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Genomic Characterization of Cisplatin Response Uncovers Priming of Cisplatin-Induced Genes in a Resistant Cell Line. Int J Mol Sci 2021; 22:ijms22115814. [PMID: 34071702 PMCID: PMC8198185 DOI: 10.3390/ijms22115814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
Cisplatin is a chemotherapy drug that kills cancer cells by damaging their DNA. In human cells, this damage is repaired primarily by nucleotide excision repair. While cisplatin is generally effective, many cancers exhibit initial or acquired resistance to it. Here, we studied cisplatin resistance in a defined cell line system. We conducted a comprehensive genomic characterization of the cisplatin-sensitive A2780 ovarian cancer cell line compared to A2780cis, its resistant derivative. The resistant cells acquired less damage, but had similar repair kinetics. Genome-wide mapping of nucleotide excision repair showed a shift in the resistant cells from global genome towards transcription-coupled repair. By mapping gene expression changes following cisplatin treatment, we identified 56 upregulated genes that have higher basal expression in the resistant cell line, suggesting they are primed for a cisplatin response. More than half of these genes are novel to cisplatin- or damage-response. Six out of seven primed genes tested were upregulated in response to cisplatin in additional cell lines, making them attractive candidates for future investigation. These novel candidates for cisplatin resistance could prove to be important prognostic markers or targets for tailored combined therapy in the future.
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Wang W, Auer P, Zhang T, Spellman S, Carlson KS, Nazha A, Bolon YT, Saber W. Impact of Epigenomic Hypermethylation at TP53 on Allogeneic Hematopoietic Cell Transplantation Outcomes for Myelodysplastic Syndromes. Transplant Cell Ther 2021; 27:659.e1-659.e6. [PMID: 33992829 PMCID: PMC8421055 DOI: 10.1016/j.jtct.2021.04.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/03/2021] [Accepted: 04/29/2021] [Indexed: 01/25/2023]
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of hematopoietic stem cell disorders for which allogeneic hematopoietic cell transplantation (HCT) is currently the sole curative treatment. Epigenetic lesions are considered a major pathogenetic determinant in many cancers, and in MDS, epigenetic-based interventions have emerged as life-prolonging therapies. However, the impact of epigenomic aberrations on HCT outcomes among patients with MDS are not well understood. We hypothesized that epigenomic signatures in MDS patients before undergoing HCT serve as a novel prognostic indicator of the risk of post-HCT MDS relapse. To evaluate these epigenomic signatures in MDS patients, we analyzed reduced representation bisulfite sequencing profiles in a matched case-control population of 94 patients. Among these HCT recipients, 47 patients with MDS who relapsed post-HCT (cases) were matched 1:1 to patients with MDS who did not relapse (controls). Only patients with wild-type TP53, RAS pathway, and JAK2 mutations were included in this study to promote the discovery of novel factors. Cases were matched with controls based on conditioning regimen intensity, age, sex, Revised International Prognostic Scoring System, Karnofsky Performance Status, graft type, and donor type. Pre-HCT whole-blood samples from cases and matched controls were obtained from the Center for International Blood and Marrow Transplant Research repository. We comprehensively identified differentially methylated regions (DMRs) by comparing the methylation patterns among matched cases and controls. Our findings show that cases displayed more hyper-DMRs pretransplantation compared with controls, even after adjusting for pre-HCT use of hypomethylating agents. Hyper-DMRs specific to cases were mapped to the transcription start site of 218 unique genes enriched in 5 different signaling pathways that may serve as regions of interest and factors to consider as prognostic determinants of post-HCT relapse in MDS patients. Interestingly, although patients selected for this cohort were wild-type for the TP53 gene, cases showed significantly greater levels of methylation at TP53 compared with controls. These findings indicate that previously identified prognostic genes for MDS, such as TP53, may affect disease relapse not only through genetic mutation, but also through epigenetic methylation mechanisms.
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Affiliation(s)
- Wei Wang
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
| | - Paul Auer
- National Marrow Donor Program/Be the Match, Minneapolis, Minnesota
| | - Tao Zhang
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
| | - Stephen Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, Minnesota
| | | | - Aziz Nazha
- Leukemia Program, Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Avon Lake, Ohio
| | - Yung-Tsi Bolon
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, Minnesota.
| | - Wael Saber
- Center for International Blood and Marrow Transplant Research, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
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Agostini F, Zagalak J, Attig J, Ule J, Luscombe NM. Intergenic RNA mainly derives from nascent transcripts of known genes. Genome Biol 2021; 22:136. [PMID: 33952325 PMCID: PMC8097831 DOI: 10.1186/s13059-021-02350-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/12/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Eukaryotic genomes undergo pervasive transcription, leading to the production of many types of stable and unstable RNAs. Transcription is not restricted to regions with annotated gene features but includes almost any genomic context. Currently, the source and function of most RNAs originating from intergenic regions in the human genome remain unclear. RESULTS We hypothesize that many intergenic RNAs can be ascribed to the presence of as-yet unannotated genes or the "fuzzy" transcription of known genes that extends beyond the annotated boundaries. To elucidate the contributions of these two sources, we assemble a dataset of more than 2.5 billion publicly available RNA-seq reads across 5 human cell lines and multiple cellular compartments to annotate transcriptional units in the human genome. About 80% of transcripts from unannotated intergenic regions can be attributed to the fuzzy transcription of existing genes; the remaining transcripts originate mainly from putative long non-coding RNA loci that are rarely spliced. We validate the transcriptional activity of these intergenic RNAs using independent measurements, including transcriptional start sites, chromatin signatures, and genomic occupancies of RNA polymerase II in various phosphorylation states. We also analyze the nuclear localization and sensitivities of intergenic transcripts to nucleases to illustrate that they tend to be rapidly degraded either on-chromatin by XRN2 or off-chromatin by the exosome. CONCLUSIONS We provide a curated atlas of intergenic RNAs that distinguishes between alternative processing of well-annotated genes from independent transcriptional units based on the combined analysis of chromatin signatures, nuclear RNA localization, and degradation pathways.
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Affiliation(s)
| | - Julian Zagalak
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Jan Attig
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jernej Ule
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- UCL Genetics Institute, Department of Genetics, Environment and Evolution, University College London, Gower Street, London, WC1E 6BT, UK
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
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104
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Cabré N, Luciano-Mateo F, Chapski DJ, Baiges-Gaya G, Fernández-Arroyo S, Hernández-Aguilera A, Castañé H, Rodríguez-Tomàs E, París M, Sabench F, Del Castillo D, Del Bas JM, Tomé M, Bodineau C, Sola-García A, López-Miranda J, Martín-Montalvo A, Durán RV, Vondriska TM, Rosa-Garrido M, Camps J, Menéndez JA, Joven J. Glutaminolysis-induced mTORC1 activation drives non-alcoholic steatohepatitis progression. J Hepatol 2021:S0168-8278(21)00302-0. [PMID: 33961941 DOI: 10.1016/j.jhep.2021.04.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS A holistic insight on the relationship between obesity and metabolic dysfunction-associated fatty liver disease is an unmet clinical need. Omics investigations can be used to investigate the multifaceted role of altered mitochondrial pathways to promote nonalcoholic steatohepatitis, a major risk factor for liver disease-associated death. There are no specific treatments but remission via surgery might offer an opportunity to examine the signaling processes that govern the complex spectrum of chronic liver diseases observed in extreme obesity. We aim to assess the emerging relationship between metabolism, methylation and liver disease. METHODS We tailed the flow of information, before and after steatohepatitis remission, from biochemical, histological, and multi-omics analyses in liver biopsies from patients with extreme obesity and successful bariatric surgery. Functional studies were performed in HepG2 cells and primary hepatocytes. RESULTS The reversal of hepatic mitochondrial dysfunction and the control of oxidative stress and inflammatory responses revealed the regulatory role of mitogen-activated protein kinases. The reversible metabolic rearrangements leading to steatohepatitis increased the glutaminolysis-induced production of α-ketoglutarate and the hyperactivation of mammalian target of rapamycin complex 1. These changes were crucial for the adenosine monophosphate-activated protein kinase/mammalian target of rapamycin-driven pathways that modulated hepatocyte survival by coordinating apoptosis and autophagy. The signaling activity of α-ketoglutarate and the associated metabolites also affected methylation-related epigenomic remodeling enzymes. Integrative analysis of hepatic transcriptome signatures and differentially methylated genomic regions distinguished patients with and without steatohepatitis. CONCLUSION We provide evidence supporting the multifaceted potential of the increased glutaminolysis-induced α-ketoglutarate production and the mammalian target of rapamycin complex 1 dysregulation as a conceivable source of the inefficient adaptive responses leading to steatohepatitis. LAY SUMMARY Steatohepatitis is a frequent and threatening complication of extreme obesity without specific treatment. Omics technologies can be used to identify therapeutic targets. We highlight increased glutaminolysis-induced α-ketoglutarate production as a potential source of signals promoting and exacerbating steatohepatitis.
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Affiliation(s)
- Noemí Cabré
- Universitat Rovira i Virgili, Department of Medicine and Surgery, Reus, Spain; Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Fedra Luciano-Mateo
- Universitat Rovira i Virgili, Department of Medicine and Surgery, Reus, Spain; Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Douglas J Chapski
- Department of Anesthesiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, US
| | - Gerard Baiges-Gaya
- Universitat Rovira i Virgili, Department of Medicine and Surgery, Reus, Spain; Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Salvador Fernández-Arroyo
- Universitat Rovira i Virgili, Department of Medicine and Surgery, Reus, Spain; Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Anna Hernández-Aguilera
- Universitat Rovira i Virgili, Department of Medicine and Surgery, Reus, Spain; Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Helena Castañé
- Universitat Rovira i Virgili, Department of Medicine and Surgery, Reus, Spain; Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Elisabet Rodríguez-Tomàs
- Universitat Rovira i Virgili, Department of Medicine and Surgery, Reus, Spain; Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Marta París
- Department of Surgery, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Fàtima Sabench
- Department of Surgery, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Daniel Del Castillo
- Department of Surgery, Hospital Universitari de Sant Joan, Institut d'Investigació Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Josep M Del Bas
- Technological Unit of Nutrition and Health, EURECAT-Technology Centre of Catalonia, Reus, Spain
| | - Mercedes Tomé
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas - Universidad Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain
| | - Clément Bodineau
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas - Universidad Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain; Institut Européen de Chimie et Biologie, INSERM U1218, Université de Bordeaux, 2 Rue Robert Escarpit, Pessac 33607, France
| | - Alejandro Sola-García
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas - Universidad Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain
| | - José López-Miranda
- Lipids and Atherosclerosis Unit, IMIBIC/Reina Sofia University Hospital. University of Cordoba, Cordoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Cordoba, Spain
| | - Alejandro Martín-Montalvo
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas - Universidad Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain
| | - Raúl V Durán
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas - Universidad Pablo de Olavide, Avda. Américo Vespucio 24, 41092 Sevilla, Spain; Institut Européen de Chimie et Biologie, INSERM U1218, Université de Bordeaux, 2 Rue Robert Escarpit, Pessac 33607, France
| | - Thomas M Vondriska
- Department of Anesthesiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, US
| | - Manuel Rosa-Garrido
- Department of Anesthesiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, US
| | - Jordi Camps
- Universitat Rovira i Virgili, Department of Medicine and Surgery, Reus, Spain; Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain.
| | - Javier A Menéndez
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group , Catalan Institute of Oncology, Girona , Spain; Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Jorge Joven
- Universitat Rovira i Virgili, Department of Medicine and Surgery, Reus, Spain; Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigacio Sanitaria Pere Virgili, Universitat Rovira i Virgili, Reus, Spain; The Campus of International Excellence Southern Catalonia, Tarragona, Spain.
