1
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Verwilt J, Mestdagh P, Vandesompele J. Artifacts and biases of the reverse transcription reaction in RNA sequencing. RNA (NEW YORK, N.Y.) 2023; 29:889-897. [PMID: 36990512 DOI: 10.1261/rna.079623.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
RNA sequencing has spurred a significant number of research areas in recent years. Most protocols rely on synthesizing a more stable complementary DNA (cDNA) copy of the RNA molecule during the reverse transcription reaction. The resulting cDNA pool is often wrongfully assumed to be quantitatively and molecularly similar to the original RNA input. Sadly, biases and artifacts confound the resulting cDNA mixture. These issues are often overlooked or ignored in the literature by those that rely on the reverse transcription process. In this review, we confront the reader with intra- and intersample biases and artifacts caused by the reverse transcription reaction during RNA sequencing experiments. To fight the reader's despair, we also provide solutions to most issues and inform on good RNA sequencing practices. We hope the reader can use this review to their advantage, thereby contributing to scientifically sound RNA studies.
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Affiliation(s)
- Jasper Verwilt
- OncoRNALab, Cancer Research Institute Ghent, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Pieter Mestdagh
- OncoRNALab, Cancer Research Institute Ghent, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Jo Vandesompele
- OncoRNALab, Cancer Research Institute Ghent, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
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2
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Haas BJ, Dobin A, Ghandi M, Van Arsdale A, Tickle T, Robinson JT, Gillani R, Kasif S, Regev A. Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector. CELL REPORTS METHODS 2023; 3:100467. [PMID: 37323575 PMCID: PMC10261907 DOI: 10.1016/j.crmeth.2023.100467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 02/28/2023] [Accepted: 04/14/2023] [Indexed: 06/17/2023]
Abstract
Here, we present FusionInspector for in silico characterization and interpretation of candidate fusion transcripts from RNA sequencing (RNA-seq) and exploration of their sequence and expression characteristics. We applied FusionInspector to thousands of tumor and normal transcriptomes and identified statistical and experimental features enriched among biologically impactful fusions. Through clustering and machine learning, we identified large collections of fusions potentially relevant to tumor and normal biological processes. We show that biologically relevant fusions are enriched for relatively high expression of the fusion transcript, imbalanced fusion allelic ratios, and canonical splicing patterns, and are deficient in sequence microhomologies between partner genes. We demonstrate that FusionInspector accurately validates fusion transcripts in silico and helps characterize numerous understudied fusions in tumor and normal tissue samples. FusionInspector is freely available as open source for screening, characterization, and visualization of candidate fusions via RNA-seq, and facilitates transparent explanation and interpretation of machine-learning predictions and their experimental sources.
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Affiliation(s)
- Brian J. Haas
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA
| | | | | | - Anne Van Arsdale
- Department of Obstetrics and Gynecology and Women’s Health, Albert Einstein Montefiore Medical Center, Bronx, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Timothy Tickle
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James T. Robinson
- School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Riaz Gillani
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02215, USA
- Boston Children’s Hospital, Boston, MA 02115, USA
| | - Simon Kasif
- Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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3
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Hunter S, Sigauke RF, Stanley JT, Allen MA, Dowell RD. Protocol variations in run-on transcription dataset preparation produce detectable signatures in sequencing libraries. BMC Genomics 2022; 23:187. [PMID: 35255806 PMCID: PMC8900324 DOI: 10.1186/s12864-022-08352-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 01/25/2022] [Indexed: 11/20/2022] Open
Abstract
Background A variety of protocols exist for producing whole genome run-on transcription datasets. However, little is known about how differences between these protocols affect the signal within the resulting libraries. Results Using run-on transcription datasets generated from the same biological system, we show that a variety of GRO- and PRO-seq preparation methods leave identifiable signatures within each library. Specifically we show that the library preparation method results in differences in quality control metrics, as well as differences in the signal distribution at the 5 ′ end of transcribed regions. These shifts lead to disparities in eRNA identification, but do not impact analyses aimed at inferring the key regulators involved in changes to transcription. Conclusions Run-on sequencing protocol variations result in technical signatures that can be used to identify both the enrichment and library preparation method of a particular data set. These technical signatures are batch effects that limit detailed comparisons of pausing ratios and eRNAs identified across protocols. However, these batch effects have only limited impact on our ability to infer which regulators underlie the observed transcriptional changes. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-022-08352-8).
