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Awazu A, Tanabe T, Kamitani M, Tezuka A, Nagano AJ. Broad distribution spectrum from Gaussian to power law appears in stochastic variations in RNA-seq data. Sci Rep 2018; 8:8339. [PMID: 29844539 PMCID: PMC5974282 DOI: 10.1038/s41598-018-26735-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 05/09/2018] [Indexed: 11/21/2022] Open
Abstract
Gene expression levels exhibit stochastic variations among genetically identical organisms under the same environmental conditions. In many recent transcriptome analyses based on RNA sequencing (RNA-seq), variations in gene expression levels among replicates were assumed to follow a negative binomial distribution, although the physiological basis of this assumption remains unclear. In this study, RNA-seq data were obtained from Arabidopsis thaliana under eight conditions (21-27 replicates), and the characteristics of gene-dependent empirical probability density function (ePDF) profiles of gene expression levels were analyzed. For A. thaliana and Saccharomyces cerevisiae, various types of ePDF of gene expression levels were obtained that were classified as Gaussian, power law-like containing a long tail, or intermediate. These ePDF profiles were well fitted with a Gauss-power mixing distribution function derived from a simple model of a stochastic transcriptional network containing a feedback loop. The fitting function suggested that gene expression levels with long-tailed ePDFs would be strongly influenced by feedback regulation. Furthermore, the features of gene expression levels are correlated with their functions, with the levels of essential genes tending to follow a Gaussian-like ePDF while those of genes encoding nucleic acid-binding proteins and transcription factors exhibit long-tailed ePDF.
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Affiliation(s)
- Akinori Awazu
- Department of Mathematical and Life Sciences, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
- Research Center for Mathematics on Chromatin Live Dynamics, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
| | - Takahiro Tanabe
- Department of Mathematical and Life Sciences, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Mari Kamitani
- Research Institute for Food and Agriculture, Ryukoku University, Yokotani 1-5, Seta Ohe-cho, Otsu, Shiga, 520-2194, Japan
| | - Ayumi Tezuka
- Research Institute for Food and Agriculture, Ryukoku University, Yokotani 1-5, Seta Ohe-cho, Otsu, Shiga, 520-2194, Japan
| | - Atsushi J Nagano
- Research Institute for Food and Agriculture, Ryukoku University, Yokotani 1-5, Seta Ohe-cho, Otsu, Shiga, 520-2194, Japan
- Faculty of Agriculture, Ryukoku University, Yokatani 1-5, Seta, Ohe-cho, Otsu-shi, Shiga, 520-2194, Japan
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4
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Xiong Y, Soumillon M, Wu J, Hansen J, Hu B, van Hasselt JGC, Jayaraman G, Lim R, Bouhaddou M, Ornelas L, Bochicchio J, Lenaeus L, Stocksdale J, Shim J, Gomez E, Sareen D, Svendsen C, Thompson LM, Mahajan M, Iyengar R, Sobie EA, Azeloglu EU, Birtwistle MR. A Comparison of mRNA Sequencing with Random Primed and 3'-Directed Libraries. Sci Rep 2017; 7:14626. [PMID: 29116112 PMCID: PMC5676863 DOI: 10.1038/s41598-017-14892-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 10/18/2017] [Indexed: 11/26/2022] Open
Abstract
Creating a cDNA library for deep mRNA sequencing (mRNAseq) is generally done by random priming, creating multiple sequencing fragments along each transcript. A 3'-end-focused library approach cannot detect differential splicing, but has potentially higher throughput at a lower cost, along with the ability to improve quantification by using transcript molecule counting with unique molecular identifiers (UMI) that correct PCR bias. Here, we compare an implementation of such a 3'-digital gene expression (3'-DGE) approach with "conventional" random primed mRNAseq. Given our particular datasets on cultured human cardiomyocyte cell lines, we find that, while conventional mRNAseq detects ~15% more genes and needs ~500,000 fewer reads per sample for equivalent statistical power, the resulting differentially expressed genes, biological conclusions, and gene signatures are highly concordant between two techniques. We also find good quantitative agreement at the level of individual genes between two techniques for both read counts and fold changes between given conditions. We conclude that, for high-throughput applications, the potential cost savings associated with 3'-DGE approach are likely a reasonable tradeoff for modest reduction in sensitivity and inability to observe alternative splicing, and should enable many larger scale studies focusing on not only differential expression analysis, but also quantitative transcriptome profiling.
