{"title":"Editorial Board: (Advanced Genetics 3/04)","authors":"","doi":"10.1002/ggn2.202370032","DOIUrl":"https://doi.org/10.1002/ggn2.202370032","url":null,"abstract":"Nadav Ahituv, University of California, San Francisco, San Francisco, CA USA Nir Barzilai, Albert Einstein College of Medicine, Bronx, NY USA Jacqueline Batley, University of Western Australia, Perth, Australia Touati Benoukraf,Memorial University of Newfoundland, St. John’s, NL, Canada Ewan Birney, EMBL-EBI, Cambridge, UK Catherine A. Brownstein, Boston Children’s Hospital, Boston, MA USA Stephen J. Chanock, National Cancer Institute, Bethesda, MD USA George Church, Harvard Medical School, Boston, MA USA Francesco Cucca, University of Sassari, Sassari, Sardinia, Italy Marcella Devoto, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy Roland Eils, Berlin Institue of Health, Berlin, Germany Jeanette Erdmann, Institute for Cardiogenetics, University of Lubeck, Lubeck, Germany Andrew Feinberg, Johns Hopkins University, Baltimore, MD USA Claudio Franceschi, University of Bologna, Bologna, Italy Paul W. Franks, Lund University, Malmö, Sweden Rachel Freathy, University of Exeter, Exeter, UK Jingyuan Fu, University Medical Center Groningen, Groningen, The Netherlands Eileen Furlong, European Molecular Biology Laboratory, Heidelberg, Germany Tom Gilbert, University of Copenhagen, The Globe Institute, Copenhagen, Denmark Joseph G. Gleeson, University of California, San Diego, Howard Hughes Medical Institute for Genomic Medicine, La Jolla, CA USA Erica Golemis, Fox Chase Cancer Center, Philadelphia, PA USA Sarah Hearne, International Maize and Wheat Improvement Centre (CIMMYT), Texcoco, Mexico Agnar Helgason, deCODE Genetics, Reykjavik, Iceland Kristina Hettne, Leiden University Libraries, Leiden, The Netherlands Sanwen Huang, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China Youssef Idaghdour, New York University, Abu Dhabi, Abu Dhabi, UAE Rosalind John, Cardiff University, Cardiff, UK Moien Kanaan, Bethlehem University, Bethlehem, Palestine Beat Keller, University of Zurich, Zurich, Switzerland Tuuli Lappalainen, New York Genome Center, Columbia University, New York, NY USA Luis F. Larrondo, Pontifica Universidad Catolica de Chile, Santiago, Chile Suet-Yi Leung, The University of Hong Kong, Hong Kong, China Ryan Lister, The University of Western Australia, Perth, Australia Jianjun Liu, Genome Institute Singapore, Singapore Naomichi Matsumoto, Yokohama City University, Yokohama, Japan Rachel S. Meyer, University of California, Los Angeles, Los Angeles, CA USA Nicola Mulder, University of Cape Town, Cape Town, South Africa Seishi Ogawa, Kyoto University, Kyoto, Japan Guilherme Oliveira, Vale Institute of Technology, Belem, Brazil Qiang Pan-Hammarstrom, Karolinska Institute, Stockholm, Sweden Len A. Pennacchio, Joint Genome Institute, Walnut Creek, CA USA Martin Pera, Jackson Lab, Bar Harbor, ME USA Danielle Posthuma, VU University Amsterdam, Amsterdam, The Netherlands Michael Purugganan, New York University, New York, NY USA Maanasa Raghavan, University of Chic","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"4 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.202370032","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50144419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A New Epigenetic Crosstalk: Chemical Modification Information Flow","authors":"Hongwoo Lee, Young-Joon Park, Pil Joon Seo","doi":"10.1002/ggn2.202200033","DOIUrl":"10.1002/ggn2.202200033","url":null,"abstract":"<p>Central dogma is the most fundamental hypothesis in the field of molecular biology and explains the genetic information flow from DNA to protein. Beyond residue-by-residue transmission of sequential information, chemical modifications of DNA, RNA, and protein are also relayed in the course of gene expression. Here, this work presents recent evidence supporting bidirectional interplay between chromatin modifications and RNA modifications. Furthermore, several RNA modifications likely affect chemical modifications of proteins. The relay of chemical modifications occurs co-transcriptionally or co-translationally, ensuring crosstalk among chemical modifications at the DNA, RNA, and protein levels. Overall, this work proposes a hypothetical framework that represents transmission of chemical modification information among chromatin, RNA, and proteins.