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Chen HF, Chang CT, Hsu KW, Peng PH, Lai JCY, Hung MC, Wu KJ. Epigenetic regulation of asymmetric cell division by the LIBR-BRD4 axis. Nucleic Acids Res 2024; 52:154-165. [PMID: 37986225 PMCID: PMC10783485 DOI: 10.1093/nar/gkad1095] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/04/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023] Open
Abstract
Asymmetric cell division (ACD) is a mechanism used by stem cells to maintain the number of progeny. However, the epigenetic mechanisms regulating ACD remain elusive. Here we show that BRD4, a BET domain protein that binds to acetylated histone, is segregated in daughter cells together with H3K56Ac and regulates ACD. ITGB1 is regulated by BRD4 to regulate ACD. A long noncoding RNA (lncRNA), LIBR (LncRNA Inhibiting BRD4), decreases the percentage of stem cells going through ACD through interacting with the BRD4 mRNAs. LIBR inhibits the translation of BRD4 through recruiting a translation repressor, RCK, and inhibiting the binding of BRD4 mRNAs to polysomes. These results identify the epigenetic regulatory modules (BRD4, lncRNA LIBR) that regulate ACD. The regulation of ACD by BRD4 suggests the therapeutic limitation of using BRD4 inhibitors to treat cancer due to the ability of these inhibitors to promote symmetric cell division that may lead to tumor progression and treatment resistance.
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Affiliation(s)
- Hsiao-Fan Chen
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406, Taiwan
| | - Chia-Ting Chang
- Graduate Institute of Translational Medicine & New Drug Development, China Medical University, Taichung 406, Taiwan
- General Education Center, Feng Chia University, Taichung 407, Taiwan
| | - Kai-Wen Hsu
- Graduate Institute of Translational Medicine & New Drug Development, China Medical University, Taichung 406, Taiwan
| | - Pei-Hua Peng
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
| | - Joseph Chieh-Yu Lai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406, Taiwan
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406, Taiwan
- Institutes of Biochemistry and Molecular Biology, Research Center for Cancer Biology, Cancer Biology and Precision Therapeutics Center, and Center for Molecular Medicine, China Medical University, Taichung 406, Taiwan
| | - Kou-Juey Wu
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
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2
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Berres S, Gromoll J, Wöste M, Sandmann S, Laurentino S. OGRE: calculate, visualize, and analyze overlap between genomic input regions and public annotations. BMC Bioinformatics 2023; 24:300. [PMID: 37496002 PMCID: PMC10369718 DOI: 10.1186/s12859-023-05422-w] [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: 04/19/2022] [Accepted: 07/18/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND Modern genome sequencing leads to an ever-growing collection of genomic annotations. Combining these elements with a set of input regions (e.g. genes) would yield new insights in genomic associations, such as those involved in gene regulation. The required data are scattered across different databases making a manual approach tiresome, unpractical, and prone to error. Semi-automatic approaches require programming skills in data parsing, processing, overlap calculation, and visualization, which most biomedical researchers lack. Our aim was to develop an automated tool providing all necessary algorithms, benefiting both bioinformaticians and researchers without bioinformatic training. RESULTS We developed overlapping annotated genomic regions (OGRE) as a comprehensive tool to associate and visualize input regions with genomic annotations. It does so by parsing regions of interest, mining publicly available annotations, and calculating possible overlaps between them. The user can thus identify location, type, and number of associated regulatory elements. Results are presented as easy to understand visualizations and result tables. We applied OGRE to recent studies and could show high reproducibility and potential new insights. To demonstrate OGRE's performance in terms of running time and output, we have conducted a benchmark and compared its features with similar tools. CONCLUSIONS OGRE's functions and built-in annotations can be applied as a downstream overlap association step, which is compatible with most genomic sequencing outputs, and can thus enrich pre-existing analyses pipelines. Compared to similar tools, OGRE shows competitive performance, offers additional features, and has been successfully applied to two recent studies. Overall, OGRE addresses the lack of tools for automatic analysis, local genomic overlap calculation, and visualization by providing an easy to use, end-to-end solution for both biologists and computational scientists.
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Affiliation(s)
- Sven Berres
- Centre of Reproductive Medicine and Andrology, University of Münster, Albert-Schweitzer-Campus 1 Building D11, 48149, Munster, Germany
| | - Jörg Gromoll
- Centre of Reproductive Medicine and Andrology, University of Münster, Albert-Schweitzer-Campus 1 Building D11, 48149, Munster, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1 Building A11, 48149, Munster, Germany
| | - Sarah Sandmann
- Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1 Building A11, 48149, Munster, Germany
| | - Sandra Laurentino
- Centre of Reproductive Medicine and Andrology, University of Münster, Albert-Schweitzer-Campus 1 Building D11, 48149, Munster, Germany.
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3
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Mendez Ruiz S, Chalk AM, Goradia A, Heraud-Farlow J, Walkley C. Over-expression of ADAR1 in mice does not initiate or accelerate cancer formation in vivo. NAR Cancer 2023; 5:zcad023. [PMID: 37275274 PMCID: PMC10233902 DOI: 10.1093/narcan/zcad023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/27/2023] [Accepted: 05/16/2023] [Indexed: 06/07/2023] Open
Abstract
Adenosine to inosine editing (A-to-I) in regions of double stranded RNA (dsRNA) is mediated by adenosine deaminase acting on RNA 1 (ADAR1) or ADAR2. ADAR1 and A-to-I editing levels are increased in many human cancers. Inhibition of ADAR1 has emerged as a high priority oncology target, however, whether ADAR1 overexpression enables cancer initiation or progression has not been directly tested. We established a series of in vivo models to allow overexpression of full-length ADAR1, or its individual isoforms, to test if increased ADAR1 expression was oncogenic. Widespread over-expression of ADAR1 or the p110 or p150 isoforms individually as sole lesions was well tolerated and did not result in cancer initiation. Therefore, ADAR1 overexpression alone is not sufficient to initiate cancer. We demonstrate that endogenous ADAR1 and A-to-I editing increased upon immortalization in murine cells, consistent with the observations from human cancers. We tested if ADAR1 over-expression could co-operate with cancer initiated by loss of tumour suppressors using a model of osteosarcoma. We did not see a disease potentiating or modifying effect of overexpressing ADAR1 or its isoforms in the models assessed. We conclude that increased ADAR1 expression and A-to-I editing in cancers is most likely a consequence of tumor formation.
