1
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Fan C, Xing X, Murphy SJH, Poursine-Laurent J, Schmidt H, Parikh BA, Yoon J, Choudhary MNK, Saligrama N, Piersma SJ, Yokoyama WM, Wang T. Cis-regulatory evolution of the recently expanded Ly49 gene family. Nat Commun 2024; 15:4839. [PMID: 38844462 PMCID: PMC11156856 DOI: 10.1038/s41467-024-48990-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
Comparative genomics has revealed the rapid expansion of multiple gene families involved in immunity. Members within each gene family often evolved distinct roles in immunity. However, less is known about the evolution of their epigenome and cis-regulation. Here we systematically profile the epigenome of the recently expanded murine Ly49 gene family that mainly encode either inhibitory or activating surface receptors on natural killer cells. We identify a set of cis-regulatory elements (CREs) for activating Ly49 genes. In addition, we show that in mice, inhibitory and activating Ly49 genes are regulated by two separate sets of proximal CREs, likely resulting from lineage-specific losses of CRE activity. Furthermore, we find that some Ly49 genes are cross-regulated by the CREs of other Ly49 genes, suggesting that the Ly49 family has begun to evolve a concerted cis-regulatory mechanism. Collectively, we demonstrate the different modes of cis-regulatory evolution for a rapidly expanding gene family.
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Affiliation(s)
- Changxu Fan
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Samuel J H Murphy
- Department of Neurology, Washington University School of Medicine, St. Louis, 63110, USA
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, 63110, USA
| | - Jennifer Poursine-Laurent
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA
| | - Heather Schmidt
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Bijal A Parikh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Jeesang Yoon
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA
| | - Mayank N K Choudhary
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Naresha Saligrama
- Department of Neurology, Washington University School of Medicine, St. Louis, 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, USA
- Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, 63110, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, 63110, USA
| | - Sytse J Piersma
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, 63110, USA.
| | - Wayne M Yokoyama
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, USA.
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA.
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63110, USA.
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2
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Scheidecker B, Poulain S, Sugimoto M, Arakawa H, Kim SH, Kawanishi T, Kato Y, Danoy M, Nishikawa M, Sakai Y. Mechanobiological stimulation in organ-on-a-chip systems reduces hepatic drug metabolic capacity in favor of regenerative specialization. Biotechnol Bioeng 2024; 121:1435-1452. [PMID: 38184801 DOI: 10.1002/bit.28653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/08/2024]
Abstract
Hepatic physiology depends on the liver's complex structural composition which among others, provides high oxygen supply rates, locally differential oxygen tension, endothelial paracrine signaling, as well as residual hemodynamic shear stress to resident hepatocytes. While functional improvements were shown by implementing these factors into hepatic culture systems, direct cause-effect relationships are often not well characterized-obfuscating their individual contribution in more complex microphysiological systems. By comparing increasingly complex hepatic in vitro culture systems that gradually implement these parameters, we investigate the influence of the cellular microenvironment to overall hepatic functionality in pharmacological applications. Here, hepatocytes were modulated in terms of oxygen tension and supplementation, endothelial coculture, and exposure to fluid shear stress delineated from oxygen influx. Results from transcriptomic and metabolomic evaluation indicate that particularly oxygen supply rates are critical to enhance cellular functionality-with cellular drug metabolism remaining comparable to physiological conditions after prolonged static culture. Endothelial signaling was found to be a major contributor to differential phenotype formation known as metabolic zonation, indicated by WNT pathway activity. Lastly, oxygen-delineated shear stress was identified to direct cellular fate towards increased hepatic plasticity and regenerative phenotypes at the cost of drug metabolic functionality - in line with regenerative effects observed in vivo. With these results, we provide a systematic evaluation of critical parameters and their impact in hepatic systems. Given their adherence to physiological effects in vivo, this highlights the importance of their implementation in biomimetic devices, such as organ-on-a-chip systems. Considering recent advances in basic liver biology, direct translation of physiological structures into in vitro models is a promising strategy to expand the capabilities of pharmacological models.
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Affiliation(s)
| | - Stéphane Poulain
- Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
- Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
| | - Hiroshi Arakawa
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Soo H Kim
- Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - Takumi Kawanishi
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Yukio Kato
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Mathieu Danoy
- Department of Chemical System Engineering, University of Tokyo, Tokyo, Japan
| | - Masaki Nishikawa
- Department of Chemical System Engineering, University of Tokyo, Tokyo, Japan
| | - Yasuyuki Sakai
- Department of Chemical System Engineering, University of Tokyo, Tokyo, Japan
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3
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Scheidecker B, Poulain S, Sugimoto M, Kido T, Kawanishi T, Miyajima A, Kim SH, Arakawa H, Kato Y, Nishikawa M, Danoy M, Sakai Y, Leclerc E. Dynamic, IPSC-derived hepatic tissue tri-culture system for the evaluation of liver physiology in vitro. Biofabrication 2024; 16:025037. [PMID: 38447229 DOI: 10.1088/1758-5090/ad30c5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 03/06/2024] [Indexed: 03/08/2024]
Abstract
Availability of hepatic tissue for the investigation of metabolic processes is severely limited. While primary hepatocytes or animal models are widely used in pharmacological applications, a change in methodology towards more sustainable and ethical assays is highly desirable. Stem cell derived hepatic cells are generally regarded as a viable alternative for the above model systems, if current limitations in functionality and maturation can be overcome. By combining microfluidic organ-on-a-chip technology with individually differentiated, multicellular hepatic tissue fractions, we aim to improve overall functionality of hepatocyte-like cells, as well as evaluate cellular composition and interactions with non-parenchymal cell populations towards the formation of mature liver tissue. Utilizing a multi-omic approach, we show the improved maturation profiles of hepatocyte-like cells maintained in a dynamic microenvironment compared to standard tissue culture setups without continuous perfusion. In order to evaluate the resulting tissue, we employ single cell sequencing to distinguish formed subpopulations and spatial localization. While cellular input was strictly defined based on established differentiation protocols of parenchyma, endothelial and stellate cell fractions, resulting hepatic tissue was shown to comprise a complex mixture of epithelial and non-parenchymal fractions with specific local enrichment of phenotypes along the microchannel. Following this approach, we show the importance of passive, paracrine developmental processes in tissue formation. Using such complex tissue models is a crucial first step to develop stem cell-derivedin vitrosystems that can compare functionally with currently used pharmacological and toxicological applications.
