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Rebboah E, Reese F, Williams K, Balderrama-Gutierrez G, McGill C, Trout D, Rodriguez I, Liang H, Wold BJ, Mortazavi A. Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq. Genome Biol 2021; 22:286. [PMID: 34620214 PMCID: PMC8495978 DOI: 10.1186/s13059-021-02505-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/20/2021] [Indexed: 11/24/2022] Open
Abstract
The rise in throughput and quality of long-read sequencing should allow unambiguous identification of full-length transcript isoforms. However, its application to single-cell RNA-seq has been limited by throughput and expense. Here we develop and characterize long-read Split-seq (LR-Split-seq), which uses combinatorial barcoding to sequence single cells with long reads. Applied to the C2C12 myogenic system, LR-split-seq associates isoforms to cell types with relative economy and design flexibility. We find widespread evidence of changing isoform expression during differentiation including alternative transcription start sites (TSS) and/or alternative internal exon usage. LR-Split-seq provides an affordable method for identifying cluster-specific isoforms in single cells.
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Affiliation(s)
- Elisabeth Rebboah
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA
| | - Fairlie Reese
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA
| | - Katherine Williams
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA
| | - Gabriela Balderrama-Gutierrez
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA
| | - Cassandra McGill
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA
| | - Diane Trout
- Division of Biology, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Isaryhia Rodriguez
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA
| | - Heidi Liang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA
| | - Barbara J Wold
- Division of Biology, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA.
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA.
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Altered visual processing in the mdx52 mouse model of Duchenne muscular dystrophy. Neurobiol Dis 2021; 152:105288. [PMID: 33556541 DOI: 10.1016/j.nbd.2021.105288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/26/2021] [Accepted: 02/03/2021] [Indexed: 02/06/2023] Open
Abstract
The mdx52 mouse model of Duchenne muscular dystrophy (DMD) is lacking exon 52 of the DMD gene that is located in a hotspot mutation region causing cognitive deficits and retinal anomalies in DMD patients. This deletion leads to the loss of the dystrophin proteins, Dp427, Dp260 and Dp140, while Dp71 is preserved. The flash electroretinogram (ERG) in mdx52 mice was previously characterized by delayed dark-adapted b-waves. A detailed description of functional ERG changes and visual performances in mdx52 mice is, however, lacking. Here an extensive full-field ERG repertoire was applied in mdx52 mice and WT littermates to analyze retinal physiology in scotopic, mesopic and photopic conditions in response to flash, sawtooth and/or sinusoidal stimuli. Behavioral contrast sensitivity was assessed using quantitative optomotor response (OMR) to sinusoidally modulated luminance gratings at 100% or 50% contrast. The mdx52 mice exhibited reduced amplitudes and delayed implicit times in dark-adapted ERG flash responses, particularly in their b-wave and oscillatory potentials, and diminished amplitudes of light-adapted flash ERGs. ERG responses to sawtooth stimuli were also diminished and delayed for both mesopic and photopic conditions in mdx52 mice and the first harmonic amplitudes to photopic sine-wave stimuli were smaller at all temporal frequencies. OMR indices were comparable between genotypes at 100% contrast but significantly reduced in mdx52 mice at 50% contrast. The complex ERG alterations and disturbed contrast vision in mdx52 mice include features observed in DMD patients and suggest altered photoreceptor-to-bipolar cell transmission possibly affecting contrast sensitivity. The mdx52 mouse is a relevant model to appraise the roles of retinal dystrophins and for preclinical studies related to DMD.
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3
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Neutral endopeptidase inhibitors blunt kidney fibrosis by reducing myofibroblast formation. Clin Sci (Lond) 2019; 133:239-252. [PMID: 30617188 DOI: 10.1042/cs20180882] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/03/2019] [Accepted: 01/06/2019] [Indexed: 02/02/2023]
Abstract
Kidney fibrosis is the common pathophysiological mechanism in end-stage renal disease characterized by excessive accumulation of myofibroblast-derived extracellular matrix. Natriuretic peptides have been demonstrated to have cyclic guanosine monophosphate (cGMP)-dependent anti-fibrotic properties likely due to interference with pro-fibrotic tissue growth factor β (TGF-β) signaling. However, in vivo, natriuretic peptides are rapidly degraded by neutral endopeptidases (NEP). In a unilateral ureteral obstruction (UUO) mouse model for kidney fibrosis we assessed the anti-fibrotic effects of SOL1, an orally active compound that inhibits NEP and endothelin-converting enzyme (ECE). Mice (n=10 per group) subjected to UUO were treated for 1 week with either solvent, NEP-/ECE-inhibitor SOL1 (two doses), reference NEP-inhibitor candoxatril or the angiotensin II receptor type 1 (AT1)-antagonist losartan. While NEP-inhibitors had no significant effect on blood pressure, they did increase urinary cGMP levels as well as endothelin-1 (ET-1) levels. Immunohistochemical staining revealed a marked decrease in renal collagen (∼55% reduction, P<0.05) and α-smooth muscle actin (α-SMA; ∼40% reduction, P<0.05). Moreover, the number of α-SMA positive cells in the kidneys of SOL1-treated groups inversely correlated with cGMP levels consistent with a NEP-dependent anti-fibrotic effect. To dissect the molecular mechanisms associated with the anti-fibrotic effects of NEP inhibition, we performed a 'deep serial analysis of gene expression (Deep SAGE)' transcriptome and targeted metabolomics analysis of total kidneys of all treatment groups. Pathway analyses linked increased cGMP and ET-1 levels with decreased nuclear receptor signaling (peroxisome proliferator-activated receptor [PPAR] and liver X receptor/retinoid X receptor [LXR/RXR] signaling) and actin cytoskeleton organization. Taken together, although our transcriptome and metabolome data indicate metabolic dysregulation, our data support the therapeutic potential of NEP inhibition in the treatment of kidney fibrosis via cGMP elevation and reduced myofibroblast formation.
