1
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Janssen P, Kliesmete Z, Vieth B, Adiconis X, Simmons S, Marshall J, McCabe C, Heyn H, Levin JZ, Enard W, Hellmann I. The effect of background noise and its removal on the analysis of single-cell expression data. Genome Biol 2023; 24:140. [PMID: 37337297 DOI: 10.1186/s13059-023-02978-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 05/26/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND In droplet-based single-cell and single-nucleus RNA-seq experiments, not all reads associated with one cell barcode originate from the encapsulated cell. Such background noise is attributed to spillage from cell-free ambient RNA or barcode swapping events. RESULTS Here, we characterize this background noise exemplified by three scRNA-seq and two snRNA-seq replicates of mouse kidneys. For each experiment, cells from two mouse subspecies are pooled, allowing to identify cross-genotype contaminating molecules and thus profile background noise. Background noise is highly variable across replicates and cells, making up on average 3-35% of the total counts (UMIs) per cell and we find that noise levels are directly proportional to the specificity and detectability of marker genes. In search of the source of background noise, we find multiple lines of evidence that the majority of background molecules originates from ambient RNA. Finally, we use our genotype-based estimates to evaluate the performance of three methods (CellBender, DecontX, SoupX) that are designed to quantify and remove background noise. We find that CellBender provides the most precise estimates of background noise levels and also yields the highest improvement for marker gene detection. By contrast, clustering and classification of cells are fairly robust towards background noise and only small improvements can be achieved by background removal that may come at the cost of distortions in fine structure. CONCLUSIONS Our findings help to better understand the extent, sources and impact of background noise in single-cell experiments and provide guidance on how to deal with it.
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Affiliation(s)
- Philipp Janssen
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Munich, Germany
| | - Zane Kliesmete
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Munich, Germany
| | - Beate Vieth
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Munich, Germany
| | - Xian Adiconis
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, USA
| | - Sean Simmons
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, USA
| | | | - Cristin McCabe
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, USA
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Joshua Z Levin
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, USA
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Munich, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Munich, Germany.
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2
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Kliesmete Z, Wange LE, Vieth B, Esgleas M, Radmer J, Hülsmann M, Geuder J, Richter D, Ohnuki M, Götz M, Hellmann I, Enard W. Regulatory and coding sequences of TRNP1 co-evolve with brain size and cortical folding in mammals. eLife 2023; 12:83593. [PMID: 36947129 PMCID: PMC10032658 DOI: 10.7554/elife.83593] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/01/2023] [Indexed: 03/23/2023] Open
Abstract
Brain size and cortical folding have increased and decreased recurrently during mammalian evolution. Identifying genetic elements whose sequence or functional properties co-evolve with these traits can provide unique information on evolutionary and developmental mechanisms. A good candidate for such a comparative approach is TRNP1, as it controls proliferation of neural progenitors in mice and ferrets. Here, we investigate the contribution of both regulatory and coding sequences of TRNP1 to brain size and cortical folding in over 30 mammals. We find that the rate of TRNP1 protein evolution (ω) significantly correlates with brain size, slightly less with cortical folding and much less with body size. This brain correlation is stronger than for >95% of random control proteins. This co-evolution is likely affecting TRNP1 activity, as we find that TRNP1 from species with larger brains and more cortical folding induce higher proliferation rates in neural stem cells. Furthermore, we compare the activity of putative cis-regulatory elements (CREs) of TRNP1 in a massively parallel reporter assay and identify one CRE that likely co-evolves with cortical folding in Old World monkeys and apes. Our analyses indicate that coding and regulatory changes that increased TRNP1 activity were positively selected either as a cause or a consequence of increases in brain size and cortical folding. They also provide an example how phylogenetic approaches can inform biological mechanisms, especially when combined with molecular phenotypes across several species.
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Affiliation(s)
- Zane Kliesmete
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Lucas Esteban Wange
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Beate Vieth
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Miriam Esgleas
- Physiological Genomics, BioMedical Center - BMC, Ludwig-Maximilians-Universität, Munich, Germany
- Institute for Stem Cell Research, Helmholtz Zentrum München, Germany Research Center for Environmental Health, Munich, Germany
| | - Jessica Radmer
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Matthias Hülsmann
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
- Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Johanna Geuder
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Daniel Richter
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Mari Ohnuki
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Magdelena Götz
- Physiological Genomics, BioMedical Center - BMC, Ludwig-Maximilians-Universität, Munich, Germany
- Institute for Stem Cell Research, Helmholtz Zentrum München, Germany Research Center for Environmental Health, Munich, Germany
- SYNERGY, Excellence Cluster of Systems Neurology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
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3
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Janjic A, Wange LE, Bagnoli JW, Geuder J, Nguyen P, Richter D, Vieth B, Vick B, Jeremias I, Ziegenhain C, Hellmann I, Enard W. Prime-seq, efficient and powerful bulk RNA sequencing. Genome Biol 2022; 23:88. [PMID: 35361256 PMCID: PMC8969310 DOI: 10.1186/s13059-022-02660-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/23/2022] [Indexed: 12/21/2022] Open
Abstract
Cost-efficient library generation by early barcoding has been central in propelling single-cell RNA sequencing. Here, we optimize and validate prime-seq, an early barcoding bulk RNA-seq method. We show that it performs equivalently to TruSeq, a standard bulk RNA-seq method, but is fourfold more cost-efficient due to almost 50-fold cheaper library costs. We also validate a direct RNA isolation step, show that intronic reads are derived from RNA, and compare cost-efficiencies of available protocols. We conclude that prime-seq is currently one of the best options to set up an early barcoding bulk RNA-seq protocol from which many labs would profit.
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Affiliation(s)
- Aleksandar Janjic
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany.,Graduate School of Systemic Neurosciences, Faculty of Biology, Ludwig-Maximilians University, Martinsried, Germany
| | - Lucas E Wange
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Johannes W Bagnoli
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Johanna Geuder
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Phong Nguyen
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Daniel Richter
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Beate Vieth
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Binje Vick
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ines Hellmann
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Wolfgang Enard
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany.
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4
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Zeller C, Richter D, Jurinovic V, Valtierra-Gutiérrez IA, Jayavelu AK, Mann M, Bagnoli JW, Hellmann I, Herold T, Enard W, Vick B, Jeremias I. Adverse stem cell clones within a single patient's tumor predict clinical outcome in AML patients. J Hematol Oncol 2022; 15:25. [PMID: 35279202 PMCID: PMC8917742 DOI: 10.1186/s13045-022-01232-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/27/2022] [Indexed: 11/28/2022] Open
Abstract
Acute myeloid leukemia (AML) patients suffer dismal prognosis upon treatment resistance. To study functional heterogeneity of resistance, we generated serially transplantable patient-derived xenograft (PDX) models from one patient with AML and twelve clones thereof, each derived from a single stem cell, as proven by genetic barcoding. Transcriptome and exome sequencing segregated clones according to their origin from relapse one or two. Undetectable for sequencing, multiplex fluorochrome-guided competitive in vivo treatment trials identified a subset of relapse two clones as uniquely resistant to cytarabine treatment. Transcriptional and proteomic profiles obtained from resistant PDX clones and refractory AML patients defined a 16-gene score that was predictive of clinical outcome in a large independent patient cohort. Thus, we identified novel genes related to cytarabine resistance and provide proof of concept that intra-tumor heterogeneity reflects inter-tumor heterogeneity in AML.
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Affiliation(s)
- Christina Zeller
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
| | - Daniel Richter
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians University (LMU), Munich, Germany
| | - Vindi Jurinovic
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany.,Institute for Medical Information Processing, Biometry and Epidemiology, LMU, Munich, Germany
| | - Ilse A Valtierra-Gutiérrez
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians University (LMU), Munich, Germany
| | - Ashok Kumar Jayavelu
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Johannes W Bagnoli
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians University (LMU), Munich, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians University (LMU), Munich, Germany
| | - Tobias Herold
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany.,Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians University (LMU), Munich, Germany
| | - Binje Vick
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany. .,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany. .,Department of Pediatrics, Dr. von Hauner Children´s Hospital, University Hospital, LMU, Munich, Germany.
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5
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Kälin R, Cai L, Li Y, Hellmann I, Glass R. TAMI-36. TAMEP ARE BRAIN TUMOR PARENCHYMAL CELLS CONTROLLING NEOPLASTIC ANGIOGENESIS AND PROGRESSION. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Aggressive brain tumors like glioblastoma depend on support by their local environment and subsets of tumor-parenchymal cells may promote specific phases of disease-progression. We investigated the glioblastoma microenvironment with transgenic lineage-tracing models, intravital imaging, single-cell transcriptomics, immunofluorescence analysis as well as histopathology and characterized a previously unacknowledged population of tumor-associated cells with a myeloid-like expression profile (TAMEP) that transiently appeared during glioblastoma growth. TAMEP of mice and humans were identified with specific markers. Strikingly, TAMEP did not derive from microglia or peripheral monocytes but were generated by a fraction of CNS-resident, SOX2-positive progenitors. Abrogation of this progenitor cell-population, by conditional Sox2-knockout, drastically reduced glioblastoma-vascularization and -size. TAMEP manipulation profoundly altered vessel function and strongly attenuated the blood-tumor barrier. Hence, our data indicate TAMEP and their progenitors as new targets for glioblastoma therapy.
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Affiliation(s)
| | - Linzhi Cai
- University Clinics Munich, Munich, Germany
| | - Yuping Li
- University Clinics Munich, Munich, Germany
| | - Ines Hellmann
- Ludwig Maximilians University Munich, Munich, Germany
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6
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Kälin R, Cai L, Li Y, von Baumgarten L, Schulz C, Hellmann I, Glass R. OTME-1. TAMEP are brain tumor parenchymal cells controlling neoplastic angiogenesis and progression. Neurooncol Adv 2021. [PMCID: PMC8255436 DOI: 10.1093/noajnl/vdab070.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Aggressive brain tumors like glioblastoma depend on support by their local environment and subsets of tumor parenchymal cells may promote specific phases of disease progression. We investigated the glioblastoma microenvironment with transgenic lineage-tracing models, intravital imaging, single-cell transcriptomics, immunofluorescence analysis as well as histopathology and characterized a previously unacknowledged population of tumor-associated cells with a myeloid-like expression profile (TAMEP) that transiently appeared during glioblastoma growth. TAMEP of mice and humans were identified with specific markers. Notably, TAMEP did not derive from microglia or peripheral monocytes but were generated by a fraction of CNS-resident, SOX2-positive progenitors. Abrogation of this progenitor cell population, by conditional Sox2-knockout, drastically reduced glioblastoma vascularization and size. Hence, TAMEP emerge as a tumor parenchymal component with a strong impact on glioblastoma progression.
