1
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Seki M, Kuze Y, Zhang X, Kurotani KI, Notaguchi M, Nishio H, Kudoh H, Suzaki T, Yoshida S, Sugano S, Matsushita T, Suzuki Y. An improved method for the highly specific detection of transcription start sites. Nucleic Acids Res 2024; 52:e7. [PMID: 37994784 PMCID: PMC10810191 DOI: 10.1093/nar/gkad1116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/17/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Precise detection of the transcriptional start site (TSS) is a key for characterizing transcriptional regulation of genes and for annotation of newly sequenced genomes. Here, we describe the development of an improved method, designated 'TSS-seq2.' This method is an iterative improvement of TSS-seq, a previously published enzymatic cap-structure conversion method to detect TSSs in base sequences. By modifying the original procedure, including by introducing split ligation at the key cap-selection step, the yield and the accuracy of the reaction has been substantially improved. For example, TSS-seq2 can be conducted using as little as 5 ng of total RNA with an overall accuracy of 96%; this yield a less-biased and more precise detection of TSS. We then applied TSS-seq2 for TSS analysis of four plant species that had not yet been analyzed by any previous TSS method.
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Affiliation(s)
- Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yuta Kuze
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Xiang Zhang
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Ken-ichi Kurotani
- Bioscience and Biotechnology Center, Nagoya University, Aichi, Japan
| | - Michitaka Notaguchi
- Bioscience and Biotechnology Center, Nagoya University, Aichi, Japan
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Nagoya, Japan
| | - Haruki Nishio
- Data Science and AI Innovation Research Promotion Center, Shiga University, Shiga, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Shiga, Japan
| | - Takuya Suzaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
- Tsukuba Plant-Innovation Research Center, University of Tsukuba, Ibaraki, Japan
| | - Satoko Yoshida
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Sumio Sugano
- Institute of Kashiwa-no-ha Omics Gate, Chiba, Japan
- Future Medicine Education and Research Organization, Chiba University, Chiba, Japan
| | - Tomonao Matsushita
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
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2
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Gvozdenov Z. Genome-Wide Mapping of 5' Isoforms with 5'-Seq. Curr Protoc 2023; 3:e750. [PMID: 37084173 DOI: 10.1002/cpz1.750] [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] [Indexed: 04/22/2023]
Abstract
The transcriptome is far more complex than previously assumed. Transcripts from the same gene can differ in terms of transcription start site, transcription end site, or pattern of splicing, and growing evidence supports the functional importance of these distinct transcript isoforms. Easily identifying these isoforms experimentally via library construction and high-throughput sequencing is crucial. Current library construction methods for identifying transcription start sites (5' transcript isoforms) involve large number of steps and (expensive) reagents, utilization of cDNA intermediates for adapter ligation, and are less suitable for studying low-abundance isoforms. Here, I describe a quick protocol for the generation of sequencing libraries to define capped 5' isoforms (5'-Seq) of various abundances in yeast and suggest a 5' isoform data analysis pipeline. The protocol relies on the utilization of a dephosphorylation-decapping method (oligo-capping) to generate a sequencing library from mRNA fragments and is a simplification of previously published 5' isoform protocols in terms of the handling steps, time, and cost. This method is exemplified using Saccharomyces cerevisiae mRNA, but it can be applied to various cellular conditions to study the effects of 5' transcript isoforms on transcriptional and/or translational regulation. © 2023 Wiley Periodicals LLC. Basic Protocol: Construction of a DNA sequencing library from capped 5' isoforms Support Protocol: Sequencing data analysis.
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Affiliation(s)
- Zlata Gvozdenov
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, Massachusetts
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3
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Haberkorn B, Löwen D, Meier L, Fromm MF, König J. Transcriptional Regulation of Liver-Type OATP1B3 (Lt-OATP1B3) and Cancer-Type OATP1B3 (Ct-OATP1B3) Studied in Hepatocyte-Derived and Colon Cancer-Derived Cell Lines. Pharmaceutics 2023; 15:pharmaceutics15030738. [PMID: 36986600 PMCID: PMC10051083 DOI: 10.3390/pharmaceutics15030738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
Due to alternative splicing, the SLCO1B3 gene encodes two protein variants; the hepatic uptake transporter liver-type OATP1B3 (Lt-OATP1B3) and the cancer-type OATP1B3 (Ct-OATP1B3) expressed in several cancerous tissues. There is limited information about the cell type-specific transcriptional regulation of both variants and about transcription factors regulating this differential expression. Therefore, we cloned DNA fragments from the promoter regions of the Lt-SLCO1B3 and the Ct-SLCO1B3 gene and investigated their luciferase activity in hepatocellular and colorectal cancer cell lines. Both promoters showed differences in their luciferase activity depending on the used cell lines. We identified the first 100 bp upstream of the transcriptional start site as the core promoter region of the Ct-SLCO1B3 gene. In silico predicted binding sites for the transcription factors ZKSCAN3, SOX9 and HNF1α localized within these fragments were further analyzed. The mutagenesis of the ZKSCAN3 binding site reduced the luciferase activity of the Ct-SLCO1B3 reporter gene construct in the colorectal cancer cell lines DLD1 and T84 to 29.9% and 14.3%, respectively. In contrast, using the liver-derived Hep3B cells, 71.6% residual activity could be measured. This indicates that the transcription factors ZKSCAN3 and SOX9 are important for the cell type-specific transcriptional regulation of the Ct-SLCO1B3 gene.
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Affiliation(s)
| | | | | | | | - Jörg König
- Correspondence: ; Tel.: +49-9131-8522077
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4
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Despic V, Jaffrey SR. mRNA ageing shapes the Cap2 methylome in mammalian mRNA. Nature 2023; 614:358-366. [PMID: 36725932 PMCID: PMC9891201 DOI: 10.1038/s41586-022-05668-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 12/16/2022] [Indexed: 02/03/2023]
Abstract
The mRNA cap structure is a major site of dynamic mRNA methylation. mRNA caps exist in either the Cap1 or Cap2 form, depending on the presence of 2'-O-methylation on the first transcribed nucleotide or both the first and second transcribed nucleotides, respectively1,2. However, the identity of Cap2-containing mRNAs and the function of Cap2 are unclear. Here we describe CLAM-Cap-seq, a method for transcriptome-wide mapping and quantification of Cap2. We find that unlike other epitranscriptomic modifications, Cap2 can occur on all mRNAs. Cap2 is formed through a slow continuous conversion of mRNAs from Cap1 to Cap2 as mRNAs age in the cytosol. As a result, Cap2 is enriched on long-lived mRNAs. Large increases in the abundance of Cap1 leads to activation of RIG-I, especially in conditions in which expression of RIG-I is increased. The methylation of Cap1 to Cap2 markedly reduces the ability of RNAs to bind to and activate RIG-I. The slow methylation rate of Cap2 allows Cap2 to accumulate on host mRNAs, yet ensures that low levels of Cap2 occur on newly expressed viral RNAs. Overall, these results reveal an immunostimulatory role for Cap1, and that Cap2 functions to reduce activation of the innate immune response.
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Affiliation(s)
- Vladimir Despic
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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5
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Schneider C, Erhard F, Binotti B, Buchberger A, Vogel J, Fischer U. An unusual mode of baseline translation adjusts cellular protein synthesis capacity to metabolic needs. Cell Rep 2022; 41:111467. [DOI: 10.1016/j.celrep.2022.111467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/14/2022] [Accepted: 09/16/2022] [Indexed: 11/25/2022] Open
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6
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Kidaka T, Sugi T, Hayashida K, Suzuki Y, Xuan X, Dubey JP, Yamagishi J. TSS-seq of Toxoplasma gondii sporozoites revealed a novel motif in stage-specific promoters. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 98:105213. [PMID: 35041968 DOI: 10.1016/j.meegid.2022.105213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Toxoplasma gondii is one of the most common zoonotic protozoan parasites. It has three major infectious stages: rapidly multiplying tachyzoites (Tz), slowly replicating bradyzoites (Bz) and a resting/free-living stage, sporozoites (Sz). The regulatory mechanisms governing stage-specific gene expression are not fully understood. Few transcriptional start sites (TSS) are known for Sz. In this study, we obtained TSS of Sz using an oligo-capping method and RNA-seq analysis. We identified 1,043,503 TSS in the Sz transcriptome. These defined 38,973 TSS clusters, of which, 11,925 were expressed in Sz and 1535 TSS differentially expressed in Sz. Based on these data, we defined promoter regions and novel sporozoite stage-specific motifs using MEME. TGTANNTACA was distributed around -55 to -75 regions from each TSS. Interestingly, the same motif was reported in another apicomplexan, Plasmodium berghei, as a cis-element of female-specific gametocyte genes, implying the presence of common regulatory machinery. Further comparative analysis should better define the distribution and function of these elements in other members of this important parasitic phylum.
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Affiliation(s)
- Taishi Kidaka
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
| | - Tatsuki Sugi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
| | - Kyoko Hayashida
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Xuenan Xuan
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Jitender P Dubey
- United States Department of Agriculture, Agricultural Research Service, Animal Parasitic Diseases Laboratory, Beltsville, MD, 20705-2350, USA
| | - Junya Yamagishi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido 001-0020, Japan.
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7
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Abstract
Transcription start site (TSS) selection influences transcript stability and translation as well as protein sequence. Alternative TSS usage is pervasive in organismal development, is a major contributor to transcript isoform diversity in humans, and is frequently observed in human diseases including cancer. In this review, we discuss the breadth of techniques that have been used to globally profile TSSs and the resulting insights into gene regulation, as well as future prospects in this area of inquiry.