</p>","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"4 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.202200033","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41177564","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Editorial Board: (Advanced Genetics 2/04)","authors":"","doi":"10.1002/ggn2.202370022","DOIUrl":"https://doi.org/10.1002/ggn2.202370022","url":null,"abstract":"Nadav Ahituv, University of California, San Francisco, San Francisco, CA USA Nir Barzilai, Albert Einstein College of Medicine, Bronx, NY USA Jacqueline Batley, University of Western Australia, Perth, Australia Touati Benoukraf,Memorial University of Newfoundland, St. John’s, NL, Canada Ewan Birney, EMBL-EBI, Cambridge, UK Catherine A. Brownstein, Boston Children’s Hospital, Boston, MA USA Stephen J. Chanock, National Cancer Institute, Bethesda, MD USA George Church, Harvard Medical School, Boston, MA USA Francesco Cucca, University of Sassari, Sassari, Sardinia, Italy Marcella Devoto, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy Roland Eils, Berlin Institue of Health, Berlin, Germany Jeanette Erdmann, Institute for Cardiogenetics, University of Lubeck, Lubeck, Germany Andrew Feinberg, Johns Hopkins University, Baltimore, MD USA Claudio Franceschi, University of Bologna, Bologna, Italy Paul W. Franks, Lund University, Malmö, Sweden Rachel Freathy, University of Exeter, Exeter, UK Jingyuan Fu, University Medical Center Groningen, Groningen, The Netherlands Eileen Furlong, European Molecular Biology Laboratory, Heidelberg, Germany Tom Gilbert, University of Copenhagen, The Globe Institute, Copenhagen, Denmark Joseph G. Gleeson, University of California, San Diego, Howard Hughes Medical Institute for Genomic Medicine, La Jolla, CA USA Erica Golemis, Fox Chase Cancer Center, Philadelphia, PA USA Sarah Hearne, International Maize and Wheat Improvement Centre (CIMMYT), Texcoco, Mexico Agnar Helgason, deCODE Genetics, Reykjavik, Iceland Kristina Hettne, Leiden University Libraries, Leiden, The Netherlands Sanwen Huang, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China Youssef Idaghdour, New York University, Abu Dhabi, Abu Dhabi, UAE Rosalind John, Cardiff University, Cardiff, UK Moien Kanaan, Bethlehem University, Bethlehem, Palestine Beat Keller, University of Zurich, Zurich, Switzerland Tuuli Lappalainen, New York Genome Center, Columbia University, New York, NY USA Luis F. Larrondo, Pontifica Universidad Catolica de Chile, Santiago, Chile Suet-Yi Leung, The University of Hong Kong, Hong Kong, China Ryan Lister, The University of Western Australia, Perth, Australia Jianjun Liu, Genome Institute Singapore, Singapore Naomichi Matsumoto, Yokohama City University, Yokohama, Japan Rachel S. Meyer, University of California, Los Angeles, Los Angeles, CA USA Nicola Mulder, University of Cape Town, Cape Town, South Africa Seishi Ogawa, Kyoto University, Kyoto, Japan Guilherme Oliveira, Vale Institute of Technology, Belem, Brazil Qiang Pan-Hammarstrom, Karolinska Institute, Stockholm, Sweden Len A. Pennacchio, Joint Genome Institute, Walnut Creek, CA USA Martin Pera, Jackson Lab, Bar Harbor, ME USA Danielle Posthuma, VU University Amsterdam, Amsterdam, The Netherlands Michael Purugganan, New York University, New York, NY USA Maanasa Raghavan, University of Chic","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.202370022","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50123038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Isa-Rita M. Russo, Deon de Jager, Anna M. van Wyk, Arrie W. Klopper, Kenneth Uiseb, Coral Birss, Ian Rushworth, Paulette Bloomer
{"title":"The Contribution of Digital Sequence Information to Conservation Biology: A Southern African Perspective","authors":"Isa-Rita M. Russo, Deon de Jager, Anna M. van Wyk, Arrie W. Klopper, Kenneth Uiseb, Coral Birss, Ian Rushworth, Paulette Bloomer","doi":"10.1002/ggn2.202200032","DOIUrl":"10.1002/ggn2.202200032","url":null,"abstract":"<p>Many recent contributions have made a compelling case that genetic diversity is not adequately reflected in international frameworks and policies, as well as in local governmental processes implementing such frameworks. Using digital sequence information (DSI) and other publicly available data is supported to assess genetic diversity, toward formulation of practical actions for long-term conservation of biodiversity, with the particular goal of maintaining ecological and evolutionary processes. Given the inclusion of specific goals and targets regarding DSI in the latest draft of the Global Biodiversity Framework negotiated at the 15<sup>th</sup> Conference of the Parties (COP15) in Montreal in December 2022 and the crucial decisions on access and benefit sharing to DSI that will be taken in the coming months and future COP meetings, a southern African perspective on how and why open access to DSI is essential for the conservation of intraspecific biodiversity (genetic diversity and structure) across country borders is provided.