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Affiliation(s)
- Shannon Mendez Ruiz
- St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria 3065, Australia
| | - Alistair M Chalk
- St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical School, University of Melbourne, Fitzroy, Victoria 3065, Australia
| | - Ankita Goradia
- St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | | | - Carl R Walkley
- To whom correspondence should be addressed. Tel: +61 3 9231 2480;
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4
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Liang Z, Chalk AM, Taylor S, Goradia A, Heraud‐Farlow JE, Walkley CR. The phenotype of the most common human ADAR1p150 Zα mutation P193A in mice is partially penetrant. EMBO Rep 2023; 24:e55835. [PMID: 36975179 PMCID: PMC10157378 DOI: 10.15252/embr.202255835] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
ADAR1 -mediated A-to-I RNA editing is a self-/non-self-discrimination mechanism for cellular double-stranded RNAs. ADAR mutations are one cause of Aicardi-Goutières Syndrome, an inherited paediatric encephalopathy, classed as a "Type I interferonopathy." The most common ADAR1 mutation is a proline 193 alanine (p.P193A) mutation, mapping to the ADAR1p150 isoform-specific Zα domain. Here, we report the development of an independent murine P195A knock-in mouse, homologous to human P193A. The Adar1P195A/P195A mice are largely normal and the mutation is well tolerated. When the P195A mutation is compounded with an Adar1 null allele (Adar1P195A/- ), approximately half the animals are runted with a shortened lifespan while the remaining Adar1P195A/- animals are normal, contrasting with previous reports. The phenotype of the Adar1P195A/- animals is both associated with the parental genotype and partly non-genetic/environmental. Complementation with an editing-deficient ADAR1 (Adar1P195A/E861A ), or the loss of MDA5, rescues phenotypes in the Adar1P195A/- mice.
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Affiliation(s)
- Zhen Liang
- St Vincent's Institute of Medical ResearchFitzroyVic.Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical SchoolUniversity of MelbourneFitzroyVic.Australia
| | - Alistair M Chalk
- St Vincent's Institute of Medical ResearchFitzroyVic.Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical SchoolUniversity of MelbourneFitzroyVic.Australia
| | - Scott Taylor
- St Vincent's Institute of Medical ResearchFitzroyVic.Australia
| | - Ankita Goradia
- St Vincent's Institute of Medical ResearchFitzroyVic.Australia
| | - Jacki E Heraud‐Farlow
- St Vincent's Institute of Medical ResearchFitzroyVic.Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical SchoolUniversity of MelbourneFitzroyVic.Australia
| | - Carl R Walkley
- St Vincent's Institute of Medical ResearchFitzroyVic.Australia
- Department of Medicine, Eastern Hill Precinct, Melbourne Medical SchoolUniversity of MelbourneFitzroyVic.Australia
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5
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Wünnemann F, Fotsing Tadjo T, Beaudoin M, Lalonde S, Lo KS, Kleinstiver BP, Lettre G. Multimodal CRISPR perturbations of GWAS loci associated with coronary artery disease in vascular endothelial cells. PLoS Genet 2023; 19:e1010680. [PMID: 36928188 PMCID: PMC10047545 DOI: 10.1371/journal.pgen.1010680] [Citation(s) in RCA: 8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 03/28/2023] [Accepted: 02/25/2023] [Indexed: 03/18/2023] Open
Abstract
Genome-wide association studies have identified >250 genetic variants associated with coronary artery disease (CAD), but the causal variants, genes and molecular mechanisms remain unknown at most loci. We performed pooled CRISPR screens to test the impact of sequences at or near CAD-associated genetic variants on vascular endothelial cell functions. Using CRISPR knockout, inhibition and activation, we targeted 1998 variants at 83 CAD loci to assess their effect on three adhesion proteins (E-selectin, ICAM1, VCAM1) and three key endothelial functions (nitric oxide and reactive oxygen species production, calcium signalling). At a false discovery rate ≤10%, we identified significant CRISPR perturbations near 42 variants located within 26 CAD loci. We used base editing to validate a putative causal variant in the promoter of the FES gene. Although a few of the loci include genes previously characterized in endothelial cells (e.g. AIDA, ARHGEF26, ADAMTS7), most are implicated in endothelial dysfunction for the first time. Detailed characterization of one of these new loci implicated the RNA helicase DHX38 in vascular endothelial cell senescence. While promising, our results also highlighted several limitations in using CRISPR perturbations to functionally dissect GWAS loci, including an unknown false negative rate and potential off-target effects.
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Affiliation(s)
| | | | | | | | - Ken Sin Lo
- Montreal Heart Institute, Montréal, Québec, Canada
| | - Benjamin P. Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, Québec, Canada
- Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
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6
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Nefzger CM, Jardé T, Srivastava A, Schroeder J, Rossello FJ, Horvay K, Prasko M, Paynter JM, Chen J, Weng CF, Sun YBY, Liu X, Chan E, Deshpande N, Chen X, Li YJ, Pflueger J, Engel RM, Knaupp AS, Tsyganov K, Nilsson SK, Lister R, Rackham OJL, Abud HE, Polo JM. Intestinal stem cell aging signature reveals a reprogramming strategy to enhance regenerative potential. NPJ Regen Med 2022; 7:31. [PMID: 35710627 PMCID: PMC9203768 DOI: 10.1038/s41536-022-00226-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 04/25/2022] [Indexed: 12/13/2022] Open
Abstract
The impact of aging on intestinal stem cells (ISCs) has not been fully elucidated. In this study, we identified widespread epigenetic and transcriptional alterations in old ISCs. Using a reprogramming algorithm, we identified a set of key transcription factors (Egr1, Irf1, FosB) that drives molecular and functional differences between old and young states. Overall, by dissecting the molecular signature of aged ISCs, our study identified transcription factors that enhance the regenerative capacity of ISCs.