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105
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Salifou K, Burnard C, Basavarajaiah P, Grasso G, Helsmoortel M, Mac V, Depierre D, Franckhauser C, Beyne E, Contreras X, Dejardin J, Rouquier S, Cuvier O, Kiernan R. Chromatin-associated MRN complex protects highly transcribing genes from genomic instability. SCIENCE ADVANCES 2021; 7:7/21/eabb2947. [PMID: 34020942 PMCID: PMC8139584 DOI: 10.1126/sciadv.abb2947] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 03/31/2021] [Indexed: 05/05/2023]
Abstract
MRN-MDC1 plays a central role in the DNA damage response (DDR) and repair. Using proteomics of isolated chromatin fragments, we identified DDR factors, such as MDC1, among those highly associating with a genomic locus upon transcriptional activation. Purification of MDC1 in the absence of exogenous DNA damage revealed interactions with factors involved in gene expression and RNA processing, in addition to DDR factors. ChIP-seq showed that MRN subunits, MRE11 and NBS1, colocalized throughout the genome, notably at TSSs and bodies of actively transcribing genes, which was dependent on the RNAPII transcriptional complex rather than transcription per se. Depletion of MRN increased RNAPII abundance at MRE11/NBS1-bound genes. Prolonged MRE11 or NBS1 depletion induced single-nucleotide polymorphisms across actively transcribing MRN target genes. These data suggest that association of MRN with the transcriptional machinery constitutively scans active genes for transcription-induced DNA damage to preserve the integrity of the coding genome.
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Affiliation(s)
- Kader Salifou
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Callum Burnard
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
- Center of Integrative Biology (CBI) CNRS/Université de Toulouse (UMR 5077), 31000, France
| | - Poornima Basavarajaiah
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Giuseppa Grasso
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Marion Helsmoortel
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Victor Mac
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - David Depierre
- Center of Integrative Biology (CBI) CNRS/Université de Toulouse (UMR 5077), 31000, France
| | - Céline Franckhauser
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Emmanuelle Beyne
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Xavier Contreras
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Jérôme Dejardin
- CNRS-UMR 9002, IGH/University of Montpellier, Biology of Repeated Sequences Lab, 34396, France
| | - Sylvie Rouquier
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Olivier Cuvier
- Center of Integrative Biology (CBI) CNRS/Université de Toulouse (UMR 5077), 31000, France
| | - Rosemary Kiernan
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France.
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106
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Patty BJ, Hainer SJ. Transcription factor chromatin profiling genome-wide using uliCUT&RUN in single cells and individual blastocysts. Nat Protoc 2021; 16:2633-2666. [PMID: 33911257 PMCID: PMC8177051 DOI: 10.1038/s41596-021-00516-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/04/2021] [Indexed: 02/02/2023]
Abstract
Determining chromatin-associated protein localization across the genome has provided insight into the functions of DNA-binding proteins and their connections to disease. However, established protocols requiring large quantities of cell or tissue samples currently limit applications for clinical and biomedical research in this field. Furthermore, most technologies have been optimized to assess abundant histone protein localization, prohibiting the investigation of nonhistone protein localization in low cell numbers. We recently described a protocol to profile chromatin-associated protein localization in as low as one cell: ultra-low-input cleavage under targets and release using nuclease (uliCUT&RUN). Optimized from chromatin immunocleavage and CUT&RUN, uliCUT&RUN is a tethered enzyme-based protocol that utilizes a combination of recombinant protein, antibody recognition and stringent purification to selectively target proteins of interest and isolate the associated DNA. Performed in native conditions, uliCUT&RUN profiles protein localization to chromatin with low input and high precision. Compared with other profiling technologies, uliCUT&RUN can determine nonhistone protein chromatin occupancies in low cell numbers, permitting the investigation into the molecular functions of a range of DNA-binding proteins within rare samples. From sample preparation to sequencing library submission, the uliCUT&RUN protocol takes <2 d to perform, with the accompanying data analysis timeline dependent on experience level.
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Affiliation(s)
- Benjamin J Patty
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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107
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Garcia-Lozano M, Natarajan P, Levi A, Katam R, Lopez-Ortiz C, Nimmakayala P, Reddy UK. Altered chromatin conformation and transcriptional regulation in watermelon following genome doubling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:588-600. [PMID: 33788333 DOI: 10.1111/tpj.15256] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Polyploidy has played a crucial role in plant evolution, development and function. Synthetic autopolyploid represents an ideal system to investigate the effects of polyploidization on transcriptional regulation. In this study, we deciphered the impact of genome duplication at phenotypic and molecular levels in watermelon. Overall, 88% of the genes in tetraploid watermelon followed a >1:1 dosage effect, and accordingly, differentially expressed genes were largely upregulated. In addition, a great number of hypomethylated regions (1688) were identified in an isogenic tetraploid watermelon. These differentially methylated regions were localized in promoters and intergenic regions and near transcriptional start sites of the identified upregulated genes, which enhances the importance of methylation in gene regulation. These changes were reflected in sophisticated higher-order chromatin structures. The genome doubling caused switching of 108 A and 626 B compartments that harbored genes associated with growth, development and stress responses.
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Affiliation(s)
- Marleny Garcia-Lozano
- Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, Charleston, WV, USA
| | - Purushothaman Natarajan
- Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, Charleston, WV, USA
| | - Amnon Levi
- USDA, ARS, U.S. Vegetable Lab, Charleston, SC, USA
| | - Ramesh Katam
- Department of Biological Sciences, Florida A&M University, Tallahassee, FL, USA
| | - Carlos Lopez-Ortiz
- Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, Charleston, WV, USA
| | - Padma Nimmakayala
- Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, Charleston, WV, USA
| | - Umesh K Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, Charleston, WV, USA
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108
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Bleu M, Mermet-Meillon F, Apfel V, Barys L, Holzer L, Bachmann Salvy M, Lopes R, Amorim Monteiro Barbosa I, Delmas C, Hinniger A, Chau S, Kaufmann M, Haenni S, Berneiser K, Wahle M, Moravec I, Vissières A, Poetsch T, Ahrné E, Carte N, Voshol J, Bechter E, Hamon J, Meyerhofer M, Erdmann D, Fischer M, Stachyra T, Freuler F, Gutmann S, Fernández C, Schmelzle T, Naumann U, Roma G, Lawrenson K, Nieto-Oberhuber C, Cobos-Correa A, Ferretti S, Schübeler D, Galli GG. PAX8 and MECOM are interaction partners driving ovarian cancer. Nat Commun 2021; 12:2442. [PMID: 33903593 PMCID: PMC8076227 DOI: 10.1038/s41467-021-22708-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/26/2021] [Indexed: 11/25/2022] Open
Abstract
The transcription factor PAX8 is critical for the development of the thyroid and urogenital system. Comprehensive genomic screens furthermore indicate an additional oncogenic role for PAX8 in renal and ovarian cancers. While a plethora of PAX8-regulated genes in different contexts have been proposed, we still lack a mechanistic understanding of how PAX8 engages molecular complexes to drive disease-relevant oncogenic transcriptional programs. Here we show that protein isoforms originating from the MECOM locus form a complex with PAX8. These include MDS1-EVI1 (also called PRDM3) for which we map its interaction with PAX8 in vitro and in vivo. We show that PAX8 binds a large number of genomic sites and forms transcriptional hubs. At a subset of these, PAX8 together with PRDM3 regulates a specific gene expression module involved in adhesion and extracellular matrix. This gene module correlates with PAX8 and MECOM expression in large scale profiling of cell lines, patient-derived xenografts (PDXs) and clinical cases and stratifies gynecological cancer cases with worse prognosis. PRDM3 is amplified in ovarian cancers and we show that the MECOM locus and PAX8 sustain in vivo tumor growth, further supporting that the identified function of the MECOM locus underlies PAX8-driven oncogenic functions in ovarian cancer.
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Affiliation(s)
- Melusine Bleu
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Fanny Mermet-Meillon
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Verena Apfel
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Louise Barys
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Laura Holzer
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Rui Lopes
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Cecile Delmas
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Alexandra Hinniger
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Suzanne Chau
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Markus Kaufmann
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Simon Haenni
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Karolin Berneiser
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
- Biozentrum, University of Basel, Basel, Switzerland
| | - Maria Wahle
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Ivana Moravec
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Alexandra Vissières
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Tania Poetsch
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Erik Ahrné
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Nathalie Carte
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Johannes Voshol
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Elisabeth Bechter
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Jacques Hamon
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Marco Meyerhofer
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Dirk Erdmann
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Matteo Fischer
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Therese Stachyra
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Felix Freuler
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Sascha Gutmann
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - César Fernández
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Tobias Schmelzle
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Ulrike Naumann
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Guglielmo Roma
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Kate Lawrenson
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA
| | | | - Amanda Cobos-Correa
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Stephane Ferretti
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, University of Basel, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Giorgio Giacomo Galli
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland.
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109
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Mesnage R, Teixeira M, Mandrioli D, Falcioni L, Ibragim M, Ducarmon QR, Zwittink RD, Amiel C, Panoff JM, Bourne E, Savage E, Mein CA, Belpoggi F, Antoniou MN. Multi-omics phenotyping of the gut-liver axis reveals metabolic perturbations from a low-dose pesticide mixture in rats. Commun Biol 2021; 4:471. [PMID: 33854195 PMCID: PMC8046807 DOI: 10.1038/s42003-021-01990-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/15/2021] [Indexed: 12/24/2022] Open
Abstract
Health effects of pesticides are not always accurately detected using the current battery of regulatory toxicity tests. We compared standard histopathology and serum biochemistry measures and multi-omics analyses in a subchronic toxicity test of a mixture of six pesticides frequently detected in foodstuffs (azoxystrobin, boscalid, chlorpyrifos, glyphosate, imidacloprid and thiabendazole) in Sprague-Dawley rats. Analysis of water and feed consumption, body weight, histopathology and serum biochemistry showed little effect. Contrastingly, serum and caecum metabolomics revealed that nicotinamide and tryptophan metabolism were affected, which suggested activation of an oxidative stress response. This was not reflected by gut microbial community composition changes evaluated by shotgun metagenomics. Transcriptomics of the liver showed that 257 genes had their expression changed. Gene functions affected included the regulation of response to steroid hormones and the activation of stress response pathways. Genome-wide DNA methylation analysis of the same liver samples showed that 4,255 CpG sites were differentially methylated. Overall, we demonstrated that in-depth molecular profiling in laboratory animals exposed to low concentrations of pesticides allows the detection of metabolic perturbations that would remain undetected by standard regulatory biochemical measures and which could thus improve the predictability of health risks from exposure to chemical pollutants.
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Affiliation(s)
- Robin Mesnage
- Gene Expression and Therapy Group, King's College London, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, Guy's Hospital, London, UK
| | - Maxime Teixeira
- UR Aliments Bioprocédés Toxicologie Environnements, EA 4651, University of Caen Normandy (UCN), Caen, France
| | | | | | - Mariam Ibragim
- Gene Expression and Therapy Group, King's College London, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, Guy's Hospital, London, UK
| | - Quinten Raymond Ducarmon
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Romy Daniëlle Zwittink
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Caroline Amiel
- UR Aliments Bioprocédés Toxicologie Environnements, EA 4651, University of Caen Normandy (UCN), Caen, France
| | - Jean-Michel Panoff
- UR Aliments Bioprocédés Toxicologie Environnements, EA 4651, University of Caen Normandy (UCN), Caen, France
| | - Emma Bourne
- Genome Centre, Barts and the London School of Medicine and Dentistry, Blizard Institute, London, UK
| | - Emanuel Savage
- Genome Centre, Barts and the London School of Medicine and Dentistry, Blizard Institute, London, UK
| | - Charles A Mein
- Genome Centre, Barts and the London School of Medicine and Dentistry, Blizard Institute, London, UK
| | | | - Michael N Antoniou
- Gene Expression and Therapy Group, King's College London, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, Guy's Hospital, London, UK.