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Affiliation(s)
- Benedikt Scheidecker
- CNRS UMI 2820, Institute of Industrial Science, University of Tokyo, 153-8505 Tokyo, Japan
| | - Stéphane Poulain
- Institute of Industrial Science, University of Tokyo, 153-8505 Tokyo, Japan
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, 997-0035 Yamagata, Japan
- Institute of Medical Science, Tokyo Medical University, 160-8402 Tokyo, Japan
| | - Taketomo Kido
- Institute for Quantitative Biosciences, University of Tokyo, 113-0032 Tokyo, Japan
| | - Takumi Kawanishi
- School of Pharmaceutical Sciences, Kanazawa University, 920-1102 Kanazawa, Japan
| | - Atsushi Miyajima
- Institute for Quantitative Biosciences, University of Tokyo, 113-0032 Tokyo, Japan
| | - Soo Hyeon Kim
- Institute of Industrial Science, University of Tokyo, 153-8505 Tokyo, Japan
| | - Hiroshi Arakawa
- School of Pharmaceutical Sciences, Kanazawa University, 920-1102 Kanazawa, Japan
| | - Yukio Kato
- School of Pharmaceutical Sciences, Kanazawa University, 920-1102 Kanazawa, Japan
| | - Masaki Nishikawa
- Department of Chemical System Engineering, University of Tokyo, 113-8654 Tokyo, Japan
| | - Mathieu Danoy
- Department of Chemical System Engineering, University of Tokyo, 113-8654 Tokyo, Japan
| | - Yasuyuki Sakai
- Department of Chemical System Engineering, University of Tokyo, 113-8654 Tokyo, Japan
| | - Eric Leclerc
- CNRS UMI 2820, Institute of Industrial Science, University of Tokyo, 153-8505 Tokyo, Japan
- CNRS UMR 7338, Laboratoire de Biomécanique et Bioingénierie, Université de Technologies de Compiègne, 60203 Compiègne, France
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4
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Peng Y, Huang Q, Liu D, Kong S, Kamada R, Ozato K, Zhang Y, Zhu J. A single-cell genomic strategy for alternative transcript start sites identification. Biotechnol J 2024; 19:e2300516. [PMID: 38472100 DOI: 10.1002/biot.202300516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/20/2024] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
Alternative transcription start sites (TSSs) usage plays a critical role in gene transcription regulation in mammals. However, precisely identifying alternative TSSs remains challenging at the genome-wide level. We report a single-cell genomic technology for alternative TSSs annotation and cell heterogeneity detection. In the method, we utilize Fluidigm C1 system to capture individual cells of interest, SMARTer cDNA synthesis kit to recover full-length cDNAs, then dual priming oligonucleotide system to specifically enrich TSSs for genomic analysis. We apply this method to a genome-wide study of alternative TSSs identification in two different IFN-β stimulated mouse embryonic fibroblasts (MEFs). The data clearly discriminate two IFN-β stimulated MEFs. Moreover, our results indicate 81% expressed genes in these two cell types containing multiple TSSs, which is much higher than previous predictions based on Cap-Analysis Gene Expression (CAGE) (58%) or empirical determination (54%) in various cell types. This indicates that alternative TSSs are more pervasive than expected and implies our strategy could position them at an unprecedented sensitivity. It would be helpful for elucidating their biological insights in future.
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Affiliation(s)
- Yanling Peng
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qitong Huang
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | - Danli Liu
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Siyuan Kong
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Rui Kamada
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Keiko Ozato
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Yubo Zhang
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
| | - Jun Zhu
- DNA Sequencing and Genomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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5
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Maeng JH, Jang HJ, Du AY, Tzeng SC, Wang T. Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome. Genome Res 2023; 33:gr.277061.122. [PMID: 38065624 PMCID: PMC10760525 DOI: 10.1101/gr.277061.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 11/13/2023] [Indexed: 01/04/2024]
Abstract
Recent studies have shown that the noncoding genome can produce unannotated proteins as antigens that induce immune response. One major source of this activity is the aberrant epigenetic reactivation of transposable elements (TEs). In tumors, TEs often provide cryptic or alternate promoters, which can generate transcripts that encode tumor-specific unannotated proteins. Thus, TE-derived transcripts (TE transcripts) have the potential to produce tumor-specific, but recurrent, antigens shared among many tumors. Identification of TE-derived tumor antigens holds the promise to improve cancer immunotherapy approaches; however, current genomics and computational tools are not optimized for their detection. Here we combined CAGE technology with full-length long-read transcriptome sequencing (long-read CAGE, or LRCAGE) and developed a suite of computational tools to significantly improve immunopeptidome detection by incorporating TE and other tumor transcripts into the proteome database. By applying our methods to human lung cancer cell line H1299 data, we show that long-read technology significantly improves mapping of promoters with low mappability scores and that LRCAGE guarantees accurate construction of uncharacterized 5' transcript structure. Augmenting a reference proteome database with newly characterized transcripts enabled us to detect noncanonical antigens from HLA-pulldown LC-MS/MS data. Lastly, we show that epigenetic treatment increased the number of noncanonical antigens, particularly those encoded by TE transcripts, which might expand the pool of targetable antigens for cancers with low mutational burden.