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Affiliation(s)
- Christian M Nefzger
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, Australia
| | - Thierry Jardé
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Akanksha Srivastava
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Jan Schroeder
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Fernando J Rossello
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Katja Horvay
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Mirsada Prasko
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jacob M Paynter
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Joseph Chen
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Chen-Fang Weng
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Yu B Y Sun
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Xiaodong Liu
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Eva Chan
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Nikita Deshpande
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, Australia
| | - Xiaoli Chen
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, Australia
| | - Y Jinhua Li
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jahnvi Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia.,Harry Perkins Institute of Medical Research, Nedlands, WA, Australia
| | - Rebekah M Engel
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Cabrini Monash University Department of Surgery, Cabrini Hospital, Malvern, VIC, Australia
| | - Anja S Knaupp
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Kirill Tsyganov
- Monash Bioinformatics Platform, Monash University, Clayton, VIC, Australia
| | - Susan K Nilsson
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia.,Biomedical Manufacturing CSIRO, Clayton, VIC, Australia
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia.,Harry Perkins Institute of Medical Research, Nedlands, WA, Australia
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Helen E Abud
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia. .,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia. .,Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia. .,Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia. .,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia. .,Adelaide Centre for Epigenetics, The University of Adelaide, Adelaide, SA, Australia. .,The South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, SA, Australia.
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7
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Min S, Xu Q, Qin L, Li Y, Li Z, Chen C, Wu H, Han J, Zhu X, Jin P, Tang B. Altered hydroxymethylome in the substantia nigra of Parkinson's disease. Hum Mol Genet 2022; 31:3494-3503. [PMID: 35661211 PMCID: PMC9558850 DOI: 10.1093/hmg/ddac122] [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] [Received: 03/03/2022] [Revised: 05/05/2022] [Accepted: 05/21/2022] [Indexed: 01/26/2023] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder, and aging and genetic and environmental exposure can contribute to its pathogenesis. DNA methylation has been suggested to play a pivotal role in neurodevelopment and neurodegenerative diseases. 5-hydroxymethylcytosine (5hmC) is generated through 5-methylcytosine (5mC) oxidization by ten-eleven translocation proteins and is particularly enriched in the brain. Although 5hmC has been linked to multiple neurological disorders, little is known about 5hmC alterations in the substantia nigra of patients with PD. To determine the specific alterations in DNA methylation and hydroxymethylation in PD brain samples, we examined the genome-wide profiles of 5mC and 5hmC in the substantia nigra of patients with PD and Alzheimer's disease (ad). We identified 4119 differentially hydroxymethylated regions (DhMRs) and no differentially methylated regions (DMRs) in the postmortem brains of patients with PD compared with those of controls. These DhMRs were PD-specific when compared with the results of AD. Gene ontology analysis revealed that several signaling pathways, such as neurogenesis and neuronal differentiation, were significantly enriched in PD DhMRs. KEGG enrichment analysis revealed substantial alterations in multiple signaling pathways, including phospholipase D (PLD), cAMP and Rap1. In addition, using a PD Drosophila model, we found that one of the 5hmC-modulated genes, PLD1, modulated α-synuclein toxicity. Our analysis suggested that 5hmC may act as an independent epigenetic marker and contribute to the pathogenesis of PD.
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Affiliation(s)
| | | | | | - Yujing Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ziyi Li
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA 30322, USA
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA 30322, USA
| | - Junhai Han
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu 210096, China
| | - Xiongwei Zhu
- To whom correspondence should be addressed at: Department of Neurology, Xiangya Hospital, Central South University, #87 Xiangya Road, Changsha, Hunan 410008, China. Tel: +86-731-84327398; ; Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA. Tel: +1 404-727-3729; ; Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA. Tel: +1-216-368-5903,
| | - Peng Jin
- To whom correspondence should be addressed at: Department of Neurology, Xiangya Hospital, Central South University, #87 Xiangya Road, Changsha, Hunan 410008, China. Tel: +86-731-84327398; ; Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA. Tel: +1 404-727-3729; ; Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA. Tel: +1-216-368-5903,
| | - Beisha Tang
- To whom correspondence should be addressed at: Department of Neurology, Xiangya Hospital, Central South University, #87 Xiangya Road, Changsha, Hunan 410008, China. Tel: +86-731-84327398; ; Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA. Tel: +1 404-727-3729; ; Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA. Tel: +1-216-368-5903,
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8
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Silva TC, Young JI, Martin ER, Chen XS, Wang L. MethReg: estimating the regulatory potential of DNA methylation in gene transcription. Nucleic Acids Res 2022; 50:e51. [PMID: 35100398 PMCID: PMC9122535 DOI: 10.1093/nar/gkac030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 10/03/2021] [Revised: 12/17/2021] [Accepted: 01/11/2022] [Indexed: 01/02/2023] Open
Abstract
Epigenome-wide association studies often detect many differentially methylated sites, and many are located in distal regulatory regions. To further prioritize these significant sites, there is a critical need to better understand the functional impact of CpG methylation. Recent studies demonstrated that CpG methylation-dependent transcriptional regulation is a widespread phenomenon. Here, we present MethReg, an R/Bioconductor package that analyzes matched DNA methylation and gene expression data, along with external transcription factor (TF) binding information, to evaluate, prioritize and annotate CpG sites with high regulatory potential. At these CpG sites, TF-target gene associations are often only present in a subset of samples with high (or low) methylation levels, so they can be missed by analyses that use all samples. Using colorectal cancer and Alzheimer's disease datasets, we show MethReg significantly enhances our understanding of the regulatory roles of DNA methylation in complex diseases.
