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Jansen C, Paraiso KD, Zhou JJ, Blitz IL, Fish MB, Charney RM, Cho JS, Yasuoka Y, Sudou N, Bright AR, Wlizla M, Veenstra GJC, Taira M, Zorn AM, Mortazavi A, Cho KWY. Uncovering the mesendoderm gene regulatory network through multi-omic data integration. Cell Rep 2022; 38:110364. [PMID: 35172134 PMCID: PMC8917868 DOI: 10.1016/j.celrep.2022.110364] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 10/30/2021] [Accepted: 01/19/2022] [Indexed: 01/01/2023] Open
Abstract
Mesendodermal specification is one of the earliest events in embryogenesis, where cells first acquire distinct identities. Cell differentiation is a highly regulated process that involves the function of numerous transcription factors (TFs) and signaling molecules, which can be described with gene regulatory networks (GRNs). Cell differentiation GRNs are difficult to build because existing mechanistic methods are low throughput, and high-throughput methods tend to be non-mechanistic. Additionally, integrating highly dimensional data composed of more than two data types is challenging. Here, we use linked self-organizing maps to combine chromatin immunoprecipitation sequencing (ChIP-seq)/ATAC-seq with temporal, spatial, and perturbation RNA sequencing (RNA-seq) data from Xenopus tropicalis mesendoderm development to build a high-resolution genome scale mechanistic GRN. We recover both known and previously unsuspected TF-DNA/TF-TF interactions validated through reporter assays. Our analysis provides insights into transcriptional regulation of early cell fate decisions and provides a general approach to building GRNs using highly dimensional multi-omic datasets.
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Affiliation(s)
- Camden Jansen
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Kitt D Paraiso
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Jeff J Zhou
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Margaret B Fish
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Rebekah M Charney
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Jin Sun Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Norihiro Sudou
- Department of Anatomy, School of Medicine, Toho University, Tokyo, Japan
| | - Ann Rose Bright
- Department of Molecular Developmental Biology, Radboud University, Nijmegen, the Netherlands
| | - Marcin Wlizla
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Gert Jan C Veenstra
- Department of Molecular Developmental Biology, Radboud University, Nijmegen, the Netherlands
| | - Masanori Taira
- Department of Biological Sciences, Chuo University, Tokyo, Japan
| | - Aaron M Zorn
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA.
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA.
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2
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Karimi K, Fortriede JD, Lotay VS, Burns KA, Wang DZ, Fisher ME, Pells TJ, James-Zorn C, Wang Y, Ponferrada VG, Chu S, Chaturvedi P, Zorn AM, Vize PD. Xenbase: a genomic, epigenomic and transcriptomic model organism database. Nucleic Acids Res 2019; 46:D861-D868. [PMID: 29059324 PMCID: PMC5753396 DOI: 10.1093/nar/gkx936] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/02/2017] [Indexed: 01/03/2023] Open
Abstract
Xenbase (www.xenbase.org) is an online resource for researchers utilizing Xenopus laevis and Xenopus tropicalis, and for biomedical scientists seeking access to data generated with these model systems. Content is aggregated from a variety of external resources and also generated by in-house curation of scientific literature and bioinformatic analyses. Over the past two years many new types of content have been added along with new tools and functionalities to reflect the impact of high-throughput sequencing. These include new genomes for both supported species (each with chromosome scale assemblies), new genome annotations, genome segmentation, dynamic and interactive visualization for RNA-Seq data, updated ChIP-Seq mapping, GO terms, protein interaction data, ORFeome support, and improved connectivity to other biomedical and bioinformatic resources.