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Affiliation(s)
- Ju Heon Maeng
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - H Josh Jang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Alan Y Du
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Shin-Cheng Tzeng
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
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6
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Lee HJ, Hou Y, Maeng JH, Shah NM, Chen Y, Lawson HA, Yang H, Yue F, Wang T. Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish. Genome Res 2022; 32:1424-1436. [PMID: 35649578 PMCID: PMC9341505 DOI: 10.1101/gr.276052.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 05/27/2022] [Indexed: 12/04/2022]
Abstract
Transposable elements (TEs) encode regulatory elements that impact gene expression in multiple species, yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here, we systematically investigate the epigenomic and transcriptomic landscape of TEs across 11 adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE-derived transcriptional units expressed across tissues. Finally, we show that novel TE-derived promoters can initiate tissue-specific transcription of alternate gene isoforms. This work provides a comprehensive profile of TE activity across normal zebrafish tissues, shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.
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Affiliation(s)
- Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;,Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Yiran Hou
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;,Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Ju Heon Maeng
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;,Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Nakul M. Shah
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;,Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Yujie Chen
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;,Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Heather A. Lawson
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA;,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois 60611, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;,Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA;,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
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7
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Abstract
Transcription start site (TSS) usage is a critical factor in the regulation of gene expression. A number of methods for global TSS mapping have been developed, but barriers of expense, technical difficulty, time, and/or cost have limited their broader adoption. To address these issues, we developed Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq). Requiring only three enzymatic steps with intervening bead cleanups, a STRIPE-seq library can be prepared from as little as 50 ng total RNA in ~5 h at a cost of ~$12 (US). In addition to profiling TSS usage, STRIPE-seq provides information on transcript levels that can be used for differential expression analysis. Thanks to its simplicity and low cost, we envision that STRIPE-seq could be employed by any molecular biology laboratory interested in profiling transcription initiation.
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Affiliation(s)
| | - Gabriel E Zentner
- Department of Biology, Indiana University, Bloomington, IN, USA.
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, USA.
- eGenesis, Inc., Cambridge, MA, USA.
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8
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Chowdhary A, Satagopam V, Schneider R. Long Non-coding RNAs: Mechanisms, Experimental, and Computational Approaches in Identification, Characterization, and Their Biomarker Potential in Cancer. Front Genet 2021; 12:649619. [PMID: 34276764 PMCID: PMC8281131 DOI: 10.3389/fgene.2021.649619] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/20/2021] [Indexed: 01/09/2023] Open
Abstract
Long non-coding RNAs are diverse class of non-coding RNA molecules >200 base pairs of length having various functions like gene regulation, dosage compensation, epigenetic regulation. Dysregulation and genomic variations of several lncRNAs have been implicated in several diseases. Their tissue and developmental specific expression are contributing factors for them to be viable indicators of physiological states of the cells. Here we present an comprehensive review the molecular mechanisms and functions, state of the art experimental and computational pipelines and challenges involved in the identification and functional annotation of lncRNAs and their prospects as biomarkers. We also illustrate the application of co-expression networks on the TCGA-LIHC dataset for putative functional predictions of lncRNAs having a therapeutic potential in Hepatocellular carcinoma (HCC).
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Affiliation(s)
- Anshika Chowdhary
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Venkata Satagopam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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9
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Danoy M, Tauran Y, Poulain S, Jellali R, Bruce J, Leduc M, Le Gall M, Koui Y, Arakawa H, Gilard F, Gakiere B, Kato Y, Plessy C, Kido T, Miyajima A, Sakai Y, Leclerc E. Investigation of the hepatic development in the coculture of hiPSCs-derived LSECs and HLCs in a fluidic microenvironment. APL Bioeng 2021; 5:026104. [PMID: 34027283 PMCID: PMC8116060 DOI: 10.1063/5.0041227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/02/2021] [Indexed: 12/29/2022] Open
Abstract
Interactions between the different liver cell types are critical to the maintenance or induction of their function in vitro. In this work, human-induced Pluripotent Stem Cells (hiPSCs)-derived Liver Sinusoidal Endothelial Cells (LSECs) and Hepatocytes-Like Cells (HLCs) were cultured and matured in a microfluidic environment. Both cell populations were differentiated in Petri dishes, detached, and inoculated in microfluidic biochips. In cocultures of both cell types, the tissue has exhibited a higher production of albumin (3.19 vs 5.31 μg/mL/106 cells in monocultures and cocultures) as well as a higher inducibility CYP450 over monocultures of HLCs. Tubular-like structures composed of LSECs and positive for the endothelial marker PECAM1, as well as a tissue more largely expressing Stabilin-2 were detected in cocultures only. In contrast, monocultures exhibited no network and less specific endothelial markers. The transcriptomic analysis did not reveal a marked difference between the profiles of both culture conditions. Nevertheless, the analysis allowed us to highlight different upstream regulators in cocultures (SP1, EBF1, and GATA3) and monocultures (PML, MECP2, and NRF1). In cocultures, the multi-omics dataset after 14 days of maturation in biochips has shown the activation of signaling related to hepatic maturation, angiogenesis, and tissue repair. In this condition, inflammatory signaling was also found to be reduced when compared to monocultures as illustrated by the activation of NFKB and by the detection of several cytokines involved in tissue injury in the latter. Finally, the extracted biological processes were discussed regarding the future development of a new generation of human in vitro hepatic models.