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110
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Hu J, Wuitchik SJS, Barry TN, Jamniczky HA, Rogers SM, Barrett RDH. Heritability of DNA methylation in threespine stickleback (Gasterosteus aculeatus). Genetics 2021; 217:1-15. [PMID: 33683369 PMCID: PMC8045681 DOI: 10.1093/genetics/iyab001] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022] Open
Abstract
Epigenetic mechanisms underlying phenotypic change are hypothesized to contribute to population persistence and adaptation in the face of environmental change. To date, few studies have explored the heritability of intergenerationally stable methylation levels in natural populations, and little is known about the relative contribution of cis- and trans-regulatory changes to methylation variation. Here, we explore the heritability of DNA methylation, and conduct methylation quantitative trait loci (meQTLs) analysis to investigate the genetic architecture underlying methylation variation between marine and freshwater ecotypes of threespine stickleback (Gasterosteus aculeatus). We quantitatively measured genome-wide DNA methylation in fin tissue using reduced representation bisulfite sequencing of F1 and F2 crosses, and their marine and freshwater source populations. We identified cytosines (CpG sites) that exhibited stable methylation levels across generations. We found that additive genetic variance explained an average of 24-35% of the methylation variance, with a number of CpG sites possibly autonomous from genetic control. We also detected both cis- and trans-meQTLs, with only trans-meQTLs overlapping with previously identified genomic regions of high differentiation between marine and freshwater ecotypes. Finally, we identified the genetic architecture underlying two key CpG sites that were differentially methylated between ecotypes. These findings demonstrate a potential role for DNA methylation in facilitating adaptation to divergent environments and improve our understanding of the heritable basis of population epigenomic variation.
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Affiliation(s)
- Juntao Hu
- National Observation and Research Station for Yangtze Estuarine Wetland Ecosystems, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Institute of Biodiversity Science, Fudan University, Shanghai 200438, China
- Redpath Museum and Department of Biology, McGill University, Montreal, QC H3A 0C4, Canada
| | - Sara J S Wuitchik
- Informatics Group, Harvard University, Cambridge, MA 02138, USA
- Department of Biology, Boston University, Boston, MA 02215, USA
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Tegan N Barry
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Heather A Jamniczky
- Department of Cell Biology and Anatomy, McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Sean M Rogers
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Rowan D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, QC H3A 0C4, Canada
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111
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Heilbrun EE, Merav M, Adar S. Exons and introns exhibit transcriptional strand asymmetry of dinucleotide distribution, damage formation and DNA repair. NAR Genom Bioinform 2021; 3:lqab020. [PMID: 33817640 PMCID: PMC8002178 DOI: 10.1093/nargab/lqab020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/24/2021] [Accepted: 03/22/2021] [Indexed: 12/29/2022] Open
Abstract
Recent cancer sequencing efforts have uncovered asymmetry in DNA damage induced mutagenesis between the transcribed and non-transcribed strands of genes. Here, we investigate the major type of damage induced by ultraviolet (UV) radiation, the cyclobutane pyrimidine dimers (CPDs), which are formed primarily in TT dinucleotides. We reveal that a transcriptional asymmetry already exists at the level of TT dinucleotide frequency and therefore also in CPD damage formation. This asymmetry is conserved in vertebrates and invertebrates and is completely reversed between introns and exons. We show the asymmetry in introns is linked to the transcription process itself, and is also found in enhancer elements. In contrast, the asymmetry in exons is not correlated to transcription, and is associated with codon usage preferences. Reanalysis of nucleotide excision repair, normalizing repair to the underlying TT frequencies, we show repair of CPDs is more efficient in exons compared to introns, contributing to the maintenance and integrity of coding regions. Our results highlight the importance of considering the primary sequence of the DNA in determining DNA damage sensitivity and mutagenic potential.
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Affiliation(s)
- Elisheva E Heilbrun
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem, Jerusalem 91120, Israel
| | - May Merav
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem, Jerusalem 91120, Israel
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem, Jerusalem 91120, Israel
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112
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Kundu P, Torres ERS, Stagaman K, Kasschau K, Okhovat M, Holden S, Ward S, Nevonen KA, Davis BA, Saito T, Saido TC, Carbone L, Sharpton TJ, Raber J. Integrated analysis of behavioral, epigenetic, and gut microbiome analyses in App NL-G-F, App NL-F, and wild type mice. Sci Rep 2021; 11:4678. [PMID: 33633159 PMCID: PMC7907263 DOI: 10.1038/s41598-021-83851-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/09/2021] [Indexed: 12/19/2022] Open
Abstract
Epigenetic mechanisms occurring in the brain as well as alterations in the gut microbiome composition might contribute to Alzheimer’s disease (AD). Human amyloid precursor protein knock-in (KI) mice contain the Swedish and Iberian mutations (AppNL-F) or those two and also the Arctic mutation (AppNL-G-F). In this study, we assessed whether behavioral and cognitive performance in 6-month-old AppNL-F, AppNL-G-F, and C57BL/6J wild-type (WT) mice was associated with the gut microbiome, and whether the genotype modulates this association. The genotype effects observed in behavioral tests were test-dependent. The biodiversity and composition of the gut microbiome linked to various aspects of mouse behavioral and cognitive performance but differences in genotype modulated these relationships. These genotype-dependent associations include members of the Lachnospiraceae and Ruminococcaceae families. In a subset of female mice, we assessed DNA methylation in the hippocampus and investigated whether alterations in hippocampal DNA methylation were associated with the gut microbiome. Among other differentially methylated regions, we identified a 1 Kb region that overlapped ing 3′UTR of the Tomm40 gene and the promoter region of the Apoe gene that and was significantly more methylated in the hippocampus of AppNL-G-F than WT mice. The integrated gut microbiome hippocampal DNA methylation analysis revealed a positive relationship between amplicon sequence variants (ASVs) within the Lachnospiraceae family and methylation at the Apoe gene. Hence, these microbes may elicit an impact on AD-relevant behavioral and cognitive performance via epigenetic changes in AD-susceptibility genes in neural tissue or that such changes in the epigenome can elicit alterations in intestinal physiology that affect the growth of these taxa in the gut microbiome.
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Affiliation(s)
- Payel Kundu
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Eileen Ruth S Torres
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Keaton Stagaman
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA
| | - Kristin Kasschau
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA
| | - Mariam Okhovat
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Sarah Holden
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Samantha Ward
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Kimberly A Nevonen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Brett A Davis
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Takashi Saito
- Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, 97239, USA.,Departments of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, USA.,Departments of Medical Informatics and Clinical Epidemiology, Portland, OR, 97239, USA.,Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, 97006, USA
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, 97331, USA.,Department of Statistics, Oregon State University, Corvallis, OR, 97331, USA
| | - Jacob Raber
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, 97239, USA. .,Departments of Neurology, Psychiatry, and Radiation Medicine, Division of Neuroscience ONPRC, Oregon Health & Science University, Portland, OR, 97239, USA. .,College of Pharmacy, Oregon State University, Corvallis, OR, 97331, USA. .,Department of Behavioral Neuroscience, L470, Oregon Health & Science University, 3181SW Sam Jackson Park Road, Portland, OR, 97239, USA.
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113
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Blumberg A, Zhao Y, Huang YF, Dukler N, Rice EJ, Chivu AG, Krumholz K, Danko CG, Siepel A. Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data. BMC Biol 2021; 19:30. [PMID: 33588838 PMCID: PMC7885420 DOI: 10.1186/s12915-021-00949-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/05/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The concentrations of distinct types of RNA in cells result from a dynamic equilibrium between RNA synthesis and decay. Despite the critical importance of RNA decay rates, current approaches for measuring them are generally labor-intensive, limited in sensitivity, and/or disruptive to normal cellular processes. Here, we introduce a simple method for estimating relative RNA half-lives that is based on two standard and widely available high-throughput assays: Precision Run-On sequencing (PRO-seq) and RNA sequencing (RNA-seq). RESULTS Our method treats PRO-seq as a measure of transcription rate and RNA-seq as a measure of RNA concentration, and estimates the rate of RNA decay required for a steady-state equilibrium. We show that this approach can be used to assay relative RNA half-lives genome-wide, with good accuracy and sensitivity for both coding and noncoding transcription units. Using a structural equation model (SEM), we test several features of transcription units, nearby DNA sequences, and nearby epigenomic marks for associations with RNA stability after controlling for their effects on transcription. We find that RNA splicing-related features are positively correlated with RNA stability, whereas features related to miRNA binding and DNA methylation are negatively correlated with RNA stability. Furthermore, we find that a measure based on U1 binding and polyadenylation sites distinguishes between unstable noncoding and stable coding transcripts but is not predictive of relative stability within the mRNA or lincRNA classes. We also identify several histone modifications that are associated with RNA stability. CONCLUSION We introduce an approach for estimating the relative half-lives of individual RNAs. Together, our estimation method and systematic analysis shed light on the pervasive impacts of RNA stability on cellular RNA concentrations.
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Affiliation(s)
- Amit Blumberg
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yixin Zhao
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yi-Fei Huang
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Present Address: Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Noah Dukler
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Alexandra G Chivu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Katie Krumholz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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114
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Interspecific Variation in One-Carbon Metabolism within the Ovarian Follicle, Oocyte, and Preimplantation Embryo: Consequences for Epigenetic Programming of DNA Methylation. Int J Mol Sci 2021; 22:ijms22041838. [PMID: 33673278 PMCID: PMC7918761 DOI: 10.3390/ijms22041838] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 02/07/2023] Open
Abstract
One-carbon (1C) metabolism provides methyl groups for the synthesis and/or methylation of purines and pyrimidines, biogenic amines, proteins, and phospholipids. Our understanding of how 1C pathways operate, however, pertains mostly to the (rat) liver. Here we report that transcripts for all bar two genes (i.e., BHMT, MAT1A) encoding enzymes in the linked methionine-folate cycles are expressed in all cell types within the ovarian follicle, oocyte, and blastocyst in the cow, sheep, and pig; as well as in rat granulosa cells (GCs) and human KGN cells (a granulosa-like tumor cell line). Betaine-homocysteine methyltransferase (BHMT) protein was absent in bovine theca and GCs, as was activity of this enzyme in GCs. Mathematical modeling predicted that absence of this enzyme would lead to more volatile S-adenosylmethionine-mediated transmethylation in response to 1C substrate (e.g., methionine) or cofactor provision. We tested the sensitivity of bovine GCs to reduced methionine (from 50 to 10 µM) and observed a diminished flux of 1C units through the methionine cycle. We then used reduced-representation bisulfite sequencing to demonstrate that this reduction in methionine during bovine embryo culture leads to genome-wide alterations to DNA methylation in >1600 genes, including a cohort of imprinted genes linked to an abnormal fetal-overgrowth phenotype. Bovine ovarian and embryonic cells are acutely sensitive to methionine, but further experimentation is required to determine the significance of interspecific variation in BHMT expression.
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115
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Genome-wide analysis of allele-specific expression of genes in the model diatom Phaeodactylum tricornutum. Sci Rep 2021; 11:2954. [PMID: 33536552 PMCID: PMC7859220 DOI: 10.1038/s41598-021-82529-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/15/2021] [Indexed: 01/04/2023] Open
Abstract
Recent advances in next generation sequencing technologies have allowed the discovery of widespread autosomal allele-specific expression (aASE) in mammals and plants with potential phenotypic effects. Extensive numbers of genes with allele-specific expression have been described in the diatom Fragilariopsis cylindrus in association with adaptation to external cues, as well as in Fistulifera solaris in the context of natural hybridization. However, the role of aASE and its extent in diatoms remain elusive. In this study, we investigate allele-specific expression in the model diatom Phaeodactylum tricornutum by the re-analysis of previously published whole genome RNA sequencing data and polymorphism calling. We found that 22% of P. tricornutum genes show moderate bias in allelic expression while 1% show nearly complete monoallelic expression. Biallelic expression associates with genes encoding components of protein metabolism while moderately biased genes associate with functions in catabolism and protein transport. We validated candidate genes by pyrosequencing and found that moderate biases in allelic expression were less stable than monoallelically expressed genes that showed consistent bias upon experimental validations at the population level and in subcloning experiments. Our approach provides the basis for the analysis of aASE in P. tricornutum and could be routinely implemented to test for variations in allele expression under different environmental conditions.