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Affiliation(s)
- Tiago C Silva
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I Young
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R Martin
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - X Steven Chen
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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9
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Moro A, Gao Z, Wang L, Yu A, Hsiung S, Ban Y, Yan A, Sologon CM, Chen XS, Malek TR. Dynamic transcriptional activity and chromatin remodeling of regulatory T cells after varied duration of interleukin-2 receptor signaling. Nat Immunol 2022; 23:802-813. [PMID: 35449416 PMCID: PMC9106907 DOI: 10.1038/s41590-022-01179-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 03/03/2021] [Accepted: 03/10/2022] [Indexed: 12/11/2022]
Abstract
Regulatory T (Treg) cells require (interleukin-2) IL-2 for their homeostasis by affecting their proliferation, survival and activation. Here we investigated transcriptional and epigenetic changes after acute, periodic and persistent IL-2 receptor (IL-2R) signaling in mouse peripheral Treg cells in vivo using IL-2 or the long-acting IL-2-based biologic mouse IL-2-CD25. We show that initially IL-2R-dependent STAT5 transcription factor-dependent pathways enhanced gene activation, chromatin accessibility and metabolic reprogramming to support Treg cell proliferation. Unexpectedly, at peak proliferation, less accessible chromatin prevailed and was associated with Treg cell contraction. Restimulation of IL-2R signaling after contraction activated signature IL-2-dependent genes and others associated with effector Treg cells, whereas genes associated with signal transduction were downregulated to somewhat temper expansion. Thus, IL-2R-dependent Treg cell homeostasis depends in part on a shift from more accessible chromatin and expansion to less accessible chromatin and contraction. Mouse IL-2-CD25 supported greater expansion and a more extensive transcriptional state than IL-2 in Treg cells, consistent with greater efficacy to control autoimmunity.
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Affiliation(s)
- Alejandro Moro
- Department of Microbiology and Immunology, University of Miami, Miami, FL, USA
| | - Zhen Gao
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Lily Wang
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Aixin Yu
- Department of Microbiology and Immunology, University of Miami, Miami, FL, USA
| | - Sunnie Hsiung
- Department of Microbiology and Immunology, University of Miami, Miami, FL, USA
| | - Yuguang Ban
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miami, FL, USA
| | - Aimin Yan
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Corneliu M Sologon
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - X Steven Chen
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miami, FL, USA
| | - Thomas R Malek
- Department of Microbiology and Immunology, University of Miami, Miami, FL, USA.
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10
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Kupkova K, Mosquera JV, Smith JP, Stolarczyk M, Danehy TL, Lawson JT, Xue B, Stubbs JT, LeRoy N, Sheffield NC. GenomicDistributions: fast analysis of genomic intervals with Bioconductor. BMC Genomics 2022; 23:299. [PMID: 35413804 PMCID: PMC9003978 DOI: 10.1186/s12864-022-08467-y] [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: 10/25/2021] [Accepted: 03/13/2022] [Indexed: 11/10/2022] Open
Abstract
Background Epigenome analysis relies on defined sets of genomic regions output by widely used assays such as ChIP-seq and ATAC-seq. Statistical analysis and visualization of genomic region sets is essential to answer biological questions in gene regulation. As the epigenomics community continues generating data, there will be an increasing need for software tools that can efficiently deal with more abundant and larger genomic region sets. Here, we introduce GenomicDistributions, an R package for fast and easy summarization and visualization of genomic region data. Results GenomicDistributions offers a broad selection of functions to calculate properties of genomic region sets, such as feature distances, genomic partition overlaps, and more. GenomicDistributions functions are meticulously optimized for best-in-class speed and generally outperform comparable functions in existing R packages. GenomicDistributions also offers plotting functions that produce editable ggplot objects. All GenomicDistributions functions follow a uniform naming scheme and can handle either single or multiple region set inputs. Conclusions GenomicDistributions offers a fast and scalable tool for exploratory genomic region set analysis and visualization. GenomicDistributions excels in user-friendliness, flexibility of outputs, breadth of functions, and computational performance. GenomicDistributions is available from Bioconductor (https://bioconductor.org/packages/release/bioc/html/GenomicDistributions.html). Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08467-y.
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Affiliation(s)
- Kristyna Kupkova
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA
| | - Jose Verdezoto Mosquera
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA
| | - Jason P Smith
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA
| | - Michał Stolarczyk
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA
| | - Tessa L Danehy
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA
| | - John T Lawson
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA.,Department of Biomedical Engineering, University of Virginia, Charlottesville, USA
| | - Bingjie Xue
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA.,Department of Biomedical Engineering, University of Virginia, Charlottesville, USA
| | - John T Stubbs
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA
| | - Nathan LeRoy
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA.,Department of Biomedical Engineering, University of Virginia, Charlottesville, USA
| | - Nathan C Sheffield
- Center for Public Health Genomics, University of Virginia, Charlottesville, USA. .,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA. .,Department of Biomedical Engineering, University of Virginia, Charlottesville, USA. .,Department of Public Health Sciences, University of Virginia, Charlottesville, USA.
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11
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Meiler A, Marchiano F, Haering M, Weitkunat M, Schnorrer F, Habermann BH. AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators. Sci Rep 2021; 11:15463. [PMID: 34326396 PMCID: PMC8322331 DOI: 10.1038/s41598-021-94805-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 02/16/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
Gene expression regulation requires precise transcriptional programs, led by transcription factors in combination with epigenetic events. Recent advances in epigenomic and transcriptomic techniques provided insight into different gene regulation mechanisms. However, to date it remains challenging to understand how combinations of transcription factors together with epigenetic events control cell-type specific gene expression. We have developed the AnnoMiner web-server, an innovative and flexible tool to annotate and integrate epigenetic, and transcription factor occupancy data. First, AnnoMiner annotates user-provided peaks with gene features. Second, AnnoMiner can integrate genome binding data from two different transcriptional regulators together with gene features. Third, AnnoMiner offers to explore the transcriptional deregulation of genes nearby, or within a specified genomic region surrounding a user-provided peak. AnnoMiner’s fourth function performs transcription factor or histone modification enrichment analysis for user-provided gene lists by utilizing hundreds of public, high-quality datasets from ENCODE for the model organisms human, mouse, Drosophila and C. elegans. Thus, AnnoMiner can predict transcriptional regulators for a studied process without the strict need for chromatin data from the same process. We compared AnnoMiner to existing tools and experimentally validated several transcriptional regulators predicted by AnnoMiner to indeed contribute to muscle morphogenesis in Drosophila. AnnoMiner is freely available at http://chimborazo.ibdm.univ-mrs.fr/AnnoMiner/.
