1
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Santinha AJ, Klingler E, Kuhn M, Farouni R, Lagler S, Kalamakis G, Lischetti U, Jabaudon D, Platt RJ. Transcriptional linkage analysis with in vivo AAV-Perturb-seq. Nature 2023; 622:367-375. [PMID: 37730998 PMCID: PMC10567566 DOI: 10.1038/s41586-023-06570-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 08/25/2023] [Indexed: 09/22/2023]
Abstract
The ever-growing compendium of genetic variants associated with human pathologies demands new methods to study genotype-phenotype relationships in complex tissues in a high-throughput manner1,2. Here we introduce adeno-associated virus (AAV)-mediated direct in vivo single-cell CRISPR screening, termed AAV-Perturb-seq, a tuneable and broadly applicable method for transcriptional linkage analysis as well as high-throughput and high-resolution phenotyping of genetic perturbations in vivo. We applied AAV-Perturb-seq using gene editing and transcriptional inhibition to systematically dissect the phenotypic landscape underlying 22q11.2 deletion syndrome3,4 genes in the adult mouse brain prefrontal cortex. We identified three 22q11.2-linked genes involved in known and previously undescribed pathways orchestrating neuronal functions in vivo that explain approximately 40% of the transcriptional changes observed in a 22q11.2-deletion mouse model. Our findings suggest that the 22q11.2-deletion syndrome transcriptional phenotype found in mature neurons may in part be due to the broad dysregulation of a class of genes associated with disease susceptibility that are important for dysfunctional RNA processing and synaptic function. Our study establishes a flexible and scalable direct in vivo method to facilitate causal understanding of biological and disease mechanisms with potential applications to identify genetic interventions and therapeutic targets for treating disease.
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Affiliation(s)
- Antonio J Santinha
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Esther Klingler
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
- VIB-KU Leuven Center for Brain & Disease Research, KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Maria Kuhn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Pharma Research and Early Development (pRED), Roche, Basel, Switzerland
| | - Rick Farouni
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Sandra Lagler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Georgios Kalamakis
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Ulrike Lischetti
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Department of Biomedicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Denis Jabaudon
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- Botnar Research Center for Child Health, Basel, Switzerland.
- Department of Chemistry, University of Basel, Basel, Switzerland.
- NCCR Molecular Systems Engineering, Basel, Switzerland.
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2
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Lazure F, Farouni R, Sahinyan K, Blackburn DM, Hernández-Corchado A, Perron G, Lu T, Osakwe A, Ragoussis J, Crist C, Perkins TJ, Jahani-Asl A, Najafabadi HS, Soleimani VD. Transcriptional reprogramming of skeletal muscle stem cells by the niche environment. Nat Commun 2023; 14:535. [PMID: 36726011 PMCID: PMC9892560 DOI: 10.1038/s41467-023-36265-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 01/23/2023] [Indexed: 02/03/2023] Open
Abstract
Adult stem cells are indispensable for tissue regeneration, but their function declines with age. The niche environment in which the stem cells reside plays a critical role in their function. However, quantification of the niche effect on stem cell function is lacking. Using muscle stem cells (MuSC) as a model, we show that aging leads to a significant transcriptomic shift in their subpopulations accompanied by locus-specific gain and loss of chromatin accessibility and DNA methylation. By combining in vivo MuSC transplantation and computational methods, we show that the expression of approximately half of all age-altered genes in MuSCs from aged male mice can be restored by exposure to a young niche environment. While there is a correlation between gene reversibility and epigenetic alterations, restoration of gene expression occurs primarily at the level of transcription. The stem cell niche environment therefore represents an important therapeutic target to enhance tissue regeneration in aging.