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116
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Hu X, Estecio MR, Chen R, Reuben A, Wang L, Fujimoto J, Carrot-Zhang J, McGranahan N, Ying L, Fukuoka J, Chow CW, Pham HHN, Godoy MCB, Carter BW, Behrens C, Zhang J, Antonoff MB, Sepesi B, Lu Y, Pass HI, Kadara H, Scheet P, Vaporciyan AA, Heymach JV, Wistuba II, Lee JJ, Futreal PA, Su D, Issa JPJ, Zhang J. Evolution of DNA methylome from precancerous lesions to invasive lung adenocarcinomas. Nat Commun 2021; 12:687. [PMID: 33514726 PMCID: PMC7846738 DOI: 10.1038/s41467-021-20907-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/17/2020] [Indexed: 12/17/2022] Open
Abstract
The evolution of DNA methylome and methylation intra-tumor heterogeneity (ITH) during early carcinogenesis of lung adenocarcinoma has not been systematically studied. We perform reduced representation bisulfite sequencing of invasive lung adenocarcinoma and its precursors, atypical adenomatous hyperplasia, adenocarcinoma in situ and minimally invasive adenocarcinoma. We observe gradual increase of methylation aberrations and significantly higher level of methylation ITH in later-stage lesions. The phylogenetic patterns inferred from methylation aberrations resemble those based on somatic mutations suggesting parallel methylation and genetic evolution. De-convolution reveal higher ratio of T regulatory cells (Tregs) versus CD8 + T cells in later-stage diseases, implying progressive immunosuppression with neoplastic progression. Furthermore, increased global hypomethylation is associated with higher mutation burden, copy number variation burden and AI burden as well as higher Treg/CD8 ratio, highlighting the potential impact of methylation on chromosomal instability, mutagenesis and tumor immune microenvironment during early carcinogenesis of lung adenocarcinomas.
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Affiliation(s)
- Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Marcos R Estecio
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Center of Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Runzhe Chen
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alexandre Reuben
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Junya Fujimoto
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jian Carrot-Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Nicholas McGranahan
- Cancer Research United Kingdom-University College London Lung Cancer Centre of Excellence, London, SW73RP, UK
| | - Lisha Ying
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, 310022, Hangzhou, China
- Zhejiang Cancer Research Institute, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), 310022, Hangzhou, China
| | - Junya Fukuoka
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 8528523, Japan
| | - Chi-Wan Chow
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hoa H N Pham
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 8528523, Japan
| | - Myrna C B Godoy
- Department of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Brett W Carter
- Department of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Carmen Behrens
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mara B Antonoff
- Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Boris Sepesi
- Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Center of Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, NY, 10016, USA
| | - Humam Kadara
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ara A Vaporciyan
- Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - John V Heymach
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ignacio I Wistuba
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Dan Su
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), 310022, Hangzhou, China.
| | | | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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Luo H, Wei W, Ye Z, Zheng J, Xu RH. Liquid Biopsy of Methylation Biomarkers in Cell-Free DNA. Trends Mol Med 2021; 27:482-500. [PMID: 33500194 DOI: 10.1016/j.molmed.2020.12.011] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 02/09/2023]
Abstract
Liquid biopsies, in particular, analysis of cell-free DNA (cfDNA), have emerged as a promising noninvasive diagnostic approach in oncology. Abnormal distribution of DNA methylation is one of the hallmarks of many cancers and methylation changes occur early during carcinogenesis. Systemic analysis of cfDNA methylation profiles is being developed for cancer early detection, monitoring for minimal residual disease (MRD), predicting treatment response and prognosis, and tracing the tissue origin. This review highlights the advantages and disadvantages of ctDNA profiling for noninvasive diagnosis of early-stage cancers and explores recent advances in the clinical application of ctDNA methylation assays. We also summarize the technologies for ctDNA methylation analysis and provide a brief overview of the bioinformatic approaches for analyzing DNA methylation sequencing data.
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Affiliation(s)
- Huiyan Luo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Wei Wei
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Ziyi Ye
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jiabo Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Rui-Hua Xu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.
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118
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Huang KK, Huang J, Wu JKL, Lee M, Tay ST, Kumar V, Ramnarayanan K, Padmanabhan N, Xu C, Tan ALK, Chan C, Kappei D, Göke J, Tan P. Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer. Genome Biol 2021; 22:44. [PMID: 33482911 PMCID: PMC7821541 DOI: 10.1186/s13059-021-02261-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/04/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Deregulated gene expression is a hallmark of cancer; however, most studies to date have analyzed short-read RNA sequencing data with inherent limitations. Here, we combine PacBio long-read isoform sequencing (Iso-Seq) and Illumina paired-end short-read RNA sequencing to comprehensively survey the transcriptome of gastric cancer (GC), a leading cause of global cancer mortality. RESULTS We performed full-length transcriptome analysis across 10 GC cell lines covering four major GC molecular subtypes (chromosomal unstable, Epstein-Barr positive, genome stable and microsatellite unstable). We identify 60,239 non-redundant full-length transcripts, of which > 66% are novel compared to current transcriptome databases. Novel isoforms are more likely to be cell line and subtype specific, expressed at lower levels with larger number of exons, with longer isoform/coding sequence lengths. Most novel isoforms utilize an alternate first exon, and compared to other alternative splicing categories, are expressed at higher levels and exhibit higher variability. Collectively, we observe alternate promoter usage in 25% of detected genes, with the majority (84.2%) of known/novel promoter pairs exhibiting potential changes in their coding sequences. Mapping these alternate promoters to TCGA GC samples, we identify several cancer-associated isoforms, including novel variants of oncogenes. Tumor-specific transcript isoforms tend to alter protein coding sequences to a larger extent than other isoforms. Analysis of outcome data suggests that novel isoforms may impart additional prognostic information. CONCLUSIONS Our results provide a rich resource of full-length transcriptome data for deeper studies of GC and other gastrointestinal malignancies.
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Affiliation(s)
- Kie Kyon Huang
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857 Singapore
| | - Jiawen Huang
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857 Singapore
| | - Jeanie Kar Leng Wu
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857 Singapore
| | - Minghui Lee
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857 Singapore
| | - Su Ting Tay
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857 Singapore
| | - Vikrant Kumar
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857 Singapore
| | - Kalpana Ramnarayanan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857 Singapore
| | - Nisha Padmanabhan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857 Singapore
| | - Chang Xu
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857 Singapore
| | - Angie Lay Keng Tan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857 Singapore
| | - Charlene Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599 Singapore
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599 Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596 Singapore
| | - Jonathan Göke
- Genome Institute of Singapore, Singapore, 138672 Singapore
| | - Patrick Tan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857 Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599 Singapore
- Genome Institute of Singapore, Singapore, 138672 Singapore
- SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore, 169609 Singapore
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119
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Passaro F, De Martino I, Zambelli F, Di Benedetto G, Barbato M, D'Erchia AM, Manzari C, Pesole G, Mutarelli M, Cacchiarelli D, Antonini D, Parisi S, Russo T. YAP contributes to DNA methylation remodeling upon mouse embryonic stem cell differentiation. J Biol Chem 2021; 296:100138. [PMID: 33268382 PMCID: PMC7948423 DOI: 10.1074/jbc.ra120.015896] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/26/2020] [Accepted: 12/02/2020] [Indexed: 02/06/2023] Open
Abstract
The Yes-associated protein (YAP), one of the major effectors of the Hippo pathway together with its related protein WW-domain-containing transcription regulator 1 (WWTR1; also known as TAZ), mediates a range of cellular processes from proliferation and death to morphogenesis. YAP and WW-domain-containing transcription regulator 1 (WWTR1; also known as TAZ) regulate a large number of target genes, acting as coactivators of DNA-binding transcription factors or as negative regulators of transcription by interacting with the nucleosome remodeling and histone deacetylase complexes. YAP is expressed in self-renewing embryonic stem cells (ESCs), although it is still debated whether it plays any crucial roles in the control of either stemness or differentiation. Here we show that the transient downregulation of YAP in mouse ESCs perturbs cellular homeostasis, leading to the inability to differentiate properly. Bisulfite genomic sequencing revealed that this transient knockdown caused a genome-wide alteration of the DNA methylation remodeling that takes place during the early steps of differentiation, suggesting that the phenotype we observed might be due to the dysregulation of some of the mechanisms involved in regulation of ESC exit from pluripotency. By gene expression analysis, we identified two molecules that could have a role in the altered genome-wide methylation profile: the long noncoding RNA ephemeron, whose rapid upregulation is crucial for the transition of ESCs into epiblast, and the methyltransferase-like protein Dnmt3l, which, during the embryo development, cooperates with Dnmt3a and Dnmt3b to contribute to the de novo DNA methylation that governs early steps of ESC differentiation. These data suggest a new role for YAP in the governance of the epigenetic dynamics of exit from pluripotency.
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Affiliation(s)
- Fabiana Passaro
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Italy.
| | - Ilaria De Martino
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Italy
| | - Federico Zambelli
- Department of Biosciences, University of Milano, Italy; Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Italy
| | - Giorgia Di Benedetto
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Italy
| | - Matteo Barbato
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Italy
| | - Anna Maria D'Erchia
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Italy; Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Italy
| | - Caterina Manzari
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Italy; Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Italy
| | - Margherita Mutarelli
- Tigem and Department of Translational Medicine, University of Napoli Federico II, Italy
| | - Davide Cacchiarelli
- Tigem and Department of Translational Medicine, University of Napoli Federico II, Italy
| | - Dario Antonini
- Department of Biology, University of Napoli Federico II, Italy
| | - Silvia Parisi
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Italy
| | - Tommaso Russo
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Italy.
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120
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Leiva F, Bravo S, Garcia KK, Moya J, Guzman O, Bascuñan N, Vidal R. Temporal genome-wide DNA methylation signature of post-smolt Pacific salmon challenged with Piscirickettsia salmonis. Epigenetics 2020; 16:1335-1346. [PMID: 33319647 DOI: 10.1080/15592294.2020.1864166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Piscirickettsiosis is the most important bacterial disease in the Chilean salmon industry, which has sorted several efforts to its control, generating enormous economic losses. Epigenetic alterations, such as DNA methylation, can play a relevant role in the modulation of the metazoans response to pathogens. Bacterial disease may activate global and local immune responses generating intricate responses with significant biological impact in the host. However, it is scarcely understood how bacterial infections influence fish epigenetic alterations. In the present study, we utilized Pacific salmon and Piscirickettsiosis as model, to gain understanding into the dynamics of DNA methylation among fish-bacterial infection interactions. A genome-wide analysis of DNA methylation patterns in female spleen tissue of Pacific salmon was achieved by reduced representation bisulphite sequencing from a time course design. We determined 2,251, 1,918, and 2,516 differentially methylated regions DMRs among infected and control Pacific salmon in 1 dpi, 5 dpi, and 15 dpi, respectively. The mean methylation difference per DMR among control and infected groups was of ~35%, with an oscillatory pattern of hypo, hyper, and hypomethylation across the disease. DMCs, among the control and infected group, showed that they were statistically enriched in intergenic regions and depleted in exons. Functional annotation of the DMR genes demonstrated three KEGG principal categories, associated directly with the host response to pathogens infections. Our results provide the first evidence of epigenetic variation in fish provoked by bacterial infection and demonstrate that this variation can be modulated across the disease.