</p>","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.202200032","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9597327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Editorial Board: (Advanced Genetics 1/04)","authors":"","doi":"10.1002/ggn2.202370012","DOIUrl":"https://doi.org/10.1002/ggn2.202370012","url":null,"abstract":"Nadav Ahituv, University of California, San Francisco, San Francisco, CA USA Nir Barzilai, Albert Einstein College of Medicine, Bronx, NY USA Jacqueline Batley, University of Western Australia, Perth, Australia Touati Benoukraf,Memorial University of Newfoundland, St. John’s, NL, Canada Ewan Birney, EMBL-EBI, Cambridge, UK Catherine A. Brownstein, Boston Children’s Hospital, Boston, MA USA Stephen J. Chanock, National Cancer Institute, Bethesda, MD USA George Church, Harvard Medical School, Boston, MA USA Francesco Cucca, University of Sassari, Sassari, Sardinia, Italy Marcella Devoto, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy Roland Eils, Berlin Institue of Health, Berlin, Germany Jeanette Erdmann, Institute for Cardiogenetics, University of Lubeck, Lubeck, Germany Andrew Feinberg, Johns Hopkins University, Baltimore, MD USA Claudio Franceschi, University of Bologna, Bologna, Italy Paul W. Franks, Lund University, Malmö, Sweden Rachel Freathy, University of Exeter, Exeter, UK Jingyuan Fu, University Medical Center Groningen, Groningen, The Netherlands Eileen Furlong, European Molecular Biology Laboratory, Heidelberg, Germany Tom Gilbert, University of Copenhagen, The Globe Institute, Copenhagen, Denmark Joseph G. Gleeson, University of California, San Diego, Howard Hughes Medical Institute for Genomic Medicine, La Jolla, CA USA Erica Golemis, Fox Chase Cancer Center, Philadelphia, PA USA Sarah Hearne, International Maize and Wheat Improvement Centre (CIMMYT), Texcoco, Mexico Agnar Helgason, deCODE Genetics, Reykjavik, Iceland Kristina Hettne, Leiden University Libraries, Leiden, The Netherlands Sanwen Huang, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China Youssef Idaghdour, New York University, Abu Dhabi, Abu Dhabi, UAE Rosalind John, Cardiff University, Cardiff, UK Moien Kanaan, Bethlehem University, Bethlehem, Palestine Beat Keller, University of Zurich, Zurich, Switzerland Tuuli Lappalainen, New York Genome Center, Columbia University, New York, NY USA Luis F. Larrondo, Pontifica Universidad Catolica de Chile, Santiago, Chile Suet-Yi Leung, The University of Hong Kong, Hong Kong, China Ryan Lister, The University of Western Australia, Perth, Australia Jianjun Liu, Genome Institute Singapore, Singapore Naomichi Matsumoto, Yokohama City University, Yokohama, Japan Rachel S. Meyer, University of California, Los Angeles, Los Angeles, CA USA Nicola Mulder, University of Cape Town, Cape Town, South Africa Seishi Ogawa, Kyoto University, Kyoto, Japan Guilherme Oliveira, Vale Institute of Technology, Belem, Brazil Qiang Pan-Hammarstrom, Karolinska Institute, Stockholm, Sweden Len A. Pennacchio, Joint Genome Institute, Walnut Creek, CA USA Martin Pera, Jackson Lab, Bar Harbor, ME USA Danielle Posthuma, VU University Amsterdam, Amsterdam, The Netherlands Michael Purugganan, New York University, New York, NY USA Maanasa Raghavan, University of Chic","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.202370012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50127642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tanner Stokes, Haoning Howard Cen, Philipp Kapranov, Iain J Gallagher, Andrew A. Pitsillides, Claude-Henry Volmar, William E Kraus, James D. Johnson, Stuart M. Phillips, Claes Wahlestedt, James A. Timmons
{"title":"Transcriptomics for Clinical and Experimental Biology Research: Hang on a Seq","authors":"Tanner Stokes, Haoning Howard Cen, Philipp Kapranov, Iain J Gallagher, Andrew A. Pitsillides, Claude-Henry Volmar, William E Kraus, James D. Johnson, Stuart M. Phillips, Claes Wahlestedt, James A. Timmons","doi":"10.1002/ggn2.202200024","DOIUrl":"10.1002/ggn2.202200024","url":null,"abstract":"<p>Sequencing the human genome empowers translational medicine, facilitating transcriptome-wide molecular diagnosis, pathway biology, and drug repositioning. Initially, microarrays are used to study the bulk transcriptome; but now short-read RNA sequencing (RNA-seq) predominates. Positioned as a superior technology, that makes the discovery of novel transcripts routine, most RNA-seq analyses are in fact modeled on the known transcriptome. Limitations of the RNA-seq methodology have emerged, while the design of, and the analysis strategies applied to, arrays have matured. An equitable comparison between these