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Xiang G, He X, Giardine BM, Isaac KJ, Taylor DJ, McCoy RC, Jansen C, Keller CA, Wixom AQ, Cockburn A, Miller A, Qi Q, He Y, Li Y, Lichtenberg J, Heuston EF, Anderson SM, Luan J, Vermunt MW, Yue F, Sauria ME, Schatz MC, Taylor J, Göttgens B, Hughes JR, Higgs DR, Weiss MJ, Cheng Y, Blobel GA, Bodine DM, Zhang Y, Li Q, Mahony S, Hardison RC. Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. bioRxiv 2024:2023.04.02.535219. [PMID: 37066352 PMCID: PMC10103973 DOI: 10.1101/2023.04.02.535219] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Knowledge of locations and activities of cis-regulatory elements (CREs) is needed to decipher basic mechanisms of gene regulation and to understand the impact of genetic variants on complex traits. Previous studies identified candidate CREs (cCREs) using epigenetic features in one species, making comparisons difficult between species. In contrast, we conducted an interspecies study defining epigenetic states and identifying cCREs in blood cell types to generate regulatory maps that are comparable between species, using integrative modeling of eight epigenetic features jointly in human and mouse in our Validated Systematic Integration (VISION) Project. The resulting catalogs of cCREs are useful resources for further studies of gene regulation in blood cells, indicated by high overlap with known functional elements and strong enrichment for human genetic variants associated with blood cell phenotypes. The contribution of each epigenetic state in cCREs to gene regulation, inferred from a multivariate regression, was used to estimate epigenetic state Regulatory Potential (esRP) scores for each cCRE in each cell type, which were used to categorize dynamic changes in cCREs. Groups of cCREs displaying similar patterns of regulatory activity in human and mouse cell types, obtained by joint clustering on esRP scores, harbored distinctive transcription factor binding motifs that were similar between species. An interspecies comparison of cCREs revealed both conserved and species-specific patterns of epigenetic evolution. Finally, we showed that comparisons of the epigenetic landscape between species can reveal elements with similar roles in regulation, even in the absence of genomic sequence alignment.
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Affiliation(s)
- Guanjue Xiang
- Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215
| | - Xi He
- Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Belinda M. Giardine
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Kathryn J. Isaac
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Dylan J. Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Rajiv C. McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Camden Jansen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Cheryl A. Keller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Alexander Q. Wixom
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - April Cockburn
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Amber Miller
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Qian Qi
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Yanghua He
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105
- Department of Human Nutrition, Food and Animal Sciences, University of Hawai`i at Mānoa, Honolulu, HI 96822, USA
| | - Yichao Li
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Jens Lichtenberg
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, Bethesda, MD 20892
| | - Elisabeth F. Heuston
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, Bethesda, MD 20892
| | - Stacie M. Anderson
- Flow Cytometry Core, National Human Genome Research Institute, Bethesda, MD 20892
| | - Jing Luan
- Department of Pediatrics, Children’s Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Marit W. Vermunt
- Department of Pediatrics, Children’s Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Evanston, IL 60611
| | - Michael E.G. Sauria
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218
| | - James Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218
| | - Berthold Göttgens
- Welcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Jim R. Hughes
- MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Douglas R. Higgs
- MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, UK
| | - Mitchell J. Weiss
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Yong Cheng
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Gerd A. Blobel
- Department of Pediatrics, Children’s Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - David M. Bodine
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, Bethesda, MD 20892
| | - Yu Zhang
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802
| | - Qunhua Li
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802
- Center for Computational Biology and Bioinformatics, Genome Sciences Institute, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
- Center for Computational Biology and Bioinformatics, Genome Sciences Institute, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802
| | - Ross C. Hardison
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
- Center for Computational Biology and Bioinformatics, Genome Sciences Institute, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802
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