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Affiliation(s)
- Felicia Lazure
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1E2, Canada
| | - Rick Farouni
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada.,McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, 740 Dr Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Korin Sahinyan
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1E2, Canada
| | - Darren M Blackburn
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1E2, Canada
| | - Aldo Hernández-Corchado
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada.,McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, 740 Dr Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Gabrielle Perron
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada.,McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, 740 Dr Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1E2, Canada.,Quantitative Life Sciences, McGill University, Montreal, Canada
| | - Adrien Osakwe
- Quantitative Life Sciences, McGill University, Montreal, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada.,McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, 740 Dr Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Colin Crist
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1E2, Canada
| | - Theodore J Perkins
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Arezu Jahani-Asl
- Department of Cellular and Molecular Medicine and University of Ottawa Brain and Mind Research Institute, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Hamed S Najafabadi
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada. .,McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, 740 Dr Penfield Avenue, Montreal, QC, H3A 0G1, Canada. .,Quantitative Life Sciences, McGill University, Montreal, Canada.
| | - Vahab D Soleimani
- Department of Human Genetics, McGill University, 3640 rue University, Montréal, QC, H3A 0C7, Canada. .,Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1E2, Canada.
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3
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Schmidt F, Zimmermann J, Tanna T, Farouni R, Conway T, Macpherson AJ, Platt RJ. Noninvasive assessment of gut function using transcriptional recording sentinel cells. Science 2022; 376:eabm6038. [PMID: 35549411 DOI: 10.1126/science.abm6038] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Transcriptional recording by CRISPR spacer acquisition from RNA endows engineered Escherichia coli with synthetic memory, which through Record-seq reveals transcriptome-scale records. Microbial sentinels that traverse the gastrointestinal tract capture a wide range of genes and pathways that describe interactions with the host, including quantitative shifts in the molecular environment that result from alterations in the host diet, induced inflammation, and microbiome complexity. We demonstrate multiplexed recording using barcoded CRISPR arrays, enabling the reconstruction of transcriptional histories of isogenic bacterial strains in vivo. Record-seq therefore provides a scalable, noninvasive platform for interrogating intestinal and microbial physiology throughout the length of the intestine without manipulations to host physiology and can determine how single microbial genetic differences alter the way in which the microbe adapts to the host intestinal environment.
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Affiliation(s)
- Florian Schmidt
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Jakob Zimmermann
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Switzerland
- Department for Biomedical Research, University of Bern, Bern, Switzerland
| | - Tanmay Tanna
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- Department of Computer Science, ETH Zurich, Universitätstrasse 6, 8092 Zurich, Switzerland
| | - Rick Farouni
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Tyrrell Conway
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Andrew J Macpherson
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Switzerland
- Botnar Research Center for Child Health, Mattenstrasse 24a, 4058 Basel, Switzerland
- Department for Biomedical Research, University of Bern, Bern, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- Botnar Research Center for Child Health, Mattenstrasse 24a, 4058 Basel, Switzerland
- Department of Chemistry, University of Basel, Petersplatz 1, 4003 Basel, Switzerland
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4
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Farouni R, Djambazian H, Ferri LE, Ragoussis J, Najafabadi HS. Model-based analysis of sample index hopping reveals its widespread artifacts in multiplexed single-cell RNA-sequencing. Nat Commun 2020; 11:2704. [PMID: 32483174 PMCID: PMC7264361 DOI: 10.1038/s41467-020-16522-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 05/09/2020] [Indexed: 12/24/2022] Open
Abstract
Index hopping is the main cause of incorrect sample assignment of sequencing reads in multiplexed pooled libraries. We introduce a statistical model for estimating the sample index-hopping rate in multiplexed droplet-based single-cell RNA-seq data and for probabilistic inference of the true sample of origin of hopped reads. We analyze several datasets and estimate the sample index hopping probability to range between 0.003–0.009, a small number that counter-intuitively gives rise to a large fraction of phantom molecules — the fraction of phantom molecules exceeds 8% in more than 25% of samples and reaches as high as 85% in low-complexity samples. Phantom molecules lead to widespread complications in downstream analyses, including transcriptome mixing across cells, emergence of phantom copies of cells from other samples, and misclassification of empty droplets as cells. We demonstrate that our approach can correct for these artifacts by accurately purging the majority of phantom molecules from the data. Sample index hopping results in various artefacts in multiplexed scRNA-seq experiments. Here, the authors introduce a statistical model to estimate sample index hopping rate in droplet-based scRNA-seq data and show that artifacts can be corrected by purging phantom molecules from the data.
