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Cingaram PR, Beckedorff F, Yue J, Liu F, Dos Santos HG, Shiekhattar R. Enhancing Transcriptome Mapping with Rapid PRO-seq Profiling of Nascent RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593182. [PMID: 38766081 PMCID: PMC11100740 DOI: 10.1101/2024.05.08.593182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Precision nuclear run-on (PRO) sequencing (PRO-seq) is a powerful technique for mapping polymerase active sites with nucleotide resolution and measuring newly synthesized transcripts at both promoters and enhancer elements. The current PRO-seq protocol is time-intensive, technically challenging, and requires a large amount of starting material. To overcome these limitations, we developed rapid PRO-seq (rPRO-seq) which utilizes pre-adenylated single-stranded DNAs (AppDNA), a dimer blocking oligonucleotide (DBO), on-bead 5' RNA end repair, and column-based purification. These modifications enabled efficient transcriptome mapping within a single day (∼12 hours) increasing ligation efficiency, abolished adapter dimers, and reduced sample loss and RNA degradation. We demonstrate the reproducibility of rPRO-seq in measuring polymerases at promoters, gene bodies, and enhancers as compared to original PRO-seq protocols. Additionally, rPRO-seq is scalable, allowing for transcriptome mapping with as little as 25,000 cells. We apply rPRO-seq to study the role of Integrator in mouse hematopoietic stem and progenitor cell (mHSPC) homeostasis, identifying Ints11 as an essential component of transcriptional regulation and RNA processing in mHSPC homeostasis. Overall, rPRO-seq represents a significant advance in the field of nascent transcript analyses and will be a valuable tool for generating patient-specific genome-wide transcription profiles with minimal sample requirements.
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Hu K, Sun W, Chen H, Luo J, Song Z, An R, Komiyama M, Liang X. Formation of an instantaneous nick for highly efficient adenylation of oligonucleotides by ligase without subsequent jointing. Chem Commun (Camb) 2024; 60:2942-2945. [PMID: 38374791 DOI: 10.1039/d4cc00590b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
By forming a nick at the adenylation site instantaneously, nucleic acids are efficiently adenylated by T4 DNA ligase. The subsequent ligation is successfully suppressed in terms of rapid conversion of the instantaneous nick to a more stable gap. It is helpful to understand enzymatic ligation dynamics, and the adenylated products can be used for various practical applications.
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Affiliation(s)
- Kunling Hu
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao, P. R. China.
| | - Wenhua Sun
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao, P. R. China.
| | - Hui Chen
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao, P. R. China.
| | - Jian Luo
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao, P. R. China.
| | - Ziting Song
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao, P. R. China.
| | - Ran An
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao, P. R. China.
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao, P. R. China
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Xingguo Liang
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao, P. R. China.
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao, P. R. China
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3
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Luo J, Chen H, An R, Liang X. Efficient preparation of AppDNA/AppRNA by T4 DNA ligase aided by a DNA involving mismatched mini-hairpin structure at its 3′ side. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jian Luo
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
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4
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Yang Z, Zhang C, Lian G, Dong S, Song M, Shao H, Wang J, Zhong T, Luo Z, Jin S, Ding C. Direct adenylation from 5'-OH-terminated oligonucleotides by a fusion enzyme containing Pfu RNA ligase and T4 polynucleotide kinase. Nucleic Acids Res 2022; 50:7560-7569. [PMID: 35819229 PMCID: PMC9303275 DOI: 10.1093/nar/gkac604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/23/2022] [Accepted: 06/30/2022] [Indexed: 11/14/2022] Open
Abstract
5′-Adenylated oligonucleotides (AppOligos) are widely used for single-stranded DNA/RNA ligation in next-generation sequencing (NGS) applications such as microRNA (miRNA) profiling. The ligation between an AppOligo adapter and target molecules (such as miRNA) no longer requires ATP, thereby minimizing potential self-ligations and simplifying library preparation procedures. AppOligos can be produced by chemical synthesis or enzymatic modification. However, adenylation via chemical synthesis is inefficient and expensive, while enzymatic modification requires pre-phosphorylated substrate and additional purification. Here we cloned and characterized the Pfu RNA ligase encoded by the PF0353 gene in the hyperthermophilic archaea Pyrococcus furiosus. We further engineered fusion enzymes containing both Pfu RNA ligase and T4 polynucleotide kinase. One fusion enzyme, 8H-AP, was thermostable and can directly catalyze 5′-OH-terminated DNA substrates to adenylated products. The newly discovered Pfu RNA ligase and the engineered fusion enzyme may be useful tools for applications using AppOligos.
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Affiliation(s)
- Zhengquan Yang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Chengliang Zhang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.,Department of Clinical Laboratory, Kunming Third People's Hospital, Kunming, Yunnan, 650041, China
| | - Guojun Lian
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Shijie Dong
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Menghui Song
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Hengrong Shao
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Jingmei Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Tao Zhong
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Zhenni Luo
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Shengnan Jin
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Chunming Ding
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
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LaBelle J, Bowser M, Brown A, Farnam L, Kho A, Li J, McGeachie M, Chase R, Piehl S, Allen K, Hobbs BD, Weiss ST, Hersh C, Tantisira K, Amr SS. Commercially Available Blocking Oligonucleotides Effectively Suppress Unwanted Hemolysis-Related miRNAs in a Large Whole-Blood RNA Cohort. J Mol Diagn 2021; 23:671-682. [PMID: 33872788 DOI: 10.1016/j.jmoldx.2021.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 03/15/2021] [Accepted: 03/25/2021] [Indexed: 12/23/2022] Open
Abstract
When sequencing small RNA libraries derived from whole blood, the most abundant microRNAs (miRs) detected are often miR-486-5p, miR-451a, and miR-92a-3p. These highly expressed erythropoietic miRs are released into the sample from red blood cell hemolysis. Next-generation sequencing of these unwanted miRs leads to a waste in sequencing cost and diminished detection of lowly expressed miRNAs, including many potential miRNA biomarkers. Previous work has developed a method to reduce targeted miRNAs using oligonucleotides that bind their target miRNA and prevent its ligation during library construction, although the extent to which oligonucleotides can be multiplexed and their effect on larger cohorts has not been thoroughly explored. We present a method for suppressing detection of three highly abundant heme miRs in a single multiplexed blocking oligonucleotide reaction. In a small paired-sample pilot (n = 8) and a large cohort of samples (n = 901), multiplexed oligos reduced detection of their target miRNAs by approximately 70%, allowing for an approximately 10-fold increase in reads mapping to nonheme miRs and increased detection of very lowly expressed miRs, with minimal off-target effects. By removing all three highly expressed erythropoietic miRNAs from next-generational sequencing libraries, this commercially available multiplexed blocking oligonucleotide method allows for greater detection of lowly expressed biomarkers, improving the efficacy, cost-efficiency, and sensitivity of biomarker studies and diagnostic tests.
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Affiliation(s)
- Jenna LaBelle
- Mass General Brigham Personalized Medicine, Partners Healthcare, Cambridge, Massachusetts
| | - Mark Bowser
- Mass General Brigham Personalized Medicine, Partners Healthcare, Cambridge, Massachusetts
| | - Alison Brown
- Mass General Brigham Personalized Medicine, Partners Healthcare, Cambridge, Massachusetts
| | - Leanna Farnam
- School of Health Sciences, Lasell University, Auburndale, Massachusetts
| | - Alvin Kho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jiang Li
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Michael McGeachie
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Robert Chase
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | | | | | - Brian D Hobbs
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Scott T Weiss
- Mass General Brigham Personalized Medicine, Partners Healthcare, Cambridge, Massachusetts; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Craig Hersh
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Kelan Tantisira
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Sami S Amr
- Mass General Brigham Personalized Medicine, Partners Healthcare, Cambridge, Massachusetts; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.