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Affiliation(s)
- Samuel Hunter
- BioFrontiers Institute, University of Colorado, Boulder, 80309, USA
| | - Rutendo F Sigauke
- Computational Bioscience Program, Anschutz Medical Campus, University of Colorado, Aurora, 80045, USA
| | - Jacob T Stanley
- Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, 80301, USA
| | - Mary A Allen
- BioFrontiers Institute, University of Colorado, Boulder, 80309, USA
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado, Boulder, 80309, USA. .,Computational Bioscience Program, Anschutz Medical Campus, University of Colorado, Aurora, 80045, USA. .,Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, 80301, USA. .,Department of Computer Science, University of Colorado, Boulder, 80309, USA.
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4
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A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers. Nat Biotechnol 2022; 40:1056-1065. [PMID: 35177836 PMCID: PMC9288987 DOI: 10.1038/s41587-022-01211-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 01/06/2022] [Indexed: 01/15/2023]
Abstract
Mounting evidence supports the idea that transcriptional patterns serve as more specific identifiers of active enhancers than histone marks; however, the optimal strategy to identify active enhancers both experimentally and computationally has not been determined. Here, we compared 13 genome-wide RNA sequencing assays in K562 cells and showed that the nuclear run-on followed by cap-selection assay (GRO/PRO-cap) has advantages in eRNA detection and active enhancer identification. We also introduced a tool, Peak Identifier for Nascent Transcript Starts (PINTS), to identify active promoters and enhancers genome-wide and pinpoint the precise location of the 5′ transcription start sites. Finally, we compiled a comprehensive enhancer candidate compendium based on the detected eRNA TSSs available in 120 cell and tissue types that can be accessed at https://pints.yulab.org. With the knowledge of the best available assays and pipelines, this large-scale annotation of candidate enhancers will pave the way for selection and characterization of their functions in a time- and labor-efficient manner in the future.
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5
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Solayman M, Litfin T, Zhou Y, Zhan J. High-throughput mapping of RNA solvent accessibility at the single-nucleotide resolution by RtcB ligation between a fixed 5'-OH-end linker and unique 3'-P-end fragments from hydroxyl radical cleavage. RNA Biol 2022; 19:1179-1189. [PMID: 36369947 PMCID: PMC9662193 DOI: 10.1080/15476286.2022.2145098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Given the challenges for the experimental determination of RNA tertiary structures, probing solvent accessibility has become increasingly important to gain functional insights. Among various chemical probes developed, backbone-cleaving hydroxyl radical is the only one that can provide unbiased detection of all accessible nucleotides. However, the readouts have been based on reverse transcription (RT) stop at the cleaving sites, which are prone to false positives due to PCR amplification bias, early drop-off of reverse transcriptase, and the use of random primers in RT reaction. Here, we introduced a fixed-primer method called RL-Seq by performing RtcB Ligation (RL) between a fixed 5'-OH-end linker and unique 3'-P-end fragments from hydroxyl radical cleavage prior to high-throughput sequencing. The application of this method to E. coli ribosomes confirmed its ability to accurately probe solvent accessibility with high sensitivity (low required sequencing depth) and accuracy (strong correlation to structure-derived values) at the single-nucleotide resolution. Moreover, a near-perfect correlation was found between the experiments with and without using unique molecular identifiers, indicating negligible PCR biases in RL-Seq. Further improvement of RL-Seq and its potential transcriptome-wide applications are discussed.
