multiple types of next-generation sequencing datasets (e.g., ChIP-seq and RNA-seq). As such, it is natural to want to interact with a heatmap’s contents using an extensive set of integrated analysis tools applicable to a broad array of genomic data types. Results We propose a user-friendly ChIP-seq and RNA-seq software suite for the interactive visualization and analysis of genomic data, including integrated features to support differential expression analysis, interactive heatmap production, principal component analysis, gene ontology analysis, and dynamic network analysis. Conclusions MicroScope is hosted online as an R Shiny web application based on the D3 JavaScript library: http://microscopebioinformatics.org/. The methods are implemented in R, and are available as part of the MicroScope project at: https://github.com/Bohdan-Khomtchouk/Microscope.
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Affiliation(s)
- Bohdan B Khomtchouk
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1120 NW 14th ST, Miami, 33136, FL, USA.
| | - James R Hennessy
- Department of Mathematics, University of Miami, 1365 Memorial Drive, Coral Gables, 33146, FL, USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1120 NW 14th ST, Miami, 33136, FL, USA
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57
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A chemical-inducible CRISPR–Cas9 system for rapid control of genome editing. Nat Chem Biol 2016; 12:980-987. [DOI: 10.1038/nchembio.2179] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 07/13/2016] [Indexed: 01/06/2023]
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58
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Characterization of a Single Genomic Locus Encoding the Clustered Protocadherin Receptor Diversity in Xenopus tropicalis. G3-GENES GENOMES GENETICS 2016; 6:2309-18. [PMID: 27261006 PMCID: PMC4978886 DOI: 10.1534/g3.116.027995] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Clustered protocadherins (cPcdhs) constitute the largest subgroup of the cadherin superfamily, and in mammals are grouped into clusters of α-, β-, and γ-types. Tens of tandemly arranged paralogous Pcdh genes of the Pcdh clusters generate a substantial diversity of receptor isoforms. cPcdhs are known to have important roles in neuronal development, and genetic alterations of cPcdhs have been found to be associated with several neurological diseases. Here, we present a first characterization of cPcdhs in Xenopus tropicalis. We determined and annotated all cPcdh isoforms, revealing that they are present in a single chromosomal locus. We validated a total of 96 isoforms, which we show are organized in three distinct clusters. The X. tropicalis cPcdh locus is composed of one α- and two distinct γ-Pcdh clusters (pcdh-γ1 and pcdh-γ2). Bioinformatics analyses assisted by genomic BAC clone sequencing showed that the X. tropicalis α- and γ-Pcdhs are conserved at the cluster level, but, unlike mammals, X. tropicalis does not contain a β-Pcdh cluster. In contrast, the number of γ-Pcdh isoforms has expanded, possibly due to lineage-specific gene duplications. Interestingly, the number of X. tropicalis α-Pcdhs is identical between X. tropicalis and mouse. Moreover, we find highly conserved as well as novel promoter elements potentially involved in regulating the cluster-specific expression of cPcdh isoforms. This study provides important information for the understanding of the evolutionary history of cPcdh genes and future mechanistic studies. It provides an annotated X. tropicalis cPcdh genomic map and a first molecular characterization essential for functional and comparative studies.
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59
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Wang J, Wang Y, Gu W, Ni B, Sun H, Yu T, Gu W, Chen L, Shao Y. Comparative Transcriptome Analysis Reveals Substantial Tissue Specificity in Human Aortic Valve. Evol Bioinform Online 2016; 12:175-84. [PMID: 27493474 PMCID: PMC4968975 DOI: 10.4137/ebo.s37594] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/01/2016] [Accepted: 02/07/2016] [Indexed: 11/21/2022] Open
Abstract
RNA sequencing (RNA-seq) has revolutionary roles in transcriptome identification and quantification of different types of tissues and cells in many organisms. Although numerous RNA-seq data derived from many types of human tissues and cell lines, little is known on the transcriptome repertoire of human aortic valve. In this study, we sequenced the total RNA prepared from two calcified human aortic valves and reported the whole transcriptome of human aortic valve. Integrating RNA-seq data of 13 human tissues from Human Body Map 2 Project, we constructed a transcriptome repertoire of human tissues, including 19,505 protein-coding genes and 4,948 long intergenic noncoding RNAs (lincRNAs). Among them, 263 lincRNAs were identified as novel noncoding transcripts in our data. By comparing transcriptome data among different human tissues, we observed substantial tissue specificity of RNA transcripts, both protein-coding genes and lincRNAs, in human aortic valve. Further analysis revealed that aortic valve-specific lincRNAs were more likely to be recently derived from repetitive elements in the primate lineage, but were less likely to be conserved at the nucleotide level. Expression profiling analysis showed significant lower expression levels of aortic valve-specific protein-coding genes and lincRNA genes, when compared with genes that were universally expressed in various tissues. Isoform-level expression analysis also showed that a majority of mRNA genes had a major isoform expressed in the human aortic valve. To our knowledge, this is the first comparative transcriptome analysis between human aortic valve and other human tissues. Our results are helpful to understand the transcriptome diversity of human tissues and the underlying mechanisms that drive tissue specificity of protein-coding genes and lincRNAs in human aortic valve.
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Affiliation(s)
- Jun Wang
- Department of Thoracic and Cardiovascular Surgery, Jiangsu Province People's Hospital and the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Ying Wang
- Nanjing Decode Genomics Biotechnology Co., Ltd., Nanjing, People's Republic of China
| | - Weidong Gu
- Department of Thoracic and Cardiovascular Surgery, Jiangsu Province People's Hospital and the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Buqing Ni
- Department of Thoracic and Cardiovascular Surgery, Jiangsu Province People's Hospital and the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Haoliang Sun
- Department of Thoracic and Cardiovascular Surgery, Jiangsu Province People's Hospital and the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Tong Yu
- Nanjing Decode Genomics Biotechnology Co., Ltd., Nanjing, People's Republic of China
| | - Wanjun Gu
- Research Center for Learning Sciences, Southeast University, Nanjing, People's Republic of China
| | - Liang Chen
- Department of Thoracic and Cardiovascular Surgery, Jiangsu Province People's Hospital and the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Yongfeng Shao
- Department of Thoracic and Cardiovascular Surgery, Jiangsu Province People's Hospital and the First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
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Blitz IL, Paraiso KD, Patrushev I, Chiu WTY, Cho KWY, Gilchrist MJ. A catalog of Xenopus tropicalis transcription factors and their regional expression in the early gastrula stage embryo. Dev Biol 2016; 426:409-417. [PMID: 27475627 PMCID: PMC5596316 DOI: 10.1016/j.ydbio.2016.07.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/01/2016] [Accepted: 07/01/2016] [Indexed: 12/30/2022]
Abstract
Gene regulatory networks (GRNs) involve highly combinatorial interactions between transcription factors and short sequence motifs in cis-regulatory modules of target genes to control cellular phenotypes. The GRNs specifying most cell types are largely unknown and are the subject of wide interest. A catalog of transcription factors is a valuable tool toward obtaining a deeper understanding of the role of these critical effectors in any biological setting. Here we present a comprehensive catalog of the transcription factors for the diploid frog Xenopus tropicalis. We identify 1235 genes encoding DNA-binding transcription factors, comparable to the numbers found in typical mammalian species. In detail, the repertoire of X. tropicalis transcription factor genes is nearly identical to human and mouse, with the exception of zinc finger family members, and a small number of species/lineage-specific gene duplications and losses relative to the mammalian repertoires. We applied this resource to the identification of transcription factors differentially expressed in the early gastrula stage embryo. We find transcription factor enrichment in Spemann's organizer, the ventral mesoderm, ectoderm and endoderm, and report 218 TFs that show regionalized expression patterns at this stage. Many of these have not been previously reported as expressed in the early embryo, suggesting thus far unappreciated roles for many transcription factors in the GRNs regulating early development. We expect our transcription factor catalog will facilitate myriad studies using Xenopus as a model system to understand basic biology and human disease.
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Affiliation(s)
- Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States.
| | - Kitt D Paraiso
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States
| | - Ilya Patrushev
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway Mill Hill, London NW7 1AA, UK
| | - William T Y Chiu
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States.
| | - Michael J Gilchrist
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway Mill Hill, London NW7 1AA, UK.