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Affiliation(s)
- Mathieu Danoy
- Authors to whom correspondence should be addressed: and
| | | | - Stephane Poulain
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Rachid Jellali
- Université de Technologie de Compiègne, CNRS, Biomechanics and Bioengineering, Centre de recherche Royallieu, CS 60319, 60203 Compiègne Cedex, Compiegne, France
| | - Johanna Bruce
- Plateforme protéomique 3P5, Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France
| | - Marjorie Leduc
- Plateforme protéomique 3P5, Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France
| | - Morgane Le Gall
- Plateforme protéomique 3P5, Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France
| | - Yuta Koui
- Laboratory of Stem Cell Therapy, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiroshi Arakawa
- Laboratory of Molecular Pharmacokinetics, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa City, Ishikawa 920-1192, Japan
| | - Francoise Gilard
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Saclay Plant Sciences, Bâtiment 630, 91405 Orsay, France
| | - Bertrand Gakiere
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Saclay Plant Sciences, Bâtiment 630, 91405 Orsay, France
| | - Yukio Kato
- Laboratory of Molecular Pharmacokinetics, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa City, Ishikawa 920-1192, Japan
| | - Charles Plessy
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Taketomo Kido
- Laboratory of Stem Cell Therapy, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Atsushi Miyajima
- Laboratory of Stem Cell Therapy, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yasuyuki Sakai
- Department of Chemical System Engineering, graduate school of Engineering, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Eric Leclerc
- Authors to whom correspondence should be addressed: and
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10
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Danoy M, Tauran Y, Poulain S, Jellali R, Bruce J, Leduc M, Le Gall M, Gilard F, Kido T, Arakawa H, Araya K, Mori D, Kato Y, Kusuhara H, Plessy C, Miyajima A, Sakai Y, Leclerc E. Multi-omics analysis of hiPSCs-derived HLCs matured on-chip revealed patterns typical of liver regeneration. Biotechnol Bioeng 2021; 118:3716-3732. [PMID: 33404112 DOI: 10.1002/bit.27667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/13/2020] [Accepted: 12/20/2020] [Indexed: 12/17/2022]
Abstract
Maturation of human-induced pluripotent stem cells (hiPSCs)-derived hepatocytes-like cells (HLCs) toward a complete hepatocyte phenotype remains a challenge as primitiveness patterns are still commonly observed. In this study, we propose a modified differentiation protocol for those cells which includes a prematuration in Petri dishes and a maturation in microfluidic biochip. For the first time, a large range of biomolecular families has been extracted from the same sample to combine transcriptomic, proteomic, and metabolomic analysis. After integration, these datasets revealed specific molecular patterns and highlighted the hepatic regeneration profile in biochips. Overall, biochips exhibited processes of cell proliferation and inflammation (via TGFB1) coupled with anti-fibrotic signaling (via angiotensin 1-7, ATR-2, and MASR). Moreover, cultures in this condition displayed physiological lipid-carbohydrate homeostasis (notably via PPAR, cholesterol metabolism, and bile synthesis) coupled with cell respiration through advanced oxidative phosphorylation (through the overexpression of proteins from the third and fourth complex). The results presented provide an original overview of the complex mechanisms involved in liver regeneration using an advanced in vitro organ-on-chip technology.
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Affiliation(s)
- Mathieu Danoy
- CNRS UMI 2820, Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, Tokyo, Japan.,Department of Chemical System Engineering, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Yannick Tauran
- CNRS UMI 2820, Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, Tokyo, Japan.,Laboratoire des Multimatériaux et Interfaces, UMR CNRS 5615, Univ Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Stéphane Poulain
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan.,Biomedical Microsystems Lab, Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Rachid Jellali
- Université de Technologie de Compiègne, CNRS, Biomechanics and Bioengineering, Centre de Recherche Royallieu-CS 60319-60203 Compiègne Cedex, Compiègne, France
| | - Johanna Bruce
- Plateforme 3P5 Proteomi'ic, Université de Paris, Institut Cochin, INSERM, U1016, CNRS, UMR8104, 22 rue Méchain, Paris, France
| | - Marjorie Leduc
- Plateforme 3P5 Proteomi'ic, Université de Paris, Institut Cochin, INSERM, U1016, CNRS, UMR8104, 22 rue Méchain, Paris, France
| | - Morgane Le Gall
- Plateforme 3P5 Proteomi'ic, Université de Paris, Institut Cochin, INSERM, U1016, CNRS, UMR8104, 22 rue Méchain, Paris, France
| | - Francoise Gilard
- Plateforme Métabolisme Métabolome, Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ. Paris-Sud, Univ. Evry, Univ. Paris-Diderot, Univ. Paris Saclay, Gif-sur-Yvette Cedex, France
| | - Taketomo Kido
- Laboratory of Stem Cell Therapy, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Arakawa
- Laboratory of Molecular Pharmacokinetics, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City, Ishikawa, Japan
| | - Karin Araya
- Laboratory of Molecular Pharmacokinetics, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City, Ishikawa, Japan
| | - Daiki Mori
- Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukio Kato
- Laboratory of Molecular Pharmacokinetics, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa City, Ishikawa, Japan
| | - Hiroyuki Kusuhara
- Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Charles Plessy
- RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, Japan
| | - Atsushi Miyajima
- Laboratory of Stem Cell Therapy, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Yasuyuki Sakai
- Department of Chemical System Engineering, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Eric Leclerc
- CNRS UMI 2820, Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, Tokyo, Japan.,Université de Technologie de Compiègne, CNRS, Biomechanics and Bioengineering, Centre de Recherche Royallieu-CS 60319-60203 Compiègne Cedex, Compiègne, France
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11
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Use of Cap Analysis Gene Expression to detect human papillomavirus promoter activity patterns at different disease stages. Sci Rep 2020; 10:17991. [PMID: 33093512 PMCID: PMC7582169 DOI: 10.1038/s41598-020-75133-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 10/12/2020] [Indexed: 11/16/2022] Open
Abstract
Transcription of human papillomavirus (HPV) genes proceeds unidirectionally from multiple promoters. Direct profiling of transcription start sites (TSSs) by Cap Analysis Gene Expression (CAGE) is a powerful strategy for examining individual HPV promoter activity. The objective of this study was to evaluate alterations of viral promoter activity during infection using CAGE technology. We used CAGE-based sequencing of 46 primary cervical samples, and quantitatively evaluated TSS patterns in the HPV transcriptome at a single-nucleotide resolution. TSS patterns were classified into two types: early promoter-dominant type (Type A) and late promoter-dominant type (Type B). The Type B pattern was more frequently found in CIN1 and CIN2 lesions than in CIN3 and cancer samples. We detected transcriptomes from multiple HPV types in five samples. Interestingly, in each sample, the TSS patterns of both HPV types were the same. The viral gene expression pattern was determined by the differentiation status of the epithelial cells, regardless of HPV type. We performed unbiased analyses of TSSs across the HPV genome in clinical samples. Visualising TSS pattern dynamics, including TSS shifts, provides new insights into how HPV infection status relates to disease state.