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Affiliation(s)
- Kamran Karimi
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
| | - Joshua D Fortriede
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Vaneet S Lotay
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
| | - Kevin A Burns
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Dong Zhou Wang
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
| | - Malcom E Fisher
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Troy J Pells
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
| | - Christina James-Zorn
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Ying Wang
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
| | - V G Ponferrada
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Stanley Chu
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
| | - Praneet Chaturvedi
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Aaron M Zorn
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Peter D Vize
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
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Harper L, Campbell J, Cannon EKS, Jung S, Poelchau M, Walls R, Andorf C, Arnaud E, Berardini TZ, Birkett C, Cannon S, Carson J, Condon B, Cooper L, Dunn N, Elsik CG, Farmer A, Ficklin SP, Grant D, Grau E, Herndon N, Hu ZL, Humann J, Jaiswal P, Jonquet C, Laporte MA, Larmande P, Lazo G, McCarthy F, Menda N, Mungall CJ, Munoz-Torres MC, Naithani S, Nelson R, Nesdill D, Park C, Reecy J, Reiser L, Sanderson LA, Sen TZ, Staton M, Subramaniam S, Tello-Ruiz MK, Unda V, Unni D, Wang L, Ware D, Wegrzyn J, Williams J, Woodhouse M, Yu J, Main D. AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database (Oxford) 2018; 2018:5096675. [PMID: 30239679 PMCID: PMC6146126 DOI: 10.1093/database/bay088] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/19/2018] [Accepted: 07/30/2018] [Indexed: 01/07/2023]
Abstract
The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require data management plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development, curation and management, with the goal of creating database products that are more Findable, Accessible, Interoperable and Reusable. We strive to promote authentic, detailed, accurate and explicit communication between all parties involved in scientific data. As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability with regard to data curation. Each section describes challenges and opportunities for these topics, along with recommendations and best practices.
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Affiliation(s)
- Lisa Harper
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | | | - Ethalinda K S Cannon
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
- Computer Science, Iowa State University, Ames, IA, USA
| | - Sook Jung
- Horticulture, Washington State University, Pullman, WA, USA
| | - Monica Poelchau
- National Agricultural Library, USDA Agricultural Research Service, Beltsville, MD, USA
| | | | - Carson Andorf
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
- Computer Science, Iowa State University, Ames, IA, USA
| | - Elizabeth Arnaud
- Bioversity International, Informatics Unit, Conservation and Availability Programme, Parc Scientifique Agropolis II, Montpellier, France
| | - Tanya Z Berardini
- The Arabidopsis Information Resource, Phoenix Bioinformatics, Fremont, CA, USA
| | | | - Steve Cannon
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - James Carson
- Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX, USA
| | - Bradford Condon
- Entomology and Plant Pathology, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Laurel Cooper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Nathan Dunn
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christine G Elsik
- Division of Animal Sciences and Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM, USA
| | | | - David Grant
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Emily Grau
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Nic Herndon
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Zhi-Liang Hu
- Animal Science, Iowa State University, Ames, USA
| | - Jodi Humann
- Horticulture, Washington State University, Pullman, WA, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Clement Jonquet
- Laboratory of Informatics, Robotics, Microelectronics of Montpellier, University of Montpellier & CNRS, Montpellier, France
| | - Marie-Angélique Laporte
- Bioversity International, Informatics Unit, Conservation and Availability Programme, Parc Scientifique Agropolis II, Montpellier, France
| | | | - Gerard Lazo
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, CA, USA
| | - Fiona McCarthy
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | | | | | | | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Rex Nelson
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Daureen Nesdill
- Marriott Library, University of Utah, Salt Lake City, UT, USA
| | - Carissa Park
- Animal Science, Iowa State University, Ames, USA
| | - James Reecy
- Animal Science, Iowa State University, Ames, USA
| | - Leonore Reiser
- The Arabidopsis Information Resource, Phoenix Bioinformatics, Fremont, CA, USA
| | | | - Taner Z Sen
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, CA, USA
| | - Margaret Staton
- Entomology and Plant Pathology, University of Tennessee Knoxville, Knoxville, TN, USA
| | | | | | - Victor Unda
- Horticulture, Washington State University, Pullman, WA, USA
| | - Deepak Unni
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Liya Wang
- Plant Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Doreen Ware
- USDA, Plant, Soil and Nutrition Research, Ithaca, NY, USA
- Plant Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jill Wegrzyn
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Jason Williams
- Cold Spring Harbor Laboratory, DNA Learning Center, Cold Spring Harbor, NY, USA
| | - Margaret Woodhouse
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jing Yu
- Horticulture, Washington State University, Pullman, WA, USA
| | - Doreen Main
- Horticulture, Washington State University, Pullman, WA, USA
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