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Affiliation(s)
- Roland Kälin
- University Clinics Munich, Munich, Bavaria, Germany
| | - Linzhi Cai
- University Clinics Munich, Munich, Bavaria, Germany
| | - Yuping Li
- University Clinics Munich, Munich, Bavaria, Germany
| | | | | | - Ines Hellmann
- Ludwig Maximilians University, Munich, Munich, Bavaria, Germany
| | - Rainer Glass
- University Clinics Munich, Munich, Bavaria, Germany
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7
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Kälin R, Cai L, Zhao D, Zhang H, Zhang W, Kirchleitner S, Siller S, Enard W, Schiemann M, Andrä I, Giachino C, Taylor V, Synowitz M, Tonn J, Baumgarten LV, Hellmann I, Glass R. Local progenitor cells shape the neoplastic vasculature and promote brain tumor growth. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.e14044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e14044 Background: Aggressive brain tumors like glioblastoma depend on support by their local environment. While the role of tumor-associated myeloid cells on glioblastoma progression is well-documented, we have only partial knowledge of the pathological impact of glioblastoma -parenchymal progenitor cells. Methods: We investigated the glioblastoma microenvironment with transgenic lineage-tracing models ( nestin-creER2, R26-tdTomato and sox2-creER2,R26-tdTomato), intravital imaging, single-cell transcriptomics, immunofluorescence and flow-cytometry as well as histopathology and characterized a previously unknown tumor-associated progenitor cell. In functional experiments, we studied the knockout of the transcription factor SOX2 in these tumor-associated cells. Results: Lineage-traced cells from mouse glioblastoma were obtained by flow-cytometry and single cell transcriptomes compared to established gene expression data from brain tumor parenchymal cells. The traced tumor-associated cells had a transcriptomic profile largely resembling myeloid cells and expressed microglia-/macrophage-markers on the protein-level. However, transgenic models and bone-marrow chimera revealed that the traced cells were clearly distinct from microglia or macrophages. The traced tumor associated cells with a myeloid expression profile derived from a SOX2-dependent progenitor cell. Consequently, conditional Sox2-knockout ablated the entire myeloid-like cell population. Remarkably, this tumor-associated cell population had a large impact on disease-progression causing significant reduction of glioblastoma –vascularization to 53%, changing vascular function and leading to a decrease in tumor volume to 42% as compared to controls. The myeloid-like progenitor cells were identified in human brain tumors by immunofluorescence and in scRNA-seq data. Conclusions: We identified a previously unacknowledged population of tumor-associated progenitor cells with a myeloid-like expression profile that transiently appeared during glioblastoma growth. These progenitors have strong impact on glioblastoma progression and point towards a new and promising therapeutic target in order to support anti-angiogenic regimen in glioblastoma.
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Affiliation(s)
- Roland Kälin
- Department of Neurosurgery, University of Munich (LMU), Munich, Germany
| | - Linzhi Cai
- Department of Neurosurgery, University of Munich (LMU), Munich, Germany
| | - Dongxu Zhao
- Department of Neurosurgery, University of Munich (LMU), Munich, Germany
| | - Huabin Zhang
- Department of Neurosurgery, University of Munich (LMU), Munich, Germany
| | - Wenlong Zhang
- Department of Neurosurgery, University of Munich (LMU), Munich, Germany
| | | | - Sebastian Siller
- Department of Neurosurgery, University of Munich (LMU), Munich, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, LMU Munich, Munich, Germany
| | | | - Immanuel Andrä
- Institute for Medical Microbiology, TU Munich, Munich, Germany
| | - Claudio Giachino
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Verdon Taylor
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Michael Synowitz
- Department of Neurosurgery, University Hospital Center Schleswig Holstein, Kiel, Germany
| | - Joerg Tonn
- Department of Neurosurgery, University of Munich (LMU), Munich, Germany
| | | | - Ines Hellmann
- Anthropology and Human Genomics, LMU Munich, Munich, Germany
| | - Rainer Glass
- Department of Neurosurgery, University of Munich (LMU), Munich, Germany
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8
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Kälin RE, Cai L, Li Y, Zhao D, Zhang H, Cheng J, Zhang W, Wu Y, Eisenhut K, Janssen P, Schmitt L, Enard W, Michels F, Flüh C, Hou M, Kirchleitner SV, Siller S, Schiemann M, Andrä I, Montanez E, Giachino C, Taylor V, Synowitz M, Tonn JC, von Baumgarten L, Schulz C, Hellmann I, Glass R. TAMEP are brain tumor parenchymal cells controlling neoplastic angiogenesis and progression. Cell Syst 2021; 12:248-262.e7. [PMID: 33592194 DOI: 10.1016/j.cels.2021.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 04/07/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
Aggressive brain tumors like glioblastoma depend on support by their local environment and subsets of tumor parenchymal cells may promote specific phases of disease progression. We investigated the glioblastoma microenvironment with transgenic lineage-tracing models, intravital imaging, single-cell transcriptomics, immunofluorescence analysis as well as histopathology and characterized a previously unacknowledged population of tumor-associated cells with a myeloid-like expression profile (TAMEP) that transiently appeared during glioblastoma growth. TAMEP of mice and humans were identified with specific markers. Notably, TAMEP did not derive from microglia or peripheral monocytes but were generated by a fraction of CNS-resident, SOX2-positive progenitors. Abrogation of this progenitor cell population, by conditional Sox2-knockout, drastically reduced glioblastoma vascularization and size. Hence, TAMEP emerge as a tumor parenchymal component with a strong impact on glioblastoma progression.
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Affiliation(s)
- Roland E Kälin
- Neurosurgical Research, University Hospital, LMU Munich, 81377 Munich, Germany; Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Linzhi Cai
- Neurosurgical Research, University Hospital, LMU Munich, 81377 Munich, Germany; Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Yuping Li
- Neurosurgical Research, University Hospital, LMU Munich, 81377 Munich, Germany; Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Dongxu Zhao
- Neurosurgical Research, University Hospital, LMU Munich, 81377 Munich, Germany; Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Huabin Zhang
- Neurosurgical Research, University Hospital, LMU Munich, 81377 Munich, Germany; Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Jiying Cheng
- Neurosurgical Research, University Hospital, LMU Munich, 81377 Munich, Germany; Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Wenlong Zhang
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, 81377 Munich, Germany; Department of Neurology, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Yingxi Wu
- Neurosurgical Research, University Hospital, LMU Munich, 81377 Munich, Germany; Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Katharina Eisenhut
- Neurosurgical Research, University Hospital, LMU Munich, 81377 Munich, Germany; Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Philipp Janssen
- Anthropology and Human Genomics, Department Biology II, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Lukas Schmitt
- Anthropology and Human Genomics, Department Biology II, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Department Biology II, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Friederike Michels
- Department of Neurosurgery, University Hospital Center Schleswig Holstein, 24105 Kiel, Germany
| | - Charlotte Flüh
- Department of Neurosurgery, University Hospital Center Schleswig Holstein, 24105 Kiel, Germany
| | - Mengzhuo Hou
- Neurosurgical Research, University Hospital, LMU Munich, 81377 Munich, Germany; Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, 81377 Munich, Germany
| | | | - Sebastian Siller
- Department of Neurosurgery, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Matthias Schiemann
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, 81675 München, Germany
| | - Immanuel Andrä
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, 81675 München, Germany
| | - Eloi Montanez
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, 81377 Munich, Germany; Department of Physiological Sciences, Faculty of Medicine and Health Sciences, University of Barcelona and Bellvitge Biomedical Research Institute (IDIBELL), 08907 Hospitalet de Llobregat, Spain
| | - Claudio Giachino
- Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Verdon Taylor
- Department of Biomedicine, University of Basel, 4058 Basel, Switzerland
| | - Michael Synowitz
- Department of Neurosurgery, University Hospital Center Schleswig Holstein, 24105 Kiel, Germany
| | - Jörg-Christian Tonn
- Department of Neurosurgery, University Hospital, LMU Munich, 81377 Munich, Germany; German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner Site Munich, 69120 Heidelberg, Germany
| | - Louisa von Baumgarten
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, 81377 Munich, Germany; Department of Neurology, University Hospital, LMU Munich, 81377 Munich, Germany; Department of Neurosurgery, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Christian Schulz
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, 81377 Munich, Germany; Medizinische Klinik und Poliklinik I, University Hospital, LMU Munich, 81377 Munich, Germany; German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 80333 Munich, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department Biology II, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Rainer Glass
- Neurosurgical Research, University Hospital, LMU Munich, 81377 Munich, Germany; Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, 81377 Munich, Germany; German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner Site Munich, 69120 Heidelberg, Germany.
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9
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Abstract
The recent rapid spread of single cell RNA sequencing (scRNA-seq) methods has created a large variety of experimental and computational pipelines for which best practices have not yet been established. Here, we use simulations based on five scRNA-seq library protocols in combination with nine realistic differential expression (DE) setups to systematically evaluate three mapping, four imputation, seven normalisation and four differential expression testing approaches resulting in ~3000 pipelines, allowing us to also assess interactions among pipeline steps. We find that choices of normalisation and library preparation protocols have the biggest impact on scRNA-seq analyses. Specifically, we find that library preparation determines the ability to detect symmetric expression differences, while normalisation dominates pipeline performance in asymmetric DE-setups. Finally, we illustrate the importance of informed choices by showing that a good scRNA-seq pipeline can have the same impact on detecting a biological signal as quadrupling the sample size.
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Affiliation(s)
- Beate Vieth
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Munich, Germany
| | - Swati Parekh
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 65, Stockholm, Sweden
| | - Wolfgang Enard
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Munich, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Munich, Germany.