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Cattin ME, Deeke SA, Dick SA, Verret-Borsos ZJA, Tennakoon G, Gupta R, Mak E, Roeske CL, Weldrick JJ, Megeney LA, Burgon PG. Expression of murine muscle-enriched A-type lamin-interacting protein (MLIP) is regulated by tissue-specific alternative transcription start sites. J Biol Chem 2018; 293:19761-19770. [PMID: 30389785 DOI: 10.1074/jbc.ra118.003758] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 10/28/2018] [Indexed: 11/06/2022] Open
Abstract
Muscle-enriched lamin-interacting protein (Mlip) is an alternatively spliced gene whose splicing specificity is dictated by tissue type. MLIP is most abundantly expressed in brain, cardiac, and skeletal muscle. In the present study, we systematically mapped the transcriptional start and stop sites of murine Mlip Rapid amplification of cDNA ends (RACE) of Mlip transcripts from the brain, heart, and skeletal muscle revealed two transcriptional start sites (TSSs), exon 1a and exon 1b, and only one transcriptional termination site. RT-PCR analysis of the usage of the two identified TSSs revealed that the heart utilizes only exon 1a for MLIP expression, whereas the brain exclusively uses exon 1b TSS. Loss of Mlip exon 1a in mice resulted in a 7-fold increase in the prevalence of centralized nuclei in muscle fibers with the Mlip exon1a-deficient satellite cells on single fibers exhibiting a significant delay in commitment to a MYOD-positive phenotype. Furthermore, we demonstrate that the A-type lamin-binding domain in MLIP is encoded in exon 1a, indicating that MLIP isoforms generated with exon 1b TSS lack the A-type lamin-binding domain. Collectively these findings suggest that Mlip tissue-specific expression and alternative splicing play a critical role in determining MLIP's functions in mice.
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Affiliation(s)
- Marie-Elodie Cattin
- From the University of Ottawa Heart Institute, Ottawa, Ontario K1Y 4W7, Canada
| | - Shelley A Deeke
- From the University of Ottawa Heart Institute, Ottawa, Ontario K1Y 4W7, Canada.,Departments of Cellular and Molecular Medicine and
| | - Sarah A Dick
- Departments of Cellular and Molecular Medicine and.,Regenerative Medicine Program, Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, Canada, and
| | | | - Gayashan Tennakoon
- From the University of Ottawa Heart Institute, Ottawa, Ontario K1Y 4W7, Canada
| | - Rishi Gupta
- From the University of Ottawa Heart Institute, Ottawa, Ontario K1Y 4W7, Canada
| | - Esther Mak
- From the University of Ottawa Heart Institute, Ottawa, Ontario K1Y 4W7, Canada
| | - Cassandra L Roeske
- From the University of Ottawa Heart Institute, Ottawa, Ontario K1Y 4W7, Canada
| | - Jonathan J Weldrick
- From the University of Ottawa Heart Institute, Ottawa, Ontario K1Y 4W7, Canada.,Departments of Cellular and Molecular Medicine and
| | - Lynn A Megeney
- Departments of Cellular and Molecular Medicine and.,Regenerative Medicine Program, Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, Canada, and.,Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Patrick G Burgon
- From the University of Ottawa Heart Institute, Ottawa, Ontario K1Y 4W7, Canada, .,Departments of Cellular and Molecular Medicine and.,Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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5
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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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Monte E, Rosa-Garrido M, Vondriska TM, Wang J. Undiscovered Physiology of Transcript and Protein Networks. Compr Physiol 2016; 6:1851-1872. [PMID: 27783861 PMCID: PMC10751805 DOI: 10.1002/cphy.c160003] [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] [Indexed: 11/07/2022]
Abstract
The past two decades have witnessed a rapid evolution in our ability to measure RNA and protein from biological systems. As a result, new principles have arisen regarding how information is processed in cells, how decisions are made, and the role of networks in biology. This essay examines this technological evolution, reviewing (and critiquing) the conceptual framework that has emerged to explain how RNA and protein networks control cellular function. We identify how future investigations into transcriptomes, proteomes, and other cellular networks will enable development of more robust, quantitative models of cellular behavior whilst also providing new avenues to use knowledge of biological networks to improve human health. © 2016 American Physiological Society. Compr Physiol 6:1851-1872, 2016.