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6
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Hardigan AA, Roberts BS, Moore DE, Ramaker RC, Jones AL, Myers RM. CRISPR/Cas9-targeted removal of unwanted sequences from small-RNA sequencing libraries. Nucleic Acids Res 2019; 47:e84. [PMID: 31165880 PMCID: PMC6698666 DOI: 10.1093/nar/gkz425] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 04/19/2019] [Accepted: 06/03/2019] [Indexed: 02/06/2023] Open
Abstract
In small RNA (smRNA) sequencing studies, highly abundant molecules such as adapter dimer products and tissue-specific microRNAs (miRNAs) inhibit accurate quantification of lowly expressed species. We previously developed a method to selectively deplete highly abundant miRNAs. However, this method does not deplete adapter dimer ligation products that, unless removed by gel-separation, comprise most of the library. Here, we have adapted and modified recently described methods for CRISPR/Cas9-based Depletion of Abundant Species by Hybridization ('DASH') to smRNA-seq, which we have termed miRNA and Adapter Dimer-DASH (MAD-DASH). In MAD-DASH, Cas9 is complexed with single guide RNAs (sgRNAs) targeting adapter dimer ligation products, alongside highly expressed tissue-specific smRNAs, for cleavage in vitro. This process dramatically reduces adapter dimer and targeted smRNA sequences, can be multiplexed, shows minimal off-target effects, improves the quantification of lowly expressed miRNAs from human plasma and tissue derived RNA, and obviates the need for gel-separation, greatly increasing sample throughput. Additionally, the method is fully customizable to other smRNA-seq preparation methods. Like depletion of ribosomal RNA for mRNA-seq and mitochondrial DNA for ATAC-seq, our method allows for greater proportional read-depth of non-targeted sequences.
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Affiliation(s)
- Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Dianna E Moore
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Angela L Jones
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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7
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Baroin-Tourancheau A, Jaszczyszyn Y, Benigni X, Amar L. Evaluating and Correcting Inherent Bias of microRNA Expression in Illumina Sequencing Analysis. Front Mol Biosci 2019; 6:17. [PMID: 31069233 PMCID: PMC6491513 DOI: 10.3389/fmolb.2019.00017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/07/2019] [Indexed: 12/02/2022] Open
Abstract
microRNA (miRNA) expression profiles based on the highly powerful Illumina sequencing technology rely on the construction of cDNA libraries in which adaptor ligation is known to deeply favor some miRNAs over others. This introduces erroneous measurements of the miRNA abundances and relative miRNA quantities in biological samples. Here, by using the commercial miRXplore Universal Reference that contains an equimolar mixture of 963 animal miRNAs and TruSeq or bulged adaptors, we describe a method for correcting ligation biases in expression profiles obtained with standard protocols of cDNA library construction and provide data for quantifying the true miRNA abundances in biological samples. Ligation biases were evaluated at three ratios of miRNA to 3′-adaptor and four numbers of polymerase chain reaction amplification cycles by calculating efficiency captures/correcting factors for each miRNA. We show that ligation biases lead to over- or under-expression covering a 105 amplitude range. We also show that, at each miRNA:3′-adaptor ratio, coefficients of variation (CVs) of efficiency captures calculated over the four number of amplification cycles using sliding windows of 10 values ranged from 0.1 for the miRNAs of high expression to 0.6 for the miRNAs of low expression. Efficiency captures of miRNAs of high and low expression in profiles are therefore differently impacted by the number of amplification cycles. Importantly, we observed that at a given number of amplification cycles, CVs of efficiency captures calculated over the three miRNA:3′-adaptor ratios displayed a steady value of 0.3 +/− 0.05 STD for miRNAs of high and low expression. This allows, at a given number of amplification cycles, accurate comparison of miRNA expression between biological samples over a substantial expression range. Finally we provide tables of correcting factors that allow to measure the abundances of 963 miRNAs in biological samples from TruSeq-based expression profiles and, an example of their use by characterizing miRNAs of the let-7, miR-26, miR-29, and miR-30 families as the more abundant miRNAs of the rat adult cerebellum.
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Affiliation(s)
- Anne Baroin-Tourancheau
- Neuroendocrinologie Moléculaire de la Prise Alimentaire, Institut des Neurosciences Paris-Saclay (Neuro-PSI), CNRS UMR 9197, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Yan Jaszczyszyn
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS UMR 9198, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Xavier Benigni
- Neuroendocrinologie Moléculaire de la Prise Alimentaire, Institut des Neurosciences Paris-Saclay (Neuro-PSI), CNRS UMR 9197, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Laurence Amar
- Neuroendocrinologie Moléculaire de la Prise Alimentaire, Institut des Neurosciences Paris-Saclay (Neuro-PSI), CNRS UMR 9197, Université Paris-Sud, Université Paris-Saclay, Orsay, France
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8
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Wang N, Cheng J, Fan R, Lu J. Capture, amplification, and global profiling of microRNAs from low quantities of whole cell lysate. Analyst 2018; 142:3203-3211. [PMID: 28765841 DOI: 10.1039/c7an00670e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that control gene expression at the post-transcriptional level via a complex regulatory network that requires genome-wide miRNA profiling to dissect. The patterns of miRNA expression at the genome scale are rich in diagnostic and prognostic information for human diseases such as cancers. This analysis, however, requires multi-step purification of RNAs from large quantities of cells, which is not only time consuming and costly but also challenging in situations where cell numbers are limited. In this study, we report direct capture, amplification, and library preparation of miRNAs from whole cell lysate without the need of pre-purification. As a result, it enables genome-wide miRNA profiling reproducibly with low quantity of cell samples (∼500 hematopoietic cells). Specifically, we conducted a systematic investigation of two key steps - cell lysis for miRNA release and 3' adaptor ligation required for direct miRNA capture and amplification. The obtained expression profile not only distinguishes cell types but also detects individual miRNA alterations in closely related isogenic cell lines. This approach, which is substantially simple as compared to the standard methods because of elimination of the need for RNA purification, is advantageous for the measurement of low quantity samples.
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Affiliation(s)
- Nayi Wang
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
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9
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Weil PP, Jaszczyszyn Y, Baroin-Tourancheau A, Postberg J, Amar L. Holistic and Affordable Analyses of MicroRNA Expression Profiles Using Tagged cDNA Libraries and a Multiplex Sequencing Strategy. Methods Mol Biol 2017; 1654:179-196. [PMID: 28986790 DOI: 10.1007/978-1-4939-7231-9_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Small and long noncoding RNAs (ncRNAs) are key regulators of gene expression. Variations in ncRNA expression patterns can consequently affect the control of many cellular processes. Not just since 2006, when Andrew Z Fire and Craig C Mello were jointly awarded The Nobel Prize in Physiology or Medicine for their discovery of RNA interference, great efforts were undertaken to unleash the biomedical applicability of small noncoding RNAs, in particular microRNAs. With the technological evolution of massive parallel sequencing technologies over the last years, which now are available for an increasing number of scientists, there is a demand for comprehensible and efficient workflows reliable even for unique and valuable clinical specimens. Here we describe a highly reproducible low-cost protocol for analyses of miRNA expression patterns using tagged cDNA libraries and a multiplex sequencing strategy following an Illumina-like protocol. This protocol easily allows the identification of expression differences from samples of tissues of 1-2 mm3 and fluids of 50-200 μL. We further provide entry points into useful computational biology applications, whose target groups explicitly involve non-bioinformaticians.