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Affiliation(s)
- Rick Farouni
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada. .,McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada.
| | - Haig Djambazian
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada.,McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Lorenzo E Ferri
- Department of Surgery, McGill University, Montreal, QC, H3G 1A4, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada.,McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Hamed S Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada. .,McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada.
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5
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Abstract
Recent reports have identified differences in the mutational spectra across human populations. Although some of these reports have been replicated in other cohorts, most have been reported only in the 1000 Genomes Project (1kGP) data. While investigating an intriguing putative population stratification within the Japanese population, we identified a previously unreported batch effect leading to spurious mutation calls in the 1kGP data and to the apparent population stratification. Because the 1kGP data are used extensively, we find that the batch effects also lead to incorrect imputation by leading imputation servers and a small number of suspicious GWAS associations. Lower quality data from the early phases of the 1kGP thus continue to contaminate modern studies in hidden ways. It may be time to retire or upgrade such legacy sequencing data.
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Affiliation(s)
- Luke Anderson-Trocmé
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Rick Farouni
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Mathieu Bourgey
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Yoichiro Kamatani
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koichiro Higasa
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jeong-Sun Seo
- Bioinformatics Institute, Macrogen Inc, Seoul, Republic of Korea
- Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Changhoon Kim
- Bioinformatics Institute, Macrogen Inc, Seoul, Republic of Korea
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Simon Gravel
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
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6
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Pinello L, Farouni R, Yuan GC. Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements. Bioinformatics 2019; 34:1930-1933. [PMID: 29360936 DOI: 10.1093/bioinformatics/bty031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/16/2018] [Indexed: 11/12/2022] Open
Abstract
Motivation With the increasing amount of genomic and epigenomic data in the public domain, a pressing challenge is to integrate these data to investigate the role of epigenetic mechanisms in regulating gene expression and maintenance of cell-identity. To this end, we have implemented a computational pipeline to systematically study epigenetic variability and uncover regulatory DNA sequences. Results Haystack is a bioinformatics pipeline to identify hotspots of epigenetic variability across different cell-types, cell-type specific cis-regulatory elements, and associated transcription factors. Haystack is generally applicable to any epigenetic mark and provides an important tool to investigate the mechanisms underlying epigenetic switches during development. This software is accompanied by a set of precomputed tracks, which may be used as a valuable resource for functional annotation of the human genome. Availability and implementation The Haystack pipeline is implemented as an open-source, multiplatform, Python package called haystack_bio freely available at https://github.com/pinellolab/haystack_bio. Contact lpinello@mgh.harvard.edu or gcyuan@jimmy.harvard.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Luca Pinello
- Department of Molecular Pathology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rick Farouni
- Department of Molecular Pathology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Guo-Cheng Yuan
- Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard T.H. Chan School of Public Health, Boston, MA, USA
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7
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Seruggia D, Oti M, Tripathi P, Canver MC, LeBlanc L, Di Giammartino DC, Bullen MJ, Nefzger CM, Sun YBY, Farouni R, Polo JM, Pinello L, Apostolou E, Kim J, Orkin SH, Das PP. TAF5L and TAF6L Maintain Self-Renewal of Embryonic Stem Cells via the MYC Regulatory Network. Mol Cell 2019; 74:1148-1163.e7. [PMID: 31005419 DOI: 10.1016/j.molcel.2019.03.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 01/24/2019] [Accepted: 03/21/2019] [Indexed: 12/16/2022]
Abstract
Self-renewal and pluripotency of the embryonic stem cell (ESC) state are established and maintained by multiple regulatory networks that comprise transcription factors and epigenetic regulators. While much has been learned regarding transcription factors, the function of epigenetic regulators in these networks is less well defined. We conducted a CRISPR-Cas9-mediated loss-of-function genetic screen that identified two epigenetic regulators, TAF5L and TAF6L, components or co-activators of the GNAT-HAT complexes for the mouse ESC (mESC) state. Detailed molecular studies demonstrate that TAF5L/TAF6L transcriptionally activate c-Myc and Oct4 and their corresponding MYC and CORE regulatory networks. Besides, TAF5L/TAF6L predominantly regulate their target genes through H3K9ac deposition and c-MYC recruitment that eventually activate the MYC regulatory network for self-renewal of mESCs. Thus, our findings uncover a role of TAF5L/TAF6L in directing the MYC regulatory network that orchestrates gene expression programs to control self-renewal for the maintenance of mESC state.
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Affiliation(s)
- Davide Seruggia
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Martin Oti
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia
| | - Pratibha Tripathi
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia
| | - Matthew C Canver
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Lucy LeBlanc
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Dafne C Di Giammartino
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Michael J Bullen
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia
| | - Christian M Nefzger
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Yu Bo Yang Sun
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Rick Farouni
- Molecular Pathology & Cancer Center, Massachusetts General Hospital & Harvard Medical School, Boston, MA 02114, USA
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Luca Pinello
- Molecular Pathology & Cancer Center, Massachusetts General Hospital & Harvard Medical School, Boston, MA 02114, USA
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA.
| | - Partha Pratim Das
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia.
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8
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Clement K, Rees H, Canver MC, Gehrke JM, Farouni R, Hsu JY, Cole MA, Liu DR, Joung JK, Bauer DE, Pinello L. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat Biotechnol 2019; 37:224-226. [PMID: 30809026 DOI: 10.1038/s41587-019-0032-3] [Citation(s) in RCA: 715] [Impact Index Per Article: 143.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Kendell Clement
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Molecular Pathology Unit, Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Holly Rees
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Matthew C Canver
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Molecular Pathology Unit, Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Jason M Gehrke
- Molecular Pathology Unit, Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Rick Farouni
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Molecular Pathology Unit, Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Jonathan Y Hsu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Molecular Pathology Unit, Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Mitchel A Cole
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - J Keith Joung
- Molecular Pathology Unit, Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Daniel E Bauer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, USA. .,Harvard Stem Cell Institute, Cambridge, MA, USA.
| | - Luca Pinello
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Molecular Pathology Unit, Center for Cancer Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA. .,Department of Pathology, Harvard Medical School, Boston, MA, USA.
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9
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Abstract
Motivation Unique molecular identifiers (UMIs) are added to DNA fragments before PCR amplification to discriminate between alleles arising from the same genomic locus and sequencing reads produced by PCR amplification. While computational methods have been developed to take into account UMI information in genome-wide and single-cell sequencing studies, they are not designed for modern amplicon-based sequencing experiments, especially in cases of high allelic diversity. Importantly, no guidelines are provided for the design of optimal UMI length for amplicon-based sequencing experiments. Results Based on the total number of DNA fragments and the distribution of allele frequencies, we present a model for the determination of the minimum UMI length required to prevent UMI collisions and reduce allelic distortion. We also introduce a user-friendly software tool called AmpUMI to assist in the design and the analysis of UMI-based amplicon sequencing studies. AmpUMI provides quality control metrics on frequency and quality of UMIs, and trims and deduplicates amplicon sequences with user specified parameters for use in downstream analysis. Availability and implementation AmpUMI is open-source and freely available at http://github.com/pinellolab/AmpUMI.
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Affiliation(s)
- Kendell Clement
- Molecular Pathology Unit and Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rick Farouni
- Molecular Pathology Unit and Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Luca Pinello
- Molecular Pathology Unit and Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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10
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11
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Baskin E, Farouni R, Mathé EA. ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data. Bioinformatics 2017; 33:740-742. [PMID: 28011773 PMCID: PMC5408819 DOI: 10.1093/bioinformatics/btw688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/26/2016] [Indexed: 11/13/2022] Open
Abstract
Summary Regulatory elements regulate gene transcription, and their location and accessibility is cell-type specific, particularly for enhancers. Mapping and comparing chromatin accessibility between different cell types may identify mechanisms involved in cellular development and disease progression. To streamline and simplify differential analysis of regulatory elements genome-wide using chromatin accessibility data, such as DNase-seq, ATAC-seq, we developed ALTRE ( ALT ered R egulatory E lements), an R package and associated R Shiny web app. ALTRE makes such analysis accessible to a wide range of users-from novice to practiced computational biologists. Availability and Implementation https://github.com/Mathelab/ALTRE. Contact ewy.mathe@osumc.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Elizabeth Baskin
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Rick Farouni
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Ewy A Mathé
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
- To whom correspondence should be addressed.
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