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Affiliation(s)
- Emma Monte
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Manuel Rosa-Garrido
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Thomas M. Vondriska
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Jessica Wang
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, USA
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7
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8
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Lennartsson A, Arner E, Fagiolini M, Saxena A, Andersson R, Takahashi H, Noro Y, Sng J, Sandelin A, Hensch TK, Carninci P. Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors. Epigenetics Chromatin 2015; 8:55. [PMID: 26673794 PMCID: PMC4678690 DOI: 10.1186/s13072-015-0043-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/09/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The capacity for plasticity in the adult brain is limited by the anatomical traces laid down during early postnatal life. Removing certain molecular brakes, such as histone deacetylases (HDACs), has proven to be effective in recapitulating juvenile plasticity in the mature visual cortex (V1). We investigated the chromatin structure and transcriptional control by genome-wide sequencing of DNase I hypersensitive sites (DHSS) and cap analysis of gene expression (CAGE) libraries after HDAC inhibition by valproic acid (VPA) in adult V1. RESULTS We found that VPA reliably reactivates the critical period plasticity and induces a dramatic change of chromatin organization in V1 yielding significantly greater accessibility distant from promoters, including at enhancer regions. VPA also induces nucleosome eviction specifically from retrotransposon (in particular SINE) elements. The transiently accessible SINE elements overlap with transcription factor-binding sites of the Fox family. Mapping of transcription start site activity using CAGE revealed transcription of epigenetic and neural plasticity-regulating genes following VPA treatment, which may help to re-program the genomic landscape and reactivate plasticity in the adult cortex. CONCLUSIONS Treatment with HDAC inhibitors increases accessibility to enhancers and repetitive elements underlying brain-specific gene expression and reactivation of visual cortical plasticity.
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Affiliation(s)
- Andreas Lennartsson
- />Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Stockholm, Sweden
- />Genome Science Lab, RIKEN, Hirosawa, Wako-shi, Saitama 351-0198 Japan
| | - Erik Arner
- />Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Michela Fagiolini
- />Lab for Neuronal Circuit Development, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198 Japan
- />F. M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Alka Saxena
- />Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Robin Andersson
- />Department of Biology and BRIC, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Hazuki Takahashi
- />Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Yukihiko Noro
- />Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Judy Sng
- />Lab for Neuronal Circuit Development, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198 Japan
- />F. M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- />Department of Pharmacology, National University of Singapore, 10 Medical Drive 05-34, Singapore, Singapore
| | - Albin Sandelin
- />Department of Biology and BRIC, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Takao K. Hensch
- />Lab for Neuronal Circuit Development, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198 Japan
- />F. M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- />Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138 USA
| | - Piero Carninci
- />Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
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9
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Yu NYL, Hallström BM, Fagerberg L, Ponten F, Kawaji H, Carninci P, Forrest ARR, Hayashizaki Y, Uhlén M, Daub CO. Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium. Nucleic Acids Res 2015; 43:6787-98. [PMID: 26117540 PMCID: PMC4538815 DOI: 10.1093/nar/gkv608] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 12/20/2022] Open
Abstract
Understanding the normal state of human tissue transcriptome profiles is essential for recognizing tissue disease states and identifying disease markers. Recently, the Human Protein Atlas and the FANTOM5 consortium have each published extensive transcriptome data for human samples using Illumina-sequenced RNA-Seq and Heliscope-sequenced CAGE. Here, we report on the first large-scale complex tissue transcriptome comparison between full-length versus 5'-capped mRNA sequencing data. Overall gene expression correlation was high between the 22 corresponding tissues analyzed (R > 0.8). For genes ubiquitously expressed across all tissues, the two data sets showed high genome-wide correlation (91% agreement), with differences observed for a small number of individual genes indicating the need to update their gene models. Among the identified single-tissue enriched genes, up to 75% showed consensus of 7-fold enrichment in the same tissue in both methods, while another 17% exhibited multiple tissue enrichment and/or high expression variety in the other data set, likely dependent on the cell type proportions included in each tissue sample. Our results show that RNA-Seq and CAGE tissue transcriptome data sets are highly complementary for improving gene model annotations and highlight biological complexities within tissue transcriptomes. Furthermore, integration with image-based protein expression data is highly advantageous for understanding expression specificities for many genes.
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Affiliation(s)
- Nancy Yiu-Lin Yu
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, 14183, Sweden Science for Life Laboratory, Karolinska Institute, Solna, 17121, Sweden
| | - Björn M Hallström
- Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, 17121, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, 17121, Sweden
| | - Fredrik Ponten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, 751 85, Sweden
| | - Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
| | - Alistair R R Forrest
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
| | - Mathias Uhlén
- Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, 17121, Sweden
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, 14183, Sweden Science for Life Laboratory, Karolinska Institute, Solna, 17121, Sweden RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
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10
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Cumbie JS, Ivanchenko MG, Megraw M. NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites. BMC Genomics 2015; 16:597. [PMID: 26268438 PMCID: PMC4534009 DOI: 10.1186/s12864-015-1670-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 05/29/2015] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Identifying the transcription start sites (TSS) of genes is essential for characterizing promoter regions. Several protocols have been developed to capture the 5' end of transcripts via Cap Analysis of Gene Expression (CAGE) or linker-ligation strategies such as Paired-End Analysis of Transcription Start Sites (PEAT), but often require large amounts of tissue. More recently, nanoCAGE was developed for sequencing on the Illumina GAIIx to overcome these difficulties. RESULTS Here we present the first publicly available adaptation of nanoCAGE for sequencing on recent ultra-high throughput platforms such as Illumina HiSeq-2000, and CapFilter, a computational pipeline that greatly increases confidence in TSS identification. We report excellent gene coverage, reproducibility, and precision in transcription start site discovery for samples from Arabidopsis thaliana roots. CONCLUSION nanoCAGE-XL together with CapFilter allows for genome wide identification of high confidence transcription start sites in large eukaryotic genomes.
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Affiliation(s)
- Jason S Cumbie
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.
| | - Maria G Ivanchenko
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.
| | - Molly Megraw
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.
- Department of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA.
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA.