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Affiliation(s)
- Patrick P Weil
- Department of Paediatrics, HELIOS Medical Centre Wuppertal, Centre for Clinical and Translational Research (CCTR), Witten/Herdecke University Hospital, Centre for Biomedical Education and Research (ZBAF), Witten, Germany
| | - Yan Jaszczyszyn
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Anne Baroin-Tourancheau
- Institut des Neurosciences Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, Université Paris-Saclay, Orsay, France
| | - Jan Postberg
- Department of Paediatrics, HELIOS Medical Centre Wuppertal, Centre for Clinical and Translational Research (CCTR), Witten/Herdecke University Hospital, Centre for Biomedical Education and Research (ZBAF), Witten, Germany.
| | - Laurence Amar
- Institut des Neurosciences Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, Université Paris-Saclay, Orsay, France.
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Winz ML, Cahová H, Nübel G, Frindert J, Höfer K, Jäschke A. Capture and sequencing of NAD-capped RNA sequences with NAD captureSeq. Nat Protoc 2016; 12:122-149. [PMID: 27977022 DOI: 10.1038/nprot.2016.163] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Here we describe a protocol for NAD captureSeq that allows for the identification of nicotinamide-adenine dinucleotide (NAD)-capped RNA sequences in total RNA samples from different organisms. NAD-capped RNA is first chemo-enzymatically biotinylated with high efficiency, permitting selective capture on streptavidin beads. Then, a highly efficient library preparation protocol tailored to immobilized, 5'-modified RNA is applied, with adaptor ligation to the RNA's 3' terminus and reverse transcription (RT) performed on-bead. Then, cDNA is released into solution, tailed, ligated to a second adaptor and PCR-amplified. After next-generation sequencing (NGS) of the DNA library, enriched sequences are identified by comparison with a control sample in which the first step of chemo-enzymatic biotinylation is omitted. Because the downstream protocol does not necessarily rely on NAD-modified but on 'clickable' or biotin-modified RNA, it can be applied to other RNA modifications or RNA-biomolecule interactions. The central part of this protocol can be completed in ∼7 d, excluding preparatory steps, sequencing and bioinformatic analysis.
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Affiliation(s)
- Marie-Luise Winz
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Hana Cahová
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Gabriele Nübel
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Jens Frindert
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Katharina Höfer
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
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11
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Substantial and robust changes in microRNA transcriptome support postnatal development of the hypothalamus in rat. Sci Rep 2016; 6:24896. [PMID: 27118433 PMCID: PMC4847009 DOI: 10.1038/srep24896] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 04/07/2016] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) modulate gene expression in male germ cells and somatic tissues of mammals on a genome-wide scale. Hundreds of miRNAs are encoded by mammalian genomes, a large fraction of which is expressed in brain. Here we have investigated the complexity and dynamics of miRNA transcriptomes that associate with neuronal network maturation of hypothalamic arcuate nucleus and median eminence (ARC/ME) in rat by analysing more than 300 miRNAs from 3-7 biological replicates at 5 postnatal time-points. The network connecting ARC/ME to other hypothalamic and extra-hypothalamic regions maturates in an environment-dependent manner. We therefore analyzed miRNA transcriptomes of progeny of dams fed either a balanced or unbalanced diet during gestation and lactation. More than 30% of the miRNAs displayed significative changes of expression between stages P8 and P14, and P21 and P28; half of the changes were greater than 3-fold. Among those miRNAs were well-known and dozens of still poorly documented miRNAs. Progeny of dams fed an unbanced diet displayed a severe growth retardation phenotype, lower levels of plasma leptin but almost identical miRNA transcriptomes. Together these data demonstrate that two substantial and robust changes in miRNA transcriptome of ARC/ME occur at a period crucial for neuronal network functional organization.
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12
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Lama L, Ryan K. Adenylylation of small RNA sequencing adapters using the TS2126 RNA ligase I. RNA (NEW YORK, N.Y.) 2016; 22:155-61. [PMID: 26567315 PMCID: PMC4691829 DOI: 10.1261/rna.054999.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/25/2015] [Indexed: 05/27/2023]
Abstract
Many high-throughput small RNA next-generation sequencing protocols use 5' preadenylylated DNA oligonucleotide adapters during cDNA library preparation. Preadenylylation of the DNA adapter's 5' end frees from ATP-dependence the ligation of the adapter to RNA collections, thereby avoiding ATP-dependent side reactions. However, preadenylylation of the DNA adapters can be costly and difficult. The currently available method for chemical adenylylation of DNA adapters is inefficient and uses techniques not typically practiced in laboratories profiling cellular RNA expression. An alternative enzymatic method using a commercial RNA ligase was recently introduced, but this enzyme works best as a stoichiometric adenylylating reagent rather than a catalyst and can therefore prove costly when several variant adapters are needed or during scale-up or high-throughput adenylylation procedures. Here, we describe a simple, scalable, and highly efficient method for the 5' adenylylation of DNA oligonucleotides using the thermostable RNA ligase 1 from bacteriophage TS2126. Adapters with 3' blocking groups are adenylylated at >95% yield at catalytic enzyme-to-adapter ratios and need not be gel purified before ligation to RNA acceptors. Experimental conditions are also reported that enable DNA adapters with free 3' ends to be 5' adenylylated at >90% efficiency.
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Affiliation(s)
- Lodoe Lama
- Department of Chemistry, The City College of New York, The City University of New York, New York, New York 10031, USA Biochemistry Ph.D. Program, The City University of New York Graduate Center, New York, New York 10016, USA
| | - Kevin Ryan
- Department of Chemistry, The City College of New York, The City University of New York, New York, New York 10031, USA Biochemistry Ph.D. Program, The City University of New York Graduate Center, New York, New York 10016, USA
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13
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Baroin-Tourancheau A, Benigni X, Doubi-Kadmiri S, Taouis M, Amar L. Lessons from microRNA Sequencing Using Illumina Technology. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/abb.2016.77030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Song Y, Liu KJ, Wang TH. Efficient synthesis of stably adenylated DNA and RNA adapters for microRNA capture using T4 RNA ligase 1. Sci Rep 2015; 5:15620. [PMID: 26500066 PMCID: PMC4620478 DOI: 10.1038/srep15620] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/29/2015] [Indexed: 11/09/2022] Open
Abstract
MicroRNA profiling methods have become increasingly important due to the rapid rise of microRNA in both basic and translational sciences. A critical step in many microRNA profiling assays is adapter ligation using pre-adenylated adapters. While pre-adenylated adapters can be chemically or enzymatically prepared, enzymatic adenylation is preferred due to its ease and high yield. However, previously reported enzymatic methods either require tedious purification steps or use thermostable ligases that can generate side products during the subsequent ligation step. We have developed a highly efficient, template- and purification-free, adapter adenylation method using T4 RNA ligase 1. This method is capable of adenylating large amounts of adapter at ~100% efficiency and can efficiently adenylate both DNA and RNA bases. We find that the adenylation reaction speed can differ between DNA and RNA and between terminal nucleotides, leading to bias if reactions are not allowed to run to completion. We further find that the addition of high PEG levels can effectively suppress these differences.