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10
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Stöhlker U, Bleher M, Doll H, Dombrowski H, Harms W, Hellmann I, Luff R, Prommer B, Seifert S, Weiler F. THE GERMAN DOSE RATE MONITORING NETWORK AND IMPLEMENTED DATA HARMONIZATION TECHNIQUES. Radiat Prot Dosimetry 2019; 183:404-416. [PMID: 30272224 PMCID: PMC6596441 DOI: 10.1093/rpd/ncy154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 07/20/2018] [Accepted: 08/07/2018] [Indexed: 06/08/2023]
Abstract
Environmental radiation monitoring networks have been established in Europe and world-wide for the purpose of protecting population and environment against ionizing radiation. Some of these networks had been established during the cold war period and were improved after the Chernobyl accident in 1986. Today, the German Federal Office for Radiation Protection (BfS) operates an early warning network with roughly 1800 ambient dose equivalent rate (ADER) stations equally distributed over the German territory. The hardware and software of all network components are developed in-house allowing the continuous optimization of all relevant components. A probe characterization and quality assurance and control program are in place. Operational and technical aspects of the network and data harmonization techniques are described. The latter allows for calculating of the terrestrial and net ADER combined with uncertainties mainly from site specific effects. Harmonized data are finally used as input to the German emergency management system and the European radiological data exchange platform.
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Affiliation(s)
- U Stöhlker
- Bundesamt für Strahlenschutz (Federal Office for Radiation Protection), Willy-Brandt-Straße 5, Salzgitter, Germany
| | - M Bleher
- Bundesamt für Strahlenschutz (Federal Office for Radiation Protection), Willy-Brandt-Straße 5, Salzgitter, Germany
| | - H Doll
- Bundesamt für Strahlenschutz (Federal Office for Radiation Protection), Willy-Brandt-Straße 5, Salzgitter, Germany
| | - H Dombrowski
- Physikalisch-Technische Bundesanstalt, Bundesallee 100, Braunschweig, Germany
| | - W Harms
- Bundesamt für Strahlenschutz (Federal Office for Radiation Protection), Willy-Brandt-Straße 5, Salzgitter, Germany
| | - I Hellmann
- Bundesamt für Strahlenschutz (Federal Office for Radiation Protection), Willy-Brandt-Straße 5, Salzgitter, Germany
| | - R Luff
- Bundesamt für Strahlenschutz (Federal Office for Radiation Protection), Willy-Brandt-Straße 5, Salzgitter, Germany
| | - B Prommer
- Bundesamt für Strahlenschutz (Federal Office for Radiation Protection), Willy-Brandt-Straße 5, Salzgitter, Germany
| | - S Seifert
- Bundesamt für Strahlenschutz (Federal Office for Radiation Protection), Willy-Brandt-Straße 5, Salzgitter, Germany
| | - F Weiler
- Bundesamt für Strahlenschutz (Federal Office for Radiation Protection), Willy-Brandt-Straße 5, Salzgitter, Germany
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11
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Bagnoli JW, Ziegenhain C, Janjic A, Wange LE, Vieth B, Parekh S, Geuder J, Hellmann I, Enard W. Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq. Nat Commun 2018; 9:2937. [PMID: 30050112 PMCID: PMC6062574 DOI: 10.1038/s41467-018-05347-6] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 06/26/2018] [Indexed: 01/09/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a central genome-wide method to characterize cellular identities and processes. Consequently, improving its sensitivity, flexibility, and cost-efficiency can advance many research questions. Among the flexible plate-based methods, single-cell RNA barcoding and sequencing (SCRB-seq) is highly sensitive and efficient. Here, we systematically evaluate experimental conditions of this protocol and find that adding polyethylene glycol considerably increases sensitivity by enhancing cDNA synthesis. Furthermore, using Terra polymerase increases efficiency due to a more even cDNA amplification that requires less sequencing of libraries. We combined these and other improvements to develop a scRNA-seq library protocol we call molecular crowding SCRB-seq (mcSCRB-seq), which we show to be one of the most sensitive, efficient, and flexible scRNA-seq methods to date.
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Affiliation(s)
- Johannes W Bagnoli
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
| | - Christoph Ziegenhain
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
- Department of Cell & Molecular Biology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Aleksandar Janjic
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
| | - Lucas E Wange
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
| | - Beate Vieth
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
| | - Swati Parekh
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany
| | - Johanna Geuder
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
| | - Ines Hellmann
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany
| | - Wolfgang Enard
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University, Großhaderner Straße 2, 82152, Martinsried, Germany.
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12
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Vieth B, Ziegenhain C, Parekh S, Enard W, Hellmann I. powsimR: power analysis for bulk and single cell RNA-seq experiments. Bioinformatics 2018; 33:3486-3488. [PMID: 29036287 DOI: 10.1093/bioinformatics/btx435] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/04/2017] [Indexed: 11/14/2022] Open
Abstract
Summary Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes in RNA-seq data. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses. Availability and implementation The R package and associated tutorial are freely available at https://github.com/bvieth/powsimR. Contact vieth@bio.lmu.de or hellmann@bio.lmu.de. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Beate Vieth
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Munich, Germany
| | - Christoph Ziegenhain
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Munich, Germany
| | - Swati Parekh
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Munich, Germany
| | - Wolfgang Enard
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Munich, Germany
| | - Ines Hellmann
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, 82152 Munich, Germany
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13
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Abstract
Single-cell RNA sequencing (scRNA-seq) is currently transforming our understanding of biology, as it is a powerful tool to resolve cellular heterogeneity and molecular networks. Over 50 protocols have been developed in recent years and also data processing and analyzes tools are evolving fast. Here, we review the basic principles underlying the different experimental protocols and how to benchmark them. We also review and compare the essential methods to process scRNA-seq data from mapping, filtering, normalization and batch corrections to basic differential expression analysis. We hope that this helps to choose appropriate experimental and computational methods for the research question at hand.
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Affiliation(s)
- Christoph Ziegenhain
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
| | - Beate Vieth
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
| | - Swati Parekh
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, Martinsried, Germany
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14
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Parekh S, Ziegenhain C, Vieth B, Enard W, Hellmann I. zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs. Gigascience 2018; 7:5005022. [PMID: 29846586 PMCID: PMC6007394 DOI: 10.1093/gigascience/giy059] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 03/16/2018] [Accepted: 05/15/2018] [Indexed: 11/21/2022] Open
Abstract
Background Single-cell RNA-sequencing (scRNA-seq) experiments typically analyze hundreds or thousands of cells after amplification of the cDNA. The high throughput is made possible by the early introduction of sample-specific bar codes (BCs), and the amplification bias is alleviated by unique molecular identifiers (UMIs). Thus, the ideal analysis pipeline for scRNA-seq data needs to efficiently tabulate reads according to both BC and UMI. Findings zUMIs is a pipeline that can handle both known and random BCs and also efficiently collapse UMIs, either just for exon mapping reads or for both exon and intron mapping reads. If BC annotation is missing, zUMIs can accurately detect intact cells from the distribution of sequencing reads. Another unique feature of zUMIs is the adaptive downsampling function that facilitates dealing with hugely varying library sizes but also allows the user to evaluate whether the library has been sequenced to saturation. To illustrate the utility of zUMIs, we analyzed a single-nucleus RNA-seq dataset and show that more than 35% of all reads map to introns. Also, we show that these intronic reads are informative about expression levels, significantly increasing the number of detected genes and improving the cluster resolution. Conclusions zUMIs flexibility makes if possible to accommodate data generated with any of the major scRNA-seq protocols that use BCs and UMIs and is the most feature-rich, fast, and user-friendly pipeline to process such scRNA-seq data.
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Affiliation(s)
- Swati Parekh
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Grosshaderner Str. 2, 82152 Martinsried, Germany
| | - Christoph Ziegenhain
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Grosshaderner Str. 2, 82152 Martinsried, Germany
| | - Beate Vieth
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Grosshaderner Str. 2, 82152 Martinsried, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Grosshaderner Str. 2, 82152 Martinsried, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department of Biology II, Ludwig-Maximilians University, Grosshaderner Str. 2, 82152 Martinsried, Germany
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15
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Greif PA, Hartmann L, Vosberg S, Stief SM, Mattes R, Hellmann I, Metzeler KH, Herold T, Bamopoulos SA, Kerbs P, Jurinovic V, Schumacher D, Pastore F, Bräundl K, Zellmeier E, Ksienzyk B, Konstandin NP, Schneider S, Graf A, Krebs S, Blum H, Neumann M, Baldus CD, Bohlander SK, Wolf S, Görlich D, Berdel WE, Wörmann BJ, Hiddemann W, Spiekermann K. Evolution of Cytogenetically Normal Acute Myeloid Leukemia During Therapy and Relapse: An Exome Sequencing Study of 50 Patients. Clin Cancer Res 2018; 24:1716-1726. [PMID: 29330206 DOI: 10.1158/1078-0432.ccr-17-2344] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/03/2017] [Accepted: 01/08/2018] [Indexed: 11/16/2022]
Abstract
Purpose: To study mechanisms of therapy resistance and disease progression, we analyzed the evolution of cytogenetically normal acute myeloid leukemia (CN-AML) based on somatic alterations.Experimental Design: We performed exome sequencing of matched diagnosis, remission, and relapse samples from 50 CN-AML patients treated with intensive chemotherapy. Mutation patterns were correlated with clinical parameters.Results: Evolutionary patterns correlated with clinical outcome. Gain of mutations was associated with late relapse. Alterations of epigenetic regulators were frequently gained at relapse with recurring alterations of KDM6A constituting a mechanism of cytarabine resistance. Low KDM6A expression correlated with adverse clinical outcome, particularly in male patients. At complete remission, persistent mutations representing preleukemic lesions were observed in 48% of patients. The persistence of DNMT3A mutations correlated with shorter time to relapse.Conclusions: Chemotherapy resistance might be acquired through gain of mutations. Insights into the evolution during therapy and disease progression lay the foundation for tailored approaches to treat or prevent relapse of CN-AML. Clin Cancer Res; 24(7); 1716-26. ©2018 AACR.