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11
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Hestand MS, Kalbfleisch TS, Coleman SJ, Zeng Z, Liu J, Orlando L, MacLeod JN. Annotation of the Protein Coding Regions of the Equine Genome. PLoS One 2015; 10:e0124375. [PMID: 26107351 PMCID: PMC4481266 DOI: 10.1371/journal.pone.0124375] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 03/01/2015] [Indexed: 12/30/2022] Open
Abstract
Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. Only a small number of genes are annotated based on equine EST and mRNA sequences. To expand the number of equine genes annotated from equine experimental evidence, we sequenced mRNA from a pool of forty-three different tissues. From these, we derived the structures of 68,594 transcripts. In addition, we identified 301,829 positions with SNPs or small indels within these transcripts relative to EquCab2. Interestingly, 780 variants extend the open reading frame of the transcript and appear to be small errors in the equine reference genome, since they are also identified as homozygous variants by genomic DNA resequencing of the reference horse. Taken together, we provide a resource of equine mRNA structures and protein coding variants that will enhance equine and cross-species transcriptional and genomic comparisons.
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Affiliation(s)
- Matthew S. Hestand
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America
| | - Theodore S. Kalbfleisch
- Biochemistry and Molecular Biology Department, School of Medicine, University of Louisville, Louisville, Kentucky, United States of America
| | - Stephen J. Coleman
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America
| | - Zheng Zeng
- Department of Computer Science, University of Kentucky, Lexington, Kentucky, United States of America
| | - Jinze Liu
- Department of Computer Science, University of Kentucky, Lexington, Kentucky, United States of America
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - James N. MacLeod
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail:
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12
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de Klerk E, Fokkema IFAC, Thiadens KAMH, Goeman JJ, Palmblad M, den Dunnen JT, von Lindern M, 't Hoen PAC. Assessing the translational landscape of myogenic differentiation by ribosome profiling. Nucleic Acids Res 2015; 43:4408-28. [PMID: 25873627 PMCID: PMC4482065 DOI: 10.1093/nar/gkv281] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/21/2015] [Indexed: 01/08/2023] Open
Abstract
The formation of skeletal muscles is associated with drastic changes in protein requirements known to be safeguarded by tight control of gene transcription and mRNA processing. The contribution of regulation of mRNA translation during myogenesis has not been studied so far. We monitored translation during myogenic differentiation of C2C12 myoblasts, using a simplified protocol for ribosome footprint profiling. Comparison of ribosome footprints to total RNA showed that gene expression is mostly regulated at the transcriptional level. However, a subset of transcripts, enriched for mRNAs encoding for ribosomal proteins, was regulated at the level of translation. Enrichment was also found for specific pathways known to regulate muscle biology. We developed a dedicated pipeline to identify translation initiation sites (TISs) and discovered 5333 unannotated TISs, providing a catalog of upstream and alternative open reading frames used during myogenesis. We identified 298 transcripts with a significant switch in TIS usage during myogenesis, which was not explained by alternative promoter usage, as profiled by DeepCAGE. Also these transcripts were enriched for ribosomal protein genes. This study demonstrates that differential mRNA translation controls protein expression of specific subsets of genes during myogenesis. Experimental protocols, analytical workflows, tools and data are available through public repositories (http://lumc.github.io/ribosome-profiling-analysis-framework/).
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Affiliation(s)
- Eleonora de Klerk
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Ivo F A C Fokkema
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Klaske A M H Thiadens
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, AMC/UvA, 1066CX 125 Amsterdam, The Netherlands
| | - Jelle J Goeman
- Biostatistics, Department for Health Evidence, Radboud University Medical Center, Postzone 133, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Johan T den Dunnen
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Marieke von Lindern
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, AMC/UvA, 1066CX 125 Amsterdam, The Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands
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13
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de Klerk E, 't Hoen PAC. Alternative mRNA transcription, processing, and translation: insights from RNA sequencing. Trends Genet 2015; 31:128-39. [PMID: 25648499 DOI: 10.1016/j.tig.2015.01.001] [Citation(s) in RCA: 216] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 12/22/2014] [Accepted: 01/05/2015] [Indexed: 12/13/2022]
Abstract
The human transcriptome comprises >80,000 protein-coding transcripts and the estimated number of proteins synthesized from these transcripts is in the range of 250,000 to 1 million. These transcripts and proteins are encoded by less than 20,000 genes, suggesting extensive regulation at the transcriptional, post-transcriptional, and translational level. Here we review how RNA sequencing (RNA-seq) technologies have increased our understanding of the mechanisms that give rise to alternative transcripts and their alternative translation. We highlight four different regulatory processes: alternative transcription initiation, alternative splicing, alternative polyadenylation, and alternative translation initiation. We discuss their transcriptome-wide distribution, their impact on protein expression, their biological relevance, and the possible molecular mechanisms leading to their alternative regulation. We conclude with a discussion of the coordination and the interdependence of these four regulatory layers.
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Affiliation(s)
- Eleonora de Klerk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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14
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de Klerk E, den Dunnen JT, 't Hoen PAC. RNA sequencing: from tag-based profiling to resolving complete transcript structure. Cell Mol Life Sci 2014; 71:3537-51. [PMID: 24827995 PMCID: PMC4143603 DOI: 10.1007/s00018-014-1637-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 04/13/2014] [Accepted: 04/28/2014] [Indexed: 12/22/2022]
Abstract
Technological advances in the sequencing field support in-depth characterization of the transcriptome. Here, we review genome-wide RNA sequencing methods used to investigate specific aspects of gene expression and its regulation, from transcription to RNA processing and translation. We discuss tag-based methods for studying transcription, alternative initiation and polyadenylation events, shotgun methods for detection of alternative splicing, full-length RNA sequencing for the determination of complete transcript structures, and targeted methods for studying the process of transcription and translation. With the ensemble of technologies available, it is now possible to obtain a comprehensive view on transcriptome complexity and the regulation of transcript diversity.