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Affiliation(s)
- Yunke Song
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kelvin J Liu
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, MD, 21218, USA.,Circulomics Inc, Baltimore, MD, 21211, USA
| | - Tza-Huei Wang
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD, 21218, USA.,Mechanical Engineering Department, Johns Hopkins University, Baltimore, MD, 21218, USA
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15
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Roberts BS, Hardigan AA, Kirby MK, Fitz-Gerald MB, Wilcox CM, Kimberly RP, Myers RM. Blocking of targeted microRNAs from next-generation sequencing libraries. Nucleic Acids Res 2015. [PMID: 26209131 PMCID: PMC4666382 DOI: 10.1093/nar/gkv724] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Highly abundant microRNAs (miRNAs) in small RNA sequencing libraries make it difficult to obtain efficient measurements of more lowly expressed species. We present a new method that allows for the selective blocking of specific, abundant miRNAs during preparation of sequencing libraries. This technique is specific with little off-target effects and has no impact on the reproducibility of the measurement of non-targeted species. In human plasma samples, we demonstrate that blocking of highly abundant hsa-miR-16–5p leads to improved detection of lowly expressed miRNAs and more precise measurement of differential expression overall. Furthermore, we establish the ability to target a second abundant miRNA and to multiplex the blocking of two miRNAs simultaneously. For small RNA sequencing, this technique could fill a similar role as do ribosomal or globin removal technologies in messenger RNA sequencing.
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Affiliation(s)
- Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Marie K Kirby
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Meredith B Fitz-Gerald
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - C Mel Wilcox
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Robert P Kimberly
- Center for Clinical and Translational Science, University of Alabama at Birmingham, Birmingham, AL 35294, USA Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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16
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Welch JD, Slevin MK, Tatomer DC, Duronio RJ, Prins JF, Marzluff WF. EnD-Seq and AppEnD: sequencing 3' ends to identify nontemplated tails and degradation intermediates. RNA (NEW YORK, N.Y.) 2015; 21:1375-89. [PMID: 26015596 PMCID: PMC4478355 DOI: 10.1261/rna.048785.114] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 04/13/2015] [Indexed: 05/20/2023]
Abstract
Existing methods for detecting RNA intermediates resulting from exonuclease degradation are low-throughput and laborious. In addition, mapping the 3' ends of RNA molecules to the genome after high-throughput sequencing is challenging, particularly if the 3' ends contain post-transcriptional modifications. To address these problems, we developed EnD-Seq, a high-throughput sequencing protocol that preserves the 3' end of RNA molecules, and AppEnD, a computational method for analyzing high-throughput sequencing data. Together these allow determination of the 3' ends of RNA molecules, including nontemplated additions. Applying EnD-Seq and AppEnD to histone mRNAs revealed that a significant fraction of cytoplasmic histone mRNAs end in one or two uridines, which have replaced the 1-2 nt at the 3' end of mature histone mRNA maintaining the length of the histone transcripts. Histone mRNAs in fly embryos and ovaries show the same pattern, but with different tail nucleotide compositions. We increase the sensitivity of EnD-Seq by using cDNA priming to specifically enrich low-abundance tails of known sequence composition allowing identification of degradation intermediates. In addition, we show the broad applicability of our computational approach by using AppEnD to gain insight into 3' additions from diverse types of sequencing data, including data from small capped RNA sequencing and some alternative polyadenylation protocols.
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Affiliation(s)
- Joshua D Welch
- Department of Computer Science, Curriculum in Bioinformatics and Computational Biology
| | | | | | - Robert J Duronio
- Department of Biology, Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Jan F Prins
- Department of Computer Science, Curriculum in Bioinformatics and Computational Biology,
| | - William F Marzluff
- Curriculum in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, Department of Biology, Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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17
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Song Y, Liu KJ, Wang TH. Elimination of ligation dependent artifacts in T4 RNA ligase to achieve high efficiency and low bias microRNA capture. PLoS One 2014; 9:e94619. [PMID: 24722341 PMCID: PMC3983213 DOI: 10.1371/journal.pone.0094619] [Citation(s) in RCA: 26] [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: 11/28/2013] [Accepted: 03/18/2014] [Indexed: 01/22/2023] Open
Abstract
Adapter ligation is a critical first step in many microRNA analysis methods including microarray, qPCR, and sequencing. Previous studies have shown that ligation bias can have dramatic effects on both the fidelity of expression profiles and reproducibility across samples. We have developed a method for high efficiency and low bias microRNA capture by 3′ adapter ligation using T4 RNA ligase that does not require pooled adapters. Using a panel of 20 microRNA, we investigated the effects of ligase type, PEG concentration, ligase amount, adapter concentration, incubation time, incubation temperature, and adapter design on capture efficiency and bias. Of these factors, high PEG% was found to be critical in suppressing ligation bias. We obtained high average capture efficiency and low CV across the 20 microRNA panel, both in idealized buffer conditions (86%±10%) and total RNA spiking conditions (64%±17%). We demonstrate that this method is reliable across microRNA species that previous studies have had difficulty capturing and that our adapter design performs significantly better than the common adapter designs. Further, we demonstrate that the optimization methodology must be specifically designed for minimizing bias in order to obtain the ideal reaction parameters.
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Affiliation(s)
- Yunke Song
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Kelvin J. Liu
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
- Circulomics Inc, Baltimore, Maryland, United States of America
- * E-mail: (THW); (KJL)
| | - Tza-Huei Wang
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (THW); (KJL)
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18
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Head SR, Komori HK, LaMere SA, Whisenant T, Van Nieuwerburgh F, Salomon DR, Ordoukhanian P. Library construction for next-generation sequencing: overviews and challenges. Biotechniques 2014; 56:61-4, 66, 68, passim. [PMID: 24502796 DOI: 10.2144/000114133] [Citation(s) in RCA: 345] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 01/21/2014] [Indexed: 01/03/2023] Open
Abstract
High-throughput sequencing, also known as next-generation sequencing (NGS), has revolutionized genomic research. In recent years, NGS technology has steadily improved, with costs dropping and the number and range of sequencing applications increasing exponentially. Here, we examine the critical role of sequencing library quality and consider important challenges when preparing NGS libraries from DNA and RNA sources. Factors such as the quantity and physical characteristics of the RNA or DNA source material as well as the desired application (i.e., genome sequencing, targeted sequencing, RNA-seq, ChIP-seq, RIP-seq, and methylation) are addressed in the context of preparing high quality sequencing libraries. In addition, the current methods for preparing NGS libraries from single cells are also discussed.
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Affiliation(s)
- Steven R Head
- NGS and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA
| | - H Kiyomi Komori
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Sarah A LaMere
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Thomas Whisenant
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Daniel R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
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19
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Abstract
As small noncoding RNAs, microRNAs (miRNAs) regulate diverse biological functions, including physiological and pathological processes. The expression and deregulation of miRNA levels contain rich information with diagnostic and prognostic relevance and can reflect pharmacological responses. The increasing interest in miRNA-related research demands global miRNA expression profiling on large numbers of samples. We describe here a robust protocol that supports high-throughput sample labeling and detection on hundreds of samples simultaneously. This method employs 96-well-based miRNA capturing from total RNA samples and on-site biochemical reactions, coupled with bead-based detection in 96-well format for hundreds of miRNAs per sample. With low-cost, high-throughput, high detection specificity, and flexibility to profile both small and large numbers of samples, this protocol can be adapted in a wide range of laboratory settings.