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Affiliation(s)
- Francisco Leiva
- Laboratory of Molecular Ecology, Genomics and Evolutionary Studies, Department of Biology, Universidad de Santiago de Chile, Santiago, Chile
| | - Scarlet Bravo
- Laboratory of Molecular Ecology, Genomics and Evolutionary Studies, Department of Biology, Universidad de Santiago de Chile, Santiago, Chile
| | - Killen Ko Garcia
- Laboratory of Molecular Ecology, Genomics and Evolutionary Studies, Department of Biology, Universidad de Santiago de Chile, Santiago, Chile
| | | | | | - Nicolás Bascuñan
- Laboratory of Molecular Ecology, Genomics and Evolutionary Studies, Department of Biology, Universidad de Santiago de Chile, Santiago, Chile
| | - Rodrigo Vidal
- Laboratory of Molecular Ecology, Genomics and Evolutionary Studies, Department of Biology, Universidad de Santiago de Chile, Santiago, Chile
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Tini G, Varma V, Lombardo R, Nolen GT, Lefebvre G, Descombes P, Métairon S, Priami C, Kaput J, Scott-Boyer MP. DNA methylation during human adipogenesis and the impact of fructose. GENES AND NUTRITION 2020; 15:21. [PMID: 33243154 PMCID: PMC7691080 DOI: 10.1186/s12263-020-00680-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 11/10/2020] [Indexed: 01/12/2023]
Abstract
BACKGROUND Increased adipogenesis and altered adipocyte function contribute to the development of obesity and associated comorbidities. Fructose modified adipocyte metabolism compared to glucose, but the regulatory mechanisms and consequences for obesity are unknown. Genome-wide methylation and global transcriptomics in SGBS pre-adipocytes exposed to 0, 2.5, 5, and 10 mM fructose, added to a 5-mM glucose-containing medium, were analyzed at 0, 24, 48, 96, 192, and 384 h following the induction of adipogenesis. RESULTS Time-dependent changes in DNA methylation compared to baseline (0 h) occurred during the final maturation of adipocytes, between 192 and 384 h. Larger percentages (0.1% at 192 h, 3.2% at 384 h) of differentially methylated regions (DMRs) were found in adipocytes differentiated in the glucose-containing control media compared to adipocytes differentiated in fructose-supplemented media (0.0006% for 10 mM, 0.001% for 5 mM, and 0.005% for 2.5 mM at 384 h). A total of 1437 DMRs were identified in 5237 differentially expressed genes at 384 h post-induction in glucose-containing (5 mM) control media. The majority of them inversely correlated with the gene expression, but 666 regions were positively correlated to the gene expression. CONCLUSIONS Our studies demonstrate that DNA methylation regulates or marks the transformation of morphologically differentiating adipocytes (seen at 192 h), to the more mature and metabolically robust adipocytes (as seen at 384 h) in a genome-wide manner. Lower (2.5 mM) concentrations of fructose have the most robust effects on methylation compared to higher concentrations (5 and 10 mM), suggesting that fructose may be playing a signaling/regulatory role at lower concentrations of fructose and as a substrate at higher concentrations.
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Affiliation(s)
- Giulia Tini
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, 38068, Rovereto, Italy.,Department of Mathematics, University of Trento, Via Sommarive 14, 38050, Povo, Italy.,Present address: Department of Experimental Oncology, IEO European Institute of Oncology IRCSS, Milan, Italy
| | - Vijayalakshmi Varma
- Division of Systems Biology, National Center for Toxicological Research, FDA, 3900 NCTR Road, Jefferson, AR, 72079, USA.,Present Address: Cardiovascular Renal and Metabolism Division of MedImmune, Astrazeneca, Gaithersburg, MD, 20878, USA
| | - Rosario Lombardo
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, 38068, Rovereto, Italy
| | - Greg T Nolen
- Division of Systems Biology, National Center for Toxicological Research, FDA, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | | | | | | | - Corrado Priami
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, 38068, Rovereto, Italy.,Department of Computer Science, University of Pisa, Pisa, Italy
| | - Jim Kaput
- Nestlé Institute of Health Science, Lausanne, Switzerland.,Present Addresses: Vydiant Inc., Folsom, CA, 95630, USA
| | - Marie-Pier Scott-Boyer
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza Manifattura 1, 38068, Rovereto, Italy. .,Present Address: CRCHU de Québec-Université Laval, Quebec City, Québec, Canada.
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122
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Wang X, Hao D, Kadarmideen HN. GeneDMRs: An R Package for Gene-Based Differentially Methylated Regions Analysis. J Comput Biol 2020; 28:304-316. [PMID: 33185472 PMCID: PMC7994424 DOI: 10.1089/cmb.2020.0081] [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] [Indexed: 12/26/2022] Open
Abstract
DNA methylation in gene or gene body could influence gene transcription. Moreover, methylation in gene regions along with CpG island regions could modulate the transcription to undetectable gene expression levels. Therefore, it is necessary to investigate the methylation levels within the gene, gene body, CpG island regions, and their overlapped regions and then identify the gene-based differentially methylated regions (GeneDMRs). In this study, R package GeneDMRs aims to facilitate computing gene-based methylation rate using next-generation sequencing-based methylome data. The user-friendly GeneDMRs package is presented to analyze the methylation levels in each gene/promoter/exon/intron/CpG island/CpG island shore or each overlapped region (e.g., gene-CpG island/promoter-CpG island/exon-CpG island/intron-CpG island/gene-CpG island shore/promoter-CpG island shore/exon-CpG island shore/intron-CpG island shore). GeneDMRs can also interpret complex interplays between methylation levels and gene expression differences or similarities across physiological conditions or disease states. We used the public reduced representation bisulfite sequencing data of mouse (GSE62392) for evaluating software and revealing novel biologically significant results to supplement the previous research. In addition, the whole-genome bisulfite sequencing data of cattle (GSE106538) given the much larger size was used for further evaluation.
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Affiliation(s)
- Xiao Wang
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Dan Hao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Haja N Kadarmideen
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
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123
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Carleton KL, Conte MA, Malinsky M, Nandamuri SP, Sandkam BA, Meier JI, Mwaiko S, Seehausen O, Kocher TD. Movement of transposable elements contributes to cichlid diversity. Mol Ecol 2020; 29:4956-4969. [PMID: 33049090 DOI: 10.1111/mec.15685] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022]
Abstract
African cichlid fishes are a prime model for studying speciation mechanisms. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for cichlid phenotypic variation. One of their most variable phenotypes is visual sensitivity, with some of the largest spectral shifts among vertebrates. These shifts arise primarily from differential expression of seven cone opsin genes. By mapping expression quantitative trait loci (eQTL) in intergeneric crosses of Lake Malawi cichlids, we previously identified four causative genetic variants that correspond to indels in the promoters of either key transcription factors or an opsin gene. In this comprehensive study, we show that these indels are the result of the movement of transposable elements (TEs) that correlate with opsin expression variation across the Malawi flock. In tracking the evolutionary history of these particular indels, we found they are endemic to Lake Malawi, suggesting that these TEs are recently active and are segregating within the Malawi cichlid lineage. However, an independent indel has arisen at a similar genomic location in one locus outside of the Malawi flock. The convergence in TE movement suggests these loci are primed for TE insertion and subsequent deletions. Increased TE mobility may be associated with interspecific hybridization, which disrupts mechanisms of TE suppression. This might provide a link between cichlid hybridization and accelerated regulatory variation. Overall, our study suggests that TEs may be an important driver of key regulatory changes, facilitating rapid phenotypic change and possibly speciation in African cichlids.
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Affiliation(s)
- Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Milan Malinsky
- Wellcome Sanger Institute, Cambridge, UK.,Zoological Institute, University of Basel, Basel, Switzerland
| | | | | | - Joana I Meier
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Salome Mwaiko
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, USA
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124
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Corbett RJ, Te Pas MFW, van den Brand H, Groenen MAM, Crooijmans RPMA, Ernst CW, Madsen O. Genome-Wide Assessment of DNA Methylation in Chicken Cardiac Tissue Exposed to Different Incubation Temperatures and CO 2 Levels. Front Genet 2020; 11:558189. [PMID: 33193638 PMCID: PMC7655987 DOI: 10.3389/fgene.2020.558189] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/30/2020] [Indexed: 12/26/2022] Open
Abstract
Temperature and CO2 concentration during incubation have profound effects on broiler chick development, and numerous studies have identified significant effects on hatch heart weight (HW) as a result of differences in these parameters. Early life environment has also been shown to affect broiler performance later in life; it has thus been suggested that epigenetic mechanisms may mediate long-term physiological changes induced by environmental stimuli. DNA methylation is an epigenetic modification that can confer heritable changes in gene expression. Using reduced-representation bisulfite sequencing (RRBS), we assessed DNA methylation patterns in cardiac tissue of 84 broiler hatchlings incubated at two egg shell temperatures (EST; 37.8°C and 38.9°C) and three CO2 concentrations (0.1%, 0.4%, and 0.8%) from day 8 of incubation onward. We assessed differential methylation between EST treatments and identified 2,175 differentially methylated (DM) CpGs (1,121 hypermethylated, 1,054 hypomethylated at 38.9° vs. 37.8°) in 269 gene promoters and 949 intragenic regions. DM genes (DMGs) were associated with heart developmental processes, including cardiomyocyte proliferation and differentiation. We identified enriched binding motifs among DM loci, including those for transcription factors associated with cell proliferation and heart development among hypomethylated CpGs that suggest increased binding ability at higher EST. We identified 9,823 DM CpGs between at least two CO2 treatments, with the greatest difference observed between 0.8 and 0.1% CO2 that disproportionately impacted genes involved in cardiac muscle development and response to low oxygen levels. Using HW measurements from the same chicks, we performed an epigenome-wide association study (EWAS) for HW, and identified 23 significantly associated CpGs, nine of which were also DM between ESTs. We found corresponding differences in transcript abundance between ESTs in three DMGs (ABLIM2, PITX2, and THRSP). Hypomethylation of an exonic CpG in PITX2 at 38.9°C was associated with increased expression, and suggests increased cell proliferation in broiler hatchlings incubated at higher temperatures. Overall, these results identified numerous epigenetic associations between chick incubation factors and heart development that may manifest in long-term differences in animal performance.
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Affiliation(s)
- Ryan J Corbett
- Genetics and Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, United States
| | - Marinus F W Te Pas
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | - Henry van den Brand
- Adaptation Physiology Group, Wageningen University & Research, Wageningen, Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | | | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
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125
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Bou Sleiman M, Jha P, Houtkooper R, Williams RW, Wang X, Auwerx J. The Gene-Regulatory Footprint of Aging Highlights Conserved Central Regulators. Cell Rep 2020; 32:108203. [PMID: 32997995 PMCID: PMC7527782 DOI: 10.1016/j.celrep.2020.108203] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/31/2020] [Accepted: 09/04/2020] [Indexed: 12/13/2022] Open
Abstract
Many genes and pathways have been linked to aging, yet our understanding of underlying molecular mechanisms is still lacking. Here, we measure changes in the transcriptome, histone modifications, and DNA methylome in three metabolic tissues of adult and aged mice. Transcriptome and methylome changes dominate the liver aging footprint, whereas heart and muscle globally increase chromatin accessibility, especially in aging pathways. In mouse and human data from multiple tissues and regulatory layers, age-related transcription factor expression changes and binding site enrichment converge on putative aging modulators, including ZIC1, CXXC1, HMGA1, MECP2, SREBF1, SREBF2, ETS2, ZBTB7A, and ZNF518B. Using Mendelian randomization, we establish possible epidemiological links between expression of some of these transcription factors or their targets, including CXXC1, ZNF518B, and BBC3, and longevity. We conclude that conserved modulators are at the core of the molecular footprint of aging, and variation in tissue-specific expression of some may affect human longevity.
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Affiliation(s)
- Maroun Bou Sleiman
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Pooja Jha
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Riekelt Houtkooper
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee, Memphis, TN 38163, USA
| | - Xu Wang
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland.
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland.