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Affiliation(s)
- Eleonora de Klerk
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
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15
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Zhernakova DV, de Klerk E, Westra HJ, Mastrokolias A, Amini S, Ariyurek Y, Jansen R, Penninx BW, Hottenga JJ, Willemsen G, de Geus EJ, Boomsma DI, Veldink JH, van den Berg LH, Wijmenga C, den Dunnen JT, van Ommen GJB, 't Hoen PAC, Franke L. DeepSAGE reveals genetic variants associated with alternative polyadenylation and expression of coding and non-coding transcripts. PLoS Genet 2013; 9:e1003594. [PMID: 23818875 PMCID: PMC3688553 DOI: 10.1371/journal.pgen.1003594] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 05/10/2013] [Indexed: 11/18/2022] Open
Abstract
Many disease-associated variants affect gene expression levels (expression quantitative trait loci, eQTLs) and expression profiling using next generation sequencing (NGS) technology is a powerful way to detect these eQTLs. We analyzed 94 total blood samples from healthy volunteers with DeepSAGE to gain specific insight into how genetic variants affect the expression of genes and lengths of 3′-untranslated regions (3′-UTRs). We detected previously unknown cis-eQTL effects for GWAS hits in disease- and physiology-associated traits. Apart from cis-eQTLs that are typically easily identifiable using microarrays or RNA-sequencing, DeepSAGE also revealed many cis-eQTLs for antisense and other non-coding transcripts, often in genomic regions containing retrotransposon-derived elements. We also identified and confirmed SNPs that affect the usage of alternative polyadenylation sites, thereby potentially influencing the stability of messenger RNAs (mRNA). We then combined the power of RNA-sequencing with DeepSAGE by performing a meta-analysis of three datasets, leading to the identification of many more cis-eQTLs. Our results indicate that DeepSAGE data is useful for eQTL mapping of known and unknown transcripts, and for identifying SNPs that affect alternative polyadenylation. Because of the inherent differences between DeepSAGE and RNA-sequencing, our complementary, integrative approach leads to greater insight into the molecular consequences of many disease-associated variants. Many genetic variants that are associated with diseases also affect gene expression levels. We used a next generation sequencing approach targeting 3′ transcript ends (DeepSAGE) to gain specific insight into how genetic variants affect the expression of genes and the usage and length of 3′-untranslated regions. We detected many associations for antisense and other non-coding transcripts, often in genomic regions containing retrotransposon-derived elements. Some of these variants are also associated with disease. We also identified and confirmed variants that affect the usage of alternative polyadenylation sites, thereby potentially influencing the stability of mRNAs. We conclude that DeepSAGE is useful for detecting eQTL effects on both known and unknown transcripts, and for identifying variants that affect alternative polyadenylation.
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Affiliation(s)
- Daria V. Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Eleonora de Klerk
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Harm-Jan Westra
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Anastasios Mastrokolias
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Shoaib Amini
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Yavuz Ariyurek
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Genome Technology Center, Leiden, The Netherlands
| | - Rick Jansen
- Department of Psychiatry, The Netherlands Study of Depression and Anxiety, VU University Medical Center, Amsterdam, The Netherlands
| | - Brenda W. Penninx
- Department of Psychiatry, The Netherlands Study of Depression and Anxiety, VU University Medical Center, Amsterdam, The Netherlands
| | - Jouke J. Hottenga
- Department of Biological Psychology, Netherlands Twin Registry, VU University, Amsterdam, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Netherlands Twin Registry, VU University, Amsterdam, The Netherlands
| | - Eco J. de Geus
- Department of Biological Psychology, Netherlands Twin Registry, VU University, Amsterdam, The Netherlands
| | - Dorret I. Boomsma
- Department of Biological Psychology, Netherlands Twin Registry, VU University, Amsterdam, The Netherlands
| | - Jan H. Veldink
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Leonard H. van den Berg
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Johan T. den Dunnen
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Genome Technology Center, Leiden, The Netherlands
| | - Gert-Jan B. van Ommen
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A. C. 't Hoen
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- * E-mail:
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16
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Eberwine J, Lovatt D, Buckley P, Dueck H, Francis C, Kim TK, Lee J, Lee M, Miyashiro K, Morris J, Peritz T, Schochet T, Spaethling J, Sul JY, Kim J. Quantitative biology of single neurons. J R Soc Interface 2012; 9:3165-83. [PMID: 22915636 PMCID: PMC3481569 DOI: 10.1098/rsif.2012.0417] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The building blocks of complex biological systems are single cells. Fundamental insights gained from single-cell analysis promise to provide the framework for understanding normal biological systems development as well as the limits on systems/cellular ability to respond to disease. The interplay of cells to create functional systems is not well understood. Until recently, the study of single cells has concentrated primarily on morphological and physiological characterization. With the application of new highly sensitive molecular and genomic technologies, the quantitative biochemistry of single cells is now accessible.
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Affiliation(s)
- James Eberwine
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, 36th and Hamilton Walk, Philadelphia, PA 19104, USA.