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Affiliation(s)
- Yanwen Guo
- Department of Genetics, Yale Stem Cell Center, Yale University, 10 Amistad Street, New Haven, CT, 06520-8005, USA
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20
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Raabe CA, Tang TH, Brosius J, Rozhdestvensky TS. Biases in small RNA deep sequencing data. Nucleic Acids Res 2013; 42:1414-26. [PMID: 24198247 PMCID: PMC3919602 DOI: 10.1093/nar/gkt1021] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
High-throughput RNA sequencing (RNA-seq) is considered a powerful tool for novel gene discovery and fine-tuned transcriptional profiling. The digital nature of RNA-seq is also believed to simplify meta-analysis and to reduce background noise associated with hybridization-based approaches. The development of multiplex sequencing enables efficient and economic parallel analysis of gene expression. In addition, RNA-seq is of particular value when low RNA expression or modest changes between samples are monitored. However, recent data uncovered severe bias in the sequencing of small non-protein coding RNA (small RNA-seq or sRNA-seq), such that the expression levels of some RNAs appeared to be artificially enhanced and others diminished or even undetectable. The use of different adapters and barcodes during ligation as well as complex RNA structures and modifications drastically influence cDNA synthesis efficacies and exemplify sources of bias in deep sequencing. In addition, variable specific RNA G/C-content is associated with unequal polymerase chain reaction amplification efficiencies. Given the central importance of RNA-seq to molecular biology and personalized medicine, we review recent findings that challenge small non-protein coding RNA-seq data and suggest approaches and precautions to overcome or minimize bias.
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Affiliation(s)
- Carsten A Raabe
- Institute of Experimental Pathology (ZMBE), University of Muenster, Von-Esmarch-Strasse 56, 48149 Muenster, Germany and Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, 13200 Penang, Malaysia
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21
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Eminaga S, Christodoulou DC, Vigneault F, Church GM, Seidman JG. Quantification of microRNA expression with next-generation sequencing. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2013; Chapter 4:Unit 4.17. [PMID: 23821442 PMCID: PMC4138881 DOI: 10.1002/0471142727.mb0417s103] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Rapid advancement of next-generation sequencing technologies has made it possible to study expression profiles of microRNAs (miRNAs) comprehensively and efficiently. Multiplexing miRNA libraries by barcoding can significantly reduce sequencing cost per sample without compromising library quality. This unit provides a step-by-step protocol for isolating miRNAs and constructing multiplexed miRNA libraries. Also described is a custom computational pipeline for analyzing the multiplexed miRNA library sequencing reads generated by Illumina-based technology.
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Affiliation(s)
- Seda Eminaga
- Department of Genetics, Harvard Medical School, Boston, MA, USA
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22
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23
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Abstract
Mature microRNAs (miRNAs) are single-stranded RNA molecules of 20-23-nucleotide (nt) length that control gene expression in many cellular processes. These molecules typically reduce the translation and stability of mRNAs, including those of genes that mediate processes in tumorigenesis, such as inflammation, cell cycle regulation, stress response, differentiation, apoptosis, and invasion. miRNA targeting is initiated through specific base-pairing interactions between the 5' end ("seed" region) of the miRNA and sites within coding and untranslated regions (UTRs) of mRNAs; target sites in the 3' UTR lead to more effective mRNA destabilization. Since miRNAs frequently target hundreds of mRNAs, miRNA regulatory pathways are complex. To provide a critical overview of miRNA dysregulation in cancer, we first discuss the methods currently available for studying the role of miRNAs in cancer and then review miRNA genomic organization, biogenesis, and mechanism of target recognition, examining how these processes are altered in tumorigenesis. Given the critical role miRNAs play in tumorigenesis processes and their disease specific expression, they hold potential as therapeutic targets and novel biomarkers.
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24
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Hafner M, Renwick N, Farazi TA, Mihailović A, Pena JTG, Tuschl T. Barcoded cDNA library preparation for small RNA profiling by next-generation sequencing. Methods 2012; 58:164-70. [PMID: 22885844 PMCID: PMC3508525 DOI: 10.1016/j.ymeth.2012.07.030] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 11/28/2022] Open
Abstract
The characterization of post-transcriptional gene regulation by small regulatory (20-30 nt) RNAs, particularly miRNAs and piRNAs, has become a major focus of research in recent years. A prerequisite for characterizing small RNAs is their identification and quantification across different developmental stages, and in normal and disease tissues, as well as model cell lines. Here we present a step-by-step protocol for generating barcoded small RNA cDNA libraries compatible with Illumina HiSeq sequencing, thereby facilitating miRNA and other small RNA profiling of large sample collections.
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Affiliation(s)
- Markus Hafner
- Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, Box 186, NY 10065, USA
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25
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Chen YR, Zheng Y, Liu B, Zhong S, Giovannoni J, Fei Z. A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters. PLANT METHODS 2012; 8:41. [PMID: 22995534 PMCID: PMC3462708 DOI: 10.1186/1746-4811-8-41] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 08/22/2012] [Indexed: 05/23/2023]
Abstract
BACKGROUND Deep sequencing is a powerful tool for novel small RNA discovery. Illumina small RNA sequencing library preparation requires a pre-adenylated 3' end adapter containing a 5',5'-adenyl pyrophosphoryl moiety. In the absence of ATP, this adapter can be ligated to the 3' hydroxyl group of small RNA, while RNA self-ligation and concatenation are repressed. Pre-adenylated adapters are one of the most essential and costly components required for library preparation, and few are commercially available. RESULTS We demonstrate that DNA oligo with 5' phosphate and 3' amine groups can be enzymatically adenylated by T4 RNA ligase 1 to generate customized pre-adenylated adapters. We have constructed and sequenced a small RNA library for tomato (Solanum lycopersicum) using the T4 RNA ligase 1 adenylated adapter. CONCLUSION We provide an efficient and low-cost method for small RNA sequencing library preparation, which takes two days to complete and costs around $20 per library. This protocol has been tested in several plant species for small RNA sequencing including sweet potato, pepper, watermelon, and cowpea, and could be readily applied to any RNA samples.
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Affiliation(s)
- Yun-Ru Chen
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
| | - Yi Zheng
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
| | - Bao Liu
- Northeast Normal University, Changchun, China
| | - Silin Zhong
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
| | - Jim Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
- USDA Robert W. Holley Center for Agriculture and Health, Ithaca, USA
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
- USDA Robert W. Holley Center for Agriculture and Health, Ithaca, USA
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26
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Amar L, Benoit C, Beaumont G, Vacher C, Crepin D, Taouis M, Baroin-Tourancheau A. MicroRNA expression profiling of hypothalamic arcuate and paraventricular nuclei from single rats using Illumina sequencing technology. J Neurosci Methods 2012; 209:134-43. [DOI: 10.1016/j.jneumeth.2012.05.033] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 05/30/2012] [Accepted: 05/30/2012] [Indexed: 11/16/2022]
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27
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Small RNA expression profiling by high-throughput sequencing: implications of enzymatic manipulation. J Nucleic Acids 2012; 2012:360358. [PMID: 22778911 PMCID: PMC3388297 DOI: 10.1155/2012/360358] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 03/05/2012] [Indexed: 01/20/2023] Open
Abstract
Eukaryotic regulatory small RNAs (sRNAs) play significant roles in many fundamental cellular processes. As such, they have emerged as useful biomarkers for diseases and cell differentiation states. sRNA-based biomarkers outperform traditional messenger RNA-based biomarkers by testing fewer targets with greater accuracy and providing earlier detection for disease states. Therefore, expression profiling of sRNAs is fundamentally important to further advance the understanding of biological processes, as well as diagnosis and treatment of diseases. High-throughput sequencing (HTS) is a powerful approach for both sRNA discovery and expression profiling. Here, we discuss the general considerations for sRNA-based HTS profiling methods from RNA preparation to sequencing library construction, with a focus on the causes of systematic error. By examining the enzymatic manipulation steps of sRNA expression profiling, this paper aims to demystify current HTS-based sRNA profiling approaches and to aid researchers in the informed design and interpretation of profiling experiments.