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Jiang P, Nelson JD, Leng N, Collins M, Swanson S, Dewey CN, Thomson JA, Stewart R. Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability. Dev Biol 2016; 426:143-154. [PMID: 27475628 DOI: 10.1016/j.ydbio.2016.05.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 05/20/2016] [Accepted: 05/21/2016] [Indexed: 12/14/2022]
Abstract
The axolotl (Ambystoma mexicanum) has long been the subject of biological research, primarily owing to its outstanding regenerative capabilities. However, the gene expression programs governing its embryonic development are particularly underexplored, especially when compared to other amphibian model species. Therefore, we performed whole transcriptome polyA+ RNA sequencing experiments on 17 stages of embryonic development. As the axolotl genome is unsequenced and its gene annotation is incomplete, we built de novo transcriptome assemblies for each stage and garnered functional annotation by comparing expressed contigs with known genes in other organisms. In evaluating the number of differentially expressed genes over time, we identify three waves of substantial transcriptome upheaval each followed by a period of relative transcriptome stability. The first wave of upheaval is between the one and two cell stage. We show that the number of differentially expressed genes per unit time is higher between the one and two cell stage than it is across the mid-blastula transition (MBT), the period of zygotic genome activation. We use total RNA sequencing to demonstrate that the vast majority of genes with increasing polyA+ signal between the one and two cell stage result from polyadenylation rather than de novo transcription. The first stable phase begins after the two cell stage and continues until the mid-blastula transition, corresponding with the pre-MBT phase of transcriptional quiescence in amphibian development. Following this is a peak of differential gene expression corresponding with the activation of the zygotic genome and a phase of transcriptomic stability from stages 9-11. We observe a third wave of transcriptomic change between stages 11 and 14, followed by a final stable period. The last two stable phases have not been documented in amphibians previously and correspond to times of major morphogenic change in the axolotl embryo: gastrulation and neurulation. These results yield new insights into global gene expression during early stages of amphibian embryogenesis and will help to further develop the axolotl as a model species for developmental and regenerative biology.
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Affiliation(s)
- Peng Jiang
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States
| | - Jeffrey D Nelson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States
| | - Ning Leng
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States
| | - Michael Collins
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States
| | - Scott Swanson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States
| | - Colin N Dewey
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, United States
| | - James A Thomson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States; Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI, United States; Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, United States
| | - Ron Stewart
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States.
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Yang A, Zhou Z, Pan Y, Jiang J, Dong Y, Guan X, Sun H, Gao S, Chen Z. RNA sequencing analysis to capture the transcriptome landscape during skin ulceration syndrome progression in sea cucumber Apostichopus japonicus. BMC Genomics 2016; 17:459. [PMID: 27296384 PMCID: PMC4906609 DOI: 10.1186/s12864-016-2810-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 06/02/2016] [Indexed: 12/14/2022] Open
Abstract
Background Sea cucumber Apostichopus japonicus is an important economic species in China, which is affected by various diseases; skin ulceration syndrome (SUS) is the most serious. In this study, we characterized the transcriptomes in A. japonicus challenged with Vibrio splendidus to elucidate the changes in gene expression throughout the three stages of SUS progression. Results RNA sequencing of 21 cDNA libraries from various tissues and developmental stages of SUS-affected A. japonicus yielded 553 million raw reads, of which 542 million high-quality reads were generated by deep-sequencing using the Illumina HiSeq™ 2000 platform. The reference transcriptome comprised a combination of the Illumina reads, 454 sequencing data and Sanger sequences obtained from the public database to generate 93,163 unigenes (average length, 1,052 bp; N50 = 1,575 bp); 33,860 were annotated. Transcriptome comparisons between healthy and SUS-affected A. japonicus revealed greater differences in gene expression profiles in the body walls (BW) than in the intestines (Int), respiratory trees (RT) and coelomocytes (C). Clustering of expression models revealed stable up-regulation as the main pattern occurring in the BW throughout the three stages of SUS progression. Significantly affected pathways were associated with signal transduction, immune system, cellular processes, development and metabolism. Ninety-two differentially expressed genes (DEGs) were divided into four functional categories: attachment/pathogen recognition (17), inflammatory reactions (38), oxidative stress response (7) and apoptosis (30). Using quantitative real-time PCR, twenty representative DEGs were selected to validate the sequencing results. The Pearson’s correlation coefficient (R) of the 20 DEGs ranged from 0.811 to 0.999, which confirmed the consistency and accuracy between these two approaches. Conclusions Dynamic changes in global gene expression occur during SUS progression in A. japonicus. Elucidation of these changes is important in clarifying the molecular mechanisms associated with the development of SUS in sea cucumber. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2810-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aifu Yang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, Peoples' Republic of China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, Peoples' Republic of China.
| | - Yongjia Pan
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, Peoples' Republic of China
| | - Jingwei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, Peoples' Republic of China
| | - Ying Dong
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, Peoples' Republic of China
| | - Xiaoyan Guan
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, Peoples' Republic of China
| | - Hongjuan Sun
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, Peoples' Republic of China
| | - Shan Gao
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, Peoples' Republic of China
| | - Zhong Chen
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, 116023, Peoples' Republic of China
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63
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Reid CD, Karra K, Chang J, Piskol R, Li Q, Li JB, Cherry JM, Baker JC. XenMine: A genomic interaction tool for the Xenopus community. Dev Biol 2016; 426:155-164. [PMID: 27157655 DOI: 10.1016/j.ydbio.2016.02.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/06/2016] [Accepted: 02/26/2016] [Indexed: 11/17/2022]
Abstract
The Xenopus community has embraced recent advances in sequencing technology, resulting in the accumulation of numerous RNA-Seq and ChIP-Seq datasets. However, easily accessing and comparing datasets generated by multiple laboratories is challenging. Thus, we have created a central space to view, search and analyze data, providing essential information on gene expression changes and regulatory elements present in the genome. XenMine (www.xenmine.org) is a user-friendly website containing published genomic datasets from both Xenopus tropicalis and Xenopus laevis. We have established an analysis pipeline where all published datasets are uniformly processed with the latest genome releases. Information from these datasets can be extracted and compared using an array of pre-built or custom templates. With these search tools, users can easily extract sequences for all putative regulatory domains surrounding a gene of interest, identify the expression values of a gene of interest over developmental time, and analyze lists of genes for gene ontology terms and publications. Additionally, XenMine hosts an in-house genome browser that allows users to visualize all available ChIP-Seq data, extract specifically marked sequences, and aid in identifying important regulatory elements within the genome. Altogether, XenMine is an excellent tool for visualizing, accessing and querying analyzed datasets rapidly and efficiently.
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Affiliation(s)
- Christine D Reid
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Kalpana Karra
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Jessica Chang
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Robert Piskol
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Qin Li
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - J Michael Cherry
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Julie C Baker
- Department of Genetics, Stanford University, Stanford CA 94305, USA.
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64
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Accurate Profiling of Gene Expression and Alternative Polyadenylation with Whole Transcriptome Termini Site Sequencing (WTTS-Seq). Genetics 2016; 203:683-97. [PMID: 27098915 PMCID: PMC4896187 DOI: 10.1534/genetics.116.188508] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 03/17/2016] [Indexed: 01/23/2023] Open
Abstract
Construction of next-generation sequencing (NGS) libraries involves RNA manipulation, which often creates noisy, biased, and artifactual data that contribute to errors in transcriptome analysis. In this study, a total of 19 whole transcriptome termini site sequencing (WTTS-seq) and seven RNA sequencing (RNA-seq) libraries were prepared from Xenopus tropicalis adult and embryo samples to determine the most effective library preparation method to maximize transcriptomics investigation. We strongly suggest that appropriate primers/adaptors are designed to inhibit amplification detours and that PCR overamplification is minimized to maximize transcriptome coverage. Furthermore, genome annotation must be improved so that missing data can be recovered. In addition, a complete understanding of sequencing platforms is critical to limit the formation of false-positive results. Technically, the WTTS-seq method enriches both poly(A)+ RNA and complementary DNA, adds 5′- and 3′-adaptors in one step, pursues strand sequencing and mapping, and profiles both gene expression and alternative polyadenylation (APA). Although RNA-seq is cost prohibitive, tends to produce false-positive results, and fails to detect APA diversity and dynamics, its combination with WTTS-seq is necessary to validate transcriptome-wide APA.