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17
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Nolte-'t Hoen ENM, Buermans HPJ, Waasdorp M, Stoorvogel W, Wauben MHM, 't Hoen PAC. Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions. Nucleic Acids Res 2012; 40:9272-85. [PMID: 22821563 PMCID: PMC3467056 DOI: 10.1093/nar/gks658] [Citation(s) in RCA: 538] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cells release RNA-carrying vesicles and membrane-free RNA/protein complexes into the extracellular milieu. Horizontal vesicle-mediated transfer of such shuttle RNA between cells allows dissemination of genetically encoded messages, which may modify the function of target cells. Other studies used array analysis to establish the presence of microRNAs and mRNA in cell-derived vesicles from many sources. Here, we used an unbiased approach by deep sequencing of small RNA released by immune cells. We found a large variety of small non-coding RNA species representing pervasive transcripts or RNA cleavage products overlapping with protein coding regions, repeat sequences or structural RNAs. Many of these RNAs were enriched relative to cellular RNA, indicating that cells destine specific RNAs for extracellular release. Among the most abundant small RNAs in shuttle RNA were sequences derived from vault RNA, Y-RNA and specific tRNAs. Many of the highly abundant small non-coding transcripts in shuttle RNA are evolutionary well-conserved and have previously been associated to gene regulatory functions. These findings allude to a wider range of biological effects that could be mediated by shuttle RNA than previously expected. Moreover, the data present leads for unraveling how cells modify the function of other cells via transfer of specific non-coding RNA species.
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Affiliation(s)
- Esther N M Nolte-'t Hoen
- Department of Biochemistry & Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands.
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18
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Lim JS, Choi BS, Lee JS, Shin C, Yang TJ, Rhee JS, Lee JS, Choi IY. Survey of the Applications of NGS to Whole-Genome Sequencing and Expression Profiling. Genomics Inform 2012; 10:1-8. [PMID: 23105922 PMCID: PMC3475479 DOI: 10.5808/gi.2012.10.1.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 02/15/2012] [Accepted: 02/17/2012] [Indexed: 01/16/2023] Open
Abstract
Recently, the technologies of DNA sequence variation and gene expression profiling have been used widely as approaches in the expertise of genome biology and genetics. The application to genome study has been particularly developed with the introduction of the next-generation DNA sequencer (NGS) Roche/454 and Illumina/Solexa systems, along with bioinformation analysis technologies of whole-genome de novo assembly, expression profiling, DNA variation discovery, and genotyping. Both massive whole-genome shotgun paired-end sequencing and mate paired-end sequencing data are important steps for constructing de novo assembly of novel genome sequencing data. It is necessary to have DNA sequence information from a multiplatform NGS with at least 2× and 30× depth sequence of genome coverage using Roche/454 and Illumina/Solexa, respectively, for effective an way of de novo assembly. Massive short-length reading data from the Illumina/Solexa system is enough to discover DNA variation, resulting in reducing the cost of DNA sequencing. Whole-genome expression profile data are useful to approach genome system biology with quantification of expressed RNAs from a whole-genome transcriptome, depending on the tissue samples. The hybrid mRNA sequences from Rohce/454 and Illumina/Solexa are more powerful to find novel genes through de novo assembly in any whole-genome sequenced species. The 20× and 50× coverage of the estimated transcriptome sequences using Roche/454 and Illumina/Solexa, respectively, is effective to create novel expressed reference sequences. However, only an average 30× coverage of a transcriptome with short read sequences of Illumina/Solexa is enough to check expression quantification, compared to the reference expressed sequence tag sequence.
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Affiliation(s)
- Jong-Sung Lim
- National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
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19
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5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc 2012; 7:542-61. [PMID: 22362160 DOI: 10.1038/nprot.2012.005] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cap-analysis gene expression (CAGE) provides accurate high-throughput measurement of RNA expression. CAGE allows mapping of all the initiation sites of both capped coding and noncoding RNAs. In addition, transcriptional start sites within promoters are characterized at single-nucleotide resolution. The latter allows the regulatory inputs driving gene expression to be studied, which in turn enables the construction of transcriptional networks. Here we provide an optimized protocol for the construction of CAGE libraries on the basis of the preparation of 27-nt-long tags corresponding to initial bases at the 5' ends of capped RNAs. We have optimized the methods using simple steps based on filtration, which altogether takes 4 d to complete. The CAGE tags can be readily sequenced with Illumina sequencers, and upon modification they are also amenable to sequencing using other platforms.
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20
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Itoh M, Kojima M, Nagao-Sato S, Saijo E, Lassmann T, Kanamori-Katayama M, Kaiho A, Lizio M, Kawaji H, Carninci P, Forrest ARR, Hayashizaki Y. Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer. PLoS One 2012; 7:e30809. [PMID: 22303458 PMCID: PMC3268765 DOI: 10.1371/journal.pone.0030809] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 12/21/2011] [Indexed: 11/19/2022] Open
Abstract
Background Cap analysis of gene expression (CAGE) is a 5′ sequence tag technology to globally determine transcriptional starting sites in the genome and their expression levels and has most recently been adapted to the HeliScope single molecule sequencer. Despite significant simplifications in the CAGE protocol, it has until now been a labour intensive protocol. Methodology In this study we set out to adapt the protocol to a robotic workflow, which would increase throughput and reduce handling. The automated CAGE cDNA preparation system we present here can prepare 96 ‘HeliScope ready’ CAGE cDNA libraries in 8 days, as opposed to 6 weeks by a manual operator.We compare the results obtained using the same RNA in manual libraries and across multiple automation batches to assess reproducibility. Conclusions We show that the sequencing was highly reproducible and comparable to manual libraries with an 8 fold increase in productivity. The automated CAGE cDNA preparation system can prepare 96 CAGE sequencing samples simultaneously. Finally we discuss how the system could be used for CAGE on Illumina/SOLiD platforms, RNA-seq and full-length cDNA generation.