technologies is provided, highlighting advantages that modern arrays hold over RNA-seq. Array protocols more accurately quantify constitutively expressed protein coding genes across tissue replicates, and are more reliable for studying lower expressed genes. Arrays reveal long noncoding RNAs (lncRNA) are neither sparsely nor lower expressed than protein coding genes. Heterogeneous coverage of constitutively expressed genes observed with RNA-seq, undermines the validity and reproducibility of pathway analyses. The factors driving these observations, many of which are relevant to long-read or single-cell sequencing are discussed. As proposed herein, a reappreciation of bulk transcriptomic methods is required, including wider use of the modern high-density array data—to urgently revise existing anatomical RNA reference atlases and assist with more accurate study of lncRNAs.</p>","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"4 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.202200024","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10301654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jacqueline Batley, Andrew L. Hufton, Guilherme Oliveira, Rajeev K. Varshney
{"title":"Global Action on Biodiversity May Hinge on Genetic Data Sharing Agreement","authors":"Jacqueline Batley, Andrew L. Hufton, Guilherme Oliveira, Rajeev K. Varshney","doi":"10.1002/ggn2.202200031","DOIUrl":"10.1002/ggn2.202200031","url":null,"abstract":"<p>This month, parties to the Convention on Biological Diversity (CBD) are meeting in Montreal with the aim of concluding negotiations on an important new action plan for global biodiversity conservation, known as the post-2020 Global Biodiversity Framework (GBF). In these negotiations, genetic data from plants, animals, fungi and microorganisms, known as digital sequence information (DSI) in policy circles, has emerged as a central source of tension. A number of parties are demanding that benefits arising from the use of these genetic data be better shared with the countries where the genetic material was collected.</p><p>The Nagoya Protocol, a component of the CBD, recognized the right of countries to share in the benefits derived from their nation's genetic resources, and established a framework by which countries can regulate and track the use of physical “genetic resources” (i.e., biological samples, strains, plant lines, etc., containing genetic material). This framework, however, is complex and, in the opinion of many, has proven inefficient at driving meaningful benefit sharing.<sup>[</sup><span><sup>1</sup></span><sup>]</sup></p><p>Researchers and other stakeholders have raised serious concerns about applying such a framework to DSI.<sup>[</sup><span><sup>2, 3</sup></span><sup>]</sup> Some of the proposals on the table could spell an end to the culture of open sequence sharing that has defined non-human genetics research for decades, and which is widely agreed to have massive positive effects on research progress and economic value creation. A poorly developed solution could therefore have a negative impact on biodiversity research that is crucial to the aims of the CBD. Representatives of indigenous peoples and local communities have also been active in the discussions on this topic and argue that the rights and roles of their communities must be respected in any final agreement.<sup>[</sup><span><sup>4</sup></span><sup>]</sup></p><p>That this issue alone could stymie global biodiversity conservation efforts is not in doubt. Talks in August on a major ocean biodiversity treaty failed to make progress because of lack of agreement on DSI,<sup>[</sup><span><sup>5</sup></span><sup>]</sup> and African negotiators have warned that they will not agree to a GBF that lacks a concrete solution to DSI.<sup>[</sup><span><sup>6</sup></span><sup>]</sup> The issue has also proven contentious in a recent meeting of the Governing Body session of the International Treaty on Plant Genetic Resources for Food and Agriculture.<sup>[</sup><span><sup>7</sup></span><sup>]</sup> It is clear that an effective benefit sharing solution must be part of any global action plan to conserve biodiversity.</p><p>But grounds for optimism remain. Scientists and major research organizations are arguing that it is possible to build a solution that will drive benefit-sharing, protect open science and promote biodiversity conservation.<sup>[</sup><span><sup>4, 8, 9</sup></span>","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"3 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9993466/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9455821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}