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65
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Hao Y, Wu W, Li H, Yuan J, Luo J, Zhao Y, Chen R. NPInter v3.0: an upgraded database of noncoding RNA-associated interactions. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw057. [PMID: 27087310 PMCID: PMC4834207 DOI: 10.1093/database/baw057] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/20/2016] [Indexed: 02/01/2023]
Abstract
Despite the fact that a large quantity of noncoding RNAs (ncRNAs) have been identified, their functions remain unclear. To enable researchers to have a better understanding of ncRNAs’ functions, we updated the NPInter database to version 3.0, which contains experimentally verified interactions between ncRNAs (excluding tRNAs and rRNAs), especially long noncoding RNAs (lncRNAs) and other biomolecules (proteins, mRNAs, miRNAs and genomic DNAs). In NPInter v3.0, interactions pertaining to ncRNAs are not only manually curated from scientific literature but also curated from high-throughput technologies. In addition, we also curated lncRNA–miRNA interactions from in silico predictions supported by AGO CLIP-seq data. When compared with NPInter v2.0, the interactions are more informative (with additional information on tissues or cell lines, binding sites, conservation, co-expression values and other features) and more organized (with divisions on data sets by data sources, tissues or cell lines, experiments and other criteria). NPInter v3.0 expands the data set to 491,416 interactions in 188 tissues (or cell lines) from 68 kinds of experimental technologies. NPInter v3.0 also improves the user interface and adds new web services, including a local UCSC Genome Browser to visualize binding sites. Additionally, NPInter v3.0 defined a high-confidence set of interactions and predicted the functions of lncRNAs in human and mouse based on the interactions curated in the database. NPInter v3.0 is available at http://www.bioinfo.org/NPInter/. Database URL: http://www.bioinfo.org/NPInter/
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Affiliation(s)
- Yajing Hao
- Key Laboratory of RNA Biology Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Wu
- Key Laboratory of RNA Biology Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Li
- University of Chinese Academy of Sciences, Beijing, 100049, China Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Advanced Computing Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jiao Yuan
- Key Laboratory of RNA Biology Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianjun Luo
- Key Laboratory of RNA Biology Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi Zhao
- Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Advanced Computing Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
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Lang T, Klasson S, Larsson E, Johansson MEV, Hansson GC, Samuelsson T. Searching the Evolutionary Origin of Epithelial Mucus Protein Components-Mucins and FCGBP. Mol Biol Evol 2016; 33:1921-36. [PMID: 27189557 PMCID: PMC4948705 DOI: 10.1093/molbev/msw066] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The gel-forming mucins are large glycosylated proteins that are essential components of the mucus layers covering epithelial cells. Using novel methods of identifying mucins based on profile hidden Markov models, we have found a large number of such proteins in Metazoa, aiding in their classification and allowing evolutionary studies. Most vertebrates have 5–6 gel-forming mucin genes and the genomic arrangement of these genes is well conserved throughout vertebrates. An exception is the frog Xenopus tropicalis with an expanded repertoire of at least 26 mucins of this type. Furthermore, we found that the ovomucin protein, originally identified in chicken, is characteristic of reptiles, birds, and amphibians. Muc6 is absent in teleost fish, but we now show that it is present in animals such as ghost sharks, demonstrating an early origin in vertebrate evolution. Public RNA-Seq data were analyzed with respect to mucins in zebrafish, frog, and chicken, thus allowing comparison in regard of tissue and developmental specificity. Analyses of invertebrate proteins reveal that gel-forming-mucin type of proteins is widely distributed also in this group. Their presence in Cnidaria, Porifera, and in Ctenophora (comb jellies) shows that these proteins were present early in metazoan evolution. Finally, we examined the evolution of the FCGBP protein, abundant in mucus and related to gel-forming mucins in terms of structure and localization. We demonstrate that FCGBP, ubiquitous in vertebrates, has a conserved N-terminal domain. Interestingly, this domain is also present as an N-terminal sequence in a number of bacterial proteins.
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Affiliation(s)
- Tiange Lang
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
| | - Sofia Klasson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Erik Larsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Malin E V Johansson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Gunnar C Hansson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Tore Samuelsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
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67
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Vize PD, Zorn AM. Xenopus genomic data and browser resources. Dev Biol 2016; 426:194-199. [PMID: 27039265 DOI: 10.1016/j.ydbio.2016.03.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/26/2016] [Accepted: 03/30/2016] [Indexed: 10/22/2022]
Abstract
The two species of Xenopus most commonly used in biomedical research are the diploid Xenopus (Silurana) tropicalis and the tetraploid Xenopus laevis. The X. tropicalis genome sequence has been available since 2010 and this year the X. laevis, genome from two distinct genetic backgrounds has been published. Multiple genome assemblies available for both species and transcriptomic and epigenetic data sets are growing rapidly, all of which are available from a variety of web resources. This review describes the contents of these resources, how to locate and download genomic data, and also how to view and manipulate these data on various public genome browsers, with an emphasis on Xenbase, the Xenopus model organism database.
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Affiliation(s)
- Peter D Vize
- Departments of Biological Science and Computer Science, University of Calgary, Alberta, Canada.
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
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68
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Identification and analysis of mouse non-coding RNA using transcriptome data. SCIENCE CHINA-LIFE SCIENCES 2016; 59:589-603. [DOI: 10.1007/s11427-015-4929-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 10/22/2015] [Indexed: 01/08/2023]
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69
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Bakhtiarizadeh MR, Hosseinpour B, Arefnezhad B, Shamabadi N, Salami SA. In silico prediction of long intergenic non-coding RNAs in sheep. Genome 2016; 59:263-75. [PMID: 27002388 DOI: 10.1139/gen-2015-0141] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Long non-coding RNAs (lncRNAs) are transcribed RNA molecules >200 nucleotides in length that do not encode proteins and serve as key regulators of diverse biological processes. Recently, thousands of long intergenic non-coding RNAs (lincRNAs), a type of lncRNAs, have been identified in mammalians using massive parallel large sequencing technologies. The availability of the genome sequence of sheep (Ovis aries) has allowed us genomic prediction of non-coding RNAs. This is the first study to identify lincRNAs using RNA-seq data of eight different tissues of sheep, including brain, heart, kidney, liver, lung, ovary, skin, and white adipose. A computational pipeline was employed to characterize 325 putative lincRNAs with high confidence from eight important tissues of sheep using different criteria such as GC content, exon number, gene length, co-expression analysis, stability, and tissue-specific scores. Sixty-four putative lincRNAs displayed tissues-specific expression. The highest number of tissues-specific lincRNAs was found in skin and brain. All novel lincRNAs that aligned to the human and mouse lincRNAs had conserved synteny. These closest protein-coding genes were enriched in 11 significant GO terms such as limb development, appendage development, striated muscle tissue development, and multicellular organismal development. The findings reported here have important implications for the study of sheep genome.
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Affiliation(s)
- Mohammad Reza Bakhtiarizadeh
- a Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Pakdasht, Tehran, Iran.,e OMICS™ Research Group, Tehran, Iran
| | - Batool Hosseinpour
- b Department of Agriculture, Iranian Research Organization for Science and Technology, Tehran, Iran.,e OMICS™ Research Group, Tehran, Iran
| | - Babak Arefnezhad
- c Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,e OMICS™ Research Group, Tehran, Iran
| | - Narges Shamabadi
- d Center of Environmental Researches, University of Qom, Qom, Iran
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70
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Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. Genome Biol 2016; 17:14. [PMID: 26821746 PMCID: PMC4731934 DOI: 10.1186/s13059-016-0873-8] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/06/2016] [Indexed: 02/06/2023] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are increasingly implicated as gene regulators and may ultimately be more numerous than protein-coding genes in the human genome. Despite large numbers of reported lncRNAs, reference annotations are likely incomplete due to their lower and tighter tissue-specific expression compared to mRNAs. An unexplored factor potentially confounding lncRNA identification is inter-individual expression variability. Here, we characterize lncRNA natural expression variability in human primary granulocytes. Results We annotate granulocyte lncRNAs and mRNAs in RNA-seq data from 10 healthy individuals, identifying multiple lncRNAs absent from reference annotations, and use this to investigate three known features (higher tissue-specificity, lower expression, and reduced splicing efficiency) of lncRNAs relative to mRNAs. Expression variability was examined in seven individuals sampled three times at 1- or more than 1-month intervals. We show that lncRNAs display significantly more inter-individual expression variability compared to mRNAs. We confirm this finding in two independent human datasets by analyzing multiple tissues from the GTEx project and lymphoblastoid cell lines from the GEUVADIS project. Using the latter dataset we also show that including more human donors into the transcriptome annotation pipeline allows identification of an increasing number of lncRNAs, but minimally affects mRNA gene number. Conclusions A comprehensive annotation of lncRNAs is known to require an approach that is sensitive to low and tight tissue-specific expression. Here we show that increased inter-individual expression variability is an additional general lncRNA feature to consider when creating a comprehensive annotation of human lncRNAs or proposing their use as prognostic or disease markers. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0873-8) contains supplementary material, which is available to authorized users.
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71
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Owens NDL, Blitz IL, Lane MA, Patrushev I, Overton JD, Gilchrist MJ, Cho KWY, Khokha MK. Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development. Cell Rep 2016; 14:632-647. [PMID: 26774488 PMCID: PMC4731879 DOI: 10.1016/j.celrep.2015.12.050] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 11/02/2015] [Accepted: 12/07/2015] [Indexed: 01/19/2023] Open
Abstract
Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack a comprehensive understanding of transcript kinetics, which limits quantitative biology. This is an acute challenge in embryonic development, where rapid changes in gene expression dictate cell fate decisions. By ultra-high-frequency sampling of Xenopus embryos and absolute normalization of sequence reads, we present smooth gene expression trajectories in absolute transcript numbers. During a developmental period approximating the first 8 weeks of human gestation, transcript kinetics vary by eight orders of magnitude. Ordering genes by expression dynamics, we find that "temporal synexpression" predicts common gene function. Remarkably, a single parameter, the characteristic timescale, can classify transcript kinetics globally and distinguish genes regulating development from those involved in cellular metabolism. Overall, our analysis provides unprecedented insight into the reorganization of maternal and embryonic transcripts and redefines our ability to perform quantitative biology.