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Affiliation(s)
- Masayoshi Itoh
- Omics Science Center, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan
- * E-mail: (MI); (YH)
| | - Miki Kojima
- Omics Science Center, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | | | - Eri Saijo
- K. K. Dnaform, Ono-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Timo Lassmann
- Omics Science Center, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | | | - Ai Kaiho
- Omics Science Center, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Marina Lizio
- Omics Science Center, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Hideya Kawaji
- Omics Science Center, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Piero Carninci
- Omics Science Center, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | | | - Yoshihide Hayashizaki
- Omics Science Center, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan
- * E-mail: (MI); (YH)
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21
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Pareek CS, Smoczynski R, Tretyn A. Sequencing technologies and genome sequencing. J Appl Genet 2011; 52:413-35. [PMID: 21698376 PMCID: PMC3189340 DOI: 10.1007/s13353-011-0057-x] [Citation(s) in RCA: 370] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 05/27/2011] [Accepted: 05/31/2011] [Indexed: 12/21/2022]
Abstract
The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. In the relatively short time frame since 2005, the HT-NGS technologies are revolutionizing the human and animal genome researches by analysis of chromatin immunoprecipitation coupled to DNA microarray (ChIP-chip) or sequencing (ChIP-seq), RNA sequencing (RNA-seq), whole genome genotyping, genome wide structural variation, de novo assembling and re-assembling of genome, mutation detection and carrier screening, detection of inherited disorders and complex human diseases, DNA library preparation, paired ends and genomic captures, sequencing of mitochondrial genome and personal genomics. In this review, we addressed the important features of HT-NGS like, first generation DNA sequencers, birth of HT-NGS, second generation HT-NGS platforms, third generation HT-NGS platforms: including single molecule Heliscope™, SMRT™ and RNAP sequencers, Nanopore, Archon Genomics X PRIZE foundation, comparison of second and third HT-NGS platforms, applications, advances and future perspectives of sequencing technologies on human and animal genome research.
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Affiliation(s)
- Chandra Shekhar Pareek
- Laboratory of Functional Genomics, Institute of General and Molecular Biology, Nicolaus Copernicus University, Torun, Poland.
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22
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de Morrée A, Droog M, Grand Moursel L, Bisschop IJM, Impagliazzo A, Frants RR, Klooster R, van der Maarel SM. Self-regulated alternative splicing at the AHNAK locus. FASEB J 2011; 26:93-103. [PMID: 21940993 DOI: 10.1096/fj.11-187971] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
AHNAK is a 700-kDa protein involved in cytoarchitecture and calcium signaling. It is secondarily reduced in muscle of dysferlinopathy patients and accumulates in muscle of calpainopathy patients, both affected by a muscular dystrophy. AHNAK directly interacts with dysferlin. This interaction is lost on cleavage of AHNAK by the protease calpain 3, explaining the molecular observations in patients. Currently, little is known of AHNAK regulation. We describe the self-regulation of multiple mRNA transcripts emanating from the AHNAK locus in muscle cells. We show that the AHNAK gene consists of a 17-kb exon flanked by multiple small exons. This genetic structure is shared by AHNAK2 and Periaxin, which share a common ancestor. Two major AHNAK transcripts are differentially expressed during muscle differentiation that encode for a small (17-kDa) and a large (700-kDa) protein isoform. These proteins interact in the cytoplasm, but the small AHNAK is also present in the nucleus. During muscle differentiation the small AHNAK is strongly increased, thereby establishing a positive feedback loop to regulate mRNA splicing of its own locus. A small 17-kDa isoform of Periaxin similarly traffics between the cytoplasm and the nucleus to regulate mRNA splicing. Thus, AHNAK constitutes a novel mechanism in post-transcriptional control of gene expression.
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Affiliation(s)
- Antoine de Morrée
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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23
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Siebert S, Robinson MD, Tintori SC, Goetz F, Helm RR, Smith SA, Shaner N, Haddock SHD, Dunn CW. Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows. PLoS One 2011; 6:e22953. [PMID: 21829563 PMCID: PMC3146525 DOI: 10.1371/journal.pone.0022953] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 07/01/2011] [Indexed: 02/02/2023] Open
Abstract
We investigated differential gene expression between functionally specialized feeding polyps and swimming medusae in the siphonophore Nanomia bijuga (Cnidaria) with a hybrid long-read/short-read sequencing strategy. We assembled a set of partial gene reference sequences from long-read data (Roche 454), and generated short-read sequences from replicated tissue samples that were mapped to the references to quantify expression. We collected and compared expression data with three short-read expression workflows that differ in sample preparation, sequencing technology, and mapping tools. These workflows were Illumina mRNA-Seq, which generates sequence reads from random locations along each transcript, and two tag-based approaches, SOLiD SAGE and Helicos DGE, which generate reads from particular tag sites. Differences in expression results across workflows were mostly due to the differential impact of missing data in the partial reference sequences. When all 454-derived gene reference sequences were considered, Illumina mRNA-Seq detected more than twice as many differentially expressed (DE) reference sequences as the tag-based workflows. This discrepancy was largely due to missing tag sites in the partial reference that led to false negatives in the tag-based workflows. When only the subset of reference sequences that unambiguously have tag sites was considered, we found broad congruence across workflows, and they all identified a similar set of DE sequences. Our results are promising in several regards for gene expression studies in non-model organisms. First, we demonstrate that a hybrid long-read/short-read sequencing strategy is an effective way to collect gene expression data when an annotated genome sequence is not available. Second, our replicated sampling indicates that expression profiles are highly consistent across field-collected animals in this case. Third, the impacts of partial reference sequences on the ability to detect DE can be mitigated through workflow choice and deeper reference sequencing.