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Affiliation(s)
- Arno Meiler
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Fabio Marchiano
- Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France
| | - Margaux Haering
- Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France
| | - Manuela Weitkunat
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Frank Schnorrer
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.,Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France
| | - Bianca H Habermann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany. .,Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France.
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12
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Chalk AM, Taylor S, Heraud-Farlow JE, Walkley CR. The majority of A-to-I RNA editing is not required for mammalian homeostasis. Genome Biol 2019; 20:268. [PMID: 31815657 PMCID: PMC6900863 DOI: 10.1186/s13059-019-1873-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/29/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Adenosine-to-inosine (A-to-I) RNA editing, mediated by ADAR1 and ADAR2, occurs at tens of thousands to millions of sites across mammalian transcriptomes. A-to-I editing can change the protein coding potential of a transcript and alter RNA splicing, miRNA biology, RNA secondary structure and formation of other RNA species. In vivo, the editing-dependent protein recoding of GRIA2 is the essential function of ADAR2, while ADAR1 editing prevents innate immune sensing of endogenous RNAs by MDA5 in both human and mouse. However, a significant proportion of A-to-I editing sites can be edited by both ADAR1 and ADAR2, particularly within the brain where both are highly expressed. The physiological function(s) of these shared sites, including those evolutionarily conserved, is largely unknown. RESULTS To generate completely A-to-I editing-deficient mammals, we crossed the viable rescued ADAR1-editing-deficient animals (Adar1E861A/E861AIfih1-/-) with rescued ADAR2-deficient (Adarb1-/-Gria2R/R) animals. Unexpectedly, the global absence of editing was well tolerated. Adar1E861A/E861AIfih1-/-Adarb1-/-Gria2R/R were recovered at Mendelian ratios and age normally. Detailed transcriptome analysis demonstrated that editing was absent in the brains of the compound mutants and that ADAR1 and ADAR2 have similar editing site preferences and patterns. CONCLUSIONS We conclude that ADAR1 and ADAR2 are non-redundant and do not compensate for each other's essential functions in vivo. Physiologically essential A-to-I editing comprises a small subset of the editome, and the majority of editing is dispensable for mammalian homeostasis. Moreover, in vivo biologically essential protein recoding mediated by A-to-I editing is an exception in mammals.
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Affiliation(s)
- Alistair M Chalk
- St. Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, VIC, 3065, Australia
- Department of Medicine, St. Vincent's Hospital, Melbourne Medical School, University of Melbourne, Fitzroy, VIC, 3065, Australia
| | - Scott Taylor
- St. Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, VIC, 3065, Australia
| | - Jacki E Heraud-Farlow
- St. Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, VIC, 3065, Australia.
- Department of Medicine, St. Vincent's Hospital, Melbourne Medical School, University of Melbourne, Fitzroy, VIC, 3065, Australia.
| | - Carl R Walkley
- St. Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, VIC, 3065, Australia.
- Department of Medicine, St. Vincent's Hospital, Melbourne Medical School, University of Melbourne, Fitzroy, VIC, 3065, Australia.
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, 3000, Australia.
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13
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Mercatelli D, Scalambra L, Triboli L, Ray F, Giorgi FM. Gene regulatory network inference resources: A practical overview. Biochim Biophys Acta Gene Regul Mech 2019; 1863:194430. [PMID: 31678629 DOI: 10.1016/j.bbagrm.2019.194430] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 02/08/2023]
Abstract
Transcriptional regulation is a fundamental molecular mechanism involved in almost every aspect of life, from homeostasis to development, from metabolism to behavior, from reaction to stimuli to disease progression. In recent years, the concept of Gene Regulatory Networks (GRNs) has grown popular as an effective applied biology approach for describing the complex and highly dynamic set of transcriptional interactions, due to its easy-to-interpret features. Since cataloguing, predicting and understanding every GRN connection in all species and cellular contexts remains a great challenge for biology, researchers have developed numerous tools and methods to infer regulatory processes. In this review, we catalogue these methods in six major areas, based on the dominant underlying information leveraged to infer GRNs: Coexpression, Sequence Motifs, Chromatin Immunoprecipitation (ChIP), Orthology, Literature and Protein-Protein Interaction (PPI) specifically focused on transcriptional complexes. The methods described here cover a wide range of user-friendliness: from web tools that require no prior computational expertise to command line programs and algorithms for large scale GRN inferences. Each method for GRN inference described herein effectively illustrates a type of transcriptional relationship, with many methods being complementary to others. While a truly holistic approach for inferring and displaying GRNs remains one of the greatest challenges in the field of systems biology, we believe that the integration of multiple methods described herein provides an effective means with which experimental and computational biologists alike may obtain the most complete pictures of transcriptional relationships. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.
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Affiliation(s)
- Daniele Mercatelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Laura Scalambra
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Luca Triboli
- Centre for Integrative Biology (CIBIO), University of Trento, Italy
| | - Forest Ray
- Department of Systems Biology, Columbia University Medical Center, New York, NY, United States
| | - Federico M Giorgi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
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14
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Mariani L, Weinand K, Vedenko A, Barrera LA, Bulyk ML. Identification of Human Lineage-Specific Transcriptional Coregulators Enabled by a Glossary of Binding Modules and Tunable Genomic Backgrounds. Cell Syst 2019; 5:187-201.e7. [PMID: 28957653 DOI: 10.1016/j.cels.2017.06.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 02/09/2017] [Revised: 06/03/2017] [Accepted: 06/29/2017] [Indexed: 01/08/2023]
Abstract
Transcription factors (TFs) control cellular processes by binding specific DNA motifs to modulate gene expression. Motif enrichment analysis of regulatory regions can identify direct and indirect TF binding sites. Here, we created a glossary of 108 non-redundant TF-8mer "modules" of shared specificity for 671 metazoan TFs from publicly available and new universal protein binding microarray data. Analysis of 239 ENCODE TF chromatin immunoprecipitation sequencing datasets and associated RNA sequencing profiles suggest the 8mer modules are more precise than position weight matrices in identifying indirect binding motifs and their associated tethering TFs. We also developed GENRE (genomically equivalent negative regions), a tunable tool for construction of matched genomic background sequences for analysis of regulatory regions. GENRE outperformed four state-of-the-art approaches to background sequence construction. We used our TF-8mer glossary and GENRE in the analysis of the indirect binding motifs for the co-occurrence of tethering factors, suggesting novel TF-TF interactions. We anticipate that these tools will aid in elucidating tissue-specific gene-regulatory programs.