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Affiliation(s)
- Philipp A Greif
- Department of Medicine III, University Hospital, LMU Munich, München, Germany. .,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Luise Hartmann
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Vosberg
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sophie M Stief
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Raphael Mattes
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department Biology II, LMU Munich, Martinsried, Germany
| | - Klaus H Metzeler
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tobias Herold
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Paul Kerbs
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vindi Jurinovic
- Institute for Medical Information Procesing, Biometry and Epidemiology (IBE), LMU Munich, München, Germany
| | - Daniela Schumacher
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Friederike Pastore
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kathrin Bräundl
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Evelyn Zellmeier
- Department of Medicine III, University Hospital, LMU Munich, München, Germany
| | - Bianka Ksienzyk
- Department of Medicine III, University Hospital, LMU Munich, München, Germany
| | - Nikola P Konstandin
- Department of Medicine III, University Hospital, LMU Munich, München, Germany
| | - Stephanie Schneider
- Department of Medicine III, University Hospital, LMU Munich, München, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, München, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, München, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, München, Germany
| | - Martin Neumann
- German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Divison of Hematology and Oncology, Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, and Campus Virchow, Berlin, Germany
| | - Claudia D Baldus
- German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Divison of Hematology and Oncology, Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, and Campus Virchow, Berlin, Germany
| | - Stefan K Bohlander
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand
| | - Stephan Wolf
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dennis Görlich
- Institute of Biostatistics and Clinical Research, University of Münster, Münster, Germany
| | - Wolfgang E Berdel
- Department of Medicine A -Hematology, Oncology and Pneumology, University of Münster, Münster, Germany
| | - Bernhard J Wörmann
- Divison of Hematology and Oncology, Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, and Campus Virchow, Berlin, Germany
| | - Wolfgang Hiddemann
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Karsten Spiekermann
- Department of Medicine III, University Hospital, LMU Munich, München, Germany.,German Cancer Consortium (DKTK), and.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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16
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Ziegenhain C, Vieth B, Parekh S, Reinius B, Guillaumet-Adkins A, Smets M, Leonhardt H, Heyn H, Hellmann I, Enard W. Comparative Analysis of Single-Cell RNA Sequencing Methods. Mol Cell 2017; 65:631-643.e4. [PMID: 28212749 DOI: 10.1016/j.molcel.2017.01.023] [Citation(s) in RCA: 817] [Impact Index Per Article: 116.7] [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: 08/08/2016] [Revised: 12/01/2016] [Accepted: 01/17/2017] [Indexed: 02/06/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) offers new possibilities to address biological and medical questions. However, systematic comparisons of the performance of diverse scRNA-seq protocols are lacking. We generated data from 583 mouse embryonic stem cells to evaluate six prominent scRNA-seq methods: CEL-seq2, Drop-seq, MARS-seq, SCRB-seq, Smart-seq, and Smart-seq2. While Smart-seq2 detected the most genes per cell and across cells, CEL-seq2, Drop-seq, MARS-seq, and SCRB-seq quantified mRNA levels with less amplification noise due to the use of unique molecular identifiers (UMIs). Power simulations at different sequencing depths showed that Drop-seq is more cost-efficient for transcriptome quantification of large numbers of cells, while MARS-seq, SCRB-seq, and Smart-seq2 are more efficient when analyzing fewer cells. Our quantitative comparison offers the basis for an informed choice among six prominent scRNA-seq methods, and it provides a framework for benchmarking further improvements of scRNA-seq protocols.
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Affiliation(s)
- Christoph Ziegenhain
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Beate Vieth
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Swati Parekh
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Björn Reinius
- Ludwig Institute for Cancer Research, Box 240, 171 77 Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Amy Guillaumet-Adkins
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Martha Smets
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Ines Hellmann
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Wolfgang Enard
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Straße 2, 82152 Martinsried, Germany.
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17
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Ludwig AK, Zhang P, Hastert FD, Meyer S, Rausch C, Herce HD, Müller U, Lehmkuhl A, Hellmann I, Trummer C, Storm C, Leonhardt H, Cardoso MC. Binding of MBD proteins to DNA blocks Tet1 function thereby modulating transcriptional noise. Nucleic Acids Res 2017; 45:2438-2457. [PMID: 27923996 PMCID: PMC5389475 DOI: 10.1093/nar/gkw1197] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [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: 06/16/2016] [Accepted: 11/20/2016] [Indexed: 12/18/2022] Open
Abstract
Aberrant DNA methylation is a hallmark of various human disorders, indicating that the spatial and temporal regulation of methylation readers and modifiers is imperative for development and differentiation. In particular, the cross-regulation between 5-methylcytosine binders (MBD) and modifiers (Tet) has not been investigated. Here, we show that binding of Mecp2 and Mbd2 to DNA protects 5-methylcytosine from Tet1-mediated oxidation. The mechanism is not based on competition for 5-methylcytosine binding but on Mecp2 and Mbd2 directly restricting Tet1 access to DNA. We demonstrate that the efficiency of this process depends on the number of bound MBDs per DNA molecule. Accordingly, we find 5-hydroxymethylcytosine enriched at heterochromatin of Mecp2-deficient neurons of a mouse model for Rett syndrome and Tet1-induced reexpression of silenced major satellite repeats. These data unveil fundamental regulatory mechanisms of Tet enzymes and their potential pathophysiological role in Rett syndrome. Importantly, it suggests that Mecp2 and Mbd2 have an essential physiological role as guardians of the epigenome.
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Affiliation(s)
- Anne K Ludwig
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Peng Zhang
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Florian D Hastert
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Stephanie Meyer
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Henry D Herce
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Udo Müller
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Anne Lehmkuhl
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Carina Trummer
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Christian Storm
- Chemical Plant Ecology, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Heinrich Leonhardt
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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18
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Zhang P, Ludwig AK, Hastert FD, Rausch C, Lehmkuhl A, Hellmann I, Smets M, Leonhardt H, Cardoso MC. L1 retrotransposition is activated by Ten-eleven-translocation protein 1 and repressed by methyl-CpG binding proteins. Nucleus 2017; 8:548-562. [PMID: 28524723 PMCID: PMC5703239 DOI: 10.1080/19491034.2017.1330238] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
One of the major functions of DNA methylation is the repression of transposable elements, such as the long-interspersed nuclear element 1 (L1). The underlying mechanism(s), however, are unclear. Here, we addressed how retrotransposon activation and mobilization are regulated by methyl-cytosine modifying ten-eleven-translocation (Tet) proteins and how this is modulated by methyl-CpG binding domain (MBD) proteins. We show that Tet1 activates both, endogenous and engineered L1 retrotransposons. Furthermore, we found that Mecp2 and Mbd2 repress Tet1-mediated activation of L1 by preventing 5hmC formation at the L1 promoter. Finally, we demonstrate that the methyl-CpG binding domain, as well as the adjacent non-sequence specific DNA binding domain of Mecp2 are each sufficient to mediate repression of Tet1-induced L1 mobilization. Our study reveals a mechanism how L1 elements get activated in the absence of Mecp2 and suggests that Tet1 may contribute to Mecp2/Mbd2-deficiency phenotypes, such as the Rett syndrome. We propose that the balance between methylation "reader" and "eraser/writer" controls L1 retrotransposition.
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Affiliation(s)
- Peng Zhang
- a Department of Biology , Technical University Darmstadt , Darmstadt , Germany
| | - Anne K Ludwig
- a Department of Biology , Technical University Darmstadt , Darmstadt , Germany
| | - Florian D Hastert
- a Department of Biology , Technical University Darmstadt , Darmstadt , Germany
| | - Cathia Rausch
- a Department of Biology , Technical University Darmstadt , Darmstadt , Germany
| | - Anne Lehmkuhl
- a Department of Biology , Technical University Darmstadt , Darmstadt , Germany
| | - Ines Hellmann
- b Anthropology and Human Genomics, Department Biology II , LMU Munich , Germany
| | - Martha Smets
- c Human Biology and BioImaging, Department of Biology II , LMU Munich , Germany
| | - Heinrich Leonhardt
- c Human Biology and BioImaging, Department of Biology II , LMU Munich , Germany
| | - M Cristina Cardoso
- a Department of Biology , Technical University Darmstadt , Darmstadt , Germany
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19
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Bossew P, Cinelli G, Hernández-Ceballos M, Cernohlawek N, Gruber V, Dehandschutter B, Menneson F, Bleher M, Stöhlker U, Hellmann I, Weiler F, Tollefsen T, Tognoli PV, de Cort M. Estimating the terrestrial gamma dose rate by decomposition of the ambient dose equivalent rate. J Environ Radioact 2017; 166:296-308. [PMID: 26926960 DOI: 10.1016/j.jenvrad.2016.02.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/11/2016] [Accepted: 02/13/2016] [Indexed: 06/05/2023]
Abstract
An extensive network of dose rate monitoring stations continuously measures ambient dose rate across Europe, as part of the EURDEP system. Its purpose is early warning in radiological emergencies and documenting its temporal and spatial evolution. In normal conditions, when there is no contribution to the dose rate signal coming from fresh anthropogenic contamination, the data represent the radiation "background", i.e. the combined natural radiation and existing anthropogenic contamination (by global and Chernobyl fallout). These data are being stored, but have so far not been evaluated in depth, or used for any purpose. In the framework of the EU project 'European Atlas of Natural Radiation' the idea has emerged to exploit these data for generating a map of natural terrestrial gamma radiation. This component contributes to the total radiation exposure and knowing its geographical distribution can help establishing local 'radiation budgets'. A further use could be found in terrestrial dose rate as a proxy of the geogenic radon potential, as both quantities are related by partly the same source, namely uranium content of the ground. In this paper, we describe in detail the composition of the ambient dose equivalent rate as measured by the EURDEP monitors with respect to its physical nature and to its sources in the environment. We propose and compare methods to recover the terrestrial component from the gross signal. This requires detailed knowledge of detector response. We consider the probes used in the Austrian, Belgian and German dose rate networks, which are the respective national networks supplying data to EURDEP. It will be shown that although considerable progress has been made in understanding the dose rate signals, there is still space for improvement in terms of modelling and model parameters. An indispensable condition for success of the endeavour to establish a Europe-wide map of terrestrial dose rate background is progress in harmonising the European dose rate monitoring network.