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28
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Smith LM, Hartmann L, Drewe P, Bohnert R, Kahles A, Lanz C, Rätsch G. Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes. RNA Biol 2012; 9:596-609. [PMID: 22614838 DOI: 10.4161/rna.19683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Deep sequencing of transcriptomes allows quantitative and qualitative analysis of many RNA species in a sample, with parallel comparison of expression levels, splicing variants, natural antisense transcripts, RNA editing and transcriptional start and stop sites the ideal goal. By computational modeling, we show how libraries of multiple insert sizes combined with strand-specific, paired-end (SS-PE) sequencing can increase the information gained on alternative splicing, especially in higher eukaryotes. Despite the benefits of gaining SS-PE data with paired ends of varying distance, the standard Illumina protocol allows only non-strand-specific, paired-end sequencing with a single insert size. Here, we modify the Illumina RNA ligation protocol to allow SS-PE sequencing by using a custom pre-adenylated 3' adaptor. We generate parallel libraries with differing insert sizes to aid deconvolution of alternative splicing events and to characterize the extent and distribution of natural antisense transcription in C. elegans. Despite stringent requirements for detection of alternative splicing, our data increases the number of intron retention and exon skipping events annotated in the Wormbase genome annotations by 127% and 121%, respectively. We show that parallel libraries with a range of insert sizes increase transcriptomic information gained by sequencing and that by current established benchmarks our protocol gives competitive results with respect to library quality.
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Affiliation(s)
- Lisa M Smith
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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29
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Vigneault F, Ter-Ovanesyan D, Alon S, Eminaga S, Christodoulou DC, Seidman JG, Eisenberg E, Church GM. High-throughput multiplex sequencing of miRNA. CURRENT PROTOCOLS IN HUMAN GENETICS 2012; Chapter 11:11.12.1-11.12.10. [PMID: 22470142 PMCID: PMC3673877 DOI: 10.1002/0471142905.hg1112s73] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Next-generation sequencing offers many advantages over other methods of microRNA (miRNA) expression profiling, such as sample throughput and the capability to discover novel miRNAs. As the sequencing depth of current sequencing platforms exceeds what is necessary to quantify miRNAs, multiplexing several samples in one sequencing run offers a significant cost advantage. Although previous studies have achieved this goal by adding bar codes to miRNA libraries at the ligation step, this was recently shown to introduce significant bias into the miRNA expression data. This bias can be avoided, however, by bar coding the miRNA libraries at the PCR step instead. Here, we describe a user-friendly PCR bar-coding method of preparing multiplexed microRNA libraries for Illumina-based sequencing. The method also prevents the production of adapter dimers and can be completed in one day.
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Affiliation(s)
- Francois Vigneault
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA,Ragon Institute of MGH, MIT and Harvard, Massachusetts, MA 02129, USA
| | - Dmitry Ter-Ovanesyan
- Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02139, USA
| | - Shahar Alon
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Israel,Raymond and Beverly Sackler School of Physics and Astronomy, Tel-Aviv University, Israel
| | - Seda Eminaga
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - J. G. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Eli Eisenberg
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Israel,Raymond and Beverly Sackler School of Physics and Astronomy, Tel-Aviv University, Israel
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
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30
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Abiotic stress-associated microRNAs in plants: discovery, expression analysis, and evolution. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s11515-012-1210-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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31
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Van Nieuwerburgh F, Soetaert S, Podshivalova K, Ay-Lin Wang E, Schaffer L, Deforce D, Salomon DR, Head SR, Ordoukhanian P. Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing. PLoS One 2011; 6:e26969. [PMID: 22046424 PMCID: PMC3203936 DOI: 10.1371/journal.pone.0026969] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 10/06/2011] [Indexed: 01/29/2023] Open
Abstract
Here we demonstrate a method for unbiased multiplexed deep sequencing of RNA and DNA libraries using a novel, efficient and adaptable barcoding strategy called Post Amplification Ligation-Mediated (PALM). PALM barcoding is performed as the very last step of library preparation, eliminating a potential barcode-induced bias and allowing the flexibility to synthesize as many barcodes as needed. We sequenced PALM barcoded micro RNA (miRNA) and DNA reference samples and evaluated the quantitative barcode-induced bias in comparison to the same reference samples prepared using the Illumina TruSeq barcoding strategy. The Illumina TruSeq small RNA strategy introduces the barcode during the PCR step using differentially barcoded primers, while the TruSeq DNA strategy introduces the barcode before the PCR step by ligation of differentially barcoded adaptors. Results show virtually no bias between the differentially barcoded miRNA and DNA samples, both for the PALM and the TruSeq sample preparation methods. We also multiplexed miRNA reference samples using a pre-PCR barcode ligation. This barcoding strategy results in significant bias.
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32
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Newman MA, Mani V, Hammond SM. Deep sequencing of microRNA precursors reveals extensive 3' end modification. RNA (NEW YORK, N.Y.) 2011; 17:1795-803. [PMID: 21849429 PMCID: PMC3185913 DOI: 10.1261/rna.2713611] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Accepted: 07/07/2011] [Indexed: 05/20/2023]
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that post-transcriptionally regulate gene expression. An emerging mechanism to control miRNA production is the addition of an oligo-uridine tail to the 3' end of the precursor miRNA. This has been demonstrated for the Let-7 family of miRNAs in embryonic cells. Additionally, nontemplated nucleotides have been found on mature miRNA species, though in most cases it is not known if nucleotide addition occurs at the precursor step or at the mature miRNA. To examine the diversity of nucleotide addition we have developed a high-throughput sequencing method specific for miRNA precursors. Here we report that nontemplated addition is a widespread phenomenon occurring in many miRNA families. As previously reported, Let-7 family members are oligo-uridylated in embryonic cells in a Lin28-dependent manner. However, we find that the fraction of uridylated precursors increases with differentiation, independent of Lin28, and is highest in adult mouse tissues, exceeding 30% of all sequence reads for some Let-7 family members. A similar fraction of sequence reads are modified for many other miRNA families. Mono-uridylation is most common, with cytidine and adenosine modification less frequent but occurring above the expected error rate for Illumina sequencing. Nucleotide addition in cell lines is associated with 3' end degradation, in contrast to adult tissues, where modification occurs predominantly on full-length precursors. This work provides an unprecedented view of the complexity of 3' modification and trimming of miRNA precursors.
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Affiliation(s)
- Martin A. Newman
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Cell and Developmental Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Vidya Mani
- Department of Cell and Developmental Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Scott M. Hammond
- Department of Cell and Developmental Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Corresponding author.E-mail .