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12
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Wragg JW, Roos L, Vucenovic D, Cvetesic N, Lenhard B, Müller F. Embryonic tissue differentiation is characterized by transitions in cell cycle dynamic-associated core promoter regulation. Nucleic Acids Res 2020; 48:8374-8392. [PMID: 32619237 PMCID: PMC7470974 DOI: 10.1093/nar/gkaa563] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/10/2020] [Accepted: 06/19/2020] [Indexed: 12/30/2022] Open
Abstract
The core-promoter, a stretch of DNA surrounding the transcription start site (TSS), is a major integration-point for regulatory-signals controlling gene-transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell-cycling behaviour between cells of different fates. The role promoter-associated gene-regulatory-networks play in development-associated transitions in cell-cycle-dynamics is poorly understood. This study demonstrates in a vertebrate embryo, how core-promoter variations define transcriptional output in cells transitioning from a proliferative to cell-lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo segmentation, using the FUCCI transgenic cell-cycle-phase marker, revealed a spatial and lineage-specific separation in cell-cycling behaviour. To investigate the role differential promoter usage plays in this process, cap-analysis-of-gene-expression (CAGE) was performed on cells segregated by cycling dynamics. This analysis revealed a dramatic increase in tissue-specific gene expression, concurrent with slowed cycling behaviour. We revealed a distinct sharpening in TSS utilization in genes upregulated in slowly cycling, differentiating tissues, associated with enhanced utilization of the TATA-box, in addition to Sp1 binding-sites. In contrast, genes upregulated in rapidly cycling cells carry broad distribution of TSS utilization, coupled with enrichment for the CCAAT-box. These promoter features appear to correspond to cell-cycle-dynamic rather than tissue/cell-lineage origin. Moreover, we observed genes with cell-cycle-dynamic-associated transitioning in TSS distribution and differential utilization of alternative promoters. These results demonstrate the regulatory role of core-promoters in cell-cycle-dependent transcription regulation, during embryo-development.
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Affiliation(s)
| | | | - Dunja Vucenovic
- Institute of Clinical Sciences and MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Nevena Cvetesic
- Institute of Clinical Sciences and MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Boris Lenhard
- Correspondence may also be addressed to Boris Lenhard. Tel: +44 20 3313 8353;
| | - Ferenc Müller
- To whom correspondence should be addressed. Tel: +44 121 414 2895;
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13
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Policastro RA, Raborn RT, Brendel VP, Zentner GE. Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq. Genome Res 2020; 30:910-923. [PMID: 32660958 PMCID: PMC7370879 DOI: 10.1101/gr.261545.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/18/2020] [Indexed: 01/07/2023]
Abstract
Accurate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulation. However, current protocols for genome-wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5' ends from as little as 50 ng total RNA. Including depletion of uncapped RNA and reaction cleanups, a STRIPE-seq library can be constructed in about 5 h. We show application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for quantification of transcript levels and analysis of differential gene expression. In conjunction with our ready-to-use computational workflows, STRIPE-seq is a straightforward, efficient means by which to probe the landscape of transcriptional initiation.
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Affiliation(s)
| | | | - Volker P Brendel
- Department of Biology
- Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA
| | - Gabriel E Zentner
- Department of Biology
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana 46202, USA
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14
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Danoy M, Poulain S, Lereau-Bernier M, Kato S, Scheidecker B, Kido T, Miyajima A, Sakai Y, Plessy C, Leclerc E. Characterization of liver zonation-like transcriptomic patterns in HLCs derived from hiPSCs in a microfluidic biochip environment. Biotechnol Prog 2020; 36:e3013. [PMID: 32364651 DOI: 10.1002/btpr.3013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 04/20/2020] [Accepted: 04/28/2020] [Indexed: 12/17/2022]
Abstract
The liver zonation is an important phenomenon characterized by a gradient of several functions along the liver acinus. However, this gradient remains difficult to reproduce in in-vitro conditions, making the obtention of an in-vitro method to recapitulate the liver zonation a challenging issue. In this study, we evaluated the spatial evolution of the transcriptome profile of human induced pluripotent stem cells (hiPSCs) differentiated toward hepatocytes-like cells (HLCs) phenotype in a microfluidic biochip environment. Cells collected at the inlet of the biochip, where the oxygen concentration is higher, were identified by the expression of genes involved in metabolic pathways related to cellular reorganization and cell proliferation. Cells collected in the middle and at the outlet of the biochips, where oxygen concentrations are lower, were characterized by the upregulation of genes involved in cellular detoxification processes (CYP450), PPAR signaling or arginine biosynthesis. A subset of 16 transcription factors (TFs) was extracted and identified as upstream regulators to HNF1A and PPARA. These TFs are also known as regulators to target genes engaged in the Wnt/βcatenin pathway, in the TGFβ/BMP/SMAD signaling, in the transition between epithelial mesenchymal transition (EMT) and mesenchymal epithelial transition (MET), in the homeostasis of lipids, bile acids and carbohydrates homeostasis, in drug metabolism, in the estrogen processing and in the oxidative stress response. Overall, the analysis allowed to confirm a partial zonation-like pattern in hiPSCs-derived HLCs in the microfluidic biochip environment. These results provide important insights into the reproduction of liver zonation in-vitro for a better understanding of the phenomenon.
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Affiliation(s)
- Mathieu Danoy
- CNRS UMI 2820, Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - Stéphane Poulain
- RIKEN Center for Integrative Medical Sciences, Division of Genomic Medicine, Yokohama, Kanagawa, Japan
| | - Myriam Lereau-Bernier
- CNRS UMI 2820, Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - Sachi Kato
- RIKEN Center for Integrative Medical Sciences, Division of Genomic Medicine, Yokohama, Kanagawa, Japan
| | - Benedikt Scheidecker
- Department of Chemical System Engineering, graduate school of Engineering, The University of Tokyo, Tokyo, Japan
| | - Taketomo Kido
- Laboratory of Stem Cell Therapy, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Atsushi Miyajima
- Laboratory of Stem Cell Therapy, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Yasuyuki Sakai
- Department of Chemical System Engineering, graduate school of Engineering, The University of Tokyo, Tokyo, Japan
| | - Charles Plessy
- RIKEN Center for Integrative Medical Sciences, Division of Genomic Medicine, Yokohama, Kanagawa, Japan
| | - Eric Leclerc
- CNRS UMI 2820, Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, University of Tokyo, Tokyo, Japan
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15
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Poulain S, Arnaud O, Kato S, Chen I, Ishida H, Carninci P, Plessy C. Machine-driven parameter screen of biochemical reactions. Nucleic Acids Res 2020; 48:e37. [PMID: 32025730 PMCID: PMC7144897 DOI: 10.1093/nar/gkaa079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/14/2020] [Accepted: 01/29/2020] [Indexed: 11/15/2022] Open
Abstract
The development of complex methods in molecular biology is a laborious, costly, iterative and often intuition-bound process where optima are sought in a multidimensional parameter space through step-by-step optimizations. The difficulty of miniaturizing reactions under the microliter volumes usually handled in multiwell plates by robots, plus the cost of the experiments, limit the number of parameters and the dynamic ranges that can be explored. Nevertheless, because of non-linearities of the response of biochemical systems to their reagent concentrations, broad dynamic ranges are necessary. Here we use a high-performance nanoliter handling platform and computer generation of liquid transfer programs to explore in quadruplicates 648 combinations of 4 parameters of a biochemical reaction, the reverse-transcription, which lead us to uncover non-linear responses, parameter interactions and novel mechanistic insights. With the increased availability of computer-driven laboratory platforms for biotechnology, our results demonstrate the feasibility and advantage of methods development based on reproducible, computer-aided exhaustive characterization of biochemical systems.
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Affiliation(s)
- Stéphane Poulain
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences, Division of Genomic Medicine, Yokohama, Japan
- Biomedical Microsystems Lab., Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Ophélie Arnaud
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama, Japan
| | - Sachi Kato
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences, Division of Genomic Medicine, Yokohama, Japan
| | | | | | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences, Division of Genomic Medicine, Yokohama, Japan
| | - Charles Plessy
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences, Division of Genomic Medicine, Yokohama, Japan
- Okinawa Institute of Science and Technology Graduate University, Genomics and Regulatory Systems Unit, Onna-son, Japan
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16
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Pre- and peri-implantation Zika virus infection impairs fetal development by targeting trophectoderm cells. Nat Commun 2019; 10:4155. [PMID: 31519912 PMCID: PMC6744420 DOI: 10.1038/s41467-019-12063-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 08/19/2019] [Indexed: 12/23/2022] Open
Abstract
Zika virus (ZIKV) infection results in an increased risk of spontaneous abortion and poor intrauterine growth although the underlying mechanisms remain undetermined. Little is known about the impact of ZIKV infection during the earliest stages of pregnancy, at pre- and peri-implantation, because most current ZIKV pregnancy studies have focused on post-implantation stages. Here, we demonstrate that trophectoderm cells of pre-implantation human and mouse embryos can be infected with ZIKV, and propagate virus causing neural progenitor cell death. These findings are corroborated by the dose-dependent nature of ZIKV susceptibility of hESC-derived trophectoderm cells. Single blastocyst RNA-seq reveals key transcriptional changes upon ZIKV infection, including nervous system development, prior to commitment to the neural lineage. The pregnancy rate of mice is >50% lower in pre-implantation infection than infection at E4.5, demonstrating that pre-implantation ZIKV infection leads to miscarriage. Cumulatively, these data elucidate a previously unappreciated association of pre- and peri-implantation ZIKV infection and microcephaly.
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17
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Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation. Dev Cell 2019; 51:21-34.e5. [PMID: 31474564 DOI: 10.1016/j.devcel.2019.07.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/28/2019] [Accepted: 07/24/2019] [Indexed: 02/03/2023]
Abstract
Facultative heterochromatin forms and reorganizes in response to external stimuli. However, how the initial establishment of such a chromatin state is regulated in cell-cycle-arrested cells remains unexplored. Mouse gonocytes are arrested male germ cells, at which stage the genome-wide DNA methylome forms. Here, we discovered transiently accessible heterochromatin domains of several megabases in size in gonocytes and named them differentially accessible domains (DADs). Open DADs formed in gene desert and gene cluster regions, primarily at transposons, with the reprogramming of histone marks, suggesting DADs as facultative heterochromatin. De novo DNA methylation took place with two waves in gonocytes: the first region specific and the second genome-wide. DADs were resistant to the first wave and their opening preceded the second wave. In addition, the higher-order chromosome architecture was reorganized with less defined chromosome compartments in gonocytes. These findings suggest that multiple layers of chromatin reprogramming facilitate de novo DNA methylation.