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Affiliation(s)
- Md Solayman
- Institute for Glycomics, Griffith University, Parklands Dr, Southport, QLD, Australia
| | - Thomas Litfin
- Institute for Glycomics, Griffith University, Parklands Dr, Southport, QLD, Australia
| | - Yaoqi Zhou
- Institute for Glycomics, Griffith University, Parklands Dr, Southport, QLD, Australia,Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China,CONTACT Yaoqi Zhou Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Jian Zhan
- Institute for Glycomics, Griffith University, Parklands Dr, Southport, QLD, Australia,Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China,Jian Zhan Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen518055, China
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6
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Abstract
Conventional bacterial genome annotation provides information about coding sequences but ignores untranslated regions and operons. However, untranslated regions contain important regulatory elements as well as targets for many regulatory factors, such as small RNAs. Operon maps are also essential for functional gene analysis. In the last decade, considerable progress has been made in the study of bacterial transcriptomes through transcriptome sequencing (RNA-seq). Given the compact nature of bacterial genomes, many challenges still cannot be resolved through short reads generated using classical RNA-seq because of fragmentation and loss of the full-length information. Direct RNA sequencing is a technology that sequences the native RNA directly without information loss or bias. Here, we employed direct RNA sequencing to annotate the Vibrio parahaemolyticus transcriptome with its full features, including transcription start sites (TSSs), transcription termination sites, and operon maps. A total of 4,103 TSSs were identified. In comparison to short-read sequencing, full-length information provided a deeper view of TSS classification, showing that most internal and antisense TSSs were actually a result of gene overlap. Sequencing the transcriptome of V. parahaemolyticus grown with bile allowed us to study the landscape of pathogenicity island Vp-PAI. Some genes in this region were reannotated, providing more accurate annotation to increase precision in their characterization. Quantitative detection of operons in V. parahaemolyticus showed high complexity in some operons, shedding light on a greater extent of regulation within the same operon. Our study using direct RNA sequencing provides a quantitative and high-resolution landscape of the V. parahaemolyticus transcriptome. IMPORTANCEVibrio parahaemolyticus is a halophilic bacterium found in the marine environment. Outbreaks of gastroenteritis resulting from seafood poisoning by these pathogens have risen over the past 2 decades. Upon ingestion by humans—often through the consumption of raw or undercooked seafood—V. parahaemolyticus senses the host environment and expresses numerous genes, the products of which synergize to synthesize and secrete toxins that can cause acute gastroenteritis. To understand the regulation of such adaptive response, mRNA transcripts must be mapped accurately. However, due to the limitations of common sequencing methods, not all features of bacterial transcriptomes are always reported. We applied direct RNA sequencing to analyze the V. parahaemolyticus transcriptome. Mapping the full features of the transcriptome is anticipated to enhance our understanding of gene regulation in this bacterium and provides a data set for future work. Additionally, this study reveals a deeper view of a complicated transcriptome landscape, demonstrating the importance of applying such methods to other bacterial models.
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7
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Gillani R, Seong BKA, Crowdis J, Conway JR, Dharia NV, Alimohamed S, Haas BJ, Han K, Park J, Dietlein F, He MX, Imamovic A, Ma C, Bassik MC, Boehm JS, Vazquez F, Gusev A, Liu D, Janeway KA, McFarland JM, Stegmaier K, Van Allen EM. Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival. Cancer Res 2021; 81:3971-3984. [PMID: 34099491 PMCID: PMC8338889 DOI: 10.1158/0008-5472.can-21-0791] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/26/2021] [Accepted: 06/04/2021] [Indexed: 01/07/2023]
Abstract
Gene fusions frequently result from rearrangements in cancer genomes. In many instances, gene fusions play an important role in oncogenesis; in other instances, they are thought to be passenger events. Although regulatory element rearrangements and copy number alterations resulting from these structural variants are known to lead to transcriptional dysregulation across cancers, the extent to which these events result in functional dependencies with an impact on cancer cell survival is variable. Here we used CRISPR-Cas9 dependency screens to evaluate the fitness impact of 3,277 fusions across 645 cell lines from the Cancer Dependency Map. We found that 35% of cell lines harbored either a fusion partner dependency or a collateral dependency on a gene within the same topologically associating domain as a fusion partner. Fusion-associated dependencies revealed numerous novel oncogenic drivers and clinically translatable alterations. Broadly, fusions can result in partner and collateral dependencies that have biological and clinical relevance across cancer types. SIGNIFICANCE: This study provides insights into how fusions contribute to fitness in different cancer contexts beyond partner-gene activation events, identifying partner and collateral dependencies that may have direct implications for clinical care.