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Hafner M, Renwick N, Brown M, Mihailović A, Holoch D, Lin C, Pena JT, Nusbaum JD, Morozov P, Ludwig J, Ojo T, Luo S, Schroth G, Tuschl T. RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA (NEW YORK, N.Y.) 2011; 17:1697-712. [PMID: 21775473 PMCID: PMC3162335 DOI: 10.1261/rna.2799511] [Citation(s) in RCA: 256] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Sequencing of small RNA cDNA libraries is an important tool for the discovery of new RNAs and the analysis of their mutational status as well as expression changes across samples. It requires multiple enzyme-catalyzed steps, including sequential oligonucleotide adapter ligations to the 3' and 5' ends of the small RNAs, reverse transcription (RT), and PCR. We assessed biases in representation of miRNAs relative to their input concentration, using a pool of 770 synthetic miRNAs and 45 calibrator oligoribonucleotides, and tested the influence of Rnl1 and two variants of Rnl2, Rnl2(1-249) and Rnl2(1-249)K227Q, for 3'-adapter ligation. The use of the Rnl2 variants for adapter ligations yielded substantially fewer side products compared with Rnl1; however, the benefits of using Rnl2 remained largely obscured by additional biases in the 5'-adapter ligation step; RT and PCR steps did not have a significant impact on read frequencies. Intramolecular secondary structures of miRNA and/or miRNA/3'-adapter products contributed to these biases, which were highly reproducible under defined experimental conditions. We used the synthetic miRNA cocktail to derive correction factors for approximation of the absolute levels of individual miRNAs in biological samples. Finally, we evaluated the influence of 5'-terminal 5-nt barcode extensions for a set of 20 barcoded 3' adapters and observed similar biases in miRNA read distribution, thereby enabling cost-saving multiplex analysis for large-scale miRNA profiling.
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Affiliation(s)
- Markus Hafner
- Howard Hughes Medical Institute, Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Neil Renwick
- Howard Hughes Medical Institute, Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Miguel Brown
- Howard Hughes Medical Institute, Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Aleksandra Mihailović
- Howard Hughes Medical Institute, Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Daniel Holoch
- Howard Hughes Medical Institute, Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Carolina Lin
- Howard Hughes Medical Institute, Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - John T.G. Pena
- Howard Hughes Medical Institute, Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA
- Weill Cornell Medical College, Dyson Vision Research Institute, New York, New York 10065, USA
| | - Jeffrey D. Nusbaum
- Howard Hughes Medical Institute, Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Pavel Morozov
- Howard Hughes Medical Institute, Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Janos Ludwig
- Howard Hughes Medical Institute, Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Tolulope Ojo
- Howard Hughes Medical Institute, Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA
| | - Shujun Luo
- Illumina, Inc., Hayward, California 94545, USA
| | | | - Thomas Tuschl
- Howard Hughes Medical Institute, Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA
- Corresponding author.E-mail .
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Alon S, Vigneault F, Eminaga S, Christodoulou DC, Seidman JG, Church GM, Eisenberg E. Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Res 2011; 21:1506-11. [PMID: 21750102 DOI: 10.1101/gr.121715.111] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Second-generation sequencing is gradually becoming the method of choice for miRNA detection and expression profiling. Given the relatively small number of miRNAs and improvements in DNA sequencing technology, studying miRNA expression profiles of multiple samples in a single flow cell lane becomes feasible. Multiplexing strategies require marking each miRNA library with a DNA barcode. Here we report that barcodes introduced through adapter ligation confer significant bias on miRNA expression profiles. This bias is much higher than the expected Poisson noise and masks significant expression differences between miRNA libraries. This bias can be eliminated by adding barcodes during PCR amplification of libraries. The accuracy of miRNA expression measurement in multiplexed experiments becomes a function of sample number.
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Affiliation(s)
- Shahar Alon
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
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Zhelkovsky AM, McReynolds LA. Simple and efficient synthesis of 5' pre-adenylated DNA using thermostable RNA ligase. Nucleic Acids Res 2011; 39:e117. [PMID: 21724605 PMCID: PMC3177227 DOI: 10.1093/nar/gkr544] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
We report a simple method of enzymatic synthesis of pre-adenylated DNA linkers/adapters for next-generation sequencing using thermostable RNA ligase from Methanobacterium thermoautotrophicum (MthRnl). Using RNA ligase for the reaction instead of the existing chemical or T4 DNA ligase-based methods allows quantitative conversion of 5′-phosphorylated single-stranded DNA (ssDNA) to the adenylated form. The MthRnl adenylation reaction is specific for ATP and either ssDNA or RNA. In the presence of Mg+2, the reaction has a pH optimum of 6.0–6.5. Unlike reactions that use T4 DNA ligase, this protocol does not require synthesis of a template strand for adenylation. The high yield of the reaction simplifies isolation and purification of the adenylated product. Conducting the adenylation reaction at the elevated temperature (65°C) reduces structural constraints, while increased ATP concentrations allow quantitative adenylation of DNA with a 3′-unprotected end.
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36
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Kawano M, Kawazu C, Lizio M, Kawaji H, Carninci P, Suzuki H, Hayashizaki Y. Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing. Biotechniques 2011; 49:751-5. [PMID: 20964636 DOI: 10.2144/000113516] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Here we describe a method for constructing small RNA libraries for high-throughput sequencing in which we have made a significant improvement to commonly available standard protocols. We added a locked nucleic acid (LNA) oligonucleotide--named dimer eliminator--that is complementary to the adapter-dimer ligation products during the reverse transcription reaction. It reduces adapter-dimers, which often contaminate standard libraries and increase the number of non-insert sequence reads. This simple technology can be used for simultaneous multiplex sequencing of various barcoded samples as well as nonbarcoded small RNA library sequencing. In this study we also evaluated the reproducibility and quantitative design of the eight barcoded tags by comparing the Pearson's correlation values in the expression analysis between each barcoded sample. This method improves the sequencing yield and efficiency, while simplifying library construction, and makes it easier to perform large-scale small RNA analysis under multiple conditions with next-generation sequencers.
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37
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Abstract
Since the phenomenon of small RNA-mediated gene silencing was first described over 15 years ago (Lee et al. Cell 75:843-854, 1993; Wightman et al. Cell 75:855-862, 1993), it has become evident that a variety of endogenous small RNAs play an important role in establishing and maintaining cell lineages. MicroRNAs (miRNAs), in particular, have been shown to exert regulatory control over the development and function of the many specialized cells that comprise the mammalian immune system (Baltimore et al. Nat Immunol 9:839-845, 2008; Kanellopoulous and Monticelli Semin Cancer Biol 18:79-88, 2008; Xiao and Rajewsky Cell 136:26-36, 2009). The advent of next generation sequencers provides an important tool for profiling the small RNA transcriptome of many diverse cell types. Compared to traditional Sanger sequencing, next generation sequencing machines can process millions of sequence reads in parallel, generating megabases of data within just a few days. The generation of small RNA libraries for sequencing is relatively straightforward and involves the ligation of platform-specific adapter sequences to small RNAs, followed by reverse transcription of the ligated species and PCR amplification. While other hybridization-based techniques are available for profiling well-characterized small RNAs, high-throughput sequencing remains the most powerful method for discovering novel small RNAs and posttranscriptional editing.