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Affiliation(s)
| | - Gabriel E. Zentner
- Department of Biology, Indiana University, Bloomington, IN 47401, USA
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA
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8
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Patel JC, Singh A, Tulswani R, Sharma YK, Khurana P, Ragumani S. Identification of VEGFA-centric temporal hypoxia-responsive dynamic cardiopulmonary network biomarkers. Life Sci 2021; 281:119718. [PMID: 34147483 DOI: 10.1016/j.lfs.2021.119718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/31/2021] [Accepted: 06/08/2021] [Indexed: 10/21/2022]
Abstract
AIMS Hypoxia, a pathophysiological condition, is profound in several cardiopulmonary diseases (CPD). Every individual's lethality to a hypoxia state differs in terms of hypoxia exposure time, dosage units and dependent on the individual's genetic makeup. Most of the proposed markers for CPD were generally aim to distinguish disease samples from normal samples. Although, as per the 2018 GOLD guidelines, clinically useful biomarkers for several cardio pulmonary disease patients in stable condition have yet to be identified. We attempt to address these key issues through the identification of Dynamic Network Biomarkers (DNB) to detect hypoxia induced early warning signals of CPD before the catastrophic deterioration. MATERIALS AND METHODS The human microvascular endothelial tissues microarray datasets (GSE11341) of lung and cardiac expose to hypoxia (1% O2) for 3, 24 and 48 h were retrieved from the public repository. The time dependent differentially expressed genes were subjected to tissue specificity and promoter analysis to filtrate the noise levels in the networks and to dissect the tissue specific hypoxia induced genes. These filtered out genes were used to construct the dynamic segmentation networks. The hypoxia induced dynamic differentially expressed genes were validated in the lung and heart tissues of male rats. These rats were exposed to hypobaric hypoxia (simulated altitude of 25,000 or PO2 - 282 mm of Hg) progressively for 3, 24 and 48 h. KEY FINDINGS To identify the temporal key genes regulated in hypoxia, we ranked the dominant genes based on their consolidated topological features from tissue specific networks, time dependent networks and dynamic networks. Overall topological ranking described VEGFA as a single node dynamic hub and strongly communicated with tissue specific genes to carry forward their tissue specific information. We named this type of VEGFAcentric dynamic networks as "V-DNBs". As a proof of principle, our methodology helped us to identify the V-DNBs specific for lung and cardiac tissues namely V-DNBL and V-DNBC respectively. SIGNIFICANCE Our experimental studies identified VEGFA, SLC2A3, ADM and ENO2 as the minimum and sufficient candidates of V-DNBL. The dynamic expression patterns could be readily exploited to capture the pre disease state of hypoxia induced pulmonary vascular remodelling. Whereas in V-DNBC the minimum and sufficient candidates are VEGFA, SCL2A3, ADM, NDRG1, ENO2 and BHLHE40. The time dependent single node expansion indicates V-DNBC could also be the pre disease state pathological hallmark for hypoxia-associated cardiovascular remodelling. The network cross-talk and expression pattern between V-DNBL and V-DNBC are completely distinct. On the other hand, the great clinical advantage of V-DNBs for pre disease predictions, a set of samples during the healthy condition should suffice. Future clinical studies might further shed light on the predictive power of V-DNBs as prognostic and diagnostic biomarkers for CPD.
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Affiliation(s)
- Jai Chand Patel
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow Road, Timarpur, Delhi, India
| | - Ajeet Singh
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow Road, Timarpur, Delhi, India
| | - Rajkumar Tulswani
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow Road, Timarpur, Delhi, India
| | - Yogendra Kumar Sharma
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow Road, Timarpur, Delhi, India
| | - Pankaj Khurana
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow Road, Timarpur, Delhi, India
| | - Sugadev Ragumani
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow Road, Timarpur, Delhi, India.
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9
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Suzuki A, Onodera K, Matsui K, Seki M, Esumi H, Soga T, Sugano S, Kohno T, Suzuki Y, Tsuchihara K. Characterization of cancer omics and drug perturbations in panels of lung cancer cells. Sci Rep 2019; 9:19529. [PMID: 31863083 PMCID: PMC6925249 DOI: 10.1038/s41598-019-55692-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 11/21/2019] [Indexed: 01/10/2023] Open
Abstract
To better understand the disruptions of transcriptional regulations and gene expression in lung cancers, we constructed a multi-omics catalogue of the responses of lung cancer cells to a series of chemical compounds. We generated and analyzed 3,240 RNA-seq and 3,393 ATAC-seq libraries obtained from 23 cell lines treated with 95 well-annotated compounds. To demonstrate the power of the created multi-omics resource, we attempted to identify drugs that could induce the designated changes alone or in combination. The basal multi-omics information was first integrated into co-expression modules. Among these modules, we identified a stress response module that may be a promising drug intervention target, as new combinations of compounds that could be used to regulate this module and the consequent phenotypic appearance of cancer cells have been identified. We believe that the multi-omics profiles generated in this study and the strategy used to stratify them will lead to more rational and efficient development of anticancer drugs.
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Affiliation(s)
- Ayako Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Keiichi Onodera
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Bio Science & Engineering Laboratory, Fujifilm Corporation, Kanagawa, Japan
| | - Ken Matsui
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Bio Science & Engineering Laboratory, Fujifilm Corporation, Kanagawa, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Hiroyasu Esumi
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan.,Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Sumio Sugano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
| | - Katsuya Tsuchihara
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
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10
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Vahrenkamp JM, Szczotka K, Dodson MK, Jarboe EA, Soisson AP, Gertz J. FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples. Genome Res 2019; 29:1826-1835. [PMID: 31649055 PMCID: PMC6836741 DOI: 10.1101/gr.249656.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 10/03/2019] [Indexed: 12/16/2022]
Abstract
The majority of clinical cancer specimens are preserved as formalin-fixed paraffin-embedded (FFPE) samples. For clinical molecular tests to have wide-reaching impact, they must be applicable to FFPE material. Accurate quantitative measurements of RNA derived from FFPE specimens is challenging because of low yields and high amounts of degradation. Here, we present FFPEcap-seq, a method specifically designed for sequencing capped 5′ ends of RNA derived from FFPE samples. FFPEcap-seq combines enzymatic enrichment of 5′ capped RNAs with template switching to create sequencing libraries. We find that FFPEcap-seq can faithfully capture mRNA expression levels in FFPE specimens while also detecting enhancer RNAs that arise from distal regulatory regions. FFPEcap-seq is a fast and straightforward method for making high-quality 5′ end RNA-seq libraries from FFPE-derived RNA.
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Affiliation(s)
- Jeffery M Vahrenkamp
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Kathryn Szczotka
- Department of Obstetrics and Gynecology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Mark K Dodson
- Department of Obstetrics and Gynecology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Elke A Jarboe
- Department of Pathology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Andrew P Soisson
- Department of Obstetrics and Gynecology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
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11
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Thodberg M, Thieffry A, Vitting-Seerup K, Andersson R, Sandelin A. CAGEfightR: analysis of 5'-end data using R/Bioconductor. BMC Bioinformatics 2019; 20:487. [PMID: 31585526 PMCID: PMC6778389 DOI: 10.1186/s12859-019-3029-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/15/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND 5'-end sequencing assays, and Cap Analysis of Gene Expression (CAGE) in particular, have been instrumental in studying transcriptional regulation. 5'-end methods provide genome-wide maps of transcription start sites (TSSs) with base pair resolution. Because active enhancers often feature bidirectional TSSs, such data can also be used to predict enhancer candidates. The current availability of mature and comprehensive computational tools for the analysis of 5'-end data is limited, preventing efficient analysis of new and existing 5'-end data. RESULTS We present CAGEfightR, a framework for analysis of CAGE and other 5'-end data implemented as an R/Bioconductor-package. CAGEfightR can import data from BigWig files and allows for fast and memory efficient prediction and analysis of TSSs and enhancers. Downstream analyses include quantification, normalization, annotation with transcript and gene models, TSS shape statistics, linking TSSs to enhancers via co-expression, identification of enhancer clusters, and genome-browser style visualization. While built to analyze CAGE data, we demonstrate the utility of CAGEfightR in analyzing nascent RNA 5'-data (PRO-Cap). CAGEfightR is implemented using standard Bioconductor classes, making it easy to learn, use and combine with other Bioconductor packages, for example popular differential expression tools such as limma, DESeq2 and edgeR. CONCLUSIONS CAGEfightR provides a single, scalable and easy-to-use framework for comprehensive downstream analysis of 5'-end data. CAGEfightR is designed to be interoperable with other Bioconductor packages, thereby unlocking hundreds of mature transcriptomic analysis tools for 5'-end data. CAGEfightR is freely available via Bioconductor: bioconductor.org/packages/CAGEfightR .
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Affiliation(s)
- Malte Thodberg
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark.
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark.
| | - Axel Thieffry
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark
| | - Kristoffer Vitting-Seerup
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark
- Danish Cancer Society, Strandboulevarden 49 DK2100, Copenhagen Ø, Denmark
| | - Robin Andersson
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark
| | - Albin Sandelin
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark.
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2100, Copenhagen N, Denmark.
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12
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Suzuki A, Kawano S, Mitsuyama T, Suyama M, Kanai Y, Shirahige K, Sasaki H, Tokunaga K, Tsuchihara K, Sugano S, Nakai K, Suzuki Y. DBTSS/DBKERO for integrated analysis of transcriptional regulation. Nucleic Acids Res 2019; 46:D229-D238. [PMID: 29126224 PMCID: PMC5753362 DOI: 10.1093/nar/gkx1001] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/03/2017] [Indexed: 12/15/2022] Open
Abstract
DBTSS (Database of Transcriptional Start Sites)/DBKERO (Database of Kashiwa Encyclopedia for human genome mutations in Regulatory regions and their Omics contexts) is the database originally initiated with the information of transcriptional start sites and their upstream transcriptional regulatory regions. In recent years, we updated the database to assist users to elucidate biological relevance of the human genome variations or somatic mutations in cancers which may affect the transcriptional regulation. In this update, we facilitate interpretations of disease associated genomic variation, using the Japanese population as a model case. We enriched the genomic variation dataset consisting of the 13,368 individuals collected for various genome-wide association studies and the reference epigenome information in the surrounding regions using a total of 455 epigenome datasets (four tissue types from 67 healthy individuals) collected for the International Human Epigenome Consortium (IHEC). The data directly obtained from the clinical samples was associated with that obtained from various model systems, such as the drug perturbation datasets using cultured cancer cells. Furthermore, we incorporated the results obtained using the newly developed analytical methods, Nanopore/10x Genomics long-read sequencing of the human genome and single cell analyses. The database is made publicly accessible at the URL (http://dbtss.hgc.jp/).
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Affiliation(s)
- Ayako Suzuki
- Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Shin Kawano
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Chiba, Japan
| | - Toutai Mitsuyama
- Computational Regulatory Genomics Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Katsuhiko Shirahige
- Institute of Molecular and Cellular Biosciences, the University of Tokyo, Tokyo, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Katsuya Tsuchihara
- Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Sumio Sugano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, Japan
| | - Kenta Nakai
- Human Genome Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Chiba, Japan
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13
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Abstract
Application of Transcription Start Site (TSS) profiling technologies, coupled with large-scale next-generation sequencing (NGS) has yielded valuable insights into the location, structure, and activity of promoters across diverse metazoan model systems. In insects, TSS profiling has been used to characterize the promoter architecture of Drosophila melanogaster (Hoskins et al., Genome Res 21(2):182-192, 2011) and subsequently was employed to reveal widespread transposon-driven alternative promoter usage in the fruit fly (Batut et al., Genome Res 23:169-180, 2012).In this chapter we discuss the computational analysis of the experimental data derived from one of TSS profiling methods, RAMPAGE (RNA Annotation and Mapping of Promoters for Analysis of Gene Expression) that can be used for the precise, quantitative identification of promoters in insect genomes. We demonstrate this using the software tools GoRAMPAGE (Brendel and Raborn, GoRAMPAGE-A workflow for promoter detection by 5'-read mapping. https://github.com/BrendelGroup/GoRAMPAGE , 2016) and TSRchitect (Raborn and Brendel, TSRchitect: promoter identification from large-scale TSS profiling data. R Bioconductor package version 1.8.0 [Online]. Available: http://bioconductor.org/packages/release/bioc/html/TSRchitect.html , 2017), providing detailed instructions with the aim of taking the user from raw reads to processed results.