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Affiliation(s)
- Luca Mariani
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Kathryn Weinand
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Anastasia Vedenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Luis A Barrera
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115, USA; Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115, USA; Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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15
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Young JI, Sivasankaran SK, Wang L, Ali A, Mehta A, Davis DA, Dykxhoorn DM, Petito CK, Beecham GW, Martin ER, Mash DC, Pericak-Vance M, Scott WK, Montine TJ, Vance JM. Genome-wide brain DNA methylation analysis suggests epigenetic reprogramming in Parkinson disease. Neurol Genet 2019; 5:e342. [PMID: 31403079 PMCID: PMC6659138 DOI: 10.1212/nxg.0000000000000342] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 05/09/2019] [Indexed: 12/13/2022]
Abstract
Objective Given the known strong relationship of DNA methylation with environmental exposure, we investigated whether brain regions affected in Parkinson disease (PD) were differentially methylated between PD cases and controls. Methods DNA chip arrays were used to perform a genome-wide screen of DNA methylation on the dorsal motor nucleus of the vagus (DMV), substantia nigra (SN), and cingulate gyrus (CG) of pathologically confirmed PD cases and controls selected using the criteria of Beecham et al. Analysis examined differentially methylated regions (DMRs) between cases and controls for each brain area. RNA sequencing and pathway analysis were also performed for each brain area. Results Thirty-eight PD cases and 41 controls were included in the analysis. Methylation studies revealed 234 significant DMR in the DMV, 44 in the SN, and 141 in the CG between cases and controls (Sidak p < 0.05). Pathway analysis of these genes showed significant enrichment for the Wnt signaling pathway (FDR < 0.01). Conclusions Our data suggest that significant DNA methylation changes exist between cases and controls in PD, especially in the DMV, one of the areas affected earliest in PD. The etiology of these methylation changes is not yet known, but the predominance of methylation changes occurring in the DMV supports the hypothesis that vagus nerve function, perhaps involving the gastrointestinal system, is important in PD pathogenesis. These data also give independent support that genes involved in Wnt signaling are a likely factor in the neurodegenerative processes of PD.
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Affiliation(s)
- Juan I Young
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Sathesh K Sivasankaran
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Lily Wang
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Aleena Ali
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Arpit Mehta
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - David A Davis
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Carol K Petito
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Deborah C Mash
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Margaret Pericak-Vance
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - William K Scott
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Thomas J Montine
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
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Howe CG, Zhou M, Wang X, Pittman GS, Thompson IJ, Campbell MR, Bastain TM, Grubbs BH, Salam MT, Hoyo C, Bell DA, Smith AD, Breton CV. Associations between Maternal Tobacco Smoke Exposure and the Cord Blood [Formula: see text] DNA Methylome. Environ Health Perspect 2019; 127:047009. [PMID: 31039056 PMCID: PMC6785223 DOI: 10.1289/ehp3398] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 02/20/2019] [Accepted: 03/05/2019] [Indexed: 05/16/2023]
Abstract
BACKGROUND Maternal tobacco smoke exposure has been associated with altered DNA methylation. However, previous studies largely used methylation arrays, which cover a small fraction of CpGs, and focused on whole cord blood. OBJECTIVES The current study examined the impact of in utero exposure to maternal tobacco smoke on the cord blood [Formula: see text] DNA methylome. METHODS The methylomes of 20 Hispanic white newborns ([Formula: see text] exposed to any maternal tobacco smoke in pregnancy; [Formula: see text] unexposed) from the Maternal and Child Health Study (MACHS) were profiled by whole-genome bisulfite sequencing (median coverage: [Formula: see text]). Statistical analyses were conducted using the Regression Analysis of Differential Methylation (RADMeth) program because it performs well on low-coverage data (minimizes false positives and negatives). RESULTS We found that 10,381 CpGs were differentially methylated by tobacco smoke exposure [neighbor-adjusted p-values that are additionally corrected for multiple testing based on the Benjamini-Hochberg method for controlling the false discovery rate (FDR) [Formula: see text]]. From these CpGs, RADMeth identified 557 differentially methylated regions (DMRs) that were overrepresented ([Formula: see text]) in important regulatory regions, including enhancers. Of nine DMRs that could be queried in a reduced representation bisulfite sequencing (RRBS) study of adult [Formula: see text] cells ([Formula: see text] smokers; [Formula: see text] nonsmokers), four replicated ([Formula: see text]). Additionally, a CpG in the promoter of SLC7A8 (percent methylation difference: [Formula: see text] comparing exposed to unexposed) replicated ([Formula: see text]) in an EPIC (Illumina) array study of cord blood [Formula: see text] cells ([Formula: see text] exposed to sustained maternal tobacco smoke; [Formula: see text] unexposed) and in a study of adult [Formula: see text] cells across two platforms (EPIC: [Formula: see text] smokers; [Formula: see text] nonsmokers; 450K: [Formula: see text] smokers; [Formula: see text] nonsmokers). CONCLUSIONS Maternal tobacco smoke exposure in pregnancy is associated with cord blood [Formula: see text] DNA methylation in key regulatory regions, including enhancers. While we used a method that performs well on low-coverage data, we cannot exclude the possibility that some results may be false positives. However, we identified a differentially methylated CpG in amino acid transporter SLC7A8 that is highly reproducible, which may be sensitive to cigarette smoke in both cord blood and adult [Formula: see text] cells. https://doi.org/10.1289/EHP3398.