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Affiliation(s)
- Nick D L Owens
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway Mill Hill, London NW7 1AA, UK
| | - Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697 USA
| | - Maura A Lane
- Program in Vertebrate Developmental Biology, Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Ilya Patrushev
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway Mill Hill, London NW7 1AA, UK
| | - John D Overton
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Yale Center for Genome Analysis , Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Michael J Gilchrist
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway Mill Hill, London NW7 1AA, UK.
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697 USA.
| | - Mustafa K Khokha
- Program in Vertebrate Developmental Biology, Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
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72
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McCartney-Melstad E, Shaffer HB. Amphibian molecular ecology and how it has informed conservation. Mol Ecol 2015; 24:5084-109. [PMID: 26437125 DOI: 10.1111/mec.13391] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 02/02/2023]
Abstract
Molecular ecology has become one of the key tools in the modern conservationist's kit. Here we review three areas where molecular ecology has been applied to amphibian conservation: genes on landscapes, within-population processes, and genes that matter. We summarize relevant analytical methods, recent important studies from the amphibian literature, and conservation implications for each section. Finally, we include five in-depth examples of how molecular ecology has been successfully applied to specific amphibian systems.
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Affiliation(s)
- Evan McCartney-Melstad
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
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73
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Richards AJ, Herrel A, Bonneaud C. htsint: a Python library for sequencing pipelines that combines data through gene set generation. BMC Bioinformatics 2015; 16:307. [PMID: 26399714 PMCID: PMC4581156 DOI: 10.1186/s12859-015-0729-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 09/08/2015] [Indexed: 11/10/2022] Open
Abstract
Background Sequencing technologies provide a wealth of details in terms of genes, expression, splice variants, polymorphisms, and other features. A standard for sequencing analysis pipelines is to put genomic or transcriptomic features into a context of known functional information, but the relationships between ontology terms are often ignored. For RNA-Seq, considering genes and their genetic variants at the group level enables a convenient way to both integrate annotation data and detect small coordinated changes between experimental conditions, a known caveat of gene level analyses. Results We introduce the high throughput data integration tool, htsint, as an extension to the commonly used gene set enrichment frameworks. The central aim of htsint is to compile annotation information from one or more taxa in order to calculate functional distances among all genes in a specified gene space. Spectral clustering is then used to partition the genes, thereby generating functional modules. The gene space can range from a targeted list of genes, like a specific pathway, all the way to an ensemble of genomes. Given a collection of gene sets and a count matrix of transcriptomic features (e.g. expression, polymorphisms), the gene sets produced by htsint can be tested for ‘enrichment’ or conditional differences using one of a number of commonly available packages. Conclusion The database and bundled tools to generate functional modules were designed with sequencing pipelines in mind, but the toolkit nature of htsint allows it to also be used in other areas of genomics. The software is freely available as a Python library through GitHub at https://github.com/ajrichards/htsint.
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Affiliation(s)
- Adam J Richards
- Station d'Ecologie Expérimentale du CNRS, USR 2936, Route du CNRS, Moulis, 09200, France.
| | - Anthony Herrel
- UMR 7179 CNRS/MNHN, Département d'Ecologie et de Gestion de la Biodiversité 57 rue Cuvier, Case postale 55, Paris, 75231, France. .,Ghent University, Evolutionary Morphology of Vertebrates, K.L. Ledeganckstraat 35, Ghent, B-9000, Belgium.
| | - Camille Bonneaud
- Station d'Ecologie Expérimentale du CNRS, USR 2936, Route du CNRS, Moulis, 09200, France. .,Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn TR10 9FE, Cornwall, UK.
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74
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Yang J, Aguero T, King ML. The Xenopus Maternal-to-Zygotic Transition from the Perspective of the Germline. Curr Top Dev Biol 2015; 113:271-303. [PMID: 26358876 DOI: 10.1016/bs.ctdb.2015.07.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In Xenopus, the germline is specified by the inheritance of germ-plasm components synthesized at the beginning of oogenesis. Only the cells in the early embryo that receive germ plasm, the primordial germ cells (PGCs), are competent to give rise to the gametes. Thus, germ-plasm components continue the totipotent potential exhibited by the oocyte into the developing embryo at a time when most cells are preprogrammed for somatic differentiation as dictated by localized maternal determinants. When zygotic transcription begins at the mid-blastula transition, the maternally set program for somatic differentiation is realized. At this time, genetic control is ceded to the zygotic genome, and developmental potential gradually becomes more restricted within the primary germ layers. PGCs are a notable exception to this paradigm and remain transcriptionally silent until the late gastrula. How the germ-cell lineage retains full potential while somatic cells become fate restricted is a tale of translational repression, selective degradation of somatic maternal determinants, and delayed activation of zygotic transcription.
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Affiliation(s)
- Jing Yang
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Tristan Aguero
- Department of Cell Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Mary Lou King
- Department of Cell Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA.
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75
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Housman G, Ulitsky I. Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:31-40. [PMID: 26265145 DOI: 10.1016/j.bbagrm.2015.07.017] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/18/2015] [Accepted: 07/19/2015] [Indexed: 12/12/2022]
Abstract
Long noncoding RNAs (lncRNAs) are a diverse class of RNAs with increasingly appreciated functions in vertebrates, yet much of their biology remains poorly understood. In particular, it is unclear to what extent the current catalog of over 10,000 annotated lncRNAs is indeed devoid of genes coding for proteins. Here we review the available computational and experimental schemes for distinguishing between coding and noncoding transcripts and assess the conclusions from their recent genome-wide applications. We conclude that the model most consistent with the available data is that a large number of mammalian lncRNAs undergo translation, but only a very small minority of such translation events results in stable and functional peptides. The outcomes of the majority of the translation events and their potential biological purposes remain an intriguing topic for future investigation. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Gali Housman
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
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76
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Marlétaz F, Maeso I, Faas L, Isaacs HV, Holland PWH. Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution. BMC Biol 2015; 13:56. [PMID: 26231746 PMCID: PMC4522105 DOI: 10.1186/s12915-015-0165-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/08/2015] [Indexed: 01/03/2023] Open
Abstract
Background The functional consequences of whole genome duplications in vertebrate evolution are not fully understood. It remains unclear, for instance, why paralogues were retained in some gene families but extensively lost in others. Cdx homeobox genes encode conserved transcription factors controlling posterior development across diverse bilaterians. These genes are part of the ParaHox gene cluster. Multiple Cdx copies were retained after genome duplication, raising questions about how functional divergence, overlap, and redundancy respectively contributed to their retention and evolutionary fate. Results We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xenopus tropicalis followed by RNA-seq. We found that one paralogue, Cdx4, has a much stronger effect on gene expression than the others, including a strong regulatory effect on FGF and Wnt genes. Functional annotation revealed distinct and overlapping roles and subtly different temporal windows of action for each gene. The data also reveal a colinear-like effect of Cdx genes on Hox genes, with repression of Hox paralogy groups 1 and 2, and activation increasing from Hox group 5 to 11. We also highlight cases in which duplicated genes regulate distinct paralogous targets revealing pathway elaboration after whole genome duplication. Conclusions Despite shared core pathways, Cdx paralogues have acquired distinct regulatory roles during development. This implies that the degree of functional overlap between paralogues is relatively low and that gene expression pattern alone should be used with caution when investigating the functional evolution of duplicated genes. We therefore suggest that developmental programmes were extensively rewired after whole genome duplication in the early evolution of vertebrates. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0165-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ferdinand Marlétaz
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
| | - Ignacio Maeso
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK. .,Present address: Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain.
| | - Laura Faas
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
| | - Harry V Isaacs
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
| | - Peter W H Holland
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
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77
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Abstract
In mature gametes and during the oocyte-to-embryo transition, transcription is generally silenced and gene expression is post-transcriptionally regulated. However, we recently discovered that major transcription can occur immediately after fertilization, prior to pronuclear fusion, and in the first cell division of the oocyte-to-embryo transition in the nematode Ascaris suum. We postulate that the balance between transcriptional and post-transcriptional regulation during the oocyte-to-embryo transition may largely be determined by cell cycle length and thus the time available for the genome to be transcribed.