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Affiliation(s)
- P Bossew
- German Federal Office for Radiation Protection (BfS), Berlin, Munich, Freiburg, Germany
| | - G Cinelli
- European Commission, DG Joint Research Centre (JRC), Institute for Transuranium Elements, Ispra, Italy
| | - M Hernández-Ceballos
- European Commission, DG Joint Research Centre (JRC), Institute for Transuranium Elements, Ispra, Italy
| | - N Cernohlawek
- Austrian Federal Ministry of Agriculture, Forestry, Environment and Water Management, Vienna, Austria
| | - V Gruber
- Austrian Agency for Health and Food Safety (AGES), Vienna and Linz, Austria
| | - B Dehandschutter
- Belgian Federal Agency for Nuclear Control (FANC), Brussels, Belgium
| | - F Menneson
- Belgian Federal Agency for Nuclear Control (FANC), Brussels, Belgium
| | - M Bleher
- German Federal Office for Radiation Protection (BfS), Berlin, Munich, Freiburg, Germany
| | - U Stöhlker
- German Federal Office for Radiation Protection (BfS), Berlin, Munich, Freiburg, Germany
| | - I Hellmann
- German Federal Office for Radiation Protection (BfS), Berlin, Munich, Freiburg, Germany
| | - F Weiler
- German Federal Office for Radiation Protection (BfS), Berlin, Munich, Freiburg, Germany
| | - T Tollefsen
- European Commission, DG Joint Research Centre (JRC), Institute for Transuranium Elements, Ispra, Italy
| | - P V Tognoli
- European Commission, DG Joint Research Centre (JRC), Institute for Transuranium Elements, Ispra, Italy
| | - M de Cort
- European Commission, DG Joint Research Centre (JRC), Institute for Transuranium Elements, Ispra, Italy
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20
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Parekh S, Ziegenhain C, Vieth B, Enard W, Hellmann I. The impact of amplification on differential expression analyses by RNA-seq. Sci Rep 2016; 6:25533. [PMID: 27156886 PMCID: PMC4860583 DOI: 10.1038/srep25533] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [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: 01/25/2016] [Accepted: 04/20/2016] [Indexed: 01/20/2023] Open
Abstract
Currently, quantitative RNA-seq methods are pushed to work with increasingly small starting amounts of RNA that require amplification. However, it is unclear how much noise or bias amplification introduces and how this affects precision and accuracy of RNA quantification. To assess the effects of amplification, reads that originated from the same RNA molecule (PCR-duplicates) need to be identified. Computationally, read duplicates are defined by their mapping position, which does not distinguish PCR- from natural duplicates and hence it is unclear how to treat duplicated reads. Here, we generate and analyse RNA-seq data sets prepared using three different protocols (Smart-Seq, TruSeq and UMI-seq). We find that a large fraction of computationally identified read duplicates are not PCR duplicates and can be explained by sampling and fragmentation bias. Consequently, the computational removal of duplicates does improve neither accuracy nor precision and can actually worsen the power and the False Discovery Rate (FDR) for differential gene expression. Even when duplicates are experimentally identified by unique molecular identifiers (UMIs), power and FDR are only mildly improved. However, the pooling of samples as made possible by the early barcoding of the UMI-protocol leads to an appreciable increase in the power to detect differentially expressed genes.
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Affiliation(s)
- Swati Parekh
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, 82152 Martinsried, Germany
| | - Christoph Ziegenhain
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, 82152 Martinsried, Germany
| | - Beate Vieth
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, 82152 Martinsried, Germany
| | - Wolfgang Enard
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, 82152 Martinsried, Germany
| | - Ines Hellmann
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians University, Großhaderner Str. 2, 82152 Martinsried, Germany
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21
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DeGiorgio M, Huber CD, Hubisz MJ, Hellmann I, Nielsen R. SweepFinder2: increased sensitivity, robustness and flexibility. Bioinformatics 2016; 32:1895-7. [PMID: 27153702 DOI: 10.1093/bioinformatics/btw051] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 01/19/2016] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED SweepFinder is a widely used program that implements a powerful likelihood-based method for detecting recent positive selection, or selective sweeps. Here, we present SweepFinder2, an extension of SweepFinder with increased sensitivity and robustness to the confounding effects of mutation rate variation and background selection. Moreover, SweepFinder2 has increased flexibility that enables the user to specify test sites, set the distance between test sites and utilize a recombination map. AVAILABILITY AND IMPLEMENTATION SweepFinder2 is a freely-available (www.personal.psu.edu/mxd60/sf2.html) software package that is written in C and can be run from a Unix command line. CONTACT mxd60@psu.edu.
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Affiliation(s)
- Michael DeGiorgio
- Department of Biology and Institute for CyberScience, Pennsylvania State University, University Park, PA, USA
| | - Christian D Huber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Melissa J Hubisz
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Ines Hellmann
- Department Biologie II, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany and
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, CA, USA
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22
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Huber CD, DeGiorgio M, Hellmann I, Nielsen R. Detecting recent selective sweeps while controlling for mutation rate and background selection. Mol Ecol 2015; 25:142-56. [PMID: 26290347 PMCID: PMC5082542 DOI: 10.1111/mec.13351] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/31/2015] [Accepted: 08/17/2015] [Indexed: 12/19/2022]
Abstract
A composite likelihood ratio test implemented in the program sweepfinder is a commonly used method for scanning a genome for recent selective sweeps. sweepfinder uses information on the spatial pattern (along the chromosome) of the site frequency spectrum around the selected locus. To avoid confounding effects of background selection and variation in the mutation process along the genome, the method is typically applied only to sites that are variable within species. However, the power to detect and localize selective sweeps can be greatly improved if invariable sites are also included in the analysis. In the spirit of a Hudson–Kreitman–Aguadé test, we suggest adding fixed differences relative to an out‐group to account for variation in mutation rate, thereby facilitating more robust and powerful analyses. We also develop a method for including background selection, modelled as a local reduction in the effective population size. Using simulations, we show that these advances lead to a gain in power while maintaining robustness to mutation rate variation. Furthermore, the new method also provides more precise localization of the causative mutation than methods using the spatial pattern of segregating sites alone.
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Affiliation(s)
- Christian D Huber
- Max F. Perutz Laboratory, University of Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, University of Veterinary Medicine, Vienna, Austria.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA, 90095-1606, USA
| | - Michael DeGiorgio
- Departments of Biology and Statistics, Pennsylvania State University, University Park, PA, USA.,Institute for CyberScience, Pennsylvania State University, University Park, PA, USA
| | - Ines Hellmann
- Department Biologie II, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Rasmus Nielsen
- Departments of Integrative Biology and Statistics, University of California, Berkeley, CA, USA
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23
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Abstract
Detecting positive selection in species with heterogeneous habitats and complex demography is notoriously difficult and prone to statistical biases. The model plant Arabidopsis thaliana exemplifies this problem: In spite of the large amounts of data, little evidence for classic selective sweeps has been found. Moreover, many aspects of the demography are unclear, which makes it hard to judge whether the few signals are indeed signs of selection, or false positives caused by demographic events. Here, we focus on Swedish A. thaliana and we find that the demography can be approximated as a two-population model. Careful analysis of the data shows that such a two island model is characterized by a very old split time that significantly predates the last glacial maximum followed by secondary contact with strong migration. We evaluate selection based on this demography and find that this secondary contact model strongly affects the power to detect sweeps. Moreover, it affects the power differently for northern Sweden (more false positives) as compared with southern Sweden (more false negatives). However, even when the demographic history is accounted for, sweep signals in northern Sweden are stronger than in southern Sweden, with little or no positional overlap. Further simulations including the complex demography and selection confirm that this is not compatible with global selection acting on both populations, and thus can be taken as evidence for local selection within subpopulations of Swedish A. thaliana. This study demonstrates the necessity of combining demographic analyses and sweep scans for the detection of selection, particularly when selection acts predominantly local.
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Affiliation(s)
- Christian D Huber
- Mathematics and BioSciences Group, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Joachim Hermisson
- Mathematics and BioSciences Group, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria Department of Mathematics, University of Vienna, Vienna, Austria
| | - Ines Hellmann
- Department of Human Genetics & Anthropology, LMU, Munich, Germany
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24
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Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PLF, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Pääbo S. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 2013; 505:43-9. [PMID: 24352235 PMCID: PMC4031459 DOI: 10.1038/nature12886] [Citation(s) in RCA: 1130] [Impact Index Per Article: 102.7] [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: 09/05/2013] [Accepted: 11/15/2013] [Indexed: 12/13/2022]
Abstract
We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.
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Affiliation(s)
- Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Fernando Racimo
- Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Flora Jay
- Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | - Sriram Sankararaman
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Susanna Sawyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Anja Heinze
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Gabriel Renaud
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Peter H Sudmant
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Heng Li
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Swapan Mallick
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Michael Dannemann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Qiaomei Fu
- 1] Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany [2] Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Martin Kircher
- 1] Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany [2] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Martin Kuhlwilm
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael Lachmann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Ongyerth
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael Siebauer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Christoph Theunert
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Arti Tandon
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Priya Moorjani
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joseph Pickrell
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - James C Mullikin
- Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Samuel H Vohr
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Ines Hellmann
- 1] Max F. Perutz Laboratories, Mathematics and Bioscience Group, Campus Vienna Biocenter 5, Vienna 1030, Austria [2] Ludwig-Maximilians-Universität München, Martinsried, 82152 Munich, Germany
| | | | - Hélène Blanche
- Fondation Jean Dausset, Centre d'Étude du Polymorphisme Humain (CEPH), 75010 Paris, France
| | - Howard Cann
- Fondation Jean Dausset, Centre d'Étude du Polymorphisme Humain (CEPH), 75010 Paris, France
| | - Jacob O Kitzman
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Evan E Eichler
- 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA [2] Howard Hughes Medical Institute, Seattle, Washington 98195, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Trygve E Bakken
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | | | - Michael V Shunkov
- Palaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Anatoli P Derevianko
- Palaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Bence Viola
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | - David Reich
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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25
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Long Q, Rabanal FA, Meng D, Huber CD, Farlow A, Platzer A, Zhang Q, Vilhjálmsson BJ, Korte A, Nizhynska V, Voronin V, Korte P, Sedman L, Mandáková T, Lysak MA, Seren Ü, Hellmann I, Nordborg M. Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat Genet 2013; 45:884-890. [PMID: 23793030 DOI: 10.1038/ng.2678] [Citation(s) in RCA: 264] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 05/31/2013] [Indexed: 12/16/2022]
Abstract
Despite advances in sequencing, the goal of obtaining a comprehensive view of genetic variation in populations is still far from reached. We sequenced 180 lines of A. thaliana from Sweden to obtain as complete a picture as possible of variation in a single region. Whereas simple polymorphisms in the unique portion of the genome are readily identified, other polymorphisms are not. The massive variation in genome size identified by flow cytometry seems largely to be due to 45S rDNA copy number variation, with lines from northern Sweden having particularly large numbers of copies. Strong selection is evident in the form of long-range linkage disequilibrium (LD), as well as in LD between nearby compensatory mutations. Many footprints of selective sweeps were found in lines from northern Sweden, and a massive global sweep was shown to have involved a 700-kb transposition.