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18
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Danoy M, Bernier ML, Kimura K, Poulain S, Kato S, Mori D, Kido T, Plessy C, Kusuhara H, Miyajima A, Sakai Y, Leclerc E. Optimized protocol for the hepatic differentiation of induced pluripotent stem cells in a fluidic microenvironment. Biotechnol Bioeng 2019; 116:1762-1776. [DOI: 10.1002/bit.26970] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/22/2019] [Accepted: 03/14/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Mathieu Danoy
- Laboratory for Integrated Micro Mechatronic Systems, CNRS UMI 2820, Institute of Industrial Science, The University of TokyoTokyo Japan
| | - Myriam Lereau Bernier
- Laboratory for Integrated Micro Mechatronic Systems, CNRS UMI 2820, Institute of Industrial Science, The University of TokyoTokyo Japan
| | - Keiichi Kimura
- Department of Chemical System EngineeringGraduate School of Engineering, The University of TokyoTokyo Japan
| | - Stephane Poulain
- Division of Genomic MedicineRIKEN Center for Integrative Medical SciencesYokohama Japan
| | - Sachi Kato
- Division of Genomic MedicineRIKEN Center for Integrative Medical SciencesYokohama Japan
| | - Daiki Mori
- Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of TokyoTokyo Japan
| | - Taketomo Kido
- Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, The University of TokyoTokyo Japan
| | - Charles Plessy
- Division of Genomic MedicineRIKEN Center for Integrative Medical SciencesYokohama Japan
| | - Hiroyuki Kusuhara
- Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of TokyoTokyo Japan
| | - Atsushi Miyajima
- Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, The University of TokyoTokyo Japan
| | - Yasuyuki Sakai
- Department of Chemical System EngineeringGraduate School of Engineering, The University of TokyoTokyo Japan
| | - Eric Leclerc
- Laboratory for Integrated Micro Mechatronic Systems, CNRS UMI 2820, Institute of Industrial Science, The University of TokyoTokyo Japan
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19
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Kouno T, Moody J, Kwon ATJ, Shibayama Y, Kato S, Huang Y, Böttcher M, Motakis E, Mendez M, Severin J, Luginbühl J, Abugessaisa I, Hasegawa A, Takizawa S, Arakawa T, Furuno M, Ramalingam N, West J, Suzuki H, Kasukawa T, Lassmann T, Hon CC, Arner E, Carninci P, Plessy C, Shin JW. C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution. Nat Commun 2019; 10:360. [PMID: 30664627 PMCID: PMC6341120 DOI: 10.1038/s41467-018-08126-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 12/19/2018] [Indexed: 01/06/2023] Open
Abstract
Single-cell transcriptomic profiling is a powerful tool to explore cellular heterogeneity. However, most of these methods focus on the 3′-end of polyadenylated transcripts and provide only a partial view of the transcriptome. We introduce C1 CAGE, a method for the detection of transcript 5′-ends with an original sample multiplexing strategy in the C1TM microfluidic system. We first quantifiy the performance of C1 CAGE and find it as accurate and sensitive as other methods in the C1 system. We then use it to profile promoter and enhancer activities in the cellular response to TGF-β of lung cancer cells and discover subpopulations of cells differing in their response. We also describe enhancer RNA dynamics revealing transcriptional bursts in subsets of cells with transcripts arising from either strand in a mutually exclusive manner, validated using single molecule fluorescence in situ hybridization. Single-cell transcriptomic profiling allows the exploration of cellular heterogeneity but commonly focuses on the 3′-end of the transcript. Here the authors introduce C1 CAGE, which detects the 5′ transcript end in a multiplexed microfluidic system.
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Affiliation(s)
- Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Jonathan Moody
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Andrew Tae-Jun Kwon
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Youtaro Shibayama
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Sachi Kato
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Yi Huang
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,ACT Genomics Co. Ltd., 3F., No. 345, Xinhu 2nd Rd, Neihu Dist., Taipei City, 114, Taiwan
| | - Michael Böttcher
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Efthymios Motakis
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,Yong Loo Lin School of Medicine MD6, #08-01, 14 Medical Drive, National University of Singapore, Singapore, 117599, Singapore
| | - Mickaël Mendez
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,Princess Margaret Cancer Research Tower 11-401, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Joachim Luginbühl
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Satoshi Takizawa
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takahiro Arakawa
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Masaaki Furuno
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Naveen Ramalingam
- Single-Cell Research and Development, Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, 94080, CA, USA
| | - Jay West
- Single-Cell Research and Development, Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, 94080, CA, USA
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Timo Lassmann
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,Telethon Kids Institute, The University of Western Australia, Perth Children's Hospital, 15 Hospital Ave, Nedlands, 6009, WA, Australia
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Erik Arner
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Charles Plessy
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan. .,Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
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20
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Cvetesic N, Leitch HG, Borkowska M, Müller F, Carninci P, Hajkova P, Lenhard B. SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA. Genome Res 2018; 28:1943-1956. [PMID: 30404778 PMCID: PMC6280763 DOI: 10.1101/gr.235937.118] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 10/25/2018] [Indexed: 01/22/2023]
Abstract
Cap analysis of gene expression (CAGE) is a methodology for genome-wide quantitative mapping of mRNA 5′ ends to precisely capture transcription start sites at a single nucleotide resolution. In combination with high-throughput sequencing, CAGE has revolutionized our understanding of the rules of transcription initiation, led to discovery of new core promoter sequence features, and discovered transcription initiation at enhancers genome-wide. The biggest limitation of CAGE is that even the most recently improved version (nAnT-iCAGE) still requires large amounts of total cellular RNA (5 µg), preventing its application to scarce biological samples such as those from early embryonic development or rare cell types. Here, we present SLIC-CAGE, a Super-Low Input Carrier-CAGE approach to capture 5′ ends of RNA polymerase II transcripts from as little as 5–10 ng of total RNA. This dramatic increase in sensitivity is achieved by specially designed, selectively degradable carrier RNA. We demonstrate the ability of SLIC-CAGE to generate data for genome-wide promoterome with 1000-fold less material than required by existing CAGE methods, by generating a complex, high-quality library from mouse embryonic day 11.5 primordial germ cells.