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Affiliation(s)
- Jianbin Wang
- a Department of Biochemistry and Molecular Genetics ; University of Colorado School of Medicine ; Aurora , CO USA
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78
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E2a is necessary for Smad2/3-dependent transcription and the direct repression of lefty during gastrulation. Dev Cell 2015; 32:345-57. [PMID: 25669884 DOI: 10.1016/j.devcel.2014.11.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 09/24/2014] [Accepted: 11/25/2014] [Indexed: 11/20/2022]
Abstract
Transcription factor complexes have varied effects on cell fate and behavior, but how this diversification of function occurs is largely unknown. The Nodal signaling pathway has many biological functions that all converge on the transcription factors Smad2/3. Smad2/3 has many cofactors, and alternative usage of these may provide a mechanism for modulating Smad2/3 function. Here, we investigate how perturbation of the cofactor E2a affects global patterns of Smad2/3 binding and gene expression during gastrulation. We find that E2a regulates early development in two ways. E2a changes the position of Smad2/3 binding at the Nodal inhibitor lefty, resulting in direct repression of lefty that is critical for mesendoderm specification. Separately, E2a is necessary to drive transcription of Smad2/3 target genes, including critical regulators of dorsal cell fate and morphogenesis. Overall, we find that E2a functions as both a transcriptional repressor and activator to precisely regulate Nodal signaling.
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79
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Paranjpe SS, Veenstra GJC. Establishing pluripotency in early development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:626-36. [PMID: 25857441 DOI: 10.1016/j.bbagrm.2015.03.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/26/2015] [Accepted: 03/30/2015] [Indexed: 01/23/2023]
Abstract
The earliest steps of embryonic development involve important changes in chromatin and transcription factor networks, which are orchestrated to establish pluripotent cells that will form the embryo. DNA methylation, histone modifications, the pluripotency regulatory network of transcription factors, maternal factors and newly translated proteins all contribute to these transitions in dynamic ways. Moreover, these dynamics are linked to the onset of zygotic transcription. We will review recent progress in our understanding of chromatin state and regulation of gene expression in the context of embryonic development in vertebrates, in particular mouse, Xenopus and zebrafish. We include work on mouse embryonic stem cells and highlight work that illustrates how early embryonic dynamics establish gene regulatory networks and the state of pluripotency.
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Affiliation(s)
- Sarita S Paranjpe
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Gert Jan C Veenstra
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.
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80
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Mallory AC, Shkumatava A. LncRNAs in vertebrates: advances and challenges. Biochimie 2015; 117:3-14. [PMID: 25812751 DOI: 10.1016/j.biochi.2015.03.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 03/17/2015] [Indexed: 01/06/2023]
Abstract
Beyond the handful of classic and well-characterized long noncoding RNAs (lncRNAs), more recently, hundreds of thousands of lncRNAs have been identified in multiple species including bacteria, plants and vertebrates, and the number of newly annotated lncRNAs continues to increase as more transcriptomes are analyzed. In vertebrates, the expression of many lncRNAs is highly regulated, displaying discrete temporal and spatial expression patterns, suggesting roles in a wide range of developmental processes and setting them apart from classic housekeeping ncRNAs. In addition, the deregulation of a subset of these lncRNAs has been linked to the development of several diseases, including cancers, as well as developmental anomalies. However, the majority of vertebrate lncRNA functions remain enigmatic. As such, a major task at hand is to decipher the biological roles of lncRNAs and uncover the regulatory networks upon which they impinge. This review focuses on our emerging understanding of lncRNAs in vertebrate animals, highlighting some recent advances in their functional analyses across several species and emphasizing the current challenges researchers face to characterize lncRNAs and identify their in vivo functions.
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Affiliation(s)
- Allison C Mallory
- Institut Curie, 26 Rue d'Ulm, 75248 Paris Cedex 05, France; CNRS UMR3215, 75248 Paris Cedex 05, France; INSERM U934, 75248 Paris Cedex 05, France.
| | - Alena Shkumatava
- Institut Curie, 26 Rue d'Ulm, 75248 Paris Cedex 05, France; CNRS UMR3215, 75248 Paris Cedex 05, France; INSERM U934, 75248 Paris Cedex 05, France.
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81
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Amodeo AA, Jukam D, Straight AF, Skotheim JM. Histone titration against the genome sets the DNA-to-cytoplasm threshold for the Xenopus midblastula transition. Proc Natl Acad Sci U S A 2015; 112:E1086-95. [PMID: 25713373 PMCID: PMC4364222 DOI: 10.1073/pnas.1413990112] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During early development, animal embryos depend on maternally deposited RNA until zygotic genes become transcriptionally active. Before this maternal-to-zygotic transition, many species execute rapid and synchronous cell divisions without growth phases or cell cycle checkpoints. The coordinated onset of transcription, cell cycle lengthening, and cell cycle checkpoints comprise the midblastula transition (MBT). A long-standing model in the frog, Xenopus laevis, posits that MBT timing is controlled by a maternally loaded inhibitory factor that is titrated against the exponentially increasing amount of DNA. To identify MBT regulators, we developed an assay using Xenopus egg extract that recapitulates the activation of transcription only above the DNA-to-cytoplasm ratio found in embryos at the MBT. We used this system to biochemically purify factors responsible for inhibiting transcription below the threshold DNA-to-cytoplasm ratio. This unbiased approach identified histones H3 and H4 as concentration-dependent inhibitory factors. Addition or depletion of H3/H4 from the extract quantitatively shifted the amount of DNA required for transcriptional activation in vitro. Moreover, reduction of H3 protein in embryos induced premature transcriptional activation and cell cycle lengthening, and the addition of H3/H4 shortened post-MBT cell cycles. Our observations support a model for MBT regulation by DNA-based titration and suggest that depletion of free histones regulates the MBT. More broadly, our work shows how a constant concentration DNA binding molecule can effectively measure the amount of cytoplasm per genome to coordinate division, growth, and development.
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82
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Zhang M, Kothari P, Lampson MA. Spindle assembly checkpoint acquisition at the mid-blastula transition. PLoS One 2015; 10:e0119285. [PMID: 25741707 PMCID: PMC4351100 DOI: 10.1371/journal.pone.0119285] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/23/2015] [Indexed: 01/13/2023] Open
Abstract
The spindle assembly checkpoint (SAC) maintains the fidelity of chromosome segregation during mitosis. Nonpathogenic cells lacking the SAC are typically only found in cleavage stage metazoan embryos, which do not acquire functional checkpoints until the mid-blastula transition (MBT). It is unclear how proper SAC function is acquired at the MBT, though several models exist. First, SAC acquisition could rely on transcriptional activity, which increases dramatically at the MBT. Embryogenesis prior to the MBT relies primarily on maternally loaded transcripts, and if SAC signaling components are not maternally supplied, the SAC would depend on zygotic transcription at the MBT. Second, checkpoint acquisition could depend on the Chk1 kinase, which is activated at the MBT to elongate cell cycles and is required for the SAC in somatic cells. Third, SAC function could depend on a threshold nuclear to cytoplasmic (N:C) ratio, which increases during pre-MBT cleavage cycles and dictates several MBT events like zygotic transcription and cell cycle remodeling. Finally, the SAC could by regulated by a timer mechanism that coincides with other MBT events but is independent of them. Using zebrafish embryos we show that SAC acquisition at the MBT is independent of zygotic transcription, indicating that the checkpoint program is maternally supplied. Additionally, by precociously lengthening cleavage cycles with exogenous Chk1 activity, we show that cell cycle lengthening and Chk1 activity are not sufficient for SAC acquisition. Furthermore, we find that SAC acquisition can be uncoupled from the N:C ratio. Together, our findings indicate that SAC acquisition is regulated by a maternally programmed developmental timer.
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Affiliation(s)
- Maomao Zhang
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Priyanka Kothari
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Michael A. Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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83
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Zhang S, Li J, Lea R, Vleminckx K, Amaya E. Fezf2 promotes neuronal differentiation through localised activation of Wnt/β-catenin signalling during forebrain development. Development 2015; 141:4794-805. [PMID: 25468942 PMCID: PMC4299278 DOI: 10.1242/dev.115691] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Brain regionalisation, neuronal subtype diversification and circuit connectivity are crucial events in the establishment of higher cognitive functions. Here we report the requirement for the transcriptional repressor Fezf2 for proper differentiation of neural progenitor cells during the development of the Xenopus forebrain. Depletion of Fezf2 induces apoptosis in postmitotic neural progenitors, with concomitant reduction in forebrain size and neuronal differentiation. Mechanistically, we found that Fezf2 stimulates neuronal differentiation by promoting Wnt/β-catenin signalling in the developing forebrain. In addition, we show that Fezf2 promotes activation of Wnt/β-catenin signalling by repressing the expression of two negative regulators of Wnt signalling, namely lhx2 and lhx9. Our findings suggest that Fezf2 plays an essential role in controlling when and where neuronal differentiation occurs within the developing forebrain and that it does so by promoting local Wnt/β-catenin signalling via a double-repressor model.
