ALBERT

Description: The recently released human genome sequences provide us with reference data to conduct comparative genomic research on primates, which will be important to understand what genetic information makes us human. Here we present a first-generation human-chimpanzee comparative genome map and its initial analysis. The map was constructed through paired alignment of 77,461 chimpanzee bacterial artificial chromosome end sequences with publicly available human genome sequences. We detected candidate positions, including two clusters on human chromosome 21 that suggest large, nonrandom regions of difference between the two genomes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fujiyama, Asao -- Watanabe, Hidemi -- Toyoda, Atsushi -- Taylor, Todd D -- Itoh, Takehiko -- Tsai, Shih-Feng -- Park, Hong-Seog -- Yaspo, Marie-Laure -- Lehrach, Hans -- Chen, Zhu -- Fu, Gang -- Saitou, Naruya -- Osoegawa, Kazutoyo -- de Jong, Pieter J -- Suto, Yumiko -- Hattori, Masahira -- Sakaki, Yoshiyuki -- New York, N.Y. -- Science. 2002 Jan 4;295(5552):131-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. afujiyam@gsc.riken.go.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11778049" target="_blank"〉PubMed〈/a〉

Description: The functional complexity of the human transcriptome is not yet fully elucidated. We report a high-throughput sequence of the human transcriptome from a human embryonic kidney and a B cell line. We used shotgun sequencing of transcripts to generate randomly distributed reads. Of these, 50% mapped to unique genomic locations, of which 80% corresponded to known exons. We found that 66% of the polyadenylated transcriptome mapped to known genes and 34% to nonannotated genomic regions. On the basis of known transcripts, RNA-Seq can detect 25% more genes than can microarrays. A global survey of messenger RNA splicing events identified 94,241 splice junctions (4096 of which were previously unidentified) and showed that exon skipping is the most prevalent form of alternative splicing.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sultan, Marc -- Schulz, Marcel H -- Richard, Hugues -- Magen, Alon -- Klingenhoff, Andreas -- Scherf, Matthias -- Seifert, Martin -- Borodina, Tatjana -- Soldatov, Aleksey -- Parkhomchuk, Dmitri -- Schmidt, Dominic -- O'Keeffe, Sean -- Haas, Stefan -- Vingron, Martin -- Lehrach, Hans -- Yaspo, Marie-Laure -- New York, N.Y. -- Science. 2008 Aug 15;321(5891):956-60. doi: 10.1126/science.1160342. Epub 2008 Jul 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18599741" target="_blank"〉PubMed〈/a〉

