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Koyanagi KO. Inferring chromatin accessibility during murine hematopoiesis through phylogenetic analysis. BMC Res Notes 2023; 16:222. [PMID: 37726849 PMCID: PMC10507877 DOI: 10.1186/s13104-023-06507-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/12/2023] [Indexed: 09/21/2023] Open
Abstract
OBJECTIVE Diversification of cell types and changes in epigenetic states during cell differentiation processes are important for understanding development. Recently, phylogenetic analysis using DNA methylation and histone modification information has been shown useful for inferring these processes. The purpose of this study was to examine whether chromatin accessibility data can help infer these processes in murine hematopoiesis. RESULTS Chromatin accessibility data could partially infer the hematopoietic differentiation hierarchy. Furthermore, based on the ancestral state estimation of internal nodes, the open/closed chromatin states of differentiating progenitor cells could be predicted with a specificity of 0.86-0.99 and sensitivity of 0.29-0.72. These results suggest that the phylogenetic analysis of chromatin accessibility could offer important information on cell differentiation, particularly for organisms from which progenitor cells are difficult to obtain.
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Affiliation(s)
- Kanako O Koyanagi
- Faculty of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido, Japan.
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2
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Menet H, Daubin V, Tannier E. Phylogenetic reconciliation. PLoS Comput Biol 2022; 18:e1010621. [PMID: 36327227 PMCID: PMC9632901 DOI: 10.1371/journal.pcbi.1010621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Hugo Menet
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558,Villeurbanne, France
| | - Vincent Daubin
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558,Villeurbanne, France
- * E-mail: (VD); (ET)
| | - Eric Tannier
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558,Villeurbanne, France
- Inria, centre de recherche de Lyon, Villeurbanne, France
- * E-mail: (VD); (ET)
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3
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A novel regulatory gene promotes novel cell fate by suppressing ancestral fate in the sea anemone Nematostella vectensis. Proc Natl Acad Sci U S A 2022; 119:e2113701119. [PMID: 35500123 PMCID: PMC9172639 DOI: 10.1073/pnas.2113701119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In this study, we demonstrate how a new cell type can arise through duplication of an ancestral cell type followed by functional divergence of the new daughter cell. Specifically, we show that stinging cells in a cnidarian (namely, a sea anemone) emerged by duplication of an ancestral neuron followed by inhibition of the RFamide neuropeptide it once secreted. This finding is evidence that stinging cells evolved from a specific subtype of neurons and suggests other neuronal subtypes may have been coopted for other novel secretory functions. Cnidocytes (i.e., stinging cells) are an unequivocally novel cell type used by cnidarians (i.e., corals, jellyfish, and their kin) to immobilize prey. Although they are known to share a common evolutionary origin with neurons, the developmental program that promoted the emergence of cnidocyte fate is not known. Using functional genomics in the sea anemone, Nematostella vectensis, we show that cnidocytes develop by suppression of neural fate in a subset of neurons expressing RFamide. We further show that a single regulatory gene, a C2H2-type zinc finger transcription factor (ZNF845), coordinates both the gain of novel (cnidocyte-specific) traits and the inhibition of ancestral (neural) traits during cnidocyte development and that this gene arose by domain shuffling in the stem cnidarian. Thus, we report a mechanism by which a truly novel regulatory gene (ZNF845) promotes the development of a truly novel cell type (cnidocyte) through duplication of an ancestral cell lineage (neuron) and inhibition of its ancestral identity (RFamide).