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Affiliation(s)
- Stefan Siebert
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (SS); (CWD)
| | - Mark D. Robinson
- Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Sophia C. Tintori
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
| | - Freya Goetz
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
| | - Rebecca R. Helm
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
| | - Stephen A. Smith
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Nathan Shaner
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Steven H. D. Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Casey W. Dunn
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (SS); (CWD)
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24
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Maugeri N, Powell JE, 't Hoen PAC, de Geus EJC, Willemsen G, Kattenberg M, Henders AK, Wallace L, Penninx B, Hottenga JJ, Medland SE, Saviouk V, Martin NG, Visscher PM, van Ommen GJB, Frazer IH, Boomsma DI, Montgomery GW, Ferreira MAR. LPAR1 and ITGA4 regulate peripheral blood monocyte counts. Hum Mutat 2011; 32:873-6. [PMID: 21598361 DOI: 10.1002/humu.21536] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 04/29/2011] [Indexed: 12/17/2022]
Abstract
We recently mapped a quantitative trait locus for monocyte counts to chromosome 9q31 (rs7023923). Here we extend this work by showing with two independent approaches that rs7023923 regulates the expression levels of the nearby LPAR1 gene (P<0.0001), specifically implicating this gene in monocyte development. Furthermore, we tested 10 additional loci identified in the original analysis for replication in 1,122 individuals and confirm that rs6740847 near the alpha-4-integrin gene (ITGA4) associates with variation in monocyte counts (combined P=2.7×10(-10)). This variant is in complete linkage disequilibrium (r(2) =1) with a previously reported eQTL for ITGA4 (rs2124440), indicating that this is the likely causal gene in the region. Our results indicate that rs7023923 and rs6740847 respectively upregulate LPAR1 and downregulate ITGA4 expression and this increases the number of monocytes circulating in the peripheral blood. Further studies that investigate the downstream mechanism involved and the impact on immune function are warranted.
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Affiliation(s)
- Narelle Maugeri
- Queensland Institute of Medical Research, Brisbane, Australia
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25
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Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO, Carninci P, Forrest ARR, Hayashizaki Y. Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res 2011; 21:1150-9. [PMID: 21596820 DOI: 10.1101/gr.115469.110] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We report the development of a simplified cap analysis of gene expression (CAGE) protocol adapted for single-molecule sequencers that avoids second strand synthesis, ligation, digestion, and PCR. HeliScopeCAGE directly sequences the 3' end of cap trapped first-strand cDNAs. As with previous versions of CAGE, we better define transcription start sites (TSS) than known models, identify novel regions of transcription and alternative promoters, and find two major classes of TSS signal, sharp peaks and broad regions. However, using this protocol, we observe reproducible evidence of regulation at the much finer level of individual TSS positions. The libraries are quantitative over 5 orders of magnitude and highly reproducible (Pearson's correlation coefficient of 0.987). We have also scaled down the sample requirement to 5 μg of total RNA for a standard HeliScopeCAGE library and 100 ng for a low-quantity version. When the same RNA was run as 5-μg and 100-ng versions, the 100 ng was still able to detect expression for ∼60% of the 13,468 loci detected by a 5-μg library using the same threshold, allowing comparative analysis of even rare cell populations. Testing the protocol for differential gene expression measurements on triplicate HeLa and THP-1 samples, we find that the log fold change compared to Illumina microarray measurements is highly correlated (0.871). In addition, HeliScopeCAGE finds differential expression for thousands more loci including those with probes on the array. Finally, although the majority of tags are 5' associated, we also observe a low level of signal on exons that is useful for defining gene structures.
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't Hoen PAC, Hirsch M, de Meijer EJ, de Menezes RX, van Ommen GJ, den Dunnen JT. mRNA degradation controls differentiation state-dependent differences in transcript and splice variant abundance. Nucleic Acids Res 2010; 39:556-66. [PMID: 20852259 PMCID: PMC3025562 DOI: 10.1093/nar/gkq790] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Expression profiling experiments usually provide a static snapshot of messenger RNA (mRNA) levels. Improved understanding of the dynamics of mRNA synthesis and degradation will aid the development of sound bioinformatic models for control of gene expression. We studied mRNA stability in proliferating and differentiated myogenic cells using whole-genome exon arrays and reported the decay rates (half life) for ∼7000 mRNAs. We showed that the stability of many mRNAs strongly depends on the differentiation status and contributes to differences in abundance of these mRNAs. In addition, alternative splicing turns out to be coupled to mRNA degradation. Although different splice forms may be produced at comparable levels, their relative abundance is partly determined by their different stabilities in proliferating and differentiated cells. Where the 3'-untranslated region (3'-UTR) was previously thought to contain most RNA stabilizing and destabilizing elements, we showed that this also holds for transcript isoforms sharing the same 3'-UTR. There are two splice variants in Itga7, of which the isoform with an extra internal exon is highly stable in differentiated cells but preferentially degraded in the cytoplasm of proliferating cells. In conclusion, control of stability and degradation emerge as important determinants for differential expression of mRNA transcripts and splice variants.
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Affiliation(s)
- Peter A C 't Hoen
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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Implementation of postgenomic technologies for cancer research. Institutional experience. Acta Med Litu 2010. [DOI: 10.2478/v10140-010-0013-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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