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Affiliation(s)
- Riaz Gillani
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts.,Boston Children's Hospital, Boston, Massachusetts
| | - Bo Kyung A. Seong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Jett Crowdis
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jake R. Conway
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Neekesh V. Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts.,Boston Children's Hospital, Boston, Massachusetts
| | - Saif Alimohamed
- Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, North Carolina
| | - Brian J. Haas
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Kyuho Han
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Jihye Park
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Felix Dietlein
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Meng Xiao He
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Alma Imamovic
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Clement Ma
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Michael C. Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, California.,Program in Cancer Biology, Stanford University School of Medicine, Stanford, California.,Program in Chemistry, Engineering and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California
| | - Jesse S. Boehm
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - David Liu
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Katherine A. Janeway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts.,Boston Children's Hospital, Boston, Massachusetts
| | | | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts.,Boston Children's Hospital, Boston, Massachusetts
| | - Eliezer M. Van Allen
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts.,Corresponding Author: Eliezer M. Van Allen, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215. Phone: 617-632-6656; E-mail:
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8
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Cardona-Alberich A, Tourbez M, Pearce SF, Sibley CR. Elucidating the cellular dynamics of the brain with single-cell RNA sequencing. RNA Biol 2021; 18:1063-1084. [PMID: 33499699 PMCID: PMC8216183 DOI: 10.1080/15476286.2020.1870362] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/17/2020] [Accepted: 12/24/2020] [Indexed: 12/18/2022] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) has emerged in recent years as a breakthrough technology to understand RNA metabolism at cellular resolution. In addition to allowing new cell types and states to be identified, scRNA-seq can permit cell-type specific differential gene expression changes, pre-mRNA processing events, gene regulatory networks and single-cell developmental trajectories to be uncovered. More recently, a new wave of multi-omic adaptations and complementary spatial transcriptomics workflows have been developed that facilitate the collection of even more holistic information from individual cells. These developments have unprecedented potential to provide penetrating new insights into the basic neural cell dynamics and molecular mechanisms relevant to the nervous system in both health and disease. In this review we discuss this maturation of single-cell RNA-sequencing over the past decade, and review the different adaptations of the technology that can now be applied both at different scales and for different purposes. We conclude by highlighting how these methods have already led to many exciting discoveries across neuroscience that have furthered our cellular understanding of the neurological disease.
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Affiliation(s)
- Aida Cardona-Alberich
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, Edinburgh University, Edinburgh, UK
| | - Manon Tourbez
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Sarah F. Pearce
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Christopher R. Sibley
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, Edinburgh University, Edinburgh, UK
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
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9
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Gajos M, Jasnovidova O, van Bömmel A, Freier S, Vingron M, Mayer A. Conserved DNA sequence features underlie pervasive RNA polymerase pausing. Nucleic Acids Res 2021; 49:4402-4420. [PMID: 33788942 PMCID: PMC8096220 DOI: 10.1093/nar/gkab208] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/05/2021] [Accepted: 03/15/2021] [Indexed: 12/17/2022] Open
Abstract
Pausing of transcribing RNA polymerase is regulated and creates opportunities to control gene expression. Research in metazoans has so far mainly focused on RNA polymerase II (Pol II) promoter-proximal pausing leaving the pervasive nature of pausing and its regulatory potential in mammalian cells unclear. Here, we developed a pause detecting algorithm (PDA) for nucleotide-resolution occupancy data and a new native elongating transcript sequencing approach, termed nested NET-seq, that strongly reduces artifactual peaks commonly misinterpreted as pausing sites. Leveraging PDA and nested NET-seq reveal widespread genome-wide Pol II pausing at single-nucleotide resolution in human cells. Notably, the majority of Pol II pauses occur outside of promoter-proximal gene regions primarily along the gene-body of transcribed genes. Sequence analysis combined with machine learning modeling reveals DNA sequence properties underlying widespread transcriptional pausing including a new pause motif. Interestingly, key sequence determinants of RNA polymerase pausing are conserved between human cells and bacteria. These studies indicate pervasive sequence-induced transcriptional pausing in human cells and the knowledge of exact pause locations implies potential functional roles in gene expression.
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Affiliation(s)
- Martyna Gajos
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany.,Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin 14195, Germany
| | - Olga Jasnovidova
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Alena van Bömmel
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin 14195, Germany.,Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Susanne Freier
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
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10
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Shivalingam A, Taemaitree L, El-Sagheer AH, Brown T. Squaramides and Ureas: A Flexible Approach to Polymerase-Compatible Nucleic Acid Assembly. Angew Chem Int Ed Engl 2020; 59:11416-11422. [PMID: 32153132 PMCID: PMC7383975 DOI: 10.1002/anie.202000209] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/28/2020] [Indexed: 12/15/2022]
Abstract
Joining oligonucleotides together (ligation) is a powerful means of retrieving information from the nanoscale. To recover this information, the linkages created must be compatible with polymerases. However, enzymatic ligation is restrictive and current chemical ligation methods lack flexibility. Herein, a versatile ligation platform based on the formation of urea and squaramide artificial backbones from minimally modified 3′‐ and 5′‐amino oligonucleotides is described. One‐pot ligation gives a urea linkage with excellent read‐through speed, or a squaramide linkage that is read‐through under selective conditions. The squaramide linkage can be broken and reformed on demand, while stable pre‐activated precursor oligonucleotides expand the scope of the ligation reaction to reagent‐free, mild conditions. The utility of our system is demonstrated by replacing the enzymatically biased RNA‐to‐DNA reverse transcription step of RT‐qPCR with a rapid nucleic‐acid‐template‐dependent DNA chemical ligation system, that allows direct RNA detection.