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Koyanagi KO. Inferring changes in histone modification during cell differentiation by ancestral state estimation based on phylogenetic trees of cell types: Human hematopoiesis as a model case. Gene 2020; 721S:100021. [PMID: 32550550 PMCID: PMC7286071 DOI: 10.1016/j.gene.2019.100021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/23/2019] [Accepted: 05/27/2019] [Indexed: 12/13/2022]
Abstract
Revealing the landscape of epigenetic changes in cells during differentiation is important for understanding the development of organisms. In this study, to infer such epigenetic changes during human hematopoiesis, ancestral state estimation based on a phylogenetic tree was applied to map the epigenomic changes in six kinds of histone modifications onto the hierarchical cell differentiation process of hematopoiesis using epigenomes of eight types of differentiated hematopoietic cells. The histone modification changes inferred during hematopoiesis showed that changes that occurred on the branches separating different cell types reflected the characteristics of hematopoiesis in terms of genomic position and gene function. These results suggested that ancestral state estimation based on phylogenetic analysis of histone modifications in differentiated hematopoietic cells could reconstruct an appropriate landscape of histone modification changes during hematopoiesis. Since integration of the inferred changes of different histone modifications could reveal genes with specific histone marks such as active histone marks and bivalent histone marks on each internal branch of cell-type trees, this approach could provide valuable information for understanding the cell differentiation steps of each cell lineage.
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Key Words
- Ancestral state estimation
- B, B cell
- BED, browser extensible data
- CRISPR, clustered regularly interspaced short palindromic repeat
- Cell lineage
- Cell-type tree
- ChIP-seq, chromatin immunoprecipitation sequencing
- DNA, deoxyribonucleic acid
- Eo, eosinophil
- Er, erythroblast
- H3K27ac, acetylation of histone H3 at lysine 27
- H3K27me3, trimethylations of histone H3 at lysine 27
- H3K36me3, trimethylation of histone H3 at lysine 36
- H3K4me1, monomethylation of histone H3 at lysine 4
- H3K4me3, trimethylation of histone H3 at lysine 4
- H3K9me3, trimethylations of histone H3 at lysine 9
- Histone modification
- KEGG, Kyoto encyclopedia of genes and genomes
- L, lymphoid lineage
- M, myeloid lineage
- Me, megakaryocyte
- Mo, monocyte
- Ne, neutrophil
- Nk, natural killer cell
- Phyloepigenetics
- T, T cell
- TSS, transcription start sites
- kb, kilobase(s)
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5
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Moumi NA, Das B, Tasnim Promi Z, Bristy NA, Bayzid MS. Quartet-based inference of cell differentiation trees from ChIP-Seq histone modification data. PLoS One 2019; 14:e0221270. [PMID: 31557185 PMCID: PMC6762093 DOI: 10.1371/journal.pone.0221270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 08/04/2019] [Indexed: 01/23/2023] Open
Abstract
Understanding cell differentiation-the process of generation of distinct cell-types-plays a pivotal role in developmental and evolutionary biology. Transcriptomic information and epigenetic marks are useful to elucidate hierarchical developmental relationships among cell-types. Standard phylogenetic approaches such as maximum parsimony, maximum likelihood and neighbor joining have previously been applied to ChIP-Seq histone modification data to infer cell-type trees, showing how diverse types of cells are related. In this study, we demonstrate the applicability and suitability of quartet-based phylogenetic tree estimation techniques for constructing cell-type trees. We propose two quartet-based pipelines for constructing cell phylogeny. Our methods were assessed for their validity in inferring hierarchical differentiation processes of various cell-types in H3K4me3, H3K27me3, H3K36me3, and H3K27ac histone mark data. We also propose a robust metric for evaluating cell-type trees.
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Affiliation(s)
- Nazifa Ahmed Moumi
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Badhan Das
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Zarin Tasnim Promi
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Nishat Anjum Bristy
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Md. Shamsuzzoha Bayzid
- Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
- * E-mail:
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Rheaume BA, Jereen A, Bolisetty M, Sajid MS, Yang Y, Renna K, Sun L, Robson P, Trakhtenberg EF. Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes. Nat Commun 2018; 9:2759. [PMID: 30018341 PMCID: PMC6050223 DOI: 10.1038/s41467-018-05134-3] [Citation(s) in RCA: 237] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 06/12/2018] [Indexed: 12/13/2022] Open
Abstract
Retinal ganglion cells (RGCs) convey the major output of information collected from the eye to the brain. Thirty subtypes of RGCs have been identified to date. Here, we analyze 6225 RGCs (average of 5000 genes per cell) from right and left eyes by single-cell RNA-seq and classify them into 40 subtypes using clustering algorithms. We identify additional subtypes and markers, as well as transcription factors predicted to cooperate in specifying RGC subtypes. Zic1, a marker of the right eye-enriched subtype, is validated by immunostaining in situ. Runx1 and Fst, the markers of other subtypes, are validated in purified RGCs by fluorescent in situ hybridization (FISH) and immunostaining. We show the extent of gene expression variability needed for subtype segregation, and we show a hierarchy in diversification from a cell-type population to subtypes. Finally, we present a website for comparing the gene expression of RGC subtypes.