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Affiliation(s)
- Siwei Zhang
- The Healing Foundation Centre, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Jingjing Li
- The Healing Foundation Centre, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Robert Lea
- The Healing Foundation Centre, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Kris Vleminckx
- Department for Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium
| | - Enrique Amaya
- The Healing Foundation Centre, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
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84
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Characterization of tweety gene (ttyh1-3) expression in Xenopus laevis during embryonic development. Gene Expr Patterns 2014; 17:38-44. [PMID: 25541457 DOI: 10.1016/j.gep.2014.12.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 11/08/2014] [Accepted: 12/02/2014] [Indexed: 02/08/2023]
Abstract
The tweety family of genes encodes large-conductance chloride channels and has been implicated in a wide array of cellular processes including cell division, cell adhesion, regulation of calcium activity, and tumorigenesis, particularly in neuronal cells. However, their expression patterns during early development remain largely unknown. Here, we describe the spatial and temporal patterning of ttyh1, ttyh2, and ttyh3 in Xenopus laevis during early embryonic development. Ttyh1 and ttyh3 are initially expressed at the late neurula stage are and primarily localized to the developing nervous system; however ttyh1 and ttyh3 both show transient expression in the somites. By swimming tadpole stages, all three genes are expressed in the brain, spinal cord, eye, and cranial ganglia. While ttyh1 is restricted to proliferative, ventricular zones, ttyh3 is primarily localized to postmitotic regions of the developing nervous system. Ttyh2, however, is strongly expressed in cranial ganglia V, VII, IX and X. The differing temporal and spatial expression patterns of ttyh1, ttyh2, and ttyh3 suggest that they may play distinct roles throughout embryonic development.
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85
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Identification of 4438 novel lincRNAs involved in mouse pre-implantation embryonic development. Mol Genet Genomics 2014; 290:685-97. [DOI: 10.1007/s00438-014-0952-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 11/10/2014] [Indexed: 12/20/2022]
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86
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Pantalacci S, Sémon M. Transcriptomics of developing embryos and organs: A raising tool for evo-devo. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 324:363-71. [PMID: 25387424 DOI: 10.1002/jez.b.22595] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 08/19/2014] [Indexed: 12/12/2022]
Abstract
Comparative transcriptomics has become an important tool for revisiting many evo-devo questions and exploring new ones, and its importance is likely to increase in the near future, partly because RNA-seq data open many new possibilities. The aim of this opinion piece is twofold. In the first section, we discuss the particularities of transcriptomic studies in evo-devo, focusing mainly on RNA-seq data. The preliminary processing steps (getting coding sequences as well as expression levels) are challenging, because many studied species do not have a sequenced genome. The next step (interpreting expression differences) is also challenging, due to several issues with interpreting expression levels in complex tissues, managing developmental stages and species heterochronies, and the problem of conceptualizing expression differences. In the second section, we discuss some past and possible future applications of transcriptomic approaches (using microarray or RNA-seq) to three major themes in evo-devo: the evolution of the developmental toolkit, the genetic and developmental basis for phenotypic changes, and the general rules of the evolution of development. We believe that conceptual and technical tools are necessary in order to fully exploit the richness of multispecies transcriptomic time-series data.
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Affiliation(s)
- Sophie Pantalacci
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Université Lyon 1, CNRS, École Normale Supérieure de Lyon, Lyon, France
| | - Marie Sémon
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Université Lyon 1, CNRS, École Normale Supérieure de Lyon, Lyon, France
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87
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Gardini A, Shiekhattar R. The many faces of long noncoding RNAs. FEBS J 2014; 282:1647-57. [PMID: 25303371 DOI: 10.1111/febs.13101] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 09/30/2014] [Accepted: 10/03/2014] [Indexed: 12/21/2022]
Abstract
Over the past few years, the field of noncoding RNAs has grown from a niche for geneticists into a prominent domain of mainstream biology. Advances in genomic technologies have provided a more comprehensive view of the mammalian genome, improving our knowledge of regions of the genome devoid of protein-coding potential. A large body of evidence supports the proposal that noncoding RNAs account for a large proportion of the transcriptional output of any given cell and tissue type. This review will delve into the biogenesis and function of long noncoding RNAs. We will discuss our current understanding of these molecules as major chromatin players, and explore future directions in the field.
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Affiliation(s)
- Alessandro Gardini
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, FL, USA
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88
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Li A, Zhang J, Zhou Z. PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme. BMC Bioinformatics 2014; 15:311. [PMID: 25239089 PMCID: PMC4177586 DOI: 10.1186/1471-2105-15-311] [Citation(s) in RCA: 426] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 09/01/2014] [Indexed: 12/21/2022] Open
Abstract
Background High-throughput transcriptome sequencing (RNA-seq) technology promises to discover novel protein-coding and non-coding transcripts, particularly the identification of long non-coding RNAs (lncRNAs) from de novo sequencing data. This requires tools that are not restricted by prior gene annotations, genomic sequences and high-quality sequencing. Results We present an alignment-free tool called PLEK (predictor of long non-coding RNAs and messenger RNAs based on an improved k-mer scheme), which uses a computational pipeline based on an improved k-mer scheme and a support vector machine (SVM) algorithm to distinguish lncRNAs from messenger RNAs (mRNAs), in the absence of genomic sequences or annotations. The performance of PLEK was evaluated on well-annotated mRNA and lncRNA transcripts. 10-fold cross-validation tests on human RefSeq mRNAs and GENCODE lncRNAs indicated that our tool could achieve accuracy of up to 95.6%. We demonstrated the utility of PLEK on transcripts from other vertebrates using the model built from human datasets. PLEK attained >90% accuracy on most of these datasets. PLEK also performed well using a simulated dataset and two real de novo assembled transcriptome datasets (sequenced by PacBio and 454 platforms) with relatively high indel sequencing errors. In addition, PLEK is approximately eightfold faster than a newly developed alignment-free tool, named Coding-Non-Coding Index (CNCI), and 244 times faster than the most popular alignment-based tool, Coding Potential Calculator (CPC), in a single-threading running manner. Conclusions PLEK is an efficient alignment-free computational tool to distinguish lncRNAs from mRNAs in RNA-seq transcriptomes of species lacking reference genomes. PLEK is especially suitable for PacBio or 454 sequencing data and large-scale transcriptome data. Its open-source software can be freely downloaded from https://sourceforge.net/projects/plek/files/. Electronic supplementary material The online version of this article (doi:10.1186/1471-2105-15-311) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Junying Zhang
- School of Computer Science and Technology, Xidian University, Xi'an, PR China.
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89
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Wei J, Zhang X, Yu Y, Huang H, Li F, Xiang J. Comparative transcriptomic characterization of the early development in Pacific white shrimp Litopenaeus vannamei. PLoS One 2014; 9:e106201. [PMID: 25197823 PMCID: PMC4157780 DOI: 10.1371/journal.pone.0106201] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 08/01/2014] [Indexed: 01/28/2023] Open
Abstract
Penaeid shrimp has a distinctive metamorphosis stage during early development. Although morphological and biochemical studies about this ontogeny have been developed for decades, researches on gene expression level are still scarce. In this study, we have investigated the transcriptomes of five continuous developmental stages in Pacific white shrimp (Litopenaeus vannamei) with high throughput Illumina sequencing technology. The reads were assembled and clustered into 66,815 unigenes, of which 32,398 have putative homologues in nr database, 14,981 have been classified into diverse functional categories by Gene Ontology (GO) annotation and 26,257 have been associated with 255 pathways by KEGG pathway mapping. Meanwhile, the differentially expressed genes (DEGs) between adjacent developmental stages were identified and gene expression patterns were clustered. By GO term enrichment analysis, KEGG pathway enrichment analysis and functional gene profiling, the physiological changes during shrimp metamorphosis could be better understood, especially histogenesis, diet transition, muscle development and exoskeleton reconstruction. In conclusion, this is the first study that characterized the integrated transcriptomic profiles during early development of penaeid shrimp, and these findings will serve as significant references for shrimp developmental biology and aquaculture research.
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Affiliation(s)
- Jiankai Wei
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Yang Yu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Huang
- Hainan Guandtop Ocean Breeding Co. Ltd, Haikou, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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90
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Gupta R, Wills A, Ucar D, Baker J. Developmental enhancers are marked independently of zygotic Nodal signals in Xenopus. Dev Biol 2014; 395:38-49. [PMID: 25205067 DOI: 10.1016/j.ydbio.2014.08.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 08/06/2014] [Accepted: 08/31/2014] [Indexed: 02/08/2023]
Abstract
To determine the hierarchy of transcriptional regulation within the in vivo vertebrate embryo, we examined whether developmental enhancers were influenced by Nodal signaling during early embryogenesis in Xenopus tropicalis. We find that developmental enhancers, defined by the active enhancer chromatin marks H3K4me1 and H3K27ac, are established as early as blastula stage and that Smad2/3 only strongly associates with these regions at gastrula stages. Significantly, when we perturb Nodal signaling using the drug SB431542, most enhancers remain marked, including at genes known to be sensitive to Nodal signaling. Overall, as enhancers are in an active conformation prior to Nodal signaling and are established independently of Nodal signaling, we suggest that many developmental enhancers are marked maternally, prior to exposure to extrinsic signals.