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126
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Marczyk M, Patwardhan GA, Zhao J, Qu R, Li X, Wali VB, Gupta AK, Pillai MM, Kluger Y, Yan Q, Hatzis C, Pusztai L, Gunasekharan V. Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells. Cancers (Basel) 2020; 12:E2551. [PMID: 32911681 PMCID: PMC7563413 DOI: 10.3390/cancers12092551] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 12/13/2022] Open
Abstract
Cancer cells employ various defense mechanisms against drug-induced cell death. Investigating multi-omics landscapes of cancer cells before and after treatment can reveal resistance mechanisms and inform new therapeutic strategies. We assessed the effects of navitoclax, a BCL2 family inhibitor, on the transcriptome, methylome, chromatin structure, and copy number variations of MDA-MB-231 triple-negative breast cancer (TNBC) cells. Cells were sampled before treatment, at 72 h of exposure, and after 10-day drug-free recovery from treatment. We observed transient alterations in the expression of stress response genes that were accompanied by corresponding changes in chromatin accessibility. Most of these changes returned to baseline after the recovery period. We also detected lasting alterations in methylation states and genome structure that suggest permanent changes in cell population composition. Using single-cell analyses, we identified 2350 genes significantly upregulated in navitoclax-resistant cells and derived an 18-gene navitoclax resistance signature. We assessed the navitoclax-response-predictive function of this signature in four additional TNBC cell lines in vitro and in silico in 619 cell lines treated with 251 different drugs. We observed a drug-specific predictive value in both experiments, suggesting that this signature could help guiding clinical biomarker studies involving navitoclax.
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Affiliation(s)
- Michal Marczyk
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06511, USA; (M.M.); (G.A.P.); (X.L.); (V.B.W.); (A.K.G.); (M.M.P.); (C.H.); (V.G.)
- Department of Data Science and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Gauri A. Patwardhan
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06511, USA; (M.M.); (G.A.P.); (X.L.); (V.B.W.); (A.K.G.); (M.M.P.); (C.H.); (V.G.)
| | - Jun Zhao
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT 06511, USA; (J.Z.); (R.Q.); (Y.K.)
| | - Rihao Qu
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT 06511, USA; (J.Z.); (R.Q.); (Y.K.)
| | - Xiaotong Li
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06511, USA; (M.M.); (G.A.P.); (X.L.); (V.B.W.); (A.K.G.); (M.M.P.); (C.H.); (V.G.)
| | - Vikram B. Wali
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06511, USA; (M.M.); (G.A.P.); (X.L.); (V.B.W.); (A.K.G.); (M.M.P.); (C.H.); (V.G.)
| | - Abhishek K. Gupta
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06511, USA; (M.M.); (G.A.P.); (X.L.); (V.B.W.); (A.K.G.); (M.M.P.); (C.H.); (V.G.)
| | - Manoj M. Pillai
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06511, USA; (M.M.); (G.A.P.); (X.L.); (V.B.W.); (A.K.G.); (M.M.P.); (C.H.); (V.G.)
- Department of Pathology, Yale School of Medicine, New Haven, CT 06511, USA;
| | - Yuval Kluger
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT 06511, USA; (J.Z.); (R.Q.); (Y.K.)
- Department of Pathology, Yale School of Medicine, New Haven, CT 06511, USA;
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06511, USA;
| | - Christos Hatzis
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06511, USA; (M.M.); (G.A.P.); (X.L.); (V.B.W.); (A.K.G.); (M.M.P.); (C.H.); (V.G.)
| | - Lajos Pusztai
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06511, USA; (M.M.); (G.A.P.); (X.L.); (V.B.W.); (A.K.G.); (M.M.P.); (C.H.); (V.G.)
| | - Vignesh Gunasekharan
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06511, USA; (M.M.); (G.A.P.); (X.L.); (V.B.W.); (A.K.G.); (M.M.P.); (C.H.); (V.G.)
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Sagonas K, Meyer BS, Kaufmann J, Lenz TL, Häsler R, Eizaguirre C. Experimental Parasite Infection Causes Genome-Wide Changes in DNA Methylation. Mol Biol Evol 2020; 37:2287-2299. [PMID: 32227215 PMCID: PMC7531312 DOI: 10.1093/molbev/msaa084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Parasites are arguably among the strongest drivers of natural selection, constraining hosts to evolve resistance and tolerance mechanisms. Although, the genetic basis of adaptation to parasite infection has been widely studied, little is known about how epigenetic changes contribute to parasite resistance and eventually, adaptation. Here, we investigated the role of host DNA methylation modifications to respond to parasite infections. In a controlled infection experiment, we used the three-spined stickleback fish, a model species for host-parasite studies, and their nematode parasite Camallanus lacustris. We showed that the levels of DNA methylation are higher in infected fish. Results furthermore suggest correlations between DNA methylation and shifts in key fitness and immune traits between infected and control fish, including respiratory burst and functional trans-generational traits such as the concentration of motile sperm. We revealed that genes associated with metabolic, developmental, and regulatory processes (cell death and apoptosis) were differentially methylated between infected and control fish. Interestingly, genes such as the neuropeptide FF receptor 2 and the integrin alpha 1 as well as molecular pathways including the Th1 and Th2 cell differentiation were hypermethylated in infected fish, suggesting parasite-mediated repression mechanisms of immune responses. Altogether, we demonstrate that parasite infection contributes to genome-wide DNA methylation modifications. Our study brings novel insights into the evolution of vertebrate immunity and suggests that epigenetic mechanisms are complementary to genetic responses against parasite-mediated selection.
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Affiliation(s)
- Kostas Sagonas
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Britta S Meyer
- Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Joshka Kaufmann
- School of Biological, Earth & Environmental Sciences, University College Cork, Cork, Republic of Ireland
- Department for Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Robert Häsler
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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128
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van der Burg KRL, Lewis JJ, Martin A, Nijhout HF, Danko CG, Reed RD. Contrasting Roles of Transcription Factors Spineless and EcR in the Highly Dynamic Chromatin Landscape of Butterfly Wing Metamorphosis. Cell Rep 2020; 27:1027-1038.e3. [PMID: 31018121 DOI: 10.1016/j.celrep.2019.03.092] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/22/2019] [Accepted: 03/25/2019] [Indexed: 01/24/2023] Open
Abstract
Development requires highly coordinated changes in chromatin accessibility in order for proper gene regulation to occur. Here, we identify factors associated with major, discrete changes in chromatin accessibility during butterfly wing metamorphosis. By combining mRNA sequencing (mRNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and machine learning analysis of motifs, we show that distinct sets of transcription factors are predictive of chromatin opening at different developmental stages. Our data suggest an important role for nuclear hormone receptors early in metamorphosis, whereas PAS-domain transcription factors are strongly associated with later chromatin opening. Chromatin immunoprecipitation sequencing (ChIP-seq) validation of select candidate factors showed spineless binding to be a major predictor of opening chromatin. Surprisingly, binding of ecdysone receptor (EcR), a candidate accessibility factor in Drosophila, was not predictive of opening but instead marked persistent sites. This work characterizes the chromatin dynamics of insect wing metamorphosis, identifies candidate chromatin remodeling factors in insects, and presents a genome assembly of the model butterfly Junonia coenia.
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Affiliation(s)
- Karin R L van der Burg
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA.
| | - James J Lewis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA; Baker Institute for Animal Health, Cornell University, Ithaca, NY 14853, USA
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | | | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, NY 14853, USA
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
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129
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Rawoof A, Chhapekar SS, Jaiswal V, Brahma V, Kumar N, Ramchiary N. Single-base cytosine methylation analysis in fruits of three Capsicum species. Genomics 2020; 112:3342-3353. [PMID: 32561348 DOI: 10.1016/j.ygeno.2020.04.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/29/2020] [Accepted: 04/11/2020] [Indexed: 11/30/2022]
Abstract
Single-base cytosine methylation analysis across fruits of Capsicum annuum, C. chinense and C. frutescens showed global average methylation ranging from 82.8-89.1%, 77.6-83.9%, and 22.4-25% at CG, CHG and CHH contexts, respectively. High gene-body methylation at CG and CHG was observed across Capsicum species. The C. annuum showed the highest proportion (>80%) of mCs at different genomic regions compared to C. chinense and C. frutescens. Cytosine methylation for transposable-elements were lower in C. frutescens compared to C. annuum and C. chinense. A total of 510,165 CG, 583112 CHG and 277,897 CHH DMRs were identified across three Capsicum species. The differentially methylated regions (DMRs) distribution analysis revealed C. frutescens as more hypo-methylated compared to C. annuum and C. chinense, and also the presence of more intergenic DMRs in Capsicum genome. At CG and CHG context, gene expression and promoter methylation showed inverse correlations. Furthermore, the observed correlation between methylation and expression of genes suggested the potential role of methylation in Capsicum fruit development/ripening.
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Affiliation(s)
- Abdul Rawoof
- School of Life Sciences, Laboratory of Translational and Evolutionary Genomics, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sushil Satish Chhapekar
- School of Life Sciences, Laboratory of Translational and Evolutionary Genomics, Jawaharlal Nehru University, New Delhi 110067, India
| | - Vandana Jaiswal
- School of Life Sciences, Laboratory of Translational and Evolutionary Genomics, Jawaharlal Nehru University, New Delhi 110067, India; Biotechnology Division, CSIR-Institute of Himalayan Bioresource and Technology, Palampur, Himachal Pradhesh, India
| | - Vijaya Brahma
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Nitin Kumar
- School of Life Sciences, Laboratory of Translational and Evolutionary Genomics, Jawaharlal Nehru University, New Delhi 110067, India; Department of Bioengineering and Technology, Gauhati University, Gopinath Boroloi Nagar, Guwahati 7810014, Assam, India
| | - Nirala Ramchiary
- School of Life Sciences, Laboratory of Translational and Evolutionary Genomics, Jawaharlal Nehru University, New Delhi 110067, India; Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Bawana Road, New Delhi 110042, India.
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130
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Genome‑wide analysis of DNA methylation and gene expression changes in an ovalbumin‑induced asthma mouse model. Mol Med Rep 2020; 22:1709-1716. [PMID: 32705270 PMCID: PMC7411290 DOI: 10.3892/mmr.2020.11245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 02/04/2020] [Indexed: 12/12/2022] Open
Abstract
The aim of the present study was to establish an integrated network of DNA methylation and RNA expression in an ovalbumin (OVA)-induced asthma model, and to investigate the epigenetically-regulated genes involved in asthma development. Genome-wide CpG-DNA methylation profiling was conducted through the use of a methylated DNA immunoprecipitation microarray and RNA sequencing was performed using three lung samples from mice with OVA-induced asthma. A total of 35,401 differentially methylated regions (DMRs) were identified between mice with OVA-induced asthma and control mice. Of these, 3,060 were located in promoter regions and 370 of the genes containing these DMRs demonstrated an inverse correlation between methylation and gene expression. Kyoto Encyclopedia of Genes and Genomes pathway analysis identified that 368 genes were upregulated or downregulated in OVA-induced asthma samples, including genes involved in ‘chemokine signalling pathway’, ‘focal adhesion’, ‘leukocyte transendothelial migration’ and ‘vascular smooth muscle contraction signaling’ pathways. Integrated network analysis identified four hub genes, consisting of three upregulated genes [forkhead box O1 (FOXO1), SP1 transcription factor (SP1) and amyloid β precursor protein (APP)], and one downregulated gene [RUNX family transcription factor 1 (RUNX1)], all of which demonstrated an association between DNA methylation and gene expression. These genes were highly interconnected nodes in the Ingenuity Pathway Analysis module and were functionally significant. A total of four interconnected hub genes, FOXO1, RUNX1, SP1 and APP, were identified from the integrated DNA methylation and gene expression networks involved in asthma development. These results suggested that modulating these four genes could effectively control the development of asthma.