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14
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Marsh JW, Hayward RJ, Shetty AC, Mahurkar A, Humphrys MS, Myers GSA. Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments. Brief Bioinform 2019; 19:1115-1129. [PMID: 28535295 DOI: 10.1093/bib/bbx043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Indexed: 12/18/2022] Open
Abstract
Bacterial pathogens subvert host cells by manipulating cellular pathways for survival and replication; in turn, host cells respond to the invading pathogen through cascading changes in gene expression. Deciphering these complex temporal and spatial dynamics to identify novel bacterial virulence factors or host response pathways is crucial for improved diagnostics and therapeutics. Dual RNA sequencing (dRNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell. This approach builds on the high sensitivity and resolution of RNA sequencing technology and is applicable to any bacteria that interact with eukaryotic cells, encompassing parasitic, commensal or mutualistic lifestyles. Several laboratory protocols have been presented that outline the collection, extraction and sequencing of total RNA for dRNA-Seq experiments, but there is relatively little guidance available for the detailed bioinformatic analyses required. This protocol outlines a typical dRNA-Seq experiment, based on a Chlamydia trachomatis-infected host cell, with a detailed description of the necessary bioinformatic analyses with currently available software tools.
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Affiliation(s)
- James W Marsh
- The ithree institute, University of Technology Sydney
| | | | - Amol C Shetty
- Institute for Genome Sciences at the University of Maryland, Baltimore
| | - Anup Mahurkar
- Institute for Genome Sciences at the University of Maryland, Baltimore
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15
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Ali Z, Mukwaya A, Biesemeier A, Ntzouni M, Ramsköld D, Giatrellis S, Mammadzada P, Cao R, Lennikov A, Marass M, Gerri C, Hildesjö C, Taylor M, Deng Q, Peebo B, del Peso L, Kvanta A, Sandberg R, Schraermeyer U, Andre H, Steffensen JF, Lagali N, Cao Y, Kele J, Jensen LD. Intussusceptive Vascular Remodeling Precedes Pathological Neovascularization. Arterioscler Thromb Vasc Biol 2019; 39:1402-1418. [PMID: 31242036 PMCID: PMC6636809 DOI: 10.1161/atvbaha.118.312190] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Supplemental Digital Content is available in the text. Objective— Pathological neovascularization is crucial for progression and morbidity of serious diseases such as cancer, diabetic retinopathy, and age-related macular degeneration. While mechanisms of ongoing pathological neovascularization have been extensively studied, the initiating pathological vascular remodeling (PVR) events, which precede neovascularization remains poorly understood. Here, we identify novel molecular and cellular mechanisms of preneovascular PVR, by using the adult choriocapillaris as a model. Approach and Results— Using hypoxia or forced overexpression of VEGF (vascular endothelial growth factor) in the subretinal space to induce PVR in zebrafish and rats respectively, and by analyzing choriocapillaris membranes adjacent to choroidal neovascular lesions from age-related macular degeneration patients, we show that the choriocapillaris undergo robust induction of vascular intussusception and permeability at preneovascular stages of PVR. This PVR response included endothelial cell proliferation, formation of endothelial luminal processes, extensive vesiculation and thickening of the endothelium, degradation of collagen fibers, and splitting of existing extravascular columns. RNA-sequencing established a role for endothelial tight junction disruption, cytoskeletal remodeling, vesicle- and cilium biogenesis in this process. Mechanistically, using genetic gain- and loss-of-function zebrafish models and analysis of primary human choriocapillaris endothelial cells, we determined that HIF (hypoxia-induced factor)-1α-VEGF-A-VEGFR2 signaling was important for hypoxia-induced PVR. Conclusions— Our findings reveal that PVR involving intussusception and splitting of extravascular columns, endothelial proliferation, vesiculation, fenestration, and thickening is induced before neovascularization, suggesting that identifying and targeting these processes may prevent development of advanced neovascular disease in the future.
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Affiliation(s)
- Zaheer Ali
- From the Division of Cardiovascular Medicine, Department of Medical and Health Sciences (Z.A., L.D.J.), Linkoping University, Sweden
| | - Anthony Mukwaya
- Division of Ophthalmology, Department of Clinical and Experimental Medicine (A.M., A.L., B.P., N.L.), Linkoping University, Sweden
| | - Antje Biesemeier
- Experimental Vitreoretinal Surgery, Center for Ophthalmology, University of Tuebingen, Germany (A.B., U.S.)
| | - Maria Ntzouni
- Electronmicroscopy and Histology Laboratory, Faculty of Medicine (M.N.), Linkoping University, Sweden
| | - Daniel Ramsköld
- Department of Cell and Molecular Biology (D.R., S.G., R.S.), Karolinska Institutet, Stockholm, Sweden
| | - Sarantis Giatrellis
- Department of Cell and Molecular Biology (D.R., S.G., R.S.), Karolinska Institutet, Stockholm, Sweden
| | - Parviz Mammadzada
- Department of Clinical Neuroscience, Section for Ophthalmology and Vision, St. Erik Eye Hospital (P.M., A.K., H.A.), Karolinska Institutet, Stockholm, Sweden
| | - Renhai Cao
- Department of Microbiology, Tumor and Cell Biology (R.C., Y.C.), Karolinska Institutet, Stockholm, Sweden
| | - Anton Lennikov
- Division of Ophthalmology, Department of Clinical and Experimental Medicine (A.M., A.L., B.P., N.L.), Linkoping University, Sweden
| | - Michele Marass
- Department of Developmental Genetics, Max Planck Institute for Lung and Heart Research, Bad Nauheim, Germany (M.M., C.G.)
| | - Claudia Gerri
- Department of Developmental Genetics, Max Planck Institute for Lung and Heart Research, Bad Nauheim, Germany (M.M., C.G.)
| | - Camilla Hildesjö
- Division of Surgery, Orthopedics and Oncology, Department for Clinical and Experimental Medicine (C.H.), Linkoping University, Sweden
| | - Michael Taylor
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison (M.T.)
| | - Qiaolin Deng
- Department of Physiology and Pharmacology (Q.D., J.K.), Karolinska Institutet, Stockholm, Sweden
| | - Beatrice Peebo
- Division of Ophthalmology, Department of Clinical and Experimental Medicine (A.M., A.L., B.P., N.L.), Linkoping University, Sweden
| | - Luis del Peso
- Department of Biochemistry, Universidad Autónoma de Madrid, Spain (L.d.P.)
- Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM Madrid, Spain (L.d.P.)
| | - Anders Kvanta
- Department of Clinical Neuroscience, Section for Ophthalmology and Vision, St. Erik Eye Hospital (P.M., A.K., H.A.), Karolinska Institutet, Stockholm, Sweden
| | - Rickard Sandberg
- Department of Cell and Molecular Biology (D.R., S.G., R.S.), Karolinska Institutet, Stockholm, Sweden
| | - Ulrich Schraermeyer
- Experimental Vitreoretinal Surgery, Center for Ophthalmology, University of Tuebingen, Germany (A.B., U.S.)
| | - Helder Andre
- Department of Clinical Neuroscience, Section for Ophthalmology and Vision, St. Erik Eye Hospital (P.M., A.K., H.A.), Karolinska Institutet, Stockholm, Sweden
| | - John F. Steffensen
- Marine Biological Section, Biological Institute, University of Copenhagen, Helsingor, Denmark (J.F.S.)
| | - Neil Lagali
- Division of Ophthalmology, Department of Clinical and Experimental Medicine (A.M., A.L., B.P., N.L.), Linkoping University, Sweden
| | - Yihai Cao
- Department of Microbiology, Tumor and Cell Biology (R.C., Y.C.), Karolinska Institutet, Stockholm, Sweden
| | - Julianna Kele
- Department of Physiology and Pharmacology (Q.D., J.K.), Karolinska Institutet, Stockholm, Sweden
| | - Lasse Dahl Jensen
- From the Division of Cardiovascular Medicine, Department of Medical and Health Sciences (Z.A., L.D.J.), Linkoping University, Sweden
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16
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Bird JG, Basu U, Kuster D, Ramachandran A, Grudzien-Nogalska E, Towheed A, Wallace DC, Kiledjian M, Temiakov D, Patel SS, Ebright RH, Nickels BE. Highly efficient 5' capping of mitochondrial RNA with NAD + and NADH by yeast and human mitochondrial RNA polymerase. eLife 2018; 7:42179. [PMID: 30526856 PMCID: PMC6298784 DOI: 10.7554/elife.42179] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/10/2018] [Indexed: 12/16/2022] Open
Abstract
Bacterial and eukaryotic nuclear RNA polymerases (RNAPs) cap RNA with the oxidized and reduced forms of the metabolic effector nicotinamide adenine dinucleotide, NAD+ and NADH, using NAD+ and NADH as non-canonical initiating nucleotides for transcription initiation. Here, we show that mitochondrial RNAPs (mtRNAPs) cap RNA with NAD+ and NADH, and do so more efficiently than nuclear RNAPs. Direct quantitation of NAD+- and NADH-capped RNA demonstrates remarkably high levels of capping in vivo: up to ~60% NAD+ and NADH capping of yeast mitochondrial transcripts, and up to ~15% NAD+ capping of human mitochondrial transcripts. The capping efficiency is determined by promoter sequence at, and upstream of, the transcription start site and, in yeast and human cells, by intracellular NAD+ and NADH levels. Our findings indicate mtRNAPs serve as both sensors and actuators in coupling cellular metabolism to mitochondrial transcriptional outputs, sensing NAD+ and NADH levels and adjusting transcriptional outputs accordingly.