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Affiliation(s)
- Quan Long
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | | | - Dazhe Meng
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | | | - Ashley Farlow
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Alexander Platzer
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Qingrun Zhang
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Bjarni J Vilhjálmsson
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Arthur Korte
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | | | - Viktor Voronin
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Pamela Korte
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Laura Sedman
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Terezie Mandáková
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Martin A Lysak
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ümit Seren
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Ines Hellmann
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.,Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
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26
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Ofran Y, Filanovsky K, Gafter-Gvili A, Vidal L, Aviv A, Gatt M, Silbershatz I, Herishanu Y, Arad A, Tadmor T, Dally N, Nemets A, Rouvio O, Ronson A, Herzog-Tzarfati K, Akria L, Braester A, Hellmann I, Yeganeh S, Nagler A, Leiba R, Mittelman M, Merkel D. P-287 Infectious events are much more prevalent following a seven compared to five days cycle of azacitidine regardless of patient's age. Leuk Res 2013. [DOI: 10.1016/s0145-2126(13)70334-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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27
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Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karakoç E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, André C, Atencia R, Mugisha L, Junhold J, Patterson N, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer DE, Mailund T, Schierup MH, Andrés AM, Kelso J, Pääbo S. The bonobo genome compared with the chimpanzee and human genomes. Nature 2012; 486:527-31. [PMID: 22722832 DOI: 10.1038/nature11128] [Citation(s) in RCA: 284] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 04/05/2012] [Indexed: 01/09/2023]
Abstract
Two African apes are the closest living relatives of humans: the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours, and for some of these traits they show more similarity with humans than with each other. Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other.
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Affiliation(s)
- Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
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Lohmueller KE, Albrechtsen A, Li Y, Kim SY, Korneliussen T, Vinckenbosch N, Tian G, Huerta-Sanchez E, Feder AF, Grarup N, Jørgensen T, Jiang T, Witte DR, Sandbæk A, Hellmann I, Lauritzen T, Hansen T, Pedersen O, Wang J, Nielsen R. Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genet 2011; 7:e1002326. [PMID: 22022285 PMCID: PMC3192825 DOI: 10.1371/journal.pgen.1002326] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 08/16/2011] [Indexed: 12/30/2022] Open
Abstract
A major question in evolutionary biology is how natural selection has shaped patterns of genetic variation across the human genome. Previous work has documented a reduction in genetic diversity in regions of the genome with low recombination rates. However, it is unclear whether other summaries of genetic variation, like allele frequencies, are also correlated with recombination rate and whether these correlations can be explained solely by negative selection against deleterious mutations or whether positive selection acting on favorable alleles is also required. Here we attempt to address these questions by analyzing three different genome-wide resequencing datasets from European individuals. We document several significant correlations between different genomic features. In particular, we find that average minor allele frequency and diversity are reduced in regions of low recombination and that human diversity, human-chimp divergence, and average minor allele frequency are reduced near genes. Population genetic simulations show that either positive natural selection acting on favorable mutations or negative natural selection acting against deleterious mutations can explain these correlations. However, models with strong positive selection on nonsynonymous mutations and little negative selection predict a stronger negative correlation between neutral diversity and nonsynonymous divergence than observed in the actual data, supporting the importance of negative, rather than positive, selection throughout the genome. Further, we show that the widespread presence of weakly deleterious alleles, rather than a small number of strongly positively selected mutations, is responsible for the correlation between neutral genetic diversity and recombination rate. This work suggests that natural selection has affected multiple aspects of linked neutral variation throughout the human genome and that positive selection is not required to explain these observations.
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Affiliation(s)
- Kirk E Lohmueller
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America.
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29
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Abstract
Mutation rate variation has the potential to bias evolutionary inference, particularly when rates become much higher than the mean. We first confirm prior work that inferred the existence of cryptic, site-specific rate variation on the basis of coincident polymorphisms—sites that are segregating in both humans and chimpanzees. Then we extend this observation to a longer evolutionary timescale by identifying sites of coincident substitutions using four species. From these data, we develop analytic theory to infer the variance and skewness of the distribution of mutation rates. Even excluding CpG dinucleotides, we find a relatively large coefficient of variation and positive skew, which suggests that, although most sites in the genome have mutation rates near the mean, the distribution contains a long right-hand tail with a small number of sites having high mutation rates. At least for primates, these quickly mutating sites are few enough that the infinite sites model in population genetics remains appropriate.
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30
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Abstract
Population genetics has evolved from a theory-driven field with little empirical data into a data-driven discipline in which genome-scale data sets test the limits of available models and computational analysis methods. In humans and a few model organisms, analyses of whole-genome sequence polymorphism data are currently under way. And in light of the falling costs of next-generation sequencing technologies, such studies will soon become common in many other organisms as well. Here, we assess the challenges to analyzing whole-genome sequence polymorphism data, and we discuss the potential of these data to yield new insights concerning population history and the genomic prevalence of natural selection.
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Affiliation(s)
- John E Pool
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720, USA
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31
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Xia Q, Guo Y, Zhang Z, Li D, Xuan Z, Li Z, Dai F, Li Y, Cheng D, Li R, Cheng T, Jiang T, Becquet C, Xu X, Liu C, Zha X, Fan W, Lin Y, Shen Y, Jiang L, Jensen J, Hellmann I, Tang S, Zhao P, Xu H, Yu C, Zhang G, Li J, Cao J, Liu S, He N, Zhou Y, Liu H, Zhao J, Ye C, Du Z, Pan G, Zhao A, Shao H, Zeng W, Wu P, Li C, Pan M, Li J, Yin X, Li D, Wang J, Zheng H, Wang W, Zhang X, Li S, Yang H, Lu C, Nielsen R, Zhou Z, Wang J, Xiang Z, Wang J. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science 2009; 326:433-6. [PMID: 19713493 DOI: 10.1126/science.1176620] [Citation(s) in RCA: 278] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A single-base pair resolution silkworm genetic variation map was constructed from 40 domesticated and wild silkworms, each sequenced to approximately threefold coverage, representing 99.88% of the genome. We identified ~16 million single-nucleotide polymorphisms, many indels, and structural variations. We find that the domesticated silkworms are clearly genetically differentiated from the wild ones, but they have maintained large levels of genetic variability, suggesting a short domestication event involving a large number of individuals. We also identified signals of selection at 354 candidate genes that may have been important during domestication, some of which have enriched expression in the silk gland, midgut, and testis. These data add to our understanding of the domestication processes and may have applications in devising pest control strategies and advancing the use of silkworms as efficient bioreactors.
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Affiliation(s)
- Qingyou Xia
- Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China
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32
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Dannemann M, Lorenc A, Hellmann I, Khaitovich P, Lachmann M. The effects of probe binding affinity differences on gene expression measurements and how to deal with them. ACTA ACUST UNITED AC 2009; 25:2772-9. [PMID: 19689957 DOI: 10.1093/bioinformatics/btp492] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION When comparing gene expression levels between species or strains using microarrays, sequence differences between the groups can cause false identification of expression differences. Our simulated dataset shows that a sequence divergence of only 1% between species can lead to falsely reported expression differences for >50% of the transcripts-similar levels of effect have been reported previously in comparisons of human and chimpanzee expression. We propose a method for identifying probes that cause such false readings, using only the microarray data, so that problematic probes can be excluded from analysis. We then test the power of the method to detect sequence differences and to correct for falsely reported expression differences. Our method can detect 70% of the probes with sequence differences using human and chimpanzee data, while removing only 18% of probes with no sequence differences. Although only 70% of the probes with sequence differences are detected, the effect of removing probes on falsely reported expression differences is more dramatic: the method can remove 98% of the falsely reported expression differences from a simulated dataset. We argue that the method should be used even when sequence data are available. CONTACT lachmann@eva.mpg.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Michael Dannemann
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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33
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Ptak SE, Enard W, Wiebe V, Hellmann I, Krause J, Lachmann M, Pääbo S. Linkage disequilibrium extends across putative selected sites in FOXP2. Mol Biol Evol 2009; 26:2181-4. [PMID: 19608635 DOI: 10.1093/molbev/msp143] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Polymorphism data in humans suggest that the gene encoding the transcription factor FOXP2, which influences speech and language development, has been subject to a selective sweep within the last 260,000 years. It has been proposed that one or both of two substitutions that occurred on the human evolutionary lineage and changed amino acids were the targets for selection. In apparent contradiction to this is the observation that these substitutions are present in Neandertals who diverged from humans maybe 300,000-400,000 years ago. We have collected polymorphism data upstream and downstream of the substitutions. Contrary to what is expected, following a selective sweep, we find that the haplotypes extend across the two sites. We discuss possible explanations for these observations. One of them is that the selective sweep reflected in FOXP2 polymorphism data was not associated with the two amino acid substitutions.
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34
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Nielsen R, Hubisz MJ, Hellmann I, Torgerson D, Andrés AM, Albrechtsen A, Gutenkunst R, Adams MD, Cargill M, Boyko A, Indap A, Bustamante CD, Clark AG. Darwinian and demographic forces affecting human protein coding genes. Genes Dev 2009; 19:838-49. [PMID: 19279335 PMCID: PMC2675972 DOI: 10.1101/gr.088336.108] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Accepted: 02/23/2009] [Indexed: 11/24/2022]
Abstract
Past demographic changes can produce distortions in patterns of genetic variation that can mimic the appearance of natural selection unless the demographic effects are explicitly removed. Here we fit a detailed model of human demography that incorporates divergence, migration, admixture, and changes in population size to directly sequenced data from 13,400 protein coding genes from 20 European-American and 19 African-American individuals. Based on this demographic model, we use several new and established statistical methods for identifying genes with extreme patterns of polymorphism likely to be caused by Darwinian selection, providing the first genome-wide analysis of allele frequency distributions in humans based on directly sequenced data. The tests are based on observations of excesses of high frequency-derived alleles, excesses of low frequency-derived alleles, and excesses of differences in allele frequencies between populations. We detect numerous new genes with strong evidence of selection, including a number of genes related to psychiatric and other diseases. We also show that microRNA controlled genes evolve under extremely high constraints and are more likely to undergo negative selection than other genes. Furthermore, we show that genes involved in muscle development have been subject to positive selection during recent human history. In accordance with previous studies, we find evidence for negative selection against mutations in genes associated with Mendelian disease and positive selection acting on genes associated with several complex diseases.
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Affiliation(s)
- Rasmus Nielsen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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35
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Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang J, Guo Y, Feng B, Li H, Lu Y, Fang X, Liang H, Du Z, Li D, Zhao Y, Hu Y, Yang Z, Zheng H, Hellmann I, Inouye M, Pool J, Yi X, Zhao J, Duan J, Zhou Y, Qin J, Ma L, Li G, Yang Z, Zhang G, Yang B, Yu C, Liang F, Li W, Li S, Li D, Ni P, Ruan J, Li Q, Zhu H, Liu D, Lu Z, Li N, Guo G, Zhang J, Ye J, Fang L, Hao Q, Chen Q, Liang Y, Su Y, San A, Ping C, Yang S, Chen F, Li L, Zhou K, Zheng H, Ren Y, Yang L, Gao Y, Yang G, Li Z, Feng X, Kristiansen K, Wong GKS, Nielsen R, Durbin R, Bolund L, Zhang X, Li S, Yang H, Wang J. The diploid genome sequence of an Asian individual. Nature 2008; 456:60-5. [PMID: 18987735 DOI: 10.1038/nature07484] [Citation(s) in RCA: 664] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Accepted: 10/02/2008] [Indexed: 11/10/2022]
Abstract
Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics.
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Affiliation(s)
- Jun Wang
- Beijing Genomics Institute at Shenzhen, Shenzhen 518000, China.
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36
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Luetkens H, Klauss HH, Khasanov R, Amato A, Klingeler R, Hellmann I, Leps N, Kondrat A, Hess C, Köhler A, Behr G, Werner J, Büchner B. Field and temperature dependence of the superfluid density in LaFeAsO1-xFx superconductors: a muon spin relaxation study. Phys Rev Lett 2008; 101:097009. [PMID: 18851647 DOI: 10.1103/physrevlett.101.097009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Indexed: 05/26/2023]
Abstract
We present zero field and transverse field muon spin relaxation experiments on the recently discovered Fe-based superconductor LaFeAsO1-xFx (x=0.075 and x=0.1). The temperature dependence of the deduced superfluid density is consistent with a BCS s-wave or a dirty d-wave gap function, while the field dependence strongly evidences unconventional superconductivity. We obtain the in-plane penetration depth of lambda ab(0)=254(2) nm for x=0.1 and lambda ab(0)=364(8) nm for x=0.075. Further evidence for unconventional superconductivity is provided by the ratio of Tc versus the superfluid density, which is close to the Uemura line of high-Tc cuprates.
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Affiliation(s)
- H Luetkens
- Laboratory for Muon-Spin Spectroscopy, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland.
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37
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Hellmann I, Mang Y, Gu Z, Li P, de la Vega FM, Clark AG, Nielsen R. Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genes Dev 2008; 18:1020-9. [PMID: 18411405 PMCID: PMC2493391 DOI: 10.1101/gr.074187.107] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Accepted: 04/07/2008] [Indexed: 01/25/2023]
Abstract
We introduce a simple, broadly applicable method for obtaining estimates of nucleotide diversity from genomic shotgun sequencing data. The method takes into account the special nature of these data: random sampling of genomic segments from one or more individuals and a relatively high error rate for individual reads. Applying this method to data from the Celera human genome sequencing and SNP discovery project, we obtain estimates of nucleotide diversity in windows spanning the human genome and show that the diversity to divergence ratio is reduced in regions of low recombination. Furthermore, we show that the elevated diversity in telomeric regions is mainly due to elevated mutation rates and not due to decreased levels of background selection. However, we find indications that telomeres as well as centromeres experience greater impact from natural selection than intrachromosomal regions. Finally, we identify a number of genomic regions with increased or reduced diversity compared with the local level of human-chimpanzee divergence and the local recombination rate.
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Affiliation(s)
- Ines Hellmann
- Departments of Integrative Biology and Statistics, University of California, Berkeley, California 94720, USA.
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38
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Hellmann I, Täschner C, Klingeler R, Leonhardt A, Büchner B, Knupfer M. Structure and electronic properties of Li-doped vanadium oxide nanotubes. J Chem Phys 2008; 128:224701. [DOI: 10.1063/1.2931542] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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39
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Abstract
The recent availability of genome-scale genotyping data has led to the identification of regions of the human genome that seem to have been targeted by selection. These findings have increased our understanding of the evolutionary forces that affect the human genome, have augmented our knowledge of gene function and promise to increase our understanding of the genetic basis of disease. However, inferences of selection are challenged by several confounding factors, especially the complex demographic history of human populations, and concordance between studies is variable. Although such studies will always be associated with some uncertainty, steps can be taken to minimize the effects of confounding factors and improve our interpretation of their findings.
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Affiliation(s)
- Rasmus Nielsen
- Center for Comparative Genomics, University of Copenhagen, Universitetsparken 15, 2100 Kbh Ø, Denmark.
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40
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Weber M, Hellmann I, Stadler MB, Ramos L, Pääbo S, Rebhan M, Schübeler D. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 2007; 39:457-66. [PMID: 17334365 DOI: 10.1038/ng1990] [Citation(s) in RCA: 1543] [Impact Index Per Article: 90.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 01/29/2007] [Indexed: 01/11/2023]
Abstract
To gain insight into the function of DNA methylation at cis-regulatory regions and its impact on gene expression, we measured methylation, RNA polymerase occupancy and histone modifications at 16,000 promoters in primary human somatic and germline cells. We find CpG-poor promoters hypermethylated in somatic cells, which does not preclude their activity. This methylation is present in male gametes and results in evolutionary loss of CpG dinucleotides, as measured by divergence between humans and primates. In contrast, strong CpG island promoters are mostly unmethylated, even when inactive. Weak CpG island promoters are distinct, as they are preferential targets for de novo methylation in somatic cells. Notably, most germline-specific genes are methylated in somatic cells, suggesting additional functional selection. These results show that promoter sequence and gene function are major predictors of promoter methylation states. Moreover, we observe that inactive unmethylated CpG island promoters show elevated levels of dimethylation of Lys4 of histone H3, suggesting that this chromatin mark may protect DNA from methylation.
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Affiliation(s)
- Michael Weber
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
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41
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Khaitovich P, Tang K, Franz H, Kelso J, Hellmann I, Enard W, Lachmann M, Pääbo S. Positive selection on gene expression in the human brain. Curr Biol 2006; 16:R356-8. [PMID: 16618540 DOI: 10.1016/j.cub.2006.03.082] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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42
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Abstract
Levels of diversity vary across the human genome. This variation is caused by two forces: differences in mutation rates and the differential impact of natural selection. Pertinent to the question of the relative importance of these two forces is the observation that both diversity within species and interspecies divergence increase with recombination rates. This suggests that mutation and recombination are either directly coupled or linked through some third factor. Here, we test these possibilities using the recently generated sequence of the chimpanzee genome and new estimates of human diversity. We find that measures of GC and CpG content, simple-repeat structures, as well as the distance from the centromeres and the telomeres predict diversity as well as divergence. After controlling for these factors, large-scale recombination rates measured from pedigrees are still significant predictors of human diversity and human-chimpanzee divergence. Furthermore, the correlation between human diversity and recombination remains significant even after controlling for human-chimpanzee divergence. Two plausible and non-mutually exclusive explanations are, first, that natural selection has shaped the patterns of diversity seen in humans and, second, that recombination rates across the genome have changed since humans and chimpanzees shared a common ancestor, so that current recombination rates are a better predictor of diversity than of divergence. Because there are indications that recombination rates may have changed rapidly during human evolution, we favor the latter explanation.
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Affiliation(s)
- Ines Hellmann
- Max-Planck-Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
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43
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Khaitovich P, Hellmann I, Enard W, Nowick K, Leinweber M, Franz H, Weiss G, Lachmann M, Pääbo S. Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science 2005; 309:1850-4. [PMID: 16141373 DOI: 10.1126/science.1108296] [Citation(s) in RCA: 417] [Impact Index Per Article: 21.9] [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: 11/02/2022]
Abstract
The determination of the chimpanzee genome sequence provides a means to study both structural and functional aspects of the evolution of the human genome. Here we compare humans and chimpanzees with respect to differences in expression levels and protein-coding sequences for genes active in brain, heart, liver, kidney, and testis. We find that the patterns of differences in gene expression and gene sequences are markedly similar. In particular, there is a gradation of selective constraints among the tissues so that the brain shows the least differences between the species whereas liver shows the most. Furthermore, expression levels as well as amino acid sequences of genes active in more tissues have diverged less between the species than have genes active in fewer tissues. In general, these patterns are consistent with a model of neutral evolution with negative selection. However, for X-chromosomal genes expressed in testis, patterns suggestive of positive selection on sequence changes as well as expression changes are seen. Furthermore, although genes expressed in the brain have changed less than have genes expressed in other tissues, in agreement with previous work we find that genes active in brain have accumulated more changes on the human than on the chimpanzee lineage.