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Affiliation(s)
- Yuguang Xiong
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Magali Soumillon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Berkeley Lights, Inc. 5858 Horton St., Emeryville, CA, 94608, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, CA, USA
- UCI MIND, University of California, Irvine, CA, USA
| | - Jens Hansen
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bin Hu
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Johan G C van Hasselt
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gomathi Jayaraman
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan Lim
- Department of Biological Chemistry, University of California, Irvine, CA, USA
- UCI MIND, University of California, Irvine, CA, USA
| | - Mehdi Bouhaddou
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Loren Ornelas
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Los Angeles, CA, USA
| | | | - Lindsay Lenaeus
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Los Angeles, CA, USA
| | | | - Jaehee Shim
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emilda Gomez
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Los Angeles, CA, USA
| | - Dhruv Sareen
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Clive Svendsen
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Leslie M Thompson
- Department of Biological Chemistry, University of California, Irvine, CA, USA
- UCI MIND, University of California, Irvine, CA, USA
- Department of Psychiatry and Human Behavior, Neurobiology and Behavior, University of California, Irvine, CA, USA
| | - Milind Mahajan
- Department of Genetics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ravi Iyengar
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric A Sobie
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Evren U Azeloglu
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Marc R Birtwistle
- Department of Pharmacological Sciences and DToxS LINCS Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, USA.
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5
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Tanca A, Manghina V, Fraumene C, Palomba A, Abbondio M, Deligios M, Silverman M, Uzzau S. Metaproteogenomics Reveals Taxonomic and Functional Changes between Cecal and Fecal Microbiota in Mouse. Front Microbiol 2017; 8:391. [PMID: 28352255 PMCID: PMC5348496 DOI: 10.3389/fmicb.2017.00391] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/24/2017] [Indexed: 02/01/2023] Open
Abstract
Previous studies on mouse models report that cecal and fecal microbial communities may differ in the taxonomic structure, but little is known about their respective functional activities. Here, we employed a metaproteogenomic approach, including 16S rRNA gene sequencing, shotgun metagenomics and shotgun metaproteomics, to analyze the microbiota of paired mouse cecal contents (CCs) and feces, with the aim of identifying changes in taxon-specific functions. As a result, Gram-positive anaerobes were observed as considerably higher in CCs, while several key enzymes, involved in oxalate degradation, glutamate/glutamine metabolism, and redox homeostasis, and most actively expressed by Bacteroidetes, were clearly more represented in feces. On the whole, taxon and function abundance appeared to vary consistently with environmental changes expected to occur throughout the transit from the cecum to outside the intestine, especially when considering metaproteomic data. The results of this study indicate that functional and metabolic differences exist between CC and stool samples, paving the way to further metaproteogenomic investigations aimed at elucidating the functional dynamics of the intestinal microbiota.
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Affiliation(s)
- Alessandro Tanca
- Porto Conte Ricerche, Science and Technology Park of Sardinia Alghero, Italy
| | - Valeria Manghina
- Porto Conte Ricerche, Science and Technology Park of SardiniaAlghero, Italy; Department of Biomedical Sciences, University of SassariSassari, Italy
| | - Cristina Fraumene
- Porto Conte Ricerche, Science and Technology Park of Sardinia Alghero, Italy
| | - Antonio Palomba
- Porto Conte Ricerche, Science and Technology Park of Sardinia Alghero, Italy
| | - Marcello Abbondio
- Department of Biomedical Sciences, University of Sassari Sassari, Italy
| | - Massimo Deligios
- Department of Biomedical Sciences, University of Sassari Sassari, Italy
| | - Michael Silverman
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical SchoolBoston, MA, USA; Division of Infectious Diseases, Department of Pediatrics, Boston Children's HospitalBoston, MA, USA
| | - Sergio Uzzau
- Porto Conte Ricerche, Science and Technology Park of SardiniaAlghero, Italy; Department of Biomedical Sciences, University of SassariSassari, Italy
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