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Affiliation(s)
- Jeremy G Bird
- Department of Genetics and Waksman Institute, Rutgers University, United States.,Department of Chemistry and Waksman Institute, Rutgers University, United States
| | - Urmimala Basu
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, United States.,Biochemistry PhD Program, School of Graduate Studies, Rutgers University, United States
| | - David Kuster
- Department of Genetics and Waksman Institute, Rutgers University, United States.,Department of Chemistry and Waksman Institute, Rutgers University, United States.,Biochemistry Center Heidelberg, Heidelberg University, Germany
| | - Aparna Ramachandran
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, United States
| | | | - Atif Towheed
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, United States
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, United States.,Department of Pediatrics, Division of Human Genetics, The Children's Hospital of Philadelphia, Perelman School of Medicine, United States
| | | | - Dmitry Temiakov
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, United States
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, United States
| | - Richard H Ebright
- Department of Chemistry and Waksman Institute, Rutgers University, United States
| | - Bryce E Nickels
- Department of Genetics and Waksman Institute, Rutgers University, United States
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17
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Chen Y, Takikawa M, Tsutsumi S, Yamaguchi Y, Okabe A, Shimada M, Kawase T, Sada A, Ezawa I, Takano Y, Nagata K, Suzuki Y, Semba K, Aburatani H, Ohki R. PHLDA1, another PHLDA family protein that inhibits Akt. Cancer Sci 2018; 109:3532-3542. [PMID: 30207029 PMCID: PMC6215895 DOI: 10.1111/cas.13796] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 09/05/2018] [Accepted: 09/08/2018] [Indexed: 01/07/2023] Open
Abstract
The PHLDA family (pleckstrin homology‐like domain family) of genes consists of 3 members: PHLDA1, 2, and 3. Both PHLDA3 and PHLDA2 are phosphatidylinositol (PIP) binding proteins and function as repressors of Akt. They have tumor suppressive functions, mainly through Akt inhibition. Several reports suggest that PHLDA1 also has a tumor suppressive function; however, the precise molecular functions of PHLDA1 remain to be elucidated. Through a comprehensive screen for p53 target genes, we identified PHLDA1 as a novel p53 target, and we show that PHLDA1 has the ability to repress Akt in a manner similar to that of PHLDA3 and PHLDA2. PHLDA1 has a so‐called split PH domain in which the PH domain is divided into an N‐terminal (β sheets 1‐3) and a C‐terminal (β sheets 4‐7 and an α‐helix) portions. We show that the PH domain of PHLDA1 is responsible for its localization to the plasma membrane and binding to phosphatidylinositol. We also show that the function of the PH domain is essential for Akt repression. In addition, PHLDA1 expression analysis suggests that PHLDA1 has a tumor suppressive function in breast and ovarian cancers.
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Affiliation(s)
- Yu Chen
- Laboratory of Fundamental Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Masahiro Takikawa
- Laboratory of Fundamental Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Shuichi Tsutsumi
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Yoko Yamaguchi
- Laboratory of Fundamental Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Faculty of Science, Department of Biomolecular Science, Toho University, Chiba, Japan
| | - Atsushi Okabe
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.,Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Mayuna Shimada
- Laboratory of Fundamental Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Tatsuya Kawase
- Laboratory of Fundamental Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Akane Sada
- Laboratory of Fundamental Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Issei Ezawa
- Laboratory of Fundamental Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Yuhei Takano
- Laboratory of Fundamental Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kisaburo Nagata
- Faculty of Science, Department of Biomolecular Science, Toho University, Chiba, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Kentaro Semba
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Rieko Ohki
- Laboratory of Fundamental Oncology, National Cancer Center Research Institute, Tokyo, Japan
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18
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Vandenbon A, Kumagai Y, Lin M, Suzuki Y, Nakai K. Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation. Genome Biol 2018; 19:138. [PMID: 30231913 PMCID: PMC6146659 DOI: 10.1186/s13059-018-1524-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/04/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The importance of transcription factors (TFs) and epigenetic modifications in the control of gene expression is widely accepted. However, causal relationships between changes in TF binding, histone modifications, and gene expression during the response to extracellular stimuli are not well understood. Here, we analyze the ordering of these events on a genome-wide scale in dendritic cells in response to lipopolysaccharide (LPS) stimulation. RESULTS Using a ChIP-seq time series dataset, we find that the LPS-induced accumulation of different histone modifications follows clearly distinct patterns. Increases in H3K4me3 appear to coincide with transcriptional activation. In contrast, H3K9K14ac accumulates early after stimulation, and H3K36me3 at later time points. Integrative analysis with TF binding data reveals potential links between TF activation and dynamics in histone modifications. Especially, LPS-induced increases in H3K9K14ac and H3K4me3 are associated with binding by STAT1/2 and were severely impaired in Stat1-/- cells. CONCLUSIONS While the timing of short-term changes of some histone modifications coincides with changes in transcriptional activity, this is not the case for others. In the latter case, dynamics in modifications more likely reflect strict regulation by stimulus-induced TFs and their interactions with chromatin modifiers.
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Affiliation(s)
- Alexis Vandenbon
- Laboratory of Infection and Prevention, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan.
- Institute for Liberal Arts and Sciences, Kyoto University, Kyoto, 606-8507, Japan.
| | - Yutaro Kumagai
- Quantitative Immunology Research Unit, Immunology Frontier Research Center (IFReC), Osaka University, Suita, 565-0871, Japan
- Biotechnology Research Institute for Drug Discovery, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8565, Japan
| | - Mengjie Lin
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Kenta Nakai
- Laboratory of Functional Analysis in silico, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan.
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19
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Sabath N, Vilborg A, Steitz JA, Shalgi R. Caution needs to be taken when assigning transcription start sites to ends of protein-coding genes: a rebuttal. Hum Genomics 2018; 12:32. [PMID: 29945683 PMCID: PMC6020437 DOI: 10.1186/s40246-018-0164-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 06/11/2018] [Indexed: 11/18/2022] Open
Abstract
Naturally occurring stress-induced transcriptional readthrough is a recently discovered phenomenon, in which stress conditions lead to dramatic induction of long transcripts as a result of transcription termination failure. In 2015, we reported the induction of such downstream of gene (DoG) containing transcripts upon osmotic stress in human cells, while others observed similar transcripts in virus-infected and cancer cells. Using the rigorous methodology Cap-Seq, we demonstrated that DoGs result from transcriptional readthrough, not de novo initiation. More recently, we presented a genome-wide comparison of NIH3T3 mouse cells subjected to osmotic, heat, and oxidative stress and concluded that massive induction of transcriptional readthrough is a hallmark of the mammalian stress response. In their recent letter, Huang and Liu in contrast claim that DoG transcripts result from novel transcription initiation near the ends of genes. Their conclusions rest on analyses of a publicly available transcription start site (TSS-Seq) dataset from unstressed NIH3T3 cells. Here, we present evidence that this dataset identifies not only true transcription start sites, TSSs, but also 5′-ends of numerous snoRNAs, which are generally processed from introns in mammalian cells. We show that failure to recognize these erroneous assignments in the TSS-Seq dataset, as well as ignoring published Cap-Seq data on TSS mapping during osmotic stress, have led to misinterpretation by Huang and Liu. We conclude that, contrary to the claims made by Huang and Liu, TSS-Seq reads near gene ends cannot explain the existence of DoGs, nor their stress-mediated induction. Rather it is, as we originally demonstrated, transcriptional readthrough that leads to the formation of DoGs.
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Affiliation(s)
- Niv Sabath
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, 31096, Haifa, Israel
| | - Anna Vilborg
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT, 06536, USA
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT, 06536, USA
| | - Reut Shalgi
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, 31096, Haifa, Israel.
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20
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Comprehensive comparative analysis of 5'-end RNA-sequencing methods. Nat Methods 2018; 15:505-511. [PMID: 29867192 PMCID: PMC6075671 DOI: 10.1038/s41592-018-0014-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 04/10/2018] [Indexed: 12/20/2022]
Abstract
Specialized RNA-seq methods are required to identify the 5' ends of transcripts, which are critical for studies of gene regulation, but these methods have not been systematically benchmarked. We directly compared six such methods, including the performance of five methods on a single human cellular RNA sample and a new spike-in RNA assay that helps circumvent challenges resulting from uncertainties in annotation and RNA processing. We found that the 'cap analysis of gene expression' (CAGE) method performed best for mRNA and that most of its unannotated peaks were supported by evidence from other genomic methods. We applied CAGE to eight brain-related samples and determined sample-specific transcription start site (TSS) usage, as well as a transcriptome-wide shift in TSS usage between fetal and adult brain.
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21
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Tano K, Onoguchi-Mizutani R, Yeasmin F, Uchiumi F, Suzuki Y, Yada T, Akimitsu N. Identification of Minimal p53 Promoter Region Regulated by MALAT1 in Human Lung Adenocarcinoma Cells. Front Genet 2018; 8:208. [PMID: 29632545 PMCID: PMC5879451 DOI: 10.3389/fgene.2017.00208] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/27/2017] [Indexed: 12/15/2022] Open
Abstract
The MALAT1 long noncoding RNA is strongly linked to cancer progression. Here we report a MALAT1 function in repressing the promoter of p53 (TP53) tumor suppressor gene. p21 and FAS, well-known p53 targets, were upregulated by MALAT1 knockdown in A549 human lung adenocarcinoma cells. We found that these upregulations were mediated by transcriptional activation of p53 through MALAT1 depletion. In addition, we identified a minimal MALAT1-responsive region in the P1 promoter of p53 gene. Flow cytometry analysis revealed that MALAT1-depleted cells exhibited G1 cell cycle arrest. These results suggest that MALAT1 affects the expression of p53 target genes through repressing p53 promoter activity, leading to influence the cell cycle progression.
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Affiliation(s)
- Keiko Tano
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | | | - Fouzia Yeasmin
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Fumiaki Uchiumi
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Chiba-ken, Japan
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Tetsushi Yada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kitakyushu, Japan
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22
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Identification of potential regulatory mutations using multi-omics analysis and haplotyping of lung adenocarcinoma cell lines. Sci Rep 2018; 8:4926. [PMID: 29563587 PMCID: PMC5862974 DOI: 10.1038/s41598-018-23342-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 03/09/2018] [Indexed: 12/20/2022] Open
Abstract
The functional relevancy of mutations occurring in the regulatory regions in cancers remains mostly elusive. Here, we identified and analyzed regulatory mutations having transcriptional consequences in lung adenocarcinoma-derived cell lines. We phased the mutations in the regulatory regions to the downstream heterozygous SNPs in the coding regions and examined whether the ChIP-Seq variant tags of the regulatory SNVs and the RNA-Seq variant tags of their target transcripts showed biased frequency between the mutant and reference alleles. We identified 137 potential regulatory mutations affecting the transcriptional regulation of 146 RefSeq transcripts with at least 84 SNVs that create and/or disrupt potential transcription factor binding sites. For example, in the regulatory region of NFATC1 gene, a novel and active binding site for the ETS transcription factor family was created. Further examination revealed that 31 of these disruptions were presented in clinical lung adenocarcinoma samples and were associated with prognosis of patients.
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23
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Huang MY, Liu JL. Transcription start sites at the end of protein-coding genes. Hum Genomics 2018; 12:15. [PMID: 29548296 PMCID: PMC5857071 DOI: 10.1186/s40246-018-0146-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 03/09/2018] [Indexed: 12/04/2022] Open
Abstract
Previous studies demonstrated that massive induction of transcriptional readthrough generates downstream of gene-containing transcripts (DoGs) in cells under stress condition. Here, we analyzed TSS-seq (transcription start site sequencing) data from the DBTSS database. We investigated TSS tags at the end of gene for all pan-stress and untreated-cell DoGs, in comparison with expression-matched non-DoGs. We observed significantly more TSS tags at the end of pan-stress and untreated-cell DoG genes than non-DoG genes, even though their TSS tags in the promoter is the same. Importantly, the median value of TSS tags at gene end normalized to gene promoter is significantly higher than the median expression ratio of short DoG to host gene and of long DoG to host gene. Our results indicate that downstream overlapping long non-coding RNAs derived from the TSS at the gene end may be an important source of DoGs.
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Affiliation(s)
- Ming-Yu Huang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ji-Long Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.
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24
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Light Controls Protein Localization through Phytochrome-Mediated Alternative Promoter Selection. Cell 2017; 171:1316-1325.e12. [PMID: 29129375 DOI: 10.1016/j.cell.2017.10.018] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/15/2017] [Accepted: 10/12/2017] [Indexed: 12/31/2022]
Abstract
Alternative promoter usage is a proteome-expanding mechanism that allows multiple pre-mRNAs to be transcribed from a single gene. The impact of this mechanism on the proteome and whether it is positively exploited in normal organismal responses remain unclear. We found that the plant photoreceptor phytochrome induces genome-wide changes in alternative promoter selection in Arabidopsis thaliana. Through this mechanism, protein isoforms with different N termini are produced that display light-dependent differences in localization. For instance, shade-grown plants accumulate a cytoplasmic isoform of glycerate kinase (GLYK), an essential photorespiration enzyme that was previously thought to localize exclusively to the chloroplast. Cytoplasmic GLYK constitutes a photorespiratory bypass that alleviates fluctuating light-induced photoinhibition. Therefore, phytochrome controls alternative promoter selection to modulate protein localization in response to changing light conditions. This study suggests that alternative promoter usage represents another ubiquitous layer of gene expression regulation in eukaryotes that contributes to diversification of the proteome.
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Relatively frequent switching of transcription start sites during cerebellar development. BMC Genomics 2017; 18:461. [PMID: 28610618 PMCID: PMC5470264 DOI: 10.1186/s12864-017-3834-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alternative transcription start site (TSS) usage plays important roles in transcriptional control of mammalian gene expression. The growing interest in alternative TSSs and their role in genome diversification spawned many single-gene studies on differential usages of tissue-specific or temporal-specific alternative TSSs. However, exploration of the switching usage of alternative TSS usage on a genomic level, especially in the central nervous system, is largely lacking. RESULTS In this study, We have prepared a unique set of time-course data for the developing cerebellum, as part of the FANTOM5 consortium ( http://fantom.gsc.riken.jp/5/ ) that uses their innovative capturing of 5' ends of all transcripts followed by Helicos next generation sequencing. We analyzed the usage of all transcription start sites (TSSs) at each time point during cerebellar development that provided information on multiple RNA isoforms that emerged from the same gene. We developed a mathematical method that systematically compares the expression of different TSSs of a gene to identify temporal crossover and non-crossover switching events. We identified 48,489 novel TSS switching events in 5433 genes during cerebellar development. This includes 9767 crossover TSS switching events in 1511 genes, where the dominant TSS shifts over time. CONCLUSIONS We observed a relatively high prevalence of TSS switching in cerebellar development where the resulting temporally-specific gene transcripts and protein products can play important regulatory and functional roles.
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Joseph R, Srivastava OP, Pfister RR. Modeling Keratoconus Using Induced Pluripotent Stem Cells. Invest Ophthalmol Vis Sci 2017; 57:3685-97. [PMID: 27403997 PMCID: PMC5996875 DOI: 10.1167/iovs.16-19105] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
PURPOSE To model keratoconus (KC) using induced pluripotent stem cells (iPSC) generated from fibroblasts of both KC and normal human corneal stroma by a viral method. METHODS Both normal and KC corneal fibroblasts from four human donors were reprogramed directly by delivering reprogramming factors in a single virus using 2A "self-cleaving" peptides, using a single polycistronic lentiviral vector coexpressing four transcription factors (Oct 4, Sox2, Klf4, and Myc) to yield iPSC. These iPS cells were characterized by immunofluorescence detection using of stem cell markers (SSEA4, Oct4, and Sox2). The mRNA sequencing was performed and the datasets were analyzed using ingenuity pathways analysis (IPA) software. RESULTS The generated stem cell-like clones expressed the pluripotency markers, SSEA4, Oct4, Sox2, Tra-1-60, and also expressed pax6. Our transcriptome analysis showed 4300 genes, which had 2-fold change and 870 genes with a q-value of <0.05 in keratoconus iPSC compared to normal iPSC. One of the genes that showed difference in KC iPSC was FGFR2 (down-regulated by 2.4 fold), an upstream target of Pi3-Kinase pathway, was further validated in keratoconus corneal sections and also KC iPSC-derived keratocytes (down regulated by 2.0-fold). Both normal and KC-derived keratocytes expressed keratocan, signature marker for keratocytes. KC iPSC-derived keratocytes showed adverse growth and proliferation and was further confirmed by using Ly2924002, a PI3k inhibitor, which severely affected the growth and differentiation in normal iPSC. CONCLUSIONS Based on our result, we propose a model for KC in which inhibition FGFR2-Pi3-Kinase pathway affects the AKT phosphorylation, and thus affecting the keratocytes survival signals. This inhibition of the survival signals could be a potential mechanism for the KC-specific decreased cell survival and apoptosis of keratocytes.
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Affiliation(s)
- Roy Joseph
- Department of Optometry and Vision Science University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Om P Srivastava
- Department of Optometry and Vision Science University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Roswell R Pfister
- Eye Research Laboratory, Eye Research Foundation, Birmingham, Alabama, United States
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Tokizawa M, Kusunoki K, Koyama H, Kurotani A, Sakurai T, Suzuki Y, Sakamoto T, Kurata T, Yamamoto YY. Identification of Arabidopsis genic and non-genic promoters by paired-end sequencing of TSS tags. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:587-605. [PMID: 28214361 DOI: 10.1111/tpj.13511] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 02/02/2017] [Accepted: 02/06/2017] [Indexed: 06/06/2023]
Abstract
Information about transcription start sites (TSSs) provides baseline data for the analysis of promoter architecture. In this paper we used paired- and single-end deep sequencing to analyze Arabidopsis TSS tags from several libraries prepared from roots, shoots, flowers and etiolated seedlings. The clustering of approximately 33 million mapped TSS tags led to the identification of 324 461 promoters that covered 79.7% (21 672/27 206) of protein-coding genes in the Arabidopsis genome. In addition we identified intragenic, antisense and orphan promoters that were not associated with any gene models. Of these, intragenic promoters exhibited unique characteristics regarding dinucleotide sequences at TSSs and core promoter element composition, suggesting that these promoters use different mechanisms of transcriptional initiation. An analysis of base composition with regard to promoter position revealed a low GC content throughout the promoter region and several local strand biases that were evident for TATA-type promoters, but not for Coreless-type promoters. Most observed strand biases coincided with strand biases of single nucleotide polymorphism rate. Our analysis also revealed that transcription of a gene is supported by an average of 2.7 genic promoters, among which one specific promoter, designated as a top promoter, substantially determines the expression level of the gene.
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Affiliation(s)
- Mutsutomo Tokizawa
- United Graduate School of Agriculture, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan
| | - Kazutaka Kusunoki
- United Graduate School of Agriculture, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan
| | - Hiroyuki Koyama
- United Graduate School of Agriculture, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan
- Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan
| | - Atsushi Kurotani
- RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Tetsuya Sakurai
- RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yutaka Suzuki
- Institute of Medical Science, University of Tokyo, Shiroganedai 4-6-1, Minato-ku, Tokyo, 108-8639, Japan
| | - Tomoaki Sakamoto
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayam-cho 8916-5, Ikoma, Nara, 630-0192, Japan
| | - Tetsuya Kurata
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayam-cho 8916-5, Ikoma, Nara, 630-0192, Japan
| | - Yoshiharu Y Yamamoto
- United Graduate School of Agriculture, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan
- Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan
- RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- JST ALCA, Tokyo, Japan
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Kim H, Greenald D, Vettori A, Markham E, Santhakumar K, Argenton F, van Eeden F. Zebrafish as a model for von Hippel Lindau and hypoxia-inducible factor signaling. Methods Cell Biol 2017; 138:497-523. [DOI: 10.1016/bs.mcb.2016.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Thomson JM. Impacts of environment on gene expression and epigenetic modification in grazing animals. J Anim Sci 2016. [DOI: 10.2527/jas.2016-0556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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Woodby B, Scott M, Bodily J. The Interaction Between Human Papillomaviruses and the Stromal Microenvironment. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 144:169-238. [PMID: 27865458 PMCID: PMC5727914 DOI: 10.1016/bs.pmbts.2016.09.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human papillomaviruses (HPVs) are small, double-stranded DNA viruses that replicate in stratified squamous epithelia and cause a variety of malignancies. Current efforts in HPV biology are focused on understanding the virus-host interactions that enable HPV to persist for years or decades in the tissue. The importance of interactions between tumor cells and the stromal microenvironment has become increasingly apparent in recent years, but how stromal interactions impact the normal, benign life cycle of HPVs, or progression of lesions to cancer is less understood. Furthermore, how productively replicating HPV impacts cells in the stromal environment is also unclear. Here we bring together some of the relevant literature on keratinocyte-stromal interactions and their impacts on HPV biology, focusing on stromal fibroblasts, immune cells, and endothelial cells. We discuss how HPV oncogenes in infected cells manipulate other cells in their environment, and, conversely, how neighboring cells may impact the efficiency or course of HPV infection.
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Affiliation(s)
- B Woodby
- Louisiana State University Health Sciences Center, Shreveport, LA, United States
| | - M Scott
- Louisiana State University Health Sciences Center, Shreveport, LA, United States
| | - J Bodily
- Louisiana State University Health Sciences Center, Shreveport, LA, United States.
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Mwangi S, Attardo G, Suzuki Y, Aksoy S, Christoffels A. TSS seq based core promoter architecture in blood feeding Tsetse fly (Glossina morsitans morsitans) vector of Trypanosomiasis. BMC Genomics 2015; 16:722. [PMID: 26394619 PMCID: PMC4578606 DOI: 10.1186/s12864-015-1921-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 09/11/2015] [Indexed: 02/02/2023] Open
Abstract
Background Transcription initiation regulation is mediated by sequence-specific interactions between DNA-binding proteins (transcription factors) and cis-elements, where BRE, TATA, INR, DPE and MTE motifs constitute canonical core motifs for basal transcription initiation of genes. Accurate identification of transcription start site (TSS) and their corresponding promoter regions is critical for delineation of these motifs. To this end, the genome scale analysis of core promoter architecture in insects has been confined to Drosophila. The recently sequenced Tsetse fly genome provides a unique opportunity to analyze transcription initiation regulation machinery in blood-feeding insects. Results A computational method for identification of TSS in newly sequenced Tsetse fly genome was evaluated, using TSS seq tags sampled from two developmental stages namely; larvae and pupae. There were 3134 tag clusters among which 45.4 % (1424) of the tag clusters mapped to first coding exons or their proximal predicted 5′UTR regions and 1.0 % (31) tag clusters mapping to transposons, within a threshold of 100 tags per cluster. These 1393 non transposon-derived core promoters had propensity for AT nucleotides. The −1/+1 and 1/+1 positions in D. melanogaster, and G. m. morsitans had propensity for CA and AA dinucleotides respectively. The 1393 tag clusters comprised narrow promoters (5 %), broad with peak promoters (23 %) and broad without peak promoters (72 %). Two-way motif co-occurrence analysis showed that the MTE-DPE pair is over-represented in broad core promoters. The frequently occurring triplet motifs in all promoter classes are the INR-MTE-DPE, TATA-MTE-DPE and TATA-INR-DPE. Promoters without the TATA motif had higher frequency of the MTE and INR motifs than those observed in Drosophila, where the DPE motif occur more frequently in promoters without TATA motif. Gene ontology terms associated with developmental processes were overrepresented in the narrow and broad with peak promoters. Conclusions The study has identified different motif combinations associated with broad promoters in a blood-feeding insect. In the case of TATA-less core promoters, G.m. morsitans uses the MTE to compensate for the lack of a TATA motif. The increasing availability of TSS seq data allows for revision of existing gene annotation datasets with the potential of identifying new transcriptional units. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1921-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah Mwangi
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
| | - Geoffrey Attardo
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA.
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, University of Tokyo, Tokyo, Japan.
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA.
| | - Alan Christoffels
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
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Wu MZ, Chen SF, Nieh S, Benner C, Ger LP, Jan CI, Ma L, Chen CH, Hishida T, Chang HT, Lin YS, Montserrat N, Gascon P, Sancho-Martinez I, Izpisua Belmonte JC. Hypoxia Drives Breast Tumor Malignancy through a TET–TNFα–p38–MAPK Signaling Axis. Cancer Res 2015; 75:3912-24. [DOI: 10.1158/0008-5472.can-14-3208] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 05/31/2015] [Indexed: 11/16/2022]
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The genome-wide identification of promoter regions in Toxoplasma gondii. Methods Mol Biol 2015; 1201:193-205. [PMID: 25388115 DOI: 10.1007/978-1-4939-1438-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Parasites change their transcriptional systems in different developmental stages and in response to environmental changes. To investigate the molecular mechanisms that underlie transcriptional regulation, it is essential to identify the exact positions of the transcriptional start sites (TSSs) and characterize the upstream promoter regions. However, it has been essentially impossible to obtain comprehensive information using conventional methods. Here, we introduce our TSS-seq method, which combines full-length technology, oligo-capping, and rapidly developing next-generation sequencing technology. TSS-seq has enabled identification of TSS positions and upstream promoter activities as digital TSS tag counts within a reasonable cost and time frame. In this chapter, we describe in detail the TSS-seq method for the identification and characterization of the promoters in Toxoplasma gondii.
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Whole transcriptome analysis with sequencing: methods, challenges and potential solutions. Cell Mol Life Sci 2015; 72:3425-39. [PMID: 26018601 DOI: 10.1007/s00018-015-1934-y] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/25/2015] [Accepted: 05/21/2015] [Indexed: 10/23/2022]
Abstract
Whole transcriptome analysis plays an essential role in deciphering genome structure and function, identifying genetic networks underlying cellular, physiological, biochemical and biological systems and establishing molecular biomarkers that respond to diseases, pathogens and environmental challenges. Here, we review transcriptome analysis methods and technologies that have been used to conduct whole transcriptome shotgun sequencing or whole transcriptome tag/target sequencing analyses. We focus on how adaptors/linkers are added to both 5' and 3' ends of mRNA molecules for cloning or PCR amplification before sequencing. Challenges and potential solutions are also discussed. In brief, next generation sequencing platforms have accelerated releases of the large amounts of gene expression data. It is now time for the genome research community to assemble whole transcriptomes of all species and collect signature targets for each gene/transcript, and thus use known genes/transcripts to determine known transcriptomes directly in the near future.
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Sun M, Kraus WL. From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease. Endocr Rev 2015; 36:25-64. [PMID: 25426780 PMCID: PMC4309736 DOI: 10.1210/er.2014-1034] [Citation(s) in RCA: 311] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) are a relatively poorly understood class of RNAs with little or no coding capacity transcribed from a set of incompletely annotated genes. They have received considerable attention in the past few years and are emerging as potentially important players in biological regulation. Here we discuss the evolving understanding of this new class of molecular regulators that has emerged from ongoing research, which continues to expand our databases of annotated lncRNAs and provide new insights into their physical properties, molecular mechanisms of action, and biological functions. We outline the current strategies and approaches that have been employed to identify and characterize lncRNAs, which have been instrumental in revealing their multifaceted roles ranging from cis- to trans-regulation of gene expression and from epigenetic modulation in the nucleus to posttranscriptional control in the cytoplasm. In addition, we highlight the molecular and biological functions of some of the best characterized lncRNAs in physiology and disease, especially those relevant to endocrinology, reproduction, metabolism, immunology, neurobiology, muscle biology, and cancer. Finally, we discuss the tremendous diagnostic and therapeutic potential of lncRNAs in cancer and other diseases.
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Affiliation(s)
- Miao Sun
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Lertwattanasakul N, Kosaka T, Hosoyama A, Suzuki Y, Rodrussamee N, Matsutani M, Murata M, Fujimoto N, Tsuchikane K, Limtong S, Fujita N, Yamada M. Genetic basis of the highly efficient yeast Kluyveromyces marxianus: complete genome sequence and transcriptome analyses. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:47. [PMID: 25834639 PMCID: PMC4381506 DOI: 10.1186/s13068-015-0227-x] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/19/2015] [Indexed: 05/07/2023]
Abstract
BACKGROUND High-temperature fermentation technology with thermotolerant microbes has been expected to reduce the cost of bioconversion of cellulosic biomass to fuels or chemicals. Thermotolerant Kluyveromyces marxianus possesses intrinsic abilities to ferment and assimilate a wide variety of substrates including xylose and to efficiently produce proteins. These capabilities have been found to exceed those of the traditional ethanol producer Saccharomyces cerevisiae or lignocellulose-bioconvertible ethanologenic Scheffersomyces stipitis. RESULTS The complete genome sequence of K. marxianus DMKU 3-1042 as one of the most thermotolerant strains in the same species has been determined. A comparison of its genomic information with those of other yeasts and transcriptome analysis revealed that the yeast bears beneficial properties of temperature resistance, wide-range bioconversion ability, and production of recombinant proteins. The transcriptome analysis clarified distinctive metabolic pathways under three different growth conditions, static culture, high temperature, and xylose medium, in comparison to the control condition of glucose medium under a shaking condition at 30°C. Interestingly, the yeast appears to overcome the issue of reactive oxygen species, which tend to accumulate under all three conditions. CONCLUSIONS This study reveals many gene resources for the ability to assimilate various sugars in addition to species-specific genes in K. marxianus, and the molecular basis of its attractive traits for industrial applications including high-temperature fermentation. Especially, the thermotolerance trait may be achieved by an integrated mechanism consisting of various strategies. Gene resources and transcriptome data of the yeast are particularly useful for fundamental and applied researches for innovative applications.
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Affiliation(s)
- Noppon Lertwattanasakul
- />Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505 Japan
- />Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900 Thailand
| | - Tomoyuki Kosaka
- />Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515 Japan
| | - Akira Hosoyama
- />National Institute of Technology and Evaluation, Shibuya-ku, Tokyo 151-0066 Japan
| | - Yutaka Suzuki
- />Department of Medical Genome Sciences, The University of Tokyo, Chiba, 277-8562 Japan
| | - Nadchanok Rodrussamee
- />Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505 Japan
- />Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200 Thailand
| | - Minenosuke Matsutani
- />Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515 Japan
| | - Masayuki Murata
- />Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505 Japan
| | - Naoko Fujimoto
- />Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505 Japan
| | - Keiko Tsuchikane
- />National Institute of Technology and Evaluation, Shibuya-ku, Tokyo 151-0066 Japan
| | - Savitree Limtong
- />Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900 Thailand
| | - Nobuyuki Fujita
- />National Institute of Technology and Evaluation, Shibuya-ku, Tokyo 151-0066 Japan
| | - Mamoru Yamada
- />Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505 Japan
- />Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515 Japan
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Vandenbon A, Teraguchi S, Takeuchi O, Suzuki Y, Standley DM. Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation. BMC Genomics 2014; 15 Suppl 10:S4. [PMID: 25560382 PMCID: PMC4304210 DOI: 10.1186/1471-2164-15-s10-s4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent studies have underscored the role of enhancers in defining cell type-specific transcriptomes. Cell type-specific enhancers are bound by combinations of shared and cell type-specific transcription factors (TFs). However, little is known about combinatorial binding of TFs to enhancers, dynamics of TF binding following stimulation, or the downstream effects on gene expression. Here, we address these questions in two types of myeloid antigen presenting cells (APCs), macrophages and dendritic cells (DCs), before and after stimulation with lipopolysaccharide (LPS), a potent stimulator of the innate immune response. RESULTS We classified enhancers according to the combination of TFs binding them. There were significant correlations between the sets of TFs bound to enhancers prior to stimulation and expression changes of nearby genes after stimulation. Importantly, a set of enhancers pre-bound by PU.1, C/EBPβ, ATF3, IRF4, and JunB was strongly associated with induced genes and binding by stimulus-activated regulators. Our classification suggests that transient loss of ATF3 binding to a subset of these enhancers is important for regulation of early-induced genes. Changes in TF-enhancer binding after stimulation were correlated with binding by additional activated TFs and with the presence of proximally located enhancers. CONCLUSIONS The results presented in this study reveal the complexity and dynamics of TF- enhancer binding before and after stimulation in myeloid APCs.