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Affiliation(s)
- Nevena Cvetesic
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Harry G Leitch
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Malgorzata Borkowska
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston B15 2TT, United Kingdom
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama City, Kanagawa 230-0045, Japan.,RIKEN Omics Science Center, Yokohama City, Kanagawa 230-0045, Japan
| | - Petra Hajkova
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Boris Lenhard
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Sars International Centre for Marine Molecular Biology, University of Bergen, N-5008 Bergen, Norway
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21
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Bertin N, Mendez M, Hasegawa A, Lizio M, Abugessaisa I, Severin J, Sakai-Ohno M, Lassmann T, Kasukawa T, Kawaji H, Hayashizaki Y, Forrest ARR, Carninci P, Plessy C. Linking FANTOM5 CAGE peaks to annotations with CAGEscan. Sci Data 2017; 4:170147. [PMID: 28972578 PMCID: PMC5625555 DOI: 10.1038/sdata.2017.147] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/09/2017] [Indexed: 01/22/2023] Open
Abstract
The FANTOM5 expression atlas is a quantitative measurement of the activity of nearly 200,000 promoter regions across nearly 2,000 different human primary cells, tissue types and cell lines. Generation of this atlas was made possible by the use of CAGE, an experimental approach to localise transcription start sites at single-nucleotide resolution by sequencing the 5′ ends of capped RNAs after their conversion to cDNAs. While 50% of CAGE-defined promoter regions could be confidently associated to adjacent transcriptional units, nearly 100,000 promoter regions remained gene-orphan. To address this, we used the CAGEscan method, in which random-primed 5′-cDNAs are paired-end sequenced. Pairs starting in the same region are assembled in transcript models called CAGEscan clusters. Here, we present the production and quality control of CAGEscan libraries from 56 FANTOM5 RNA sources, which enhances the FANTOM5 expression atlas by providing experimental evidence associating core promoter regions with their cognate transcripts.
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Affiliation(s)
- Nicolas Bertin
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
| | - Mickaël Mendez
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
| | - Marina Lizio
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
| | - Jessica Severin
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
| | - Mizuho Sakai-Ohno
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
| | - Timo Lassmann
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan
| | - Hideya Kawaji
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center, Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan
| | - Alistair R R Forrest
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
| | - Charles Plessy
- RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center, Yokohama 230-0045, Japan
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22
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Lizio M, Deviatiiarov R, Nagai H, Galan L, Arner E, Itoh M, Lassmann T, Kasukawa T, Hasegawa A, Ros MA, Hayashizaki Y, Carninci P, Forrest ARR, Kawaji H, Gusev O, Sheng G. Systematic analysis of transcription start sites in avian development. PLoS Biol 2017; 15:e2002887. [PMID: 28873399 PMCID: PMC5600399 DOI: 10.1371/journal.pbio.2002887] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 09/15/2017] [Accepted: 08/18/2017] [Indexed: 01/07/2023] Open
Abstract
Cap Analysis of Gene Expression (CAGE) in combination with single-molecule sequencing technology allows precision mapping of transcription start sites (TSSs) and genome-wide capture of promoter activities in differentiated and steady state cell populations. Much less is known about whether TSS profiling can characterize diverse and non-steady state cell populations, such as the approximately 400 transitory and heterogeneous cell types that arise during ontogeny of vertebrate animals. To gain such insight, we used the chick model and performed CAGE-based TSS analysis on embryonic samples covering the full 3-week developmental period. In total, 31,863 robust TSS peaks (>1 tag per million [TPM]) were mapped to the latest chicken genome assembly, of which 34% to 46% were active in any given developmental stage. ZENBU, a web-based, open-source platform, was used for interactive data exploration. TSSs of genes critical for lineage differentiation could be precisely mapped and their activities tracked throughout development, suggesting that non-steady state and heterogeneous cell populations are amenable to CAGE-based transcriptional analysis. Our study also uncovered a large set of extremely stable housekeeping TSSs and many novel stage-specific ones. We furthermore demonstrated that TSS mapping could expedite motif-based promoter analysis for regulatory modules associated with stage-specific and housekeeping genes. Finally, using Brachyury as an example, we provide evidence that precise TSS mapping in combination with Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-on technology enables us, for the first time, to efficiently target endogenous avian genes for transcriptional activation. Taken together, our results represent the first report of genome-wide TSS mapping in birds and the first systematic developmental TSS analysis in any amniote species (birds and mammals). By facilitating promoter-based molecular analysis and genetic manipulation, our work also underscores the value of avian models in unravelling the complex regulatory mechanism of cell lineage specification during amniote development.
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Affiliation(s)
- Marina Lizio
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
- RIKEN Omics Science Center (OSC), Yokohama, Japan
| | - Ruslan Deviatiiarov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Hiroki Nagai
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
- RIKEN Center for Developmental Biology, Kobe, Japan
| | - Laura Galan
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-Universidad de Cantabria-SODERCAN), Santander, Spain
| | - Erik Arner
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
- RIKEN Omics Science Center (OSC), Yokohama, Japan
| | - Masayoshi Itoh
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
- RIKEN Omics Science Center (OSC), Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Japan
| | - Timo Lassmann
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
- RIKEN Omics Science Center (OSC), Yokohama, Japan
| | - Takeya Kasukawa
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
| | - Akira Hasegawa
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
| | - Marian A. Ros
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-Universidad de Cantabria-SODERCAN), Santander, Spain
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center (OSC), Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Japan
| | - Piero Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
- RIKEN Omics Science Center (OSC), Yokohama, Japan
| | - Alistair R. R. Forrest
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
- RIKEN Omics Science Center (OSC), Yokohama, Japan
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia, Australia
| | - Hideya Kawaji
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
- RIKEN Omics Science Center (OSC), Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Japan
- * E-mail: (GS); (HK); (OG)
| | - Oleg Gusev
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies (CLST), Yokohama, Japan
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Japan
- RIKEN Innovation Center, Wako, Japan
- * E-mail: (GS); (HK); (OG)
| | - Guojun Sheng
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
- RIKEN Center for Developmental Biology, Kobe, Japan
- * E-mail: (GS); (HK); (OG)
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