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Affiliation(s)
- Rakhi Gupta
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Andrea Wills
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Duygu Ucar
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julie Baker
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Department of Obstetrics and Gynecology, Stanford University, Stanford, CA 94305, USA
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91
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Lee MT, Bonneau AR, Giraldez AJ. Zygotic genome activation during the maternal-to-zygotic transition. Annu Rev Cell Dev Biol 2014; 30:581-613. [PMID: 25150012 DOI: 10.1146/annurev-cellbio-100913-013027] [Citation(s) in RCA: 388] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Embryogenesis depends on a highly coordinated cascade of genetically encoded events. In animals, maternal factors contributed by the egg cytoplasm initially control development, whereas the zygotic nuclear genome is quiescent. Subsequently, the genome is activated, embryonic gene products are mobilized, and maternal factors are cleared. This transfer of developmental control is called the maternal-to-zygotic transition (MZT). In this review, we discuss recent advances toward understanding the scope, timing, and mechanisms that underlie zygotic genome activation at the MZT in animals. We describe high-throughput techniques to measure the embryonic transcriptome and explore how regulation of the cell cycle, chromatin, and transcription factors together elicits specific patterns of embryonic gene expression. Finally, we illustrate the interplay between zygotic transcription and maternal clearance and show how these two activities combine to reprogram two terminally differentiated gametes into a totipotent embryo.
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Affiliation(s)
- Miler T Lee
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520; ,
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92
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Grau JH, Poustka AJ, Meixner M, Plötner J. LTR retroelements are intrinsic components of transcriptional networks in frogs. BMC Genomics 2014; 15:626. [PMID: 25056159 PMCID: PMC4131045 DOI: 10.1186/1471-2164-15-626] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/15/2014] [Indexed: 12/16/2022] Open
Abstract
Background LTR retroelements (LTR REs) constitute a major group of transposable elements widely distributed in eukaryotic genomes. Through their own mechanism of retrotranscription LTR REs enrich the genomic landscape by providing genetic variability, thus contributing to genome structure and organization. Nonetheless, transcriptomic activity of LTR REs still remains an obscure domain within cell, developmental, and organism biology. Results Here we present a first comparative analysis of LTR REs for anuran amphibians based on a full depth coverage transcriptome of the European pool frog, Pelophylax lessonae, the genome of the African clawed frog, Silurana tropicalis (release v7.1), and additional transcriptomes of S. tropicalis and Cyclorana alboguttata. We identified over 1000 copies of LTR REs from all four families (Bel/Pao, Ty1/Copia, Ty3/Gypsy, Retroviridae) in the genome of S. tropicalis and discovered transcripts of several of these elements in all RNA-seq datasets analyzed. Elements of the Ty3/Gypsy family were most active, especially Amn-san elements, which accounted for approximately 0.27% of the genome in Silurana. Some elements exhibited tissue specific expression patterns, for example Hydra1.1 and MuERV-like elements in Pelophylax. In S. tropicalis considerable transcription of LTR REs was observed during embryogenesis as soon as the embryonic genome became activated, i.e. at midblastula transition. In the course of embryonic development the spectrum of transcribed LTR REs changed; during gastrulation and neurulation MuERV-like and SnRV like retroviruses were abundantly transcribed while during organogenesis transcripts of the XEN1 retroviruses became much more active. Conclusions The differential expression of LTR REs during embryogenesis in concert with their tissue-specificity and the protein domains they encode are evidence for the functional roles these elements play as integrative parts of complex regulatory networks. Our results support the meanwhile widely accepted concept that retroelements are not simple “junk DNA” or “harmful genomic parasites” but essential components of the transcriptomic machinery in vertebrates. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-626) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José Horacio Grau
- Dahlem Center for Genome Research and Medical Systems Biology, Fabeckstraße 60-62, 14195 Berlin, Germany.
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93
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Smits AH, Lindeboom RGH, Perino M, van Heeringen SJ, Veenstra GJC, Vermeulen M. Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs. Nucleic Acids Res 2014; 42:9880-91. [PMID: 25056316 PMCID: PMC4150773 DOI: 10.1093/nar/gku661] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
While recent developments in genomic sequencing technology have enabled comprehensive transcriptome analyses of single cells, single cell proteomics has thus far been restricted to targeted studies. Here, we perform global absolute protein quantification of fertilized Xenopus laevis eggs using mass spectrometry-based proteomics, quantifying over 5800 proteins in the largest single cell proteome characterized to date. Absolute protein amounts in single eggs are highly consistent, thus indicating a tight regulation of global protein abundance. Protein copy numbers in single eggs range from tens of thousands to ten trillion copies per cell. Comparison between the single-cell proteome and transcriptome reveal poor expression correlation. Finally, we identify 439 proteins that significantly change in abundance during early embryogenesis. Downregulated proteins include ribosomal proteins and upregulated proteins include basal transcription factors, among others. Many of these proteins do not show regulation at the transcript level. Altogether, our data reveal that the transcriptome is a poor indicator of the proteome and that protein levels are tightly controlled in X. laevis eggs.
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Affiliation(s)
- Arne H Smits
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands Cancer Genomics Netherlands, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Rik G H Lindeboom
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands Cancer Genomics Netherlands, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Matteo Perino
- Department of Developmental Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Simon J van Heeringen
- Department of Developmental Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Gert Jan C Veenstra
- Department of Developmental Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands Cancer Genomics Netherlands, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
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94
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Lv J, Huang Z, Liu H, Liu H, Cui W, Li B, He H, Guo J, Liu Q, Zhang Y, Wu Q. Identification and characterization of long intergenic non-coding RNAs related to mouse liver development. Mol Genet Genomics 2014; 289:1225-35. [PMID: 25012394 DOI: 10.1007/s00438-014-0882-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 06/20/2014] [Indexed: 01/23/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been studied extensively over the last few years. Liver is an important organ that plays a crucial role in glucose metabolism and homeostasis; however, there are few reports of the identification and functional characterization of lncRNAs with important roles in liver development. Therefore, it is necessary to systematically identify lncRNAs that are involved in liver development. In this paper, we assembled the transcriptome using published RNA-seq data across three mouse liver developmental stages and identified 4,882 putative long intergenic non-coding RNAs (lincRNAs) expressed in at least one of the investigated stages. Combining these with Ensembl lincRNAs, we established a reference catalog of 6,602 transcribed lincRNAs in the mouse liver. We then analyzed all the lincRNAs in this reference catalog systematically and revealed that liver lincRNAs carry different genomic signatures from protein-coding genes, while the putative lincRNAs are generally comparable with known Ensembl lincRNAs. In addition, putative lincRNAs are functionally associated with essential biological processes, including RNA splicing, protein localization and fatty acid metabolic process, implying that they may play an important role in regulating liver development. The validation of selected lincRNAs that are specifically expressed in developing liver tissues further suggested the effectiveness of our approach. Our study shows that lincRNAs that are differentially expressed during three liver developmental stages could have important regulatory roles in liver development. The identified putative lincRNAs are a valuable resource for further functional studies.
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Affiliation(s)
- Jie Lv
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150001, China
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95
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Jambhekar A, Emerman AB, Schweidenback CTH, Blower MD. RNA stimulates Aurora B kinase activity during mitosis. PLoS One 2014; 9:e100748. [PMID: 24968351 PMCID: PMC4072698 DOI: 10.1371/journal.pone.0100748] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/22/2014] [Indexed: 11/19/2022] Open
Abstract
Accurate chromosome segregation is essential for cell viability. The mitotic spindle is crucial for chromosome segregation, but much remains unknown about factors that regulate spindle assembly. Recent work implicates RNA in promoting proper spindle assembly independently of mRNA translation; however, the mechanism by which RNA performs this function is currently unknown. Here, we show that RNA regulates both the localization and catalytic activity of the mitotic kinase, Aurora-B (AurB), which is present in a ribonucleoprotein (RNP) complex with many mRNAs. Interestingly, AurB kinase activity is reduced in Xenopus egg extracts treated with RNase, and its activity is stimulated in vitro by RNA binding. Spindle assembly defects following RNase-treatment are partially rescued by inhibiting MCAK, a microtubule depolymerase that is inactivated by AurB-dependent phosphorylation. These findings implicate AurB as an important RNA-dependent spindle assembly factor, and demonstrate a translation-independent role for RNA in stimulating AurB.