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MESH Headings
- Adult
- Aged
- Amino Acid Sequence
- Animals
- Base Sequence
- Child
- Chromosomes, Human, X/genetics
- Chromosomes, Mammalian/genetics
- Evolution, Molecular
- Female
- Gene Expression
- Gene Expression Profiling
- Gene Expression Regulation
- Genome
- Genome, Human
- Heart/physiology
- Humans
- Kidney/physiology
- Liver/physiology
- Male
- Middle Aged
- Models, Genetic
- Oligonucleotide Array Sequence Analysis
- Organ Specificity
- Pan troglodytes/genetics
- Prefrontal Cortex/physiology
- Promoter Regions, Genetic
- Proteins/genetics
- Selection, Genetic
- Sequence Analysis, DNA
- Species Specificity
- Testis/physiology
- Transcription, Genetic
- X Chromosome/genetics
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Affiliation(s)
- Philipp Khaitovich
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
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44
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Sakaki Y, Watanabe H, Taylor T, Hattori M, Fujiyama A, Toyoda A, Kuroki Y, Itoh T, Saitou N, Oota S, Kim CG, Kitano T, Lehrach H, Yaspo ML, Sudbrak R, Kahla A, Reinhardt R, Kube M, Platzer M, Taenzer S, Galgoczy P, Kel A, Blöecker H, Scharfe M, Nordsiek G, Hellmann I, Khaitovich P, Pääbo S, Chen Z, Wang SY, Ren SX, Zhang XL, Zheng HJ, Zhu GF, Wang BF, Zhao GP, Tsai SF, Wu K, Liu TT, Hsiao KJ, Park HS, Lee YS, Cheong JE, Choi SH. Human versus chimpanzee chromosome-wide sequence comparison and its evolutionary implication. Cold Spring Harb Symp Quant Biol 2004; 68:455-60. [PMID: 15338648 DOI: 10.1101/sqb.2003.68.455] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Y Sakaki
- RIKEN, Genomic Sciences Center, Yokohama 230-0045, Japan
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45
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Khaitovich P, Muetzel B, She X, Lachmann M, Hellmann I, Dietzsch J, Steigele S, Do HH, Weiss G, Enard W, Heissig F, Arendt T, Nieselt-Struwe K, Eichler EE, Pääbo S. Regional patterns of gene expression in human and chimpanzee brains. Genome Res 2004; 14:1462-73. [PMID: 15289471 PMCID: PMC509255 DOI: 10.1101/gr.2538704] [Citation(s) in RCA: 237] [Impact Index Per Article: 11.9] [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: 11/25/2022]
Abstract
We have analyzed gene expression in various brain regions of humans and chimpanzees. Within both human and chimpanzee individuals, the transcriptomes of the cerebral cortex are very similar to each other and differ more between individuals than among regions within an individual. In contrast, the transcriptomes of the cerebral cortex, the caudate nucleus, and the cerebellum differ substantially from each other. Between humans and chimpanzees, 10% of genes differ in their expression in at least one region of the brain. The majority of these expression differences are shared among all brain regions. Whereas genes encoding proteins involved in signal transduction and cell differentiation differ significantly between brain regions within individuals, no such pattern is seen between the species. However, a subset of genes that show expression differences between humans and chimpanzees are distributed nonrandomly across the genome. Furthermore, genes that show an elevated expression level in humans are statistically significantly enriched in regions that are recently duplicated in humans.
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Affiliation(s)
- Philipp Khaitovich
- Max-Planck-Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
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Watanabe H, Fujiyama A, Hattori M, Taylor TD, Toyoda A, Kuroki Y, Noguchi H, BenKahla A, Lehrach H, Sudbrak R, Kube M, Taenzer S, Galgoczy P, Platzer M, Scharfe M, Nordsiek G, Blöcker H, Hellmann I, Khaitovich P, Pääbo S, Reinhardt R, Zheng HJ, Zhang XL, Zhu GF, Wang BF, Fu G, Ren SX, Zhao GP, Chen Z, Lee YS, Cheong JE, Choi SH, Wu KM, Liu TT, Hsiao KJ, Tsai SF, Kim CG, OOta S, Kitano T, Kohara Y, Saitou N, Park HS, Wang SY, Yaspo ML, Sakaki Y. DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature 2004; 429:382-8. [PMID: 15164055 DOI: 10.1038/nature02564] [Citation(s) in RCA: 188] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2004] [Accepted: 04/14/2004] [Indexed: 01/29/2023]
Abstract
Human-chimpanzee comparative genome research is essential for narrowing down genetic changes involved in the acquisition of unique human features, such as highly developed cognitive functions, bipedalism or the use of complex language. Here, we report the high-quality DNA sequence of 33.3 megabases of chimpanzee chromosome 22. By comparing the whole sequence with the human counterpart, chromosome 21, we found that 1.44% of the chromosome consists of single-base substitutions in addition to nearly 68,000 insertions or deletions. These differences are sufficient to generate changes in most of the proteins. Indeed, 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level. Furthermore, we demonstrate different expansion of particular subfamilies of retrotransposons between the lineages, suggesting different impacts of retrotranspositions on human and chimpanzee evolution. The genomic changes after speciation and their biological consequences seem more complex than originally hypothesized.
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Affiliation(s)
- H Watanabe
- RIKEN, Genomic Sciences Center, Yokohama 230-0045, Japan
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Khaitovich P, Weiss G, Lachmann M, Hellmann I, Enard W, Muetzel B, Wirkner U, Ansorge W, Pääbo S. A neutral model of transcriptome evolution. PLoS Biol 2004; 2:E132. [PMID: 15138501 PMCID: PMC406393 DOI: 10.1371/journal.pbio.0020132] [Citation(s) in RCA: 250] [Impact Index Per Article: 12.5] [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: 11/21/2003] [Accepted: 03/02/2004] [Indexed: 11/30/2022] Open
Abstract
Microarray technologies allow the identification of large numbers of expression differences within and between species. Although environmental and physiological stimuli are clearly responsible for changes in the expression levels of many genes, it is not known whether the majority of changes of gene expression fixed during evolution between species and between various tissues within a species are caused by Darwinian selection or by stochastic processes. We find the following: (1) expression differences between species accumulate approximately linearly with time; (2) gene expression variation among individuals within a species correlates positively with expression divergence between species; (3) rates of expression divergence between species do not differ significantly between intact genes and expressed pseudogenes; (4) expression differences between brain regions within a species have accumulated approximately linearly with time since these regions emerged during evolution. These results suggest that the majority of expression differences observed between species are selectively neutral or nearly neutral and likely to be of little or no functional significance. Therefore, the identification of gene expression differences between species fixed by selection should be based on null hypotheses assuming functional neutrality. Furthermore, it may be possible to apply a molecular clock based on expression differences to infer the evolutionary history of tissues. Analysis of differences in gene expression between primate species suggests that the majority of them are selectively neutral and likely to have little or no functional consequences
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Affiliation(s)
| | - Gunter Weiss
- 1Max-Planck-Institute for Evolutionary AnthropologyLeipzigGermany
- 2WE Informatik, BioinformatikUniversity of Düsseldorf, DüsseldorfGermany
| | - Michael Lachmann
- 1Max-Planck-Institute for Evolutionary AnthropologyLeipzigGermany
| | - Ines Hellmann
- 1Max-Planck-Institute for Evolutionary AnthropologyLeipzigGermany
| | - Wolfgang Enard
- 1Max-Planck-Institute for Evolutionary AnthropologyLeipzigGermany
| | - Bjoern Muetzel
- 1Max-Planck-Institute for Evolutionary AnthropologyLeipzigGermany
| | - Ute Wirkner
- 3European Molecular Biology LaboratoryHeidelbergGermany
| | | | - Svante Pääbo
- 1Max-Planck-Institute for Evolutionary AnthropologyLeipzigGermany
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Hellmann I, Ebersberger I, Ptak SE, Pääbo S, Przeworski M. A neutral explanation for the correlation of diversity with recombination rates in humans. Am J Hum Genet 2003; 72:1527-35. [PMID: 12740762 PMCID: PMC1180312 DOI: 10.1086/375657] [Citation(s) in RCA: 227] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2003] [Accepted: 03/31/2003] [Indexed: 11/03/2022] Open
Abstract
One of the most striking findings to emerge from the study of genomic patterns of variation is that regions with lower recombination rates tend to have lower levels of intraspecific diversity but not of interspecies divergence. This uncoupling of variation within and between species has been widely interpreted as evidence that natural selection shapes patterns of genetic variability genomewide. We revisited the relationship between diversity, divergence, and recombination in humans, using data from closely related species and better estimates of recombination rates than previously available. We show that regions that experience less recombination have reduced divergence to chimpanzee and to baboon, as well as lower levels of diversity. This observation suggests that mutation and recombination are associated processes in humans, so that the positive correlation between diversity and recombination may have a purely neutral explanation. Consistent with this hypothesis, diversity levels no longer increase significantly with recombination rates after correction for divergence to chimpanzee.
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Affiliation(s)
- Ines Hellmann
- Max Planck Institute for Evolutionary Anthropology and Interdisciplinary Center for Bioinformatics, Leipzig
| | - Ingo Ebersberger
- Max Planck Institute for Evolutionary Anthropology and Interdisciplinary Center for Bioinformatics, Leipzig
| | - Susan E. Ptak
- Max Planck Institute for Evolutionary Anthropology and Interdisciplinary Center for Bioinformatics, Leipzig
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology and Interdisciplinary Center for Bioinformatics, Leipzig
| | - Molly Przeworski
- Max Planck Institute for Evolutionary Anthropology and Interdisciplinary Center for Bioinformatics, Leipzig
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Abstract
To better understand the evolutionary forces that affect human genes, we sequenced 5055 expressed sequence tags from the chimpanzee and compared them to their human counterparts. In conjunction with intergenic chimpanzee DNA sequences and data on human single-nucleotide polymorphisms in the genes studied, this allows us to gauge the extent to which selection affects human genes at a genome-wide scale. The comparison to intergenic DNA sequences indicates that about 39% of silent sites in protein-coding regions are deleterious and subject to negative selection. Further, when the divergence between human and chimpanzee is compared with the extent of nucleotide polymorphisms among humans in the same sequences, there is significantly higher divergence in the 5' untranslated regions (UTRs) but not in other parts of the transcript. This indicates that positive selection may have had a considerable influence on 5'UTRs. The dinucleotide CG (CpG) also exhibits a different substitution pattern within 5'UTRs as compared with other parts of the genome.
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Affiliation(s)
- Ines Hellmann
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
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Jahn J, Hellmann I, Kothe H, Maass M, Dalhoff K, Katus HA. [Infection hypothesis of coronary heart disease]. Wien Med Wochenschr 2002; 151:594-9. [PMID: 11820176] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
It is well accepted that coronary artery disease is linked to an inflammatory process. It is unproven however whether either infectious agents may cause or accelerate coronary artery disease or the inflammatory process is due to metabolic or toxic effects. Among the possible infectious agents Chlamydia pneumoniae is the most likely bacterium involved in atherosclerosis. The arguments in favour of Chlamydia pneumoniae originate from seroepidemiologic studies and from detection and isolation of bacteria from vascular lesions. This review summarises the present understanding of the role of bacterial infection for development or progression of coronary artery disease.
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Affiliation(s)
- J Jahn
- Medizinische Klinik II, Medizinische Universität Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Deutschland.
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