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Affiliation(s)
- Bruce A Rheaume
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave, Farmington, CT, 06030, USA
| | - Amyeo Jereen
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave, Farmington, CT, 06030, USA
| | - Mohan Bolisetty
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Muhammad S Sajid
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave, Farmington, CT, 06030, USA
| | - Yue Yang
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave, Farmington, CT, 06030, USA
| | - Kathleen Renna
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave, Farmington, CT, 06030, USA
| | - Lili Sun
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Institute for Systems Genomics and Department of Genetics & Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, 06032, USA
| | - Ephraim F Trakhtenberg
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave, Farmington, CT, 06030, USA.
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Chitsazian F, Sadeghi M, Elahi E. Confident gene activity prediction based on single histone modification H2BK5ac in human cell lines. BMC Bioinformatics 2017; 18:67. [PMID: 28122488 PMCID: PMC5264486 DOI: 10.1186/s12859-016-1418-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 12/10/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The histones in the core of nucleosomes may be subject to covalent post-transcriptional modifications. These modifications are thought to correlate with and possibly affect various genomic functions, including transcription. Each modification may alone or in combination with other modifications influence or be influenced by transcription. We aimed to identify correlations between single modifications or combinations of modifications at specific nucleosome sized gene regions with transcription activity based on global histone modification and transcription data of human CD4+ T cells and three other human cell lines. Transcription activity was defined in a binary fashion as either on or off. The analysis was done using the Classification and Regression Tree (CART) data mining protocol, and the Multifactorial Dimensionality Reduction (MDR) method was performed to confirm the CART results. These powerful methods have not previously been used for analysis of histone modification data. RESULTS We showed that analysis of the single histone modification H2BK5ac at only four gene regions correctly predicted transcription activity status of over 75% of genes in CD4+ T-cells. The H2BK5ac modification status also had high power for prediction of gene transcription activity in the three other cell lines studied. The informative gene regions with the H2BK5ac modification were all positioned proximal to transcription initiation sites. The CART and MDR methods were appropriate tools for the analysis performed. In the study, we also developed a non-arbitrary protocol for binary classification of genes as transcriptionally active or inactive. CONCLUSIONS The importance of H2BK5ac modification with regards to transcription control has not previously been emphasized. Analysis of this single modification at only four nucleosome sized gene regions, all of which are at or proximal to transcription initiation, has high power for prediction of gene transcription activity.
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Affiliation(s)
| | - Mehdi Sadeghi
- National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Elahe Elahi
- School of Biology, College of Science, University of Tehran, Tehran, Iran. .,Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran.
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Nair NU, Hunter L, Shao M, Grnarova P, Lin Y, Bucher P, E Moret BM. A maximum-likelihood approach for building cell-type trees by lifting. BMC Genomics 2016; 17 Suppl 1:14. [PMID: 26819094 PMCID: PMC4895258 DOI: 10.1186/s12864-015-2297-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In cell differentiation, a less specialized cell differentiates into a more specialized one, even though all cells in one organism have (almost) the same genome. Epigenetic factors such as histone modifications are known to play a significant role in cell differentiation. We previously introduce cell-type trees to represent the differentiation of cells into more specialized types, a representation that partakes of both ontogeny and phylogeny. RESULTS We propose a maximum-likelihood (ML) approach to build cell-type trees and show that this ML approach outperforms our earlier distance-based and parsimony-based approaches. We then study the reconstruction of ancestral cell types; since both ancestral and derived cell types can coexist in adult organisms, we propose a lifting algorithm to infer internal nodes. We present results on our lifting algorithm obtained both through simulations and on real datasets. CONCLUSIONS We show that our ML-based approach outperforms previously proposed techniques such as distance-based and parsimony-based methods. We show our lifting-based approach works well on both simulated and real data.