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38
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Farazi TA, Spitzer JI, Morozov P, Tuschl T. miRNAs in human cancer. J Pathol 2011; 223:102-15. [PMID: 21125669 PMCID: PMC3069496 DOI: 10.1002/path.2806] [Citation(s) in RCA: 747] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 10/06/2010] [Accepted: 10/09/2010] [Indexed: 12/13/2022]
Abstract
Mature microRNAs (miRNAs) are single-stranded RNA molecules of 20-23 nucleotide (nt) length that control gene expression in many cellular processes. These molecules typically reduce the stability of mRNAs, including those of genes that mediate processes in tumorigenesis, such as inflammation, cell cycle regulation, stress response, differentiation, apoptosis and invasion. miRNA targeting is mostly achieved through specific base-pairing interactions between the 5' end ('seed' region) of the miRNA and sites within coding and untranslated regions (UTRs) of mRNAs; target sites in the 3' UTR lead to more effective mRNA destabilization. Since miRNAs frequently target hundreds of mRNAs, miRNA regulatory pathways are complex. To provide a critical overview of miRNA dysregulation in cancer, we first discuss the methods currently available for studying the role of miRNAs in cancer and then review miRNA genomic organization, biogenesis and mechanism of target recognition, examining how these processes are altered in tumorigenesis. Given the critical role miRNAs play in tumorigenesis processes and their disease-specific expression, they hold potential as therapeutic targets and novel biomarkers.
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Affiliation(s)
- Thalia A. Farazi
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Jessica I. Spitzer
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Pavel Morozov
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Thomas Tuschl
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA
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39
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Five years of Methods. Nat Methods 2009. [DOI: 10.1038/nmeth1009-724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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40
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Schlee M, Roth A, Hornung V, Hagmann CA, Wimmenauer V, Barchet W, Coch C, Janke M, Mihailovic A, Wardle G, Juranek S, Kato H, Kawai T, Poeck H, Fitzgerald KA, Takeuchi O, Akira S, Tuschl T, Latz E, Ludwig J, Hartmann G. Recognition of 5' triphosphate by RIG-I helicase requires short blunt double-stranded RNA as contained in panhandle of negative-strand virus. Immunity 2009; 31:25-34. [PMID: 19576794 PMCID: PMC2824854 DOI: 10.1016/j.immuni.2009.05.008] [Citation(s) in RCA: 593] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Revised: 03/30/2009] [Accepted: 05/08/2009] [Indexed: 12/24/2022]
Abstract
Antiviral immunity is triggered by immunorecognition of viral nucleic acids. The cytosolic helicase RIG-I is a key sensor of viral infections and is activated by RNA containing a triphosphate at the 5' end. The exact structure of RNA activating RIG-I remains controversial. Here, we established a chemical approach for 5' triphosphate oligoribonucleotide synthesis and found that synthetic single-stranded 5' triphosphate oligoribonucleotides were unable to bind and activate RIG-I. Conversely, the addition of the synthetic complementary strand resulted in optimal binding and activation of RIG-I. Short double-strand conformation with base pairing of the nucleoside carrying the 5' triphosphate was required. RIG-I activation was impaired by a 3' overhang at the 5' triphosphate end. These results define the structure of RNA for full RIG-I activation and explain how RIG-I detects negative-strand RNA viruses that lack long double-stranded RNA but do contain blunt short double-stranded 5' triphosphate RNA in the panhandle region of their single-stranded genome.
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Affiliation(s)
- Martin Schlee
- Institute of Clinical Chemistry and Pharmacology, University of Bonn, D-53127 Bonn, Germany
| | - Andreas Roth
- Institute of Clinical Chemistry and Pharmacology, University of Bonn, D-53127 Bonn, Germany
| | - Veit Hornung
- Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | - Vera Wimmenauer
- Institute of Clinical Chemistry and Pharmacology, University of Bonn, D-53127 Bonn, Germany
| | - Winfried Barchet
- Institute of Clinical Chemistry and Pharmacology, University of Bonn, D-53127 Bonn, Germany
| | - Christoph Coch
- Institute of Clinical Chemistry and Pharmacology, University of Bonn, D-53127 Bonn, Germany
| | - Markus Janke
- Institute of Clinical Chemistry and Pharmacology, University of Bonn, D-53127 Bonn, Germany
| | - Aleksandra Mihailovic
- Howard Hughes Medical Institute, Laboratory of RNA Biology, The Rockefeller Unversity, New York, NY 10021, USA
| | - Greg Wardle
- Howard Hughes Medical Institute, Laboratory of RNA Biology, The Rockefeller Unversity, New York, NY 10021, USA
| | - Stefan Juranek
- Howard Hughes Medical Institute, Laboratory of RNA Biology, The Rockefeller Unversity, New York, NY 10021, USA
| | - Hiroki Kato
- Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Taro Kawai
- Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hendrik Poeck
- Institute of Clinical Chemistry and Pharmacology, University of Bonn, D-53127 Bonn, Germany
| | - Katherine A. Fitzgerald
- Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Osamu Takeuchi
- Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shizuo Akira
- Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Thomas Tuschl
- Howard Hughes Medical Institute, Laboratory of RNA Biology, The Rockefeller Unversity, New York, NY 10021, USA
| | - Eicke Latz
- Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Janos Ludwig
- Institute of Clinical Chemistry and Pharmacology, University of Bonn, D-53127 Bonn, Germany
- Howard Hughes Medical Institute, Laboratory of RNA Biology, The Rockefeller Unversity, New York, NY 10021, USA
| | - Gunther Hartmann
- Institute of Clinical Chemistry and Pharmacology, University of Bonn, D-53127 Bonn, Germany
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41
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Chew YV, Holmes AJ. Suppression subtractive hybridisation allows selective sampling of metagenomic subsets of interest. J Microbiol Methods 2009; 78:136-43. [PMID: 19442689 DOI: 10.1016/j.mimet.2009.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Revised: 04/29/2009] [Accepted: 05/03/2009] [Indexed: 11/29/2022]
Abstract
Metagenomic studies bypass the requirement of a pure culture for analysis, focusing instead on the genetic information present in a given sample. Metagenomics have been applied to various studies, with objectives ranging from genome reconstruction, gene prospecting and ecology. However, the use of metagenomics in comparative studies has been constrained by sequencing costs and computational limitations. Efforts are underway to improve current sequencing methods and reduce the expense involved. We suggest an alternative approach - pretreatment of the sample of interest to enrich for desired subsets prior to deep sequencing. In this study, we tested the use of suppression subtractive hybridisation (SSH) for in vitro separation of metagenomic samples based on temporal variance. Faecal samples were taken from pigs at different timepoints and extracted DNA was whole genome-amplified using multiple displacement amplification (MDA). A sample collected at 31 days of age was designated the tester while a 24 day sample was denoted the driver. Following hybridisation and subtraction, tester-specific sequences are expected to be enriched in the final sample while driver-specific and common sequences are removed. Using denaturing gel gradient electrophoresis (DGGE), we found that driver-specific bands were completely removed from all final profiles while an average of 70% of common bands were successfully subtracted. Final profiles retained an average of 70% of tester-specific sequences and new sequences contributed an average of 36% of the band mobilities found in the final profiles. Tester-unique sequences were inferred to make up 78% of the final profile after SSH. We expect that using subtractive hybridisation for separation of metagenomic samples into desired subsets will provide a more effective and targeted approach to comparative studies.
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Affiliation(s)
- Yi Vee Chew
- School of Molecular and Microbial Biosciences, Building G08, University of Sydney, Darlington, 2006, Australia.
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