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Affiliation(s)
- Caitlin G. Howe
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Meng Zhou
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Xuting Wang
- Immunity, Inflammation and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Dept. of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Gary S. Pittman
- Immunity, Inflammation and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Dept. of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Isabel J. Thompson
- Immunity, Inflammation and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Dept. of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Michelle R. Campbell
- Immunity, Inflammation and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Dept. of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Theresa M. Bastain
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Brendan H. Grubbs
- Department of Obstetrics and Gynecology, Keck School of Medicine, Los Angeles, California, USA
| | - Muhammad T. Salam
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Department of Psychiatry, Kern Medical, Bakersfield, California, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Douglas A. Bell
- Immunity, Inflammation and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Dept. of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Andrew D. Smith
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Carrie V. Breton
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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17
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Glowacka WK, Jain H, Okura M, Maimaitiming A, Mamatjan Y, Nejad R, Farooq H, Taylor MD, Aldape K, Kongkham P. 5-Hydroxymethylcytosine preferentially targets genes upregulated in isocitrate dehydrogenase 1 mutant high-grade glioma. Acta Neuropathol 2018; 135:617-634. [PMID: 29428975 PMCID: PMC5978937 DOI: 10.1007/s00401-018-1821-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 01/18/2018] [Accepted: 02/07/2018] [Indexed: 01/12/2023]
Abstract
Gliomas demonstrate epigenetic dysregulation exemplified by the Glioma CpG Island Methylator Phenotype (G-CIMP) seen in IDH1 mutant tumors. 5-Hydroxymethylcytosine (5hmC) is implicated in glioma pathogenesis; however, its role in IDH1 mutant gliomas is incompletely understood. To characterize 5hmC in IDH1 mutant gliomas further, we examine 5hmC in a cohort of IDH1 mutant and wild-type high-grade gliomas (HGG) using a quantitative locus-specific approach. Regions demonstrating high 5hmC abundance and differentially hydroxymethylated regions (DHMR) enrich for enhancers implicated in glioma pathogenesis. Among these regions, IDH1 mutant tumors possess greater 5hmC compared to wild type. 5hmC contributes to overall methylation status of G-CIMP genes. 5hmC targeting gene body regions correlates significantly with increased gene expression. In particular, a strong correlation between increased 5hmC and increased gene expression is identified for genes highly expressed in the IDH1 mutant cohort. Overall, locus-specific gain of 5hmC targeting regulatory regions and associated with overexpressed genes suggests a significant role for 5hmC in IDH1 mutant HGG.
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18
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Abstract
Motivation Analysis of next-generation sequencing data often results in a list of genomic regions. These may include differentially methylated CpGs/regions, transcription factor binding sites, interacting chromatin regions, or GWAS-associated SNPs, among others. A common analysis step is to annotate such genomic regions to genomic annotations (promoters, exons, enhancers, etc.). Existing tools are limited by a lack of annotation sources and flexible options, the time it takes to annotate regions, an artificial one-to-one region-to-annotation mapping, a lack of visualization options to easily summarize data, or some combination thereof. Results We developed the annotatr Bioconductor package to flexibly and quickly summarize and plot annotations of genomic regions. The annotatr package reports all intersections of regions and annotations, giving a better understanding of the genomic context of the regions. A variety of graphics functions are implemented to easily plot numerical or categorical data associated with the regions across the annotations, and across annotation intersections, providing insight into how characteristics of the regions differ across the annotations. We demonstrate that annotatr is up to 27× faster than comparable R packages. Overall, annotatr enables a richer biological interpretation of experiments. Availability and Implementation http://bioconductor.org/packages/annotatr/ and https://github.com/rcavalcante/annotatr. Contact rcavalca@umich.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics.,Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
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19
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Duncan CG, Kondilis-Mangum HD, Grimm SA, Bushel PR, Chrysovergis K, Roberts JD, Tyson FL, Merrick BA, Wade PA. Base-Resolution Analysis of DNA Methylation Patterns Downstream of Dnmt3a in Mouse Naïve B Cells. G3 (Bethesda) 2018; 8:805-13. [PMID: 29326230 DOI: 10.1534/g3.117.300446] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The DNA methyltransferase, Dnmt3a, is dynamically regulated throughout mammalian B cell development and upon activation by antigenic stimulation. Dnmt3a inactivation in hematopoietic stem cells has been shown to drive B cell-related malignancies, including chronic lymphocytic leukemia, and associates with specific DNA methylation patterns in transformed cells. However, while it is clear that inactivation of Dnmt3a in hematopoietic stem cells has profound functional effects, the consequences of Dnmt3a inactivation in cells of the B lineage are unclear. To assess whether loss of Dnmt3a at the earliest stages of B cell development lead to DNA methylation defects that might impair function, we selectively inactivated Dnmt3a early in mouse B cell development and then utilized whole genome bisulfite sequencing to generate base-resolution profiles of Dnmt3a+/+ and Dnmt3a−/− naïve splenic B cells. Overall, we find that global methylation patterns are largely consistent between Dnmt3a+/+ and Dnmt3a−/− naïve B cells, indicating a minimal functional effect of DNMT3A in mature B cells. However, loss of Dnmt3a induced 449 focal DNA methylation changes, dominated by loss-of-methylation events. Regions found to be hypomethylated in Dnmt3a−/− naïve splenic B cells were enriched in gene bodies of transcripts expressed in B cells, a fraction of which are implicated in B cell-related disease. Overall, the results from this study suggest that factors other than Dnmt3a are the major drivers for methylome maintenance in B cell development.