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Affiliation(s)
- Nishanth Ulhas Nair
- School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, Lausanne, CH-1015, Switzerland.
| | - Laura Hunter
- Computer Science Department, Stanford University, Stanford, USA.
| | - Mingfu Shao
- School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, Lausanne, CH-1015, Switzerland.
| | - Paulina Grnarova
- School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, Lausanne, CH-1015, Switzerland.
| | - Yu Lin
- Department of Computer Science and Engineering, University of California, San Diego, San Diego, USA.
| | - Philipp Bucher
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Bernard M E Moret
- School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, Lausanne, CH-1015, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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9
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Kin K. Inferring cell type innovations by phylogenetic methods-concepts, methods, and limitations. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:653-61. [PMID: 26462996 DOI: 10.1002/jez.b.22657] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 09/29/2015] [Indexed: 12/17/2022]
Abstract
Multicellular organisms are composed of distinct cell types that have specific roles in the body. Each cell type is a product of two kinds of historical processes-development and evolution. Although the concept of a cell type is difficult to define, the cell type concept based on the idea of the core regulatory network (CRN), a gene regulatory network that determines the identity of a cell type, illustrates the essential aspects of the cell type concept. The first step toward elucidating cell type evolution is to reconstruct the evolutionary relationships of cell types, or the cell type tree. The sister cell type model assumes that a new cell type evolves through divergence from a multifunctional ancestral cell type, creating tree-like evolutionary relationships between cell types. The process of generating a cell type tree can also be understood as the sequential addition of a new branching point on an ancestral cell differentiation hierarchy in evolution. A cell type tree thus represents an intertwined history of cell type evolution and development. Cell type trees can be reconstructed from high-throughput sequencing data, and the reconstruction of a cell type tree leads to the discovery of genes that are functionally important for a cell type. Although many issues including the lack of cross-species comparisons and the lack of a proper model for cell type evolution remain, the study of the origin of a new cell type using phylogenetic methods offers a promising new research avenue in developmental evolution. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 653-661, 2015. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Koryu Kin
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut.,Yale Systems Biology Institute, Yale University, West Haven, Connecticut
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Kin K, Nnamani MC, Lynch VJ, Michaelides E, Wagner GP. Cell-type phylogenetics and the origin of endometrial stromal cells. Cell Rep 2015; 10:1398-409. [PMID: 25732829 DOI: 10.1016/j.celrep.2015.01.062] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 12/23/2014] [Accepted: 01/28/2015] [Indexed: 12/23/2022] Open
Abstract
A challenge of genome annotation is the identification of genes performing specific biological functions. Here, we propose a phylogenetic approach that utilizes RNA-seq data to infer the historical relationships among cell types and to trace the pattern of gene-expression changes on the tree. The hypothesis is that gene-expression changes coincidental with the origin of a cell type will be important for the function of the derived cell type. We apply this approach to the endometrial stromal cells (ESCs), which are critical for the initiation and maintenance of pregnancy. Our approach identified well-known regulators of ESCs, PGR and FOXO1, as well as genes not yet implicated in female fertility, including GATA2 and TFAP2C. Knockdown analysis confirmed that they are essential for ESC differentiation. We conclude that phylogenetic analysis of cell transcriptomes is a powerful tool for discovery of genes performing cell-type-specific functions.
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Affiliation(s)
- Koryu Kin
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA; Yale Systems Biology Institute, Yale University, New Haven, CT 06516, USA
| | - Mauris C Nnamani
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA; Yale Systems Biology Institute, Yale University, New Haven, CT 06516, USA
| | - Vincent J Lynch
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA; Yale Systems Biology Institute, Yale University, New Haven, CT 06516, USA; Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | | | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA; Yale Systems Biology Institute, Yale University, New Haven, CT 06516, USA.
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