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Affiliation(s)
- Alexis Vandenbon
- Laboratory of Systems Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871, Japan
- Immuno-Genomics Research Unit, Immunology Frontier Research Center, Osaka University, Suita, 565-0871, Japan
| | - Shunsuke Teraguchi
- Quantitative Immunology Research Unit, Immunology Frontier Research Center, Osaka University, Suita, 565-0871, Japan
| | - Osamu Takeuchi
- Laboratory of Infection and Prevention, Institute for Virus Research, Kyoto University, Kyoto, 606-8507, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8568, Japan
| | - Daron M Standley
- Laboratory of Systems Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871, Japan
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Abstract
AbstractMethylation-specific PCR (MSP) is still the method of choice for a single gene methylation study. The proper design of the primer pairs is a prerequisite for obtaining reliable PCR results. Despite numerous protocols describing the rules for MSP primer design, none of them provide a comprehensive approach to the problem. Our aim was to depict a workflow for the primer design that is concise and easy to follow. In order to achieve this goal, adequate tools for promoter sequence retrieval, MSP primer design and subsequent in silico analysis are presented and discussed. Furthermore, a few instructive examples regarding a good versus a poor primer design are provided. Finally, primer design is demonstrated according to the proposed workflow. This article aims to provide researchers, interested in a single gene methylation studies, with useful information regarding successful primer design.
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Lawhorn IEB, Ferreira JP, Wang CL. Evaluation of sgRNA target sites for CRISPR-mediated repression of TP53. PLoS One 2014; 9:e113232. [PMID: 25398078 PMCID: PMC4232525 DOI: 10.1371/journal.pone.0113232] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 10/21/2014] [Indexed: 12/21/2022] Open
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeats) platform has been developed as a general method to direct proteins of interest to gene targets. While the native CRISPR system delivers a nuclease that cleaves and potentially mutates target genes, researchers have recently employed catalytically inactive CRISPR-associated 9 nuclease (dCas9) in order to target and repress genes without DNA cleavage or mutagenesis. With the intent of improving repression efficiency in mammalian cells, researchers have also fused dCas9 with a KRAB repressor domain. Here, we evaluated different genomic sgRNA targeting sites for repression of TP53. The sites spanned a 200-kb distance, which included the promoter, transcript sequence, and regions flanking the endogenous human TP53 gene. We showed that repression up to 86% can be achieved with dCas9 alone (i.e., without use of the KRAB domain) by targeting the complex to sites near the TP53 transcriptional start site. This work demonstrates that efficient transcriptional repression of endogenous human genes can be achieved by the targeted delivery of dCas9. Yet, the efficiency of repression strongly depends on the choice of the sgRNA target site.
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Affiliation(s)
- Ingrid E. B. Lawhorn
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
| | - Joshua P. Ferreira
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
| | - Clifford L. Wang
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
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Suzuki A, Wakaguri H, Yamashita R, Kawano S, Tsuchihara K, Sugano S, Suzuki Y, Nakai K. DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data. Nucleic Acids Res 2014; 43:D87-91. [PMID: 25378318 PMCID: PMC4383915 DOI: 10.1093/nar/gku1080] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DBTSS (http://dbtss.hgc.jp/) was originally constructed as a collection of uniquely determined transcriptional start sites (TSSs) in humans and some other species in 2002. Since then, it has been regularly updated and in recent updates epigenetic information has also been incorporated because such information is useful for characterizing the biological relevance of these TSSs/downstream genes. In the newest release, Release 9, we further integrated public and original single nucleotide variation (SNV) data into our database. For our original data, we generated SNV data from genomic analyses of various cancer types, including 97 lung adenocarcinomas and 57 lung small cell carcinomas from Japanese patients as well as 26 cell lines of lung cancer origin. In addition, we obtained publically available SNV data from other cancer types and germline variations in total of 11,322 individuals. With these updates, users can examine the association between sequence variation pattern in clinical lung cancers with its corresponding TSS-seq, RNA-seq, ChIP-seq and BS-seq data. Consequently, DBTSS is no longer a mere storage site for TSS information but has evolved into an integrative platform of a variety of genome activity data.
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Affiliation(s)
- Ayako Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Hiroyuki Wakaguri
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Riu Yamashita
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Shin Kawano
- Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan
| | - Katsuya Tsuchihara
- Division of TR, The Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Kenta Nakai
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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Yamagishi J, Wakaguri H, Yokoyama N, Yamashita R, Suzuki Y, Xuan X, Igarashi I. The Babesia bovis gene and promoter model: an update from full-length EST analysis. BMC Genomics 2014; 15:678. [PMID: 25124460 PMCID: PMC4148916 DOI: 10.1186/1471-2164-15-678] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 07/08/2014] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Babesia bovis is an apicomplexan parasite that causes babesiosis in infected cattle. Genomes of pathogens contain promising information that can facilitate the development of methods for controlling infections. Although the genome of B. bovis is publically available, annotated gene models are not highly reliable prior to experimental validation. Therefore, we validated a preproposed gene model of B. bovis and extended the associated annotations on the basis of experimentally obtained full-length expressed sequence tags (ESTs). RESULTS From in vitro cultured merozoites, 12,286 clones harboring full-length cDNAs were sequenced from both ends using the Sanger method, and 6,787 full-length cDNAs were assembled. These were then clustered, and a nonredundant referential data set of 2,115 full-length cDNA sequences was constructed. The comparison of the preproposed gene model with our data set identified 310 identical genes, 342 almost identical genes, 1,054 genes with potential structural inconsistencies, and 409 novel genes. The median length of 5' untranslated regions (UTRs) was 152 nt. Subsequently, we identified 4,086 transcription start sites (TSSs) and 2,023 transcriptionally active regions (TARs) by examining 5' ESTs. We identified ATGGGG and CCCCAT sites as consensus motifs in TARs that were distributed around -50 bp from TSSs. In addition, we found ACACA, TGTGT, and TATAT sites, which were distributed periodically around TSSs in cycles of approximately 150 bp. Moreover, related periodical distributions were not observed in mammalian promoter regions. CONCLUSIONS The observations in this study indicate the utility of integrated bioinformatics and experimental data for improving genome annotations. In particular, full-length cDNAs with one-base resolution for TSSs enabled the identification of consensus motifs in promoter sequences and demonstrated clear distributions of identified motifs. These observations allowed the illustration of a model promoter composition, which supports the differences in transcriptional regulation frameworks between apicomplexan parasites and mammals.
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Affiliation(s)
- Junya Yamagishi
- />Tohoku Medical Megabank Organization, Tohoku University, 6-3-09, aza Aoba, Sendai, Miyagi 980-8579 Japan
- />National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho west 2-13, Obihiro, Hokkaido 080-8555 Japan
| | - Hiroyuki Wakaguri
- />Department of Medical Genome Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 Japan
| | - Naoaki Yokoyama
- />National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho west 2-13, Obihiro, Hokkaido 080-8555 Japan
| | - Riu Yamashita
- />Tohoku Medical Megabank Organization, Tohoku University, 6-3-09, aza Aoba, Sendai, Miyagi 980-8579 Japan
| | - Yutaka Suzuki
- />Department of Medical Genome Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 Japan
| | - Xuenan Xuan
- />National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho west 2-13, Obihiro, Hokkaido 080-8555 Japan
| | - Ikuo Igarashi
- />National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho west 2-13, Obihiro, Hokkaido 080-8555 Japan
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Jakobi T, Brinkrolf K, Tauch A, Noll T, Stoye J, Pühler A, Goesmann A. Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing. J Biotechnol 2014; 190:64-75. [PMID: 25086342 DOI: 10.1016/j.jbiotec.2014.07.437] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/18/2014] [Accepted: 07/20/2014] [Indexed: 11/30/2022]
Abstract
Chinese hamster ovary (CHO) cell lines are one of the major production tools for monoclonal antibodies, recombinant proteins, and therapeutics. Although many efforts have significantly improved the availability of sequence information for CHO cells in the last years, forthcoming draft genomes still lack the information depth known from the mouse or human genomes. Many genes annotated for CHO cells and the Chinese hamster reference genome still are in silico predictions, only insufficiently verified by biological experiments. The correct annotation of transcription start sites (TSSs) is of special interest for CHO cells, as these directly define the location of the eukaryotic core promoter. Our study aims to elucidate these largely unexplored regions, trying to shed light on promoter landscapes in the Chinese hamster genome. Based on a 5' enriched dual library RNA sequencing approach 6547 TSSs were identified, of which over 90% were assigned to known genes. These TSSs were used to perform extensive promoter studies using a novel, modular bioinformatics pipeline, incorporating analyses of important regulatory elements of the eukaryotic core promoter on per-gene level and on genomic scale.
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Affiliation(s)
- Tobias Jakobi
- Institut für Bioinformatik, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33594 Bielefeld, Germany.
| | - Karina Brinkrolf
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33594 Bielefeld, Germany.
| | - Andreas Tauch
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33594 Bielefeld, Germany.
| | - Thomas Noll
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33594 Bielefeld, Germany.
| | - Jens Stoye
- Institut für Bioinformatik, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33594 Bielefeld, Germany; Technische Fakultät, Universität Bielefeld, 33594 Bielefeld, Germany.
| | - Alfred Pühler
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33594 Bielefeld, Germany.
| | - Alexander Goesmann
- Bioinformatik und Systembiologie, Justus-Liebig-Universität Gießen, 35392 Gießen, Germany.
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Hasegawa Y, Tang D, Takahashi N, Hayashizaki Y, Forrest ARR, Suzuki H. CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes. Sci Rep 2014; 4:5228. [PMID: 24957798 PMCID: PMC4067614 DOI: 10.1038/srep05228] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 04/04/2014] [Indexed: 12/22/2022] Open
Abstract
Standard culture of human induced pluripotent stem cells (hiPSCs) requires basic Fibroblast Growth Factor (bFGF) to maintain the pluripotent state, whereas hiPSC more closely resemble epiblast stem cells than true naïve state ES which requires LIF to maintain pluripotency. Here we show that chemokine (C-C motif) ligand 2 (CCL2) enhances the expression of pluripotent marker genes through the phosphorylation of the signal transducer and activator of transcription 3 (STAT3) protein. Moreover, comparison of transcriptomes between hiPSCs cultured with CCL2 versus with bFGF, we found that CCL2 activates hypoxia related genes, suggesting that CCL2 enhanced pluripotency by inducing a hypoxic-like response.Further, we show that hiPSCs cultured with CCL2 can differentiate at a higher efficiency than culturing withjust bFGF and we show CCL2 can be used in feeder-free conditions [corrected]. Taken together, our finding indicates the novel functions of CCL2 in enhancing its pluripotency in hiPSCs.