Description: Epigenetic alterations, that is, disruption of DNA methylation and chromatin architecture, are now acknowledged as a universal feature of tumorigenesis. Medulloblastoma, a clinically challenging, malignant childhood brain tumour, is no exception. Despite much progress from recent genomics studies, with recurrent changes identified in each of the four distinct tumour subgroups (WNT-pathway-activated, SHH-pathway-activated, and the less-well-characterized Group 3 and Group 4), many cases still lack an obvious genetic driver. Here we present whole-genome bisulphite-sequencing data from thirty-four human and five murine tumours plus eight human and three murine normal controls, augmented with matched whole-genome, RNA and chromatin immunoprecipitation sequencing data. This comprehensive data set allowed us to decipher several features underlying the interplay between the genome, epigenome and transcriptome, and its effects on medulloblastoma pathophysiology. Most notable were highly prevalent regions of hypomethylation correlating with increased gene expression, extending tens of kilobases downstream of transcription start sites. Focal regions of low methylation linked to transcription-factor-binding sites shed light on differential transcriptional networks between subgroups, whereas increased methylation due to re-normalization of repressed chromatin in DNA methylation valleys was positively correlated with gene expression. Large, partially methylated domains affecting up to one-third of the genome showed increased mutation rates and gene silencing in a subgroup-specific fashion. Epigenetic alterations also affected novel medulloblastoma candidate genes (for example, LIN28B), resulting in alternative promoter usage and/or differential messenger RNA/microRNA expression. Analysis of mouse medulloblastoma and precursor-cell methylation demonstrated a somatic origin for many alterations. Our data provide insights into the epigenetic regulation of transcription and genome organization in medulloblastoma pathogenesis, which are probably also of importance in a wider developmental and disease context.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hovestadt, Volker -- Jones, David T W -- Picelli, Simone -- Wang, Wei -- Kool, Marcel -- Northcott, Paul A -- Sultan, Marc -- Stachurski, Katharina -- Ryzhova, Marina -- Warnatz, Hans-Jorg -- Ralser, Meryem -- Brun, Sonja -- Bunt, Jens -- Jager, Natalie -- Kleinheinz, Kortine -- Erkek, Serap -- Weber, Ursula D -- Bartholomae, Cynthia C -- von Kalle, Christof -- Lawerenz, Chris -- Eils, Jurgen -- Koster, Jan -- Versteeg, Rogier -- Milde, Till -- Witt, Olaf -- Schmidt, Sabine -- Wolf, Stephan -- Pietsch, Torsten -- Rutkowski, Stefan -- Scheurlen, Wolfram -- Taylor, Michael D -- Brors, Benedikt -- Felsberg, Jorg -- Reifenberger, Guido -- Borkhardt, Arndt -- Lehrach, Hans -- Wechsler-Reya, Robert J -- Eils, Roland -- Yaspo, Marie-Laure -- Landgraf, Pablo -- Korshunov, Andrey -- Zapatka, Marc -- Radlwimmer, Bernhard -- Pfister, Stefan M -- Lichter, Peter -- England -- Nature. 2014 Jun 26;510(7506):537-41. doi: 10.1038/nature13268. Epub 2014 May 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany [2]. ; 1] Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany [2]. ; Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany. ; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany. ; Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, Berlin 14195, Germany. ; Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich Heine University Dusseldorf, Moorenstrasse 5, Dusseldorf 40225, Germany. ; Department of Neuropathology, NN Burdenko Neurosurgical Institute, 4th Tverskaya-Yamskaya 16, Moscow 125047, Russia. ; Tumor Initiation and Maintenance Program, National Cancer Institute (NCI)-Designated Cancer Center, Sanford-Burnham Medical Research Institute, 2880 Torrey Pines Scenic Drive, La Jolla, California 92037, USA. ; 1] Queensland Brain Institute, University of Queensland, QBI Building, St Lucia, Queensland 4072, Australia [2] Department of Oncogenomics, AMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands. ; Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany. ; 1] Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany [2] Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany. ; 1] Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany [2] European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg 69117, Germany. ; 1] Division of Translational Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany [2] National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, Heidelberg 69120, Germany. ; Data Management Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany. ; Department of Oncogenomics, AMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands. ; 1] Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, Im Neuenheimer Feld 430, Heidelberg 69120, Germany [2] Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany. ; Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany. ; Department of Neuropathology, University of Bonn Medical Center, Sigmund-Freud-Strasse 25, Bonn 53105, Germany. ; Department of Paediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg 20246, Germany. ; Cnopf'sche Kinderklinik, Nurnberg Children's Hospital, St.-Johannis-Muhlgasse 19, Nurnberg 90419, Germany. ; 1] Program in Developmental and Stem Cell Biology, The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada [2] Division of Neurosurgery, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada [3] Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada. ; 1] Department of Neuropathology, Heinrich Heine University Dusseldorf, Moorenstrasse 5, Dusseldorf 40225, Germany [2] German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany. ; 1] Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany [2] Institute of Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Heidelberg 69120, Germany [3] Bioquant Center, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg 69120, Germany [4] Heidelberg Center for Personalised Oncology (DKFZ-HIPO), Im Neuenheimer Feld 280, Heidelberg 69120, Germany. ; 1] Department of Neuropathology, University of Heidelberg, Im Neuenheimer Feld 220, Heidelberg 69120, Germany [2] Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 220-221, Heidelberg, 69120 Germany. ; 1] Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany [2] Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, Im Neuenheimer Feld 430, Heidelberg 69120, Germany. ; 1] Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany [2] Heidelberg Center for Personalised Oncology (DKFZ-HIPO), Im Neuenheimer Feld 280, Heidelberg 69120, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24847876" target="_blank"〉PubMed〈/a〉