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20
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Sjaarda CP, Hecht P, McNaughton AJM, Zhou A, Hudson ML, Will MJ, Smith G, Ayub M, Liang P, Chen N, Beversdorf D, Liu X. Interplay between maternal Slc6a4 mutation and prenatal stress: a possible mechanism for autistic behavior development. Sci Rep 2017; 7:8735. [PMID: 28821725 PMCID: PMC5562880 DOI: 10.1038/s41598-017-07405-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 02/10/2017] [Accepted: 06/23/2017] [Indexed: 02/05/2023] Open
Abstract
The low activity allele of the maternal polymorphism, 5HTTLPR, in the serotonin transporter, SLC6A4, coupled with prenatal stress is reported to increase the risk for children to develop autism spectrum disorder (ASD). Similarly, maternal Slc6a4 knock-out and prenatal stress in rodents results in offspring demonstrating ASD-like characteristics. The present study uses an integrative genomics approach to explore mechanistic changes in early brain development in mouse embryos exposed to this maternal gene-environment phenomenon. Restraint stress was applied to pregnant Slc6a4 +/+ and Slc6a4 +/- mice and post-stress embryonic brains were assessed for whole genome level profiling of methylome, transcriptome and miRNA using Next Generation Sequencing. Embryos of stressed Slc6a4 +/+ dams exhibited significantly altered methylation profiles and differential expression of 157 miRNAs and 1009 genes affecting neuron development and cellular adhesion pathways, which may function as a coping mechanism to prenatal stress. In striking contrast, the response of embryos of stressed Slc6a4 +/- dams was found to be attenuated, shown by significantly reduced numbers of differentially expressed genes (458) and miRNA (0) and genome hypermethylation. This attenuated response may pose increased risks on typical brain development resulting in development of ASD-like characteristics in offspring of mothers with deficits in serotonin related pathways during stressful pregnancies.
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Affiliation(s)
- Calvin P Sjaarda
- Department of Psychiatry, Queen's University, Kingston, Ontario, Canada.,Queen's Genomics Lab at Ongwanada (QGLO), Ongwanada Resource Center, Kingston, Ontario, Canada
| | - Patrick Hecht
- Interdisciplinary Neuroscience Program, University of Missouri, Columbia, Missouri, USA
| | - Amy J M McNaughton
- Department of Psychiatry, Queen's University, Kingston, Ontario, Canada.,Queen's Genomics Lab at Ongwanada (QGLO), Ongwanada Resource Center, Kingston, Ontario, Canada
| | - Audrina Zhou
- Department of Psychiatry, Queen's University, Kingston, Ontario, Canada.,Queen's Genomics Lab at Ongwanada (QGLO), Ongwanada Resource Center, Kingston, Ontario, Canada
| | - Melissa L Hudson
- Department of Psychiatry, Queen's University, Kingston, Ontario, Canada.,Queen's Genomics Lab at Ongwanada (QGLO), Ongwanada Resource Center, Kingston, Ontario, Canada
| | - Matt J Will
- Psychological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Garth Smith
- Department of Pediatrics, Queen's University, Kingston, Ontario, Canada.,Child Development Centre, Hotel Dieu Hospital, Kingston, Ontario, Canada
| | - Muhammad Ayub
- Department of Psychiatry, Queen's University, Kingston, Ontario, Canada
| | - Ping Liang
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
| | - Nansheng Chen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - David Beversdorf
- Interdisciplinary Neuroscience Program, University of Missouri, Columbia, Missouri, USA.,Departments of Radiology, Neurology, and Psychological Sciences, and the Thompson Center for Autism and Neurodevelopmental Disorders, and William and Nancy Thompson Endowed Chair in Radiology, University of Missouri, Columbia, Missouri, USA
| | - Xudong Liu
- Department of Psychiatry, Queen's University, Kingston, Ontario, Canada. .,Queen's Genomics Lab at Ongwanada (QGLO), Ongwanada Resource Center, Kingston, Ontario, Canada.
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21
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Abstract
The annotation of genomic ranges of interest represents a recurring task for bioinformatics analyses. These ranges can originate from various sources, including peaks called for transcription factor binding sites (TFBS) or histone modification ChIP-seq experiments, chromatin structure and accessibility experiments (such as ATAC-seq), but also from other types of predictions that result in genomic ranges. While peak annotation primarily driven by ChiP-seq was extensively explored, many approaches remain simplistic ("most closely located TSS"), rely on fixed pre-built references, or require complex scripting tasks on behalf of the user. An adaptable, fast, and universal tool, capable to annotate genomic ranges in the respective biological context is critically missing. UROPA (Universal RObust Peak Annotator) is a command line based tool, intended for universal genomic range annotation. Based on a configuration file, different target features can be prioritized with multiple integrated queries. These can be sensitive for feature type, distance, strand specificity, feature attributes (e.g. protein_coding) or anchor position relative to the feature. UROPA can incorporate reference annotation files (GTF) from different sources (Gencode, Ensembl, RefSeq), as well as custom reference annotation files. Statistics and plots transparently summarize the annotation process. UROPA is implemented in Python and R.
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Affiliation(s)
- Maria Kondili
- Max Planck Institute for Heart and Lung Research, Bioinformatics Core Unit (BCU), Ludwigstrasse 43, 61231, Bad Nauheim, Germany
| | - Annika Fust
- Max Planck Institute for Heart and Lung Research, Bioinformatics Core Unit (BCU), Ludwigstrasse 43, 61231, Bad Nauheim, Germany
| | - Jens Preussner
- Max Planck Institute for Heart and Lung Research, Bioinformatics Core Unit (BCU), Ludwigstrasse 43, 61231, Bad Nauheim, Germany
| | - Carsten Kuenne
- Max Planck Institute for Heart and Lung Research, Bioinformatics Core Unit (BCU), Ludwigstrasse 43, 61231, Bad Nauheim, Germany
| | - Thomas Braun
- Max Planck Institute for Heart and Lung Research, Department of Cardiac Development and Remodeling, Ludwigstrasse 43, 61231, Bad Nauheim, Germany.
| | - Mario Looso
- Max Planck Institute for Heart and Lung Research, Bioinformatics Core Unit (BCU), Ludwigstrasse 43, 61231, Bad Nauheim, Germany.
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