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Affiliation(s)
- Arun Shivalingam
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Lapatrada Taemaitree
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Department of Science and Mathematics, Suez University, Faculty of Petroleum and Mining Engineering, Suez, 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
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11
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Shivalingam A, Taemaitree L, El‐Sagheer AH, Brown T. Squaramides and Ureas: A Flexible Approach to Polymerase‐Compatible Nucleic Acid Assembly. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Arun Shivalingam
- Department of Chemistry University of Oxford Chemistry Research Laboratory 12 Mansfield Road Oxford OX1 3TA UK
| | - Lapatrada Taemaitree
- Department of Chemistry University of Oxford Chemistry Research Laboratory 12 Mansfield Road Oxford OX1 3TA UK
| | - Afaf H. El‐Sagheer
- Department of Chemistry University of Oxford Chemistry Research Laboratory 12 Mansfield Road Oxford OX1 3TA UK
- Department of Science and Mathematics Suez University Faculty of Petroleum and Mining Engineering Suez 43721 Egypt
| | - Tom Brown
- Department of Chemistry University of Oxford Chemistry Research Laboratory 12 Mansfield Road Oxford OX1 3TA UK
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12
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Wang L, Felts SJ, Van Keulen VP, Pease LR, Zhang Y. Exploring the effect of library preparation on RNA sequencing experiments. Genomics 2019; 111:1752-1759. [PMID: 30529531 PMCID: PMC6551333 DOI: 10.1016/j.ygeno.2018.11.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 10/27/2022]
Abstract
RNA sequencing (RNA-seq) has become the widely preferred choice for surveying the genome-wide transcriptome complexity in many organisms. However, the broad adaptation of this methodology into the clinic still needs further evaluation of potential effect of sample preparation factors on its analytical reliability using patient samples. In this study, we examined the impact of three major sample preparation factors (i.e., cDNA library storage time, the quantity of input RNA, and cryopreservation of cell samples) on sequence biases, gene expression profiles, and enriched biological functions using RNAs isolated from primary B cell and CD4+ cell blood samples of healthy subjects. Our comprehensive comparison results suggested that different cDNA library storage time, quantity of input RNA, and cryopreservation of cell samples did not significantly alter gene transcriptional expression profiles generated by RNA-seq experiments. These findings shed new lights on the potential applications of RNA-seq technique to patient samples in a regular clinical setting.
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Affiliation(s)
- Lei Wang
- Division of Biostatistics and Bioinformatics, University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, United States; Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, United States.
| | - Sara J Felts
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, United States.
| | - Virginia P Van Keulen
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, United States.
| | - Larry R Pease
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, United States.
| | - Yuji Zhang
- Division of Biostatistics and Bioinformatics, University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, United States; Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, United States.
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13
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Wissink EM, Vihervaara A, Tippens ND, Lis JT. Nascent RNA analyses: tracking transcription and its regulation. Nat Rev Genet 2019; 20:705-723. [PMID: 31399713 PMCID: PMC6858503 DOI: 10.1038/s41576-019-0159-6] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2019] [Indexed: 12/19/2022]
Abstract
The programmes that direct an organism's development and maintenance are encoded in its genome. Decoding of this information begins with regulated transcription of genomic DNA into RNA. Although transcription and its control can be tracked indirectly by measuring stable RNAs, it is only by directly measuring nascent RNAs that the immediate regulatory changes in response to developmental, environmental, disease and metabolic signals are revealed. Multiple complementary methods have been developed to quantitatively track nascent transcription genome-wide at nucleotide resolution, all of which have contributed novel insights into the mechanisms of gene regulation and transcription-coupled RNA processing. Here we critically evaluate the array of strategies used for investigating nascent transcription and discuss the recent conceptual advances they have provided.
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Affiliation(s)
- Erin M Wissink
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Anniina Vihervaara
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Nathaniel D Tippens
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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Shivram H, Le SV, Iyer VR. PRC2 activates interferon-stimulated genes indirectly by repressing miRNAs in glioblastoma. PLoS One 2019; 14:e0222435. [PMID: 31513636 PMCID: PMC6742368 DOI: 10.1371/journal.pone.0222435] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/30/2019] [Indexed: 12/21/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) is a chromatin binding complex that represses gene expression by methylating histone H3 at K27 to establish repressed chromatin domains. PRC2 can either regulate genes directly through the methyltransferase activity of its component EZH2 or indirectly by regulating other gene regulators. Gene expression analysis of glioblastoma (GBM) cells lacking EZH2 showed that PRC2 regulates hundreds of interferon-stimulated genes (ISGs). We found that PRC2 directly represses several ISGs and also indirectly activates a distinct set of ISGs. Assessment of EZH2 binding proximal to miRNAs showed that PRC2 directly represses miRNAs encoded in the chromosome 14 imprinted DLK1-DIO3 locus. We found that repression of this locus by PRC2 occurs in immortalized GBM-derived cell lines as well as in primary bulk tumors from GBM and anaplastic astrocytoma patients. Through repression of these miRNAs and several other miRNAs, PRC2 activates a set of ISGs that are targeted by these miRNAs. This PRC2-miRNA-ISG network is likely to be important in regulating gene expression programs in GBM.
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Affiliation(s)
- Haridha Shivram
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Livestrong Cancer Institutes, University of Texas at Austin, Austin, Texas, United States of America
| | - Steven V. Le
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Livestrong Cancer Institutes, University of Texas at Austin, Austin, Texas, United States of America
| | - Vishwanath R. Iyer
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Livestrong Cancer Institutes, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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15
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Improved TGIRT-seq methods for comprehensive transcriptome profiling with decreased adapter dimer formation and bias correction. Sci Rep 2019; 9:7953. [PMID: 31138886 PMCID: PMC6538698 DOI: 10.1038/s41598-019-44457-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/17/2019] [Indexed: 02/08/2023] Open
Abstract
Thermostable group II intron reverse transcriptases (TGIRTs) with high fidelity and processivity have been used for a variety of RNA sequencing (RNA-seq) applications, including comprehensive profiling of whole-cell, exosomal, and human plasma RNAs; quantitative tRNA-seq based on the ability of TGIRT enzymes to give full-length reads of tRNAs and other structured small ncRNAs; high-throughput mapping of post-transcriptional modifications; and RNA structure mapping. Here, we improved TGIRT-seq methods for comprehensive transcriptome profiling by rationally designing RNA-seq adapters that minimize adapter dimer formation. Additionally, we developed biochemical and computational methods for remediating 5′- and 3′-end biases, the latter based on a random forest regression model that provides insight into the contribution of different factors to these biases. These improvements, some of which may be applicable to other RNA-seq methods, increase the efficiency of TGIRT-seq library construction and improve coverage of very small RNAs, such as miRNAs. Our findings provide insight into the biochemical basis of 5′- and 3′-end biases in RNA-seq and suggest general approaches for remediating biases and decreasing adapter dimer formation.
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16
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Shivram H, Le SV, Iyer VR. MicroRNAs reinforce repression of PRC2 transcriptional targets independently and through a feed-forward regulatory network. Genome Res 2019; 29:184-192. [PMID: 30651280 PMCID: PMC6360819 DOI: 10.1101/gr.238311.118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 12/21/2018] [Indexed: 12/17/2022]
Abstract
Gene expression can be regulated at multiple levels, but it is not known if and how there is broad coordination between regulation at the transcriptional and post-transcriptional levels. Transcription factors and chromatin regulate gene expression transcriptionally, whereas microRNAs (miRNAs) are small regulatory RNAs that function post-transcriptionally. Systematically identifying the post-transcriptional targets of miRNAs and the mechanism of transcriptional regulation of the same targets can shed light on regulatory networks connecting transcriptional and post-transcriptional control. We used individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) for the RNA-induced silencing complex (RISC) component AGO2 and global miRNA depletion to identify genes directly targeted by miRNAs. We found that Polycomb repressive complex 2 (PRC2) and its associated histone mark, H3K27me3, is enriched at hundreds of miRNA-repressed genes. We show that these genes are directly repressed by PRC2 and constitute a significant proportion of direct PRC2 targets. For just over half of the genes corepressed by PRC2 and miRNAs, PRC2 promotes their miRNA-mediated repression by increasing expression of the miRNAs that are likely to target them. miRNAs also repress the remainder of the PRC2 target genes, but independently of PRC2. Thus, miRNAs post-transcriptionally reinforce silencing of PRC2-repressed genes that are inefficiently repressed at the level of chromatin, by either forming a feed-forward regulatory network with PRC2 or repressing them independently of PRC2.
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Affiliation(s)
- Haridha Shivram
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Steven V Le
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Vishwanath R Iyer
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
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