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Affiliation(s)
- Ashwini Jambhekar
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Amy B. Emerman
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Caterina T. H. Schweidenback
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael D. Blower
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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96
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Collart C, Owens NDL, Bhaw-Rosun L, Cooper B, De Domenico E, Patrushev I, Sesay AK, Smith JN, Smith JC, Gilchrist MJ. High-resolution analysis of gene activity during the Xenopus mid-blastula transition. Development 2014; 141:1927-39. [PMID: 24757007 PMCID: PMC3994770 DOI: 10.1242/dev.102012] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss of synchronous cell divisions. Little is known about what triggers the activation of transcription or how newly expressed genes interact with each other. Here, we use high-resolution expression profiling to identify three waves of gene activity: a post-fertilisation wave involving polyadenylation of maternal transcripts; a broad wave of zygotic transcription detectable as early as the seventh cleavage and extending beyond the MBT at the twelfth cleavage; and a shorter post-MBT wave of transcription that becomes apparent as development proceeds. Our studies have also allowed us to define a set of maternal mRNAs that are deadenylated shortly after fertilisation, and are likely to be degraded thereafter. Experimental analysis indicates that the polyadenylation of maternal transcripts is necessary for the establishment of proper levels of zygotic transcription at the MBT, and that genes activated in the second wave of expression, including Brachyury and Mixer, contribute to the regulation of genes expressed in the third. Together, our high-resolution time series and experimental studies have yielded a deeper understanding of the temporal organisation of gene regulatory networks in the early Xenopus embryo.
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Affiliation(s)
- Clara Collart
- Division of Systems Biology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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97
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Tena JJ, González-Aguilera C, Fernández-Miñán A, Vázquez-Marín J, Parra-Acero H, Cross JW, Rigby PWJ, Carvajal JJ, Wittbrodt J, Gómez-Skarmeta JL, Martínez-Morales JR. Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period. Genome Res 2014; 24:1075-85. [PMID: 24709821 PMCID: PMC4079964 DOI: 10.1101/gr.163915.113] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The complex relationship between ontogeny and phylogeny has been the subject of attention and controversy since von Baer’s formulations in the 19th century. The classic concept that embryogenesis progresses from clade general features to species-specific characters has often been revisited. It has become accepted that embryos from a clade show maximum morphological similarity at the so-called phylotypic period (i.e., during mid-embryogenesis). According to the hourglass model, body plan conservation would depend on constrained molecular mechanisms operating at this period. More recently, comparative transcriptomic analyses have provided conclusive evidence that such molecular constraints exist. Examining cis-regulatory architecture during the phylotypic period is essential to understand the evolutionary source of body plan stability. Here we compare transcriptomes and key epigenetic marks (H3K4me3 and H3K27ac) from medaka (Oryzias latipes) and zebrafish (Danio rerio), two distantly related teleosts separated by an evolutionary distance of 115–200 Myr. We show that comparison of transcriptome profiles correlates with anatomical similarities and heterochronies observed at the phylotypic stage. Through comparative epigenomics, we uncover a pool of conserved regulatory regions (≈700), which are active during the vertebrate phylotypic period in both species. Moreover, we show that their neighboring genes encode mainly transcription factors with fundamental roles in tissue specification. We postulate that these regulatory regions, active in both teleost genomes, represent key constrained nodes of the gene networks that sustain the vertebrate body plan.
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Affiliation(s)
- Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CSIC/UPO/JA), 41013 Sevilla, Spain
| | | | - Ana Fernández-Miñán
- Centro Andaluz de Biología del Desarrollo (CSIC/UPO/JA), 41013 Sevilla, Spain
| | | | - Helena Parra-Acero
- Centro Andaluz de Biología del Desarrollo (CSIC/UPO/JA), 41013 Sevilla, Spain
| | - Joe W Cross
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Peter W J Rigby
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Jaime J Carvajal
- Centro Andaluz de Biología del Desarrollo (CSIC/UPO/JA), 41013 Sevilla, Spain; Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Joachim Wittbrodt
- Centre for Organismal Studies, COS, University of Heidelberg, 69120 Heidelberg, Germany
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98
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Quantitative proteomics of Xenopus laevis embryos: expression kinetics of nearly 4000 proteins during early development. Sci Rep 2014; 4:4365. [PMID: 24626130 PMCID: PMC3953746 DOI: 10.1038/srep04365] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 02/17/2014] [Indexed: 02/07/2023] Open
Abstract
While there is a rich literature on transcription dynamics during the development of many organisms, protein data is limited. We used iTRAQ isotopic labeling and mass spectrometry to generate the largest developmental proteomic dataset for any animal. Expression dynamics of nearly 4,000 proteins of Xenopuslaevis was generated from fertilized egg to neurula embryo. Expression clusters into groups. The cluster profiles accurately reflect the major events that mark changes in gene expression patterns during early Xenopus development. We observed decline in the expression of ten DNA replication factors after the midblastula transition (MBT), including a marked decline of the licensing factor XCdc6. Ectopic expression of XCdc6 leads to apoptosis; temporal changes in this protein are critical for proper development. Measurement of expression in single embryos provided no evidence for significant protein heterogeneity between embryos at the same stage of development.
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99
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Park SJ, Komata M, Inoue F, Yamada K, Nakai K, Ohsugi M, Shirahige K. Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis. Genes Dev 2014; 27:2736-48. [PMID: 24352427 PMCID: PMC3877761 DOI: 10.1101/gad.227926.113] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The mechanisms underlying parental genome coordination upon mammalian fertilization remain elusive due to difficulties in preparing large numbers of high-quality preimplantation cells. Here, Park et al. collect an unprecedented number of mouse oocytes and establish detailed transcriptional profiles for four early embryonic stages and parthenogenetic development. Bioinformatic analysis identifies a distinctive gene regulatory network activated in embryos after fertilization compared with parthenotes. This large-scale profile of early mouse embryos yields a valuable resource for developmental biology and stem cell research. Fertilization precisely choreographs parental genomes by using gamete-derived cellular factors and activating genome regulatory programs. However, the mechanism remains elusive owing to the technical difficulties of preparing large numbers of high-quality preimplantation cells. Here, we collected >14 × 104 high-quality mouse metaphase II oocytes and used these to establish detailed transcriptional profiles for four early embryo stages and parthenogenetic development. By combining these profiles with other public resources, we found evidence that gene silencing appeared to be mediated in part by noncoding RNAs and that this was a prerequisite for post-fertilization development. Notably, we identified 817 genes that were differentially expressed in embryos after fertilization compared with parthenotes. The regulation of these genes was distinctly different from those expressed in parthenotes, suggesting functional specialization of particular transcription factors prior to first cell cleavage. We identified five transcription factors that were potentially necessary for developmental progression: Foxd1, Nkx2-5, Sox18, Myod1, and Runx1. Our very large-scale whole-transcriptome profile of early mouse embryos yielded a novel and valuable resource for studies in developmental biology and stem cell research. The database is available at http://dbtmee.hgc.jp.
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Affiliation(s)
- Sung-Joon Park
- Human Genome Center, the Institute of Medical Science, the University of Tokyo, Tokyo 108-8639, Japan
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100
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Paranjpe SS, Jacobi UG, van Heeringen SJ, Veenstra GJC. A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development. BMC Genomics 2013; 14:762. [PMID: 24195446 PMCID: PMC3907017 DOI: 10.1186/1471-2164-14-762] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 10/26/2013] [Indexed: 12/21/2022] Open
Abstract
Background Dynamics of polyadenylation vs. deadenylation determine the fate of several developmentally regulated genes. Decay of a subset of maternal mRNAs and new transcription define the maternal-to-zygotic transition, but the full complement of polyadenylated and deadenylated coding and non-coding transcripts has not yet been assessed in Xenopus embryos. Results To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted total RNA were harvested across six developmental stages and subjected to high throughput sequencing. The maternally loaded transcriptome is highly diverse and consists of both polyadenylated and deadenylated transcripts. Many maternal genes show peak expression in the oocyte and include genes which are known to be the key regulators of events like oocyte maturation and fertilization. Of all the transcripts that increase in abundance between early blastula and larval stages, about 30% of the embryonic genes are induced by fourfold or more by the late blastula stage and another 35% by late gastrulation. Using a gene model validation and discovery pipeline, we identified novel transcripts and putative long non-coding RNAs (lncRNA). These lncRNA transcripts were stringently selected as spliced transcripts generated from independent promoters, with limited coding potential and a codon bias characteristic of noncoding sequences. Many lncRNAs are conserved and expressed in a developmental stage-specific fashion. Conclusions These data reveal dynamics of transcriptome polyadenylation and abundance and provides a high-confidence catalogue of novel and long non-coding RNAs.
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Affiliation(s)
- Sarita S Paranjpe
- Radboud University Nijmegen, Dept, of Molecular Developmental Biology, Faculty of Science, Nijmegen Center for Molecular Life Sciences, The Netherlands.
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