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Affiliation(s)
- Yuki Hasegawa
- 1] Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa, 230-0045 Japan [2] RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa, 230-0045 Japan
| | - Dave Tang
- 1] Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa, 230-0045 Japan [2] RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa, 230-0045 Japan
| | - Naoko Takahashi
- 1] Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa, 230-0045 Japan [2] RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa, 230-0045 Japan
| | - Yoshihide Hayashizaki
- 1] Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa, 230-0045 Japan [2] RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako-shi, Saitama, 551-0198 Japan
| | - Alistair R R Forrest
- 1] Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa, 230-0045 Japan [2] RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa, 230-0045 Japan
| | | | - Harukazu Suzuki
- 1] Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa, 230-0045 Japan [2] RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa, 230-0045 Japan
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Seki M, Masaki H, Arauchi T, Nakauchi H, Sugano S, Suzuki Y. A comparison of the rest complex binding patterns in embryonic stem cells and epiblast stem cells. PLoS One 2014; 9:e95374. [PMID: 24752154 PMCID: PMC3994037 DOI: 10.1371/journal.pone.0095374] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/26/2014] [Indexed: 10/29/2022] Open
Abstract
We detected and characterized the binding sites of the representative Rest complex components Rest, Sin3A, and Lsd1. We compared their binding patterns in mouse embryonic stem (ES) cells and epiblast stem (EpiS) cells. We found few Rest sites unique to the EpiS cells. The ES-unique site features were distinct from those of the common sites, namely, the signal intensities were weaker, and the characteristic gene function categories differed. Our analyses showed that the Rest binding sites do not always overlap with the Sin3A and Lsd1 binding sites. The Sin3A binding pattern differed remarkably between the ES and EpiS cells and was accompanied by significant changes in acetylated-histone patterns in the surrounding regions. A series of transcriptome analyses in the same cell types unexpectedly showed that the putative target gene transcript levels were not dramatically different despite dynamic changes in the Rest complex binding patterns and chromatin statuses, which suggests that Rest is not the sole determinant of repression at its targets. Nevertheless, we identified putative Rest targets with explicitly enhanced transcription upon Rest knock-down in 143 and 60 common and ES-unique Rest target genes, respectively. Among such sites, several genes are involved in ES cell proliferation. In addition, we also found that long, intergenic non-coding RNAs were apparent Rest targets and shared similar features with the protein-coding target genes. Interestingly, such non-coding target genes showed less conservation through evolution than protein-coding targets. As a result of differences in the components and targets of the Rest complex, its functional roles may differ in ES and EpiS cells.
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Affiliation(s)
- Masahide Seki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, Japan
| | - Hideki Masaki
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, the University of Tokyo, Minato-ku, Tokyo, Japan
| | - Takako Arauchi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, Japan
| | - Hiromitsu Nakauchi
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, the University of Tokyo, Minato-ku, Tokyo, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, Japan
- * E-mail:
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45
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Gotoh L, Inoue K, Helman G, Mora S, Maski K, Soul JS, Bloom M, Evans SH, Goto YI, Caldovic L, Hobson GM, Vanderver A. GJC2 promoter mutations causing Pelizaeus-Merzbacher-like disease. Mol Genet Metab 2014; 111:393-398. [PMID: 24374284 PMCID: PMC4183365 DOI: 10.1016/j.ymgme.2013.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 12/03/2013] [Accepted: 12/03/2013] [Indexed: 10/25/2022]
Abstract
OBJECTIVE Pelizaeus-Merzbacher-like disease is a rare hypomyelinating leukodystrophy caused by autosomal recessive mutations in GJC2, encoding a gap junction protein essential for production of a mature myelin sheath. A previously identified GJC2 mutation (c.-167A>G) in the promoter region is hypothesized to disrupt a putative SOX10 binding site; however, the lack of additional mutations in this region and contradictory functional data have limited the interpretation of this variant. METHODS We describe two independent Pelizaeus-Merzbacher-like disease families with a novel promoter region mutation and updated in vitro functional assays. RESULTS A novel GJC2 mutation (c.-170A>G) in the promoter region was identified in Pelizaeus-Merzbacher-like disease patients. In vitro functional assays using human GJC2 promoter constructs demonstrated that this mutation and the previously described c.-167A>G mutation similarly diminished the transcriptional activity driven by SOX10 and the binding affinity for SOX10. INTERPRETATION These findings support the role of GJC2 promoter mutations in Pelizaeus-Merzbacher-like disease. GJC2 promoter region mutation screening should be included in the evaluation of patients with unexplained hypomyelinating leukodystrophies.
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Affiliation(s)
- Leo Gotoh
- Department of Mental Retardation and Birth Defects Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Ken Inoue
- Department of Mental Retardation and Birth Defects Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Guy Helman
- Department of Neurology, Children's National Medical Center, Washington, DC, USA
| | - Sara Mora
- Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Kiran Maski
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Janet S Soul
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Miriam Bloom
- Department of Pediatrics, Children's National Medical Center, Washington, DC, USA
| | - Sarah H Evans
- Department of Physical Medicine and Rehabilitation, Children's National Medical Center, Washington, DC, USA
| | - Yu-Ichi Goto
- Department of Mental Retardation and Birth Defects Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Ljubica Caldovic
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC, USA
| | - Grace M Hobson
- Nemours Biomedical Research, Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Center for Genetic Medicine Research, Children's National Medical Center, Washington, DC, USA; Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Adeline Vanderver
- Department of Neurology, Children's National Medical Center, Washington, DC, USA; Department of Pediatrics, Children's National Medical Center, Washington, DC, USA; Jefferson Medical College, Thomas Jefferson University, Philadelphia, PA, USA.
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46
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Liang KC, Suzuki Y, Kumagai Y, Nakai K. Analysis of changes in transcription start site distribution by a classification approach. Gene 2014; 537:29-40. [DOI: 10.1016/j.gene.2013.12.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 12/16/2013] [Indexed: 10/25/2022]
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47
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Elzawahry A, Patil A, Kumagai Y, Suzuki Y, Nakai K. Innate immunity interactome dynamics. GENE REGULATION AND SYSTEMS BIOLOGY 2014; 8:1-15. [PMID: 24453478 PMCID: PMC3885269 DOI: 10.4137/grsb.s12850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Innate immune response involves protein–protein interactions, deoxyribonucleic acid (DNA)–protein interactions and signaling cascades. So far, thousands of protein–protein interactions have been curated as a static interaction map. However, protein–protein interactions involved in innate immune response are dynamic. We recorded the dynamics in the interactome during innate immune response by combining gene expression data of lipopolysaccharide (LPS)-stimulated dendritic cells with protein–protein interactions data. We identified the differences in interactome during innate immune response by constructing differential networks and identifying protein modules, which were up-/down-regulated at each stage during the innate immune response. For each protein complex, we identified enriched biological processes and pathways. In addition, we identified core interactions that are conserved throughout the innate immune response and their enriched gene ontology terms and pathways. We defined two novel measures to assess the differences between network maps at different time points. We found that the protein interaction network at 1 hour after LPS stimulation has the highest interactions protein ratio, which indicates a role for proteins with large number of interactions in innate immune response. A pairwise differential matrix allows for the global visualization of the differences between different networks. We investigated the toll-like receptor subnetwork and found that S100A8 is down-regulated in dendritic cells after LPS stimulation. Identified protein complexes have a crucial role not only in innate immunity, but also in circadian rhythms, pathways involved in cancer, and p53 pathways. The study confirmed previous work that reported a strong correlation between cancer and immunity.
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Affiliation(s)
- Asmaa Elzawahry
- Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan. ; Graduate school of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Ashwini Patil
- Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yutaro Kumagai
- Laboratory of Host Defence, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan. ; Global Center of Excellence Program, Frontier Biomedical Science Underlying Organelle Network Biology, Osaka University, Suita, Osaka, Japan
| | - Yutaka Suzuki
- Graduate school of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan
| | - Kenta Nakai
- Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan. ; Graduate school of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan
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Tolba MEM, Kobayashi S, Imada M, Suzuki Y, Sugano S. Giardia lamblia transcriptome analysis using TSS-Seq and RNA-Seq. PLoS One 2013; 8:e76184. [PMID: 24116096 PMCID: PMC3792122 DOI: 10.1371/journal.pone.0076184] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 08/21/2013] [Indexed: 11/19/2022] Open
Abstract
Giardia lamblia is a protozoan parasite that is found worldwide and has both medical and veterinary importance. We applied the transcription start sequence (TSS-seq) and RNA sequence (RNA-seq) techniques to study the transcriptome of the assemblage A WB strain trophozoite. We identified 8000 transcription regions (TR) with significant transcription. Of these regions, 1881 TRs were more than 500 nucleotides upstream of an annotated ORF. Combining both techniques helped us to identify 24 ORFs that should be re-annotated and 60 new ORFs. From the 8000 TRs, we were able to identify an AT-rich consensus that includes the transcription initiation site. It is possible that transcription that was previously thought to be bidirectional is actually unidirectional.
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Affiliation(s)
- Mohammed E. M. Tolba
- Department of Medical Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
- Department of Parasitology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Seiki Kobayashi
- Department of Infectious Diseases, School of Medicine, Keio University, Tokyo, Japan
| | - Mihoko Imada
- Department of Infectious Diseases, School of Medicine, Keio University, Tokyo, Japan
| | - Yutaka Suzuki
- Department of Medical Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Sumio Sugano
- Department of Medical Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
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Tissue-specific differences in the regulation of KIBRA gene expression involve transcription factor TCF7L2 and a complex alternative promoter system. J Mol Med (Berl) 2013; 92:185-96. [DOI: 10.1007/s00109-013-1089-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 09/02/2013] [Accepted: 09/11/2013] [Indexed: 10/26/2022]
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50
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Pokrywka A, Kaliszewski P, Majorczyk E, Zembroń-Łacny A. Genes in sport and doping. Biol Sport 2013; 30:155-61. [PMID: 24744482 PMCID: PMC3944571 DOI: 10.5604/20831862.1059606] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2013] [Indexed: 11/19/2022] Open
Abstract
Genes control biological processes such as muscle production of energy, mitochondria biogenesis, bone formation, erythropoiesis, angiogenesis, vasodilation, neurogenesis, etc. DNA profiling for athletes reveals genetic variations that may be associated with endurance ability, muscle performance and power exercise, tendon susceptibility to injuries and psychological aptitude. Already, over 200 genes relating to physical performance have been identified by several research groups. Athletes’ genotyping is developing as a tool for the formulation of personalized training and nutritional programmes to optimize sport training as well as for the prediction of exercise-related injuries. On the other hand, development of molecular technology and gene therapy creates a risk of non-therapeutic use of cells, genes and genetic elements to improve athletic performance. Therefore, the World Anti-Doping Agency decided to include prohibition of gene doping within their World Anti-Doping Code in 2003. In this review article, we will provide a current overview of genes for use in athletes’ genotyping and gene doping possibilities, including their development and detection techniques.
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