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131
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Wang X, Kadarmideen HN. Characterization of Global DNA Methylation in Different Gene Regions Reveals Candidate Biomarkers in Pigs with High and Low Levels of Boar Taint. Vet Sci 2020; 7:E77. [PMID: 32545802 PMCID: PMC7356388 DOI: 10.3390/vetsci7020077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/09/2020] [Indexed: 12/11/2022] Open
Abstract
DNA methylation of different gene components, including different exons and introns, or different lengths of exons and introns is associated with differences in gene expression. To investigate the methylation of porcine gene components associated with the boar taint (BT) trait, this study used reduced representation bisulfite sequencing (RRBS) data from nine porcine testis samples in three BT groups (low, medium and high BT). The results showed that the methylation levels of the first exons and first introns were lower than those of the other exons and introns. The first exons/introns of CpG island regions had even lower levels of methylation. A total of 123 differentially methylated promoters (DMPs), 194 differentially methylated exons (DMEs) and 402 differentially methylated introns (DMIs) were identified, of which 80 DMPs (DMP-CpGis), 112 DMEs (DME-CpGis) and 166 DMIs (DMI-CpGis) were discovered in CpG islands. Importantly, GPX1 contained one each of DMP, DME, DMI, DMP-CpGi, DME-CpGi and DMI-CpGi. Gene-GO term relationships and pathways analysis showed DMP-CpGi-related genes are mainly involved in methylation-related biological functions. In addition, gene-gene interaction networks consisted of nodes that were hypo-methylated GPX1, hypo-methylated APP, hypo-methylated ATOX1, hyper-methylated ADRB2, hyper-methylated RPS6KA1 and hyper-methylated PNMT. They could be used as candidate biomarkers for reducing boar taint in pigs, after further validation in large cohorts.
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Affiliation(s)
| | - Haja N. Kadarmideen
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
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132
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Li X, Pritykin Y, Concepcion CP, Lu Y, La Rocca G, Zhang M, King B, Cook PJ, Au YW, Popow O, Paulo JA, Otis HG, Mastroleo C, Ogrodowski P, Schreiner R, Haigis KM, Betel D, Leslie CS, Ventura A. High-Resolution In Vivo Identification of miRNA Targets by Halo-Enhanced Ago2 Pull-Down. Mol Cell 2020; 79:167-179.e11. [PMID: 32497496 DOI: 10.1016/j.molcel.2020.05.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 03/18/2020] [Accepted: 05/06/2020] [Indexed: 12/19/2022]
Abstract
The identification of microRNA (miRNA) targets by Ago2 crosslinking-immunoprecipitation (CLIP) methods has provided major insights into the biology of this important class of non-coding RNAs. However, these methods are technically challenging and not easily applicable to an in vivo setting. To overcome these limitations and facilitate the investigation of miRNA functions in vivo, we have developed a method based on a genetically engineered mouse harboring a conditional Halo-Ago2 allele expressed from the endogenous Ago2 locus. By using a resin conjugated to the HaloTag ligand, Ago2-miRNA-mRNA complexes can be purified from cells and tissues expressing the endogenous Halo-Ago2 allele. We demonstrate the reproducibility and sensitivity of this method in mouse embryonic stem cells, developing embryos, adult tissues, and autochthonous mouse models of human brain and lung cancers. This method and the datasets we have generated will facilitate the characterization of miRNA-mRNA networks in vivo under physiological and pathological conditions.
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Affiliation(s)
- Xiaoyi Li
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yuri Pritykin
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Carla P Concepcion
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yuheng Lu
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Gaspare La Rocca
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Minsi Zhang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Bryan King
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Peter J Cook
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Yu Wah Au
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Internal Medicine (Nephrology), Leiden University Medical Center, Zuid-Holland, 2333 ZA, the Netherlands
| | - Olesja Popow
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hannah G Otis
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Chiara Mastroleo
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Paul Ogrodowski
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ryan Schreiner
- Margaret Dyson Vision Research Institute, Department of Ophthalmology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Kevin M Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Doron Betel
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA; Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Andrea Ventura
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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133
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Magalhães RDM, Mattos EC, Rozanski A, Galante PAF, Palmisano G, Cruz AK, Colli W, Camargo AA, Alves MJM. Global changes in nitration levels and DNA binding profile of Trypanosoma cruzi histones induced by incubation with host extracellular matrix. PLoS Negl Trop Dis 2020; 14:e0008262. [PMID: 32469928 PMCID: PMC7286532 DOI: 10.1371/journal.pntd.0008262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 06/10/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023] Open
Abstract
Adhesion of T. cruzi trypomastigotes to components of the extracellular matrix (ECM) is an important step in mammalian host cell invasion. We have recently described a significant increase in the tyrosine nitration levels of histones H2A and H4 when trypomastigotes are incubated with components of the ECM. In this work, we used chromatin immunoprecipitation (ChIP) with an anti-nitrotyrosine antibody followed by mass spectrometry to identify nitrated DNA binding proteins in T. cruzi and to detect alterations in nitration levels induced upon parasite incubation with the ECM. Histone H1, H2B, H2A and H3 were detected among the 9 most abundant nitrated DNA binding proteins using this proteomic approach. One nitrated tyrosine residue (Y29) was identified in Histone H2B in the MS/MS spectrum. In addition, we observed a significant increase in the nitration levels of histones H1, H2B, H2A and H4 upon parasite incubation with ECM. Finally, we used ChIP-Seq to map global changes in the DNA binding profile of nitrated proteins. We observed a significant change in the binding pattern of nitrated proteins to DNA after parasite incubation with ECM. This work provides the first global profile of nitrated DNA binding proteins in T. cruzi and additional evidence for modification in the nitration profile of histones upon parasite incubation with ECM. Our data also indicate that the parasite interaction with the ECM induces alterations in chromatin structure, possibly affecting nuclear functions.
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Affiliation(s)
- Rubens Daniel Miserani Magalhães
- Departamento de Bioquímica Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
- Centro de Oncologia Molecular, Hospital Sírio Libanês, São Paulo, Brazil
- Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Eliciane Cevolani Mattos
- Departamento de Bioquímica Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Andrei Rozanski
- Centro de Oncologia Molecular, Hospital Sírio Libanês, São Paulo, Brazil
| | | | - Giuseppe Palmisano
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Angela Kaysel Cruz
- Departamento de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Walter Colli
- Departamento de Bioquímica Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Anamaria Aranha Camargo
- Centro de Oncologia Molecular, Hospital Sírio Libanês, São Paulo, Brazil
- * E-mail: (AAC), (MJMA)
| | - Maria Júlia Manso Alves
- Departamento de Bioquímica Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
- * E-mail: (AAC), (MJMA)
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134
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van der Weegen Y, Golan-Berman H, Mevissen TET, Apelt K, González-Prieto R, Goedhart J, Heilbrun EE, Vertegaal ACO, van den Heuvel D, Walter JC, Adar S, Luijsterburg MS. The cooperative action of CSB, CSA, and UVSSA target TFIIH to DNA damage-stalled RNA polymerase II. Nat Commun 2020; 11:2104. [PMID: 32355176 PMCID: PMC7192910 DOI: 10.1038/s41467-020-15903-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 03/27/2020] [Indexed: 12/13/2022] Open
Abstract
The response to DNA damage-stalled RNA polymerase II (RNAPIIo) involves the assembly of the transcription-coupled repair (TCR) complex on actively transcribed strands. The function of the TCR proteins CSB, CSA and UVSSA and the manner in which the core DNA repair complex, including transcription factor IIH (TFIIH), is recruited are largely unknown. Here, we define the assembly mechanism of the TCR complex in human isogenic knockout cells. We show that TCR is initiated by RNAPIIo-bound CSB, which recruits CSA through a newly identified CSA-interaction motif (CIM). Once recruited, CSA facilitates the association of UVSSA with stalled RNAPIIo. Importantly, we find that UVSSA is the key factor that recruits the TFIIH complex in a manner that is stimulated by CSB and CSA. Together these findings identify a sequential and highly cooperative assembly mechanism of TCR proteins and reveal the mechanism for TFIIH recruitment to DNA damage-stalled RNAPIIo to initiate repair. The response to DNA damage-stalled RNA polymerase II leads to the assembly of the transcription-coupled repair (TCR) complex on actively transcribed strands. Here, the authors reveal the complex assembly mechanism of the TCR complex in human cells.
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Affiliation(s)
- Yana van der Weegen
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Hadar Golan-Berman
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, 91120, Israel
| | - Tycho E T Mevissen
- Howard Hughes Medical Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Katja Apelt
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Joachim Goedhart
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Elisheva E Heilbrun
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, 91120, Israel
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Johannes C Walter
- Howard Hughes Medical Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, 91120, Israel
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands.
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135
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Bywater MJ, Burkhart DL, Straube J, Sabò A, Pendino V, Hudson JE, Quaife-Ryan GA, Porrello ER, Rae J, Parton RG, Kress TR, Amati B, Littlewood TD, Evan GI, Wilson CH. Reactivation of Myc transcription in the mouse heart unlocks its proliferative capacity. Nat Commun 2020; 11:1827. [PMID: 32286286 PMCID: PMC7156407 DOI: 10.1038/s41467-020-15552-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 03/19/2020] [Indexed: 12/14/2022] Open
Abstract
It is unclear why some tissues are refractory to the mitogenic effects of the oncogene Myc. Here we show that Myc activation induces rapid transcriptional responses followed by proliferation in some, but not all, organs. Despite such disparities in proliferative response, Myc is bound to DNA at open elements in responsive (liver) and non-responsive (heart) tissues, but fails to induce a robust transcriptional and proliferative response in the heart. Using heart as an exemplar of a non-responsive tissue, we show that Myc-driven transcription is re-engaged in mature cardiomyocytes by elevating levels of the positive transcription elongation factor (P-TEFb), instating a large proliferative response. Hence, P-TEFb activity is a key limiting determinant of whether the heart is permissive for Myc transcriptional activation. These data provide a greater understanding of how Myc transcriptional activity is determined and indicate modification of P-TEFb levels could be utilised to drive regeneration of adult cardiomyocytes for the treatment of heart myopathies.
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Affiliation(s)
- Megan J Bywater
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Deborah L Burkhart
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Jasmin Straube
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Arianna Sabò
- Department of Experimental Oncology, European Institute of Oncology (IEO) - IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Vera Pendino
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139, Milan, Italy
| | - James E Hudson
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | | | - Enzo R Porrello
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, VIC, 3052, Australia
- Department of Physiology, School of Biomedical Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - James Rae
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, 4072, QLD, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, 4072, QLD, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, St Lucia, 4072, QLD, Australia
| | - Theresia R Kress
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139, Milan, Italy
| | - Bruno Amati
- Department of Experimental Oncology, European Institute of Oncology (IEO) - IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Trevor D Littlewood
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Gerard I Evan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
| | - Catherine H Wilson
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
- Department of Pharmacology, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1PD, UK.
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136
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Roy KR, Chanfreau GF. Robust mapping of polyadenylated and non-polyadenylated RNA 3' ends at nucleotide resolution by 3'-end sequencing. Methods 2020; 176:4-13. [PMID: 31128237 PMCID: PMC6874744 DOI: 10.1016/j.ymeth.2019.05.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/10/2019] [Accepted: 05/20/2019] [Indexed: 10/26/2022] Open
Abstract
3'-end poly(A)+ sequencing is an efficient and economical method for global measurement of mRNA levels and alternative poly(A) site usage. A common method involves oligo(dT)19V reverse-transcription (RT)-based library preparation and high-throughput sequencing with a custom primer ending in (dT)19. While the majority of library products have the first sequenced nucleotide reflect the bona fide poly(A) site (pA), a substantial fraction of sequencing reads arise from various mis-priming events. These can result in incorrect pA site calls anywhere from several nucleotides downstream to several kilobases upstream from the bona fide pA site. While these mis-priming events can be mitigated by increasing annealing stringency (e.g. increasing temperature from 37 °C to 42 °C), they still persist at an appreciable level (∼10%) and computational methods must be used to prevent artifactual calls. Here we present a bioinformatics workflow for precise mapping of poly(A)+ 3' ends and handling of artifacts due to oligo(dT) mis-priming and sample polymorphisms. We test pA site calling with three different read mapping programs (STAR, BWA, and BBMap), and show that the way in which each handles terminal mismatches and soft clipping has a substantial impact on identifying correct pA sites, with BWA requiring the least post-processing to correct artifacts. We demonstrate the use of this pipeline for mapping pA sites in the model eukaryote S. cerevisiae, and further apply this technology to non-polyadenylated transcripts by employing in vitro polyadenylation prior to library prep (IVP-seq). As proof of principle, we show that a fraction of tRNAs harbor CCU 3' tails instead of the canonical CCA tail, and globally identify 3' ends of splicing intermediates arising from inefficiently spliced transcripts.
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Affiliation(s)
- Kevin R Roy
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569, United States; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095-1570, United States
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569, United States; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095-1570, United States.
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137
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Kovač A, Miskey C, Menzel M, Grueso E, Gogol-Döring A, Ivics Z. RNA-guided retargeting of S leeping Beauty transposition in human cells. eLife 2020; 9:e53868. [PMID: 32142408 PMCID: PMC7077980 DOI: 10.7554/elife.53868] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/05/2020] [Indexed: 12/12/2022] Open
Abstract
An ideal tool for gene therapy would enable efficient gene integration at predetermined sites in the human genome. Here we demonstrate biased genome-wide integration of the Sleeping Beauty (SB) transposon by combining it with components of the CRISPR/Cas9 system. We provide proof-of-concept that it is possible to influence the target site selection of SB by fusing it to a catalytically inactive Cas9 (dCas9) and by providing a single guide RNA (sgRNA) against the human Alu retrotransposon. Enrichment of transposon integrations was dependent on the sgRNA, and occurred in an asymmetric pattern with a bias towards sites in a relatively narrow, 300 bp window downstream of the sgRNA targets. Our data indicate that the targeting mechanism specified by CRISPR/Cas9 forces integration into genomic regions that are otherwise poor targets for SB transposition. Future modifications of this technology may allow the development of methods for specific gene insertion for precision genetic engineering.
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Affiliation(s)
- Adrian Kovač
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
| | - Csaba Miskey
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
| | | | - Esther Grueso
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
| | | | - Zoltán Ivics
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich InstituteLangenGermany
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138
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ChromID identifies the protein interactome at chromatin marks. Nat Biotechnol 2020; 38:728-736. [PMID: 32123383 PMCID: PMC7289633 DOI: 10.1038/s41587-020-0434-2] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/23/2020] [Indexed: 01/05/2023]
Abstract
Chromatin modifications regulate genome function by recruiting protein factors to the genome. However, the protein composition at distinct chromatin modifications remains to be fully characterized. Here, we use natural protein domains as modular building blocks to develop engineered chromatin readers (eCRs) selective for DNA methylation and histone tri-methylation at H3K4, H3K9 a H3K27 residues. We first demonstrate their utility as selective chromatin binders in living cells by stably expressing eCRs in mouse embryonic stem cells and measuring their subnuclear localisation, genomic distribution and histone modification–binding preference. By fusing eCRs to the biotin ligase BASU, we establish ChromID, a method for identifying the chromatin-dependent protein interactome based on proximity biotinylation, and apply it to distinct chromatin modifications in mouse stem cells. Using a synthetic dual-modification reader, we also uncover the protein composition at bivalent promoters marked by H3K4me3 and H3K27me3. These results highlight the ability of ChromID to obtain a detailed view of protein interaction networks on chromatin.
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139
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Heckwolf MJ, Meyer BS, Häsler R, Höppner MP, Eizaguirre C, Reusch TBH. Two different epigenetic information channels in wild three-spined sticklebacks are involved in salinity adaptation. SCIENCE ADVANCES 2020; 6:eaaz1138. [PMID: 32219167 PMCID: PMC7083608 DOI: 10.1126/sciadv.aaz1138] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/26/2019] [Indexed: 05/30/2023]
Abstract
Epigenetic inheritance has been proposed to contribute to adaptation and acclimation via two information channels: (i) inducible epigenetic marks that enable transgenerational plasticity and (ii) noninducible epigenetic marks resulting from random epimutations shaped by selection. We studied both postulated channels by sequencing methylomes and genomes of Baltic three-spined sticklebacks (Gasterosteus aculeatus) along a salinity cline. Wild populations differing in salinity tolerance revealed differential methylation (pop-DMS) at genes enriched for osmoregulatory processes. A two-generation experiment demonstrated that 62% of these pop-DMS were noninducible by salinity manipulation, suggesting that they are the result of either direct selection or associated genomic divergence at cis- or trans-regulatory sites. Two-thirds of the remaining inducible pop-DMS increased in similarity to patterns detected in wild populations from corresponding salinities. The level of similarity accentuated over consecutive generations, indicating a mechanism of transgenerational plasticity. While we can attribute natural DNA methylation patterns to the two information channels, their interplay with genomic variation in salinity adaptation is still unresolved.
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Affiliation(s)
- Melanie J. Heckwolf
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Britta S. Meyer
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Robert Häsler
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Marc P. Höppner
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Thorsten B. H. Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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140
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Bonetti A, Agostini F, Suzuki AM, Hashimoto K, Pascarella G, Gimenez J, Roos L, Nash AJ, Ghilotti M, Cameron CJF, Valentine M, Medvedeva YA, Noguchi S, Agirre E, Kashi K, Samudyata, Luginbühl J, Cazzoli R, Agrawal S, Luscombe NM, Blanchette M, Kasukawa T, Hoon MD, Arner E, Lenhard B, Plessy C, Castelo-Branco G, Orlando V, Carninci P. RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions. Nat Commun 2020; 11:1018. [PMID: 32094342 PMCID: PMC7039879 DOI: 10.1038/s41467-020-14337-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/18/2019] [Indexed: 12/18/2022] Open
Abstract
Mammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromatin remodeling. To investigate the function of such RNAs, methods to massively map the genomic interacting sites of multiple transcripts have been developed; however, these methods have some limitations. Here, we introduce RNA And DNA Interacting Complexes Ligated and sequenced (RADICL-seq), a technology that maps genome-wide RNA–chromatin interactions in intact nuclei. RADICL-seq is a proximity ligation-based methodology that reduces the bias for nascent transcription, while increasing genomic coverage and unique mapping rate efficiency compared with existing methods. RADICL-seq identifies distinct patterns of genome occupancy for different classes of transcripts as well as cell type–specific RNA-chromatin interactions, and highlights the role of transcription in the establishment of chromatin structure. Mammalian genomes encode tens of thousands of ncRNAs that have important roles in regulation of gene expression and chromatin organization. Here, the authors present RADICLseq to map RNA-chromatin interactions in intact nuclei to shed light on these fine-tuned processes.
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Affiliation(s)
- Alessandro Bonetti
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan. .,Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | | | - Ana Maria Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.,Department of Medicine (H7), Karolinska Institutet, Stockholm, 141 86, Sweden
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Giovanni Pascarella
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Juliette Gimenez
- Epigenetics and Genome Reprogramming Laboratory, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Leonie Roos
- Faculty of Medicine, Imperial College London, Institute of Clinical Sciences, London, W12 0NN, UK.,MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Alex J Nash
- Faculty of Medicine, Imperial College London, Institute of Clinical Sciences, London, W12 0NN, UK.,MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Marco Ghilotti
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Christopher J F Cameron
- School of Computer Science, McGill University, Montréal, QC, Canada.,Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montréal, QC, Canada
| | - Matthew Valentine
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Yulia A Medvedeva
- Institute of Bioengineering, Research Centre of Biotechnology, Russian Academy of Science, 117312, Moscow, Russia.,Department of Computational Biology, Vavilov Institute of General Genetics, Russian Academy of Science, 119991, Moscow, Russia.,Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Moscow Region, Russia
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Eneritz Agirre
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kaori Kashi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Samudyata
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Joachim Luginbühl
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Riccardo Cazzoli
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,UCL Genetics Institute, University College London, London, WC1E 6BT, UK.,Okinawa Institute of Science and Technology, Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | | | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Michiel de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Erik Arner
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Boris Lenhard
- Faculty of Medicine, Imperial College London, Institute of Clinical Sciences, London, W12 0NN, UK.,MRC London Institute of Medical Sciences, London, W12 0NN, UK.,Sars International Centre for Marine Molecular Biology, University of Bergen, 5008, Bergen, Norway
| | - Charles Plessy
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Valerio Orlando
- Epigenetics and Genome Reprogramming Laboratory, IRCCS Fondazione Santa Lucia, Rome, Italy. .,KAUST Environmental Epigenetics Program, King Abdullah University of Science and Technology (KAUST), Division of Biological Environmental Sciences and Engineering, 23955-6900, Thuwal, Saudi Arabia.
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
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141
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Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer. Nat Commun 2020; 11:320. [PMID: 31949157 PMCID: PMC6965612 DOI: 10.1038/s41467-019-14098-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 12/17/2019] [Indexed: 02/07/2023] Open
Abstract
Endocrine therapy resistance frequently develops in estrogen receptor positive (ER+) breast cancer, but the underlying molecular mechanisms are largely unknown. Here, we show that 3-dimensional (3D) chromatin interactions both within and between topologically associating domains (TADs) frequently change in ER+ endocrine-resistant breast cancer cells and that the differential interactions are enriched for resistance-associated genetic variants at CTCF-bound anchors. Ectopic chromatin interactions are preferentially enriched at active enhancers and promoters and ER binding sites, and are associated with altered expression of ER-regulated genes, consistent with dynamic remodelling of ER pathways accompanying the development of endocrine resistance. We observe that loss of 3D chromatin interactions often occurs coincidently with hypermethylation and loss of ER binding. Alterations in active A and inactive B chromosomal compartments are also associated with decreased ER binding and atypical interactions and gene expression. Together, our results suggest that 3D epigenome remodelling is a key mechanism underlying endocrine resistance in ER+ breast cancer.
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142
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Rashid F, Ramakrishnan A, Fields C, Irudayaraj J. Acute PFOA exposure promotes epigenomic alterations in mouse kidney tissues. Toxicol Rep 2020; 7:125-132. [PMID: 31938689 PMCID: PMC6953769 DOI: 10.1016/j.toxrep.2019.12.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/30/2019] [Accepted: 12/31/2019] [Indexed: 01/09/2023] Open
Abstract
Perfluorooctanoic acid (PFOA), a manufactured perfluorochemical is a common surfactant and environmental pollutant found in various consumer products and water sources. Epidemiological studies have demonstrated its association with kidney dysfunction. However, the mechanisms that trigger kidney dysfunction following PFOA exposure is a gap in the field. The work presented explores the potential epigenetic indicators of kidney disease due to exposure to PFOA. In this study, 30 days old CD-1 mice were exposed to 1, 5, 10, or 20 mg/kg/day of PFOA for 10 days. Following acute oral exposure, epigenetic alterations and expression levels of various markers of fibroblast activation were evaluated in kidney tissues. We noted that PFOA-exposed mice exhibited differential methylation yielding 879 differentially methylated regions compared to vehicle. The mRNA expression revealed significant increase in Dnmt1 with decreased Rasal1 expression at higher levels of PFOA exposure suggestive of Rasal1 hypermethylation (an early indicator of fibroblast activation in kidney). Like Dnmt1, we also observed significant increase in Hdac1, 3 and 4. These are class I & II HDACs which are known to be critically altered in some renal diseases. Further, the mRNA expression levels of TGF-β and α-SMA significantly increased compared to vehicle. The KEGG and Go enrichment pathway analysis of reduced representation bisulfite data also revealed pathways implicated in renal fibrosis. Our study shows clear evidence of epigenetic alterations (DNA methylation and HDAC expression changes) in tissues from mouse kidney following PFOA exposure. Our results also suggest that epigenetