Transposable elements reveal a stem cell specific class of long noncoding RNAs Research David Kelley123 and John Rinn123* * Corresponding author: John Rinn john_rinn@harvard.edu Author Affiliations 1 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA 2 Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA 3 Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA For all author emails, please log on. Genome Biology 2012, 13:R107 doi:10.1186/gb-2012-13-11-r107 Published: 26 November 2012 Abstract Background Numerous studies over the past decade have elucidated a large set of long intergenic noncoding RNAs (lincRNAs) in the human genome. Results Conclusions TEs pervade lincRNAs, dividing them into classes, and may have shaped lincRNA evolution and function by conferring tissue-specific expression from extant transcriptional regulatory signals. close Sign up to receive new article alerts from Genome Biology
Génome: pour en finir avec l'ADN "poubelle" - Fondamental L’étude de notre génome est un peu comme une histoire sans fin… Les généticiens n’en finissent pas d’approfondir la connaissance de l’ADN, comme en témoigne la trentaine d’articles publiés les 6 et 7 septembre par le consortium ENCODE dans plusieurs revues scientifiques comme Nature, Genome Research, Genome Biology ou Science. Objectif de ce vaste effort collectif, mobilisant 440 chercheurs dans plusieurs pays : identifier tous les «éléments fonctionnels» du génome humain. Et offrir une base de données à la communauté scientifique. Codez-vous pour une protéine ? De quoi s’agit-il exactement ? Cette partie du génome –appelé ADN codant- ne représente que 1 à 2% de la totalité de l’ADN. ENCODE (ENCyclopaedia Of DNA Elements), lancé dès 2003, permet d’en savoir plus sur cette partie de l’ADN. Chausser les lunettes 3D Si la séquence du génome est représentée en deux dimensions, la réalité est toute autre.
5[prime] tRNA halves are present as abundant complexes in serum, concentrated in blood cells, and modulated by aging and calorie restriction Research article Joseph M Dhahbi1*, Stephen R Spindler1, Hani Atamna2, Amy Yamakawa1, Dario Boffelli3, Patricia Mote1 and David IK Martin3 * Corresponding author: Joseph M Dhahbi jdhahbi@ucr.edu Author Affiliations 1 Department of Biochemistry, University of California at Riverside, Riverside, CA, 92521, USA 2 Department of Basic Sciences, Neuroscience, The Commonwealth Medical College, Scranton, Scranton, PA, 18510, USA 3 Center for Genetics, Childrens Hospital Oakland Research Institute, Oakland, CA, 94609, USA For all author emails, please log on. BMC Genomics 2013, 14:298 doi:10.1186/1471-2164-14-298 Published: 2 May 2013 Abstract Background Small RNAs complex with proteins to mediate a variety of functions in animals and plants. Results In sequencing small RNAs extracted from mouse serum, we identified abundant 5′ tRNA halves derived from a small subset of tRNAs, implying that they are produced by tRNA type-specific biogenesis and/or release. Conclusions Keywords: close
An integrative analysis of cellular contexts, miRNAs and mRNAs reveals network clusters associated with antiestrogen-resistant breast cancer cells Research article Seungyoon Nam12*, Xinghua Long23, ChangHyuk Kwon1, Sun Kim4 and Kenneth P Nephew2 * Corresponding author: Seungyoon Nam seungyoon.nam@ncc.re.kr Author Affiliations 1 Cancer Genomics Branch, National Cancer Center, Goyang-si, Gyeonggi-do, 410-769, Korea 2 Department of Cellular and Integrative Physiology, Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA 3 Zhongnan Hospital, Wuhan University, Wuhan, 430071, China 4 Department of Computer Science and Engineering, Bioinformatics Institute, Seoul National University, Seoul, 151-742, Korea For all author emails, please log on. BMC Genomics 2012, 13:732 doi:10.1186/1471-2164-13-732 Published: 27 December 2012 Abstract Background A major goal of the field of systems biology is to translate genome-wide profiling data (e.g., mRNAs, miRNAs) into interpretable functional networks. Results Conclusions Keywords: Bioinformatics; miRNA; Network; Breast cancer; Antiestrogen resistance close
Nature Publishing Group : science journals, jobs, and information Gene promoters show chromosome-specificity and reveal chromosome territories in humans Research article Paul Gagniuc1* and Constantin Ionescu-Tirgoviste2 * Corresponding author: Paul Gagniuc paul_gagniuc@acad.ro Author Affiliations 1 Institute of Genetics, University of Bucharest, Bucharest, 060101, Romania 2 National Institute of Diabetes, Nutrition and Metabolic Diseases ”N.C. For all author emails, please log on. BMC Genomics 2013, 14:278 doi:10.1186/1471-2164-14-278 Published: 24 April 2013 Abstract Background Gene promoters have guided evolution processes for millions of years. Results In order to measure the structural similarity of gene promoters, we used two-dimensional image-based patterns obtained through Kappa Index of Coincidence (Kappa IC) and (C+G)% values. Conclusions In this paper we showed that gene promoters appear to be specific to each chromosome. close Sign up to receive new article alerts from BMC Genomics
Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression Research article Guan-Zheng Luo1†, Markus Hafner2†, Zhimin Shi3, Miguel Brown2, Gui-Hai Feng1, Thomas Tuschl2, Xiu-Jie Wang1* and XiaoChing Li3* * Corresponding authors: Xiu-Jie Wang xjwang@genetics.ac.cn - XiaoChing Li Xli4@lsuhsc.edu † Equal contributors Author Affiliations 1 State Kay Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China 2 Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY, 10065, USA 3 Neuroscience Center of Excellence, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA For all author emails, please log on. BMC Genomics 2012, 13:727 doi:10.1186/1471-2164-13-727 Published: 26 December 2012 Abstract Background MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression post-transcriptionally in a wide range of biological processes. Results Conclusions Keywords: close Sign up to receive new article alerts from BMC Genomics
Recherche One of the leading biomedical research centres in Europe, IGBMC explores very diverse themes, combining fundamental and applied research in life sciences. The 48 research teams conduct research on various topics, ranging from structural analysis of proteins to human genetics, stem cells, biophysics and epigenetics. The scientific results of the Institute have already allowed significant advances, notably in the understanding of many human pathologies such as certain cancers or rare genetic diseases. Discover IGBMC's research teams: Team list Discover the research carried out in IGBMC's 4 departments: Research programs across departments: 3 transversal programs are being set-up around the following strategic priorities: Cellular signaling and nuclear dynamics (emerging program) Mouse models of human diseases Bioinformatics and biocomputing IGBMC publications
BMC Evolutionary Biology | Abstract | Phylogenomics of strongylocentrotid sea urchins Research article Kord M Kober12* and Giacomo Bernardi1 * Corresponding author: Kord M Kober kord.kober@nursing.ucsf.edu Author Affiliations 1 Department of Ecology & Evolutionary Biology, University Of California Santa Cruz, Santa Cruz, CA, USA 2 Department of Physiological Nursing, University Of California San Francisco, San Francisco, CA, USA For all author emails, please log on. BMC Evolutionary Biology 2013, 13:88 doi:10.1186/1471-2148-13-88 Published: 23 April 2013 Abstract Background Strongylocentrotid sea urchins have a long tradition as model organisms for studying many fundamental processes in biology including fertilization, embryology, development and genome regulation but the phylogenetic relationships of the group remain largely unresolved. Results Conclusions Nuclear genome data contains phylogenetic signal informative for understanding the evolutionary history of this group. Keywords: close Sign up to receive new article alerts from BMC Evolutionary Biology
Comprehensive structural annotation of Pichia pastoris transcriptome and the response to various carbon sources using deep paired-end RNA sequencing Research article Shuli Liang1†, Bin Wang1†, Li Pan1, Yanrui Ye1, Minghui He3, Shuangyan Han1, Suiping Zheng1, Xiaoning Wang12* and Ying Lin1* * Corresponding authors: Xiaoning Wang xnwang@scut.edu.cn - Ying Lin feylin@scut.edu.cn † Equal contributors Author Affiliations 1 School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong 510006, China 2 School of life Science, General Hospital of PLA, Beijing 100853, China 3 Beijing Genomics Institute at Shenzhen, Shenzhen 518000, China For all author emails, please log on. BMC Genomics 2012, 13:738 doi:10.1186/1471-2164-13-738 Published: 31 December 2012 Abstract Background The methylotrophic yeast Pichia pastoris is widely used as a bioengineering platform for producing industrial and biopharmaceutical proteins, studying protein expression and secretion mechanisms, and analyzing metabolite synthesis and peroxisome biogenesis. Results Conclusions Keywords: close Sign up to receive new article alerts from BMC Genomics
Functional transcriptomic analysis of the role of MAB-5/Hox in Q neuroblast migration in Caenorhabditis elegans Research article Joel V Tamayo, Mahekta Gujar, Stuart J Macdonald and Erik A Lundquist* * Corresponding author: Erik A Lundquist erikl@ku.edu Author Affiliations Department of Molecular Biosciences, Programs in Genetics and Molecular, Cellular, and Developmental Biology, The University of Kansas, 1200 Sunnyside Avenue, Lawrence KS 66045, USA For all author emails, please log on. BMC Genomics 2013, 14:304 doi:10.1186/1471-2164-14-304 Published: 4 May 2013 Abstract Background Directed cell migration is a fundamental process in normal development and in tumor metastasis. Results Transcriptome profiling is a widely-used and potent tool to identify genes involved in developmental and pathological processes, and is most informative when RNA can be isolated from individual cell or tissue types. Conclusions close Sign up to receive new article alerts from BMC Genomics
Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice Research article Tingting Lu1*, Chuanrang Zhu1, Guojun Lu1, Yunli Guo1, Yan Zhou1, Zhiyong Zhang2, Yan Zhao1, Wenjun Li1, Ying Lu1, Weihua Tang2, Qi Feng1 and Bin Han1* * Corresponding authors: Tingting Lu ttlu@ncgr.ac.cn - Bin Han bhan@ncgr.ac.cn Author Affiliations 1 National Center for Gene Research & Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233, China 2 National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233, China For all author emails, please log on. BMC Genomics 2012, 13:721 doi:10.1186/1471-2164-13-721 Published: 22 December 2012 Abstract Background Cis-natural antisense transcripts (cis-NATs) are RNAs transcribed from the antisense strand of a gene locus, and are complementary to the RNA transcribed from the sense strand. Results Conclusions Keywords: close
The transcriptome of Leishmania major in the axenic promastigote stage: transcript annotation and relative expression levels by RNA-seq Research article Alberto Rastrojo1, Fernando Carrasco-Ramiro1, Diana Martín1, Antonio Crespillo1, Rosa M Reguera2, Begoña Aguado1* and Jose M Requena1* * Corresponding authors: Begoña Aguado baguado@cbm.uam.es - Jose M Requena jmrequena@cbm.uam.es Author Affiliations 1 Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain 2 Departamento de Ciencias Biomédicas, Universidad de León, 24071 León, Spain For all author emails, please log on. BMC Genomics 2013, 14:223 doi:10.1186/1471-2164-14-223 Published: 4 April 2013 Abstract Background Although the genome sequence of the protozoan parasite Leishmania major was determined several years ago, the knowledge of its transcriptome was incomplete, both regarding the real number of genes and their primary structure. Results Here, we describe the first comprehensive transcriptome analysis of a parasite from the genus Leishmania. Conclusions Keywords: close Sign up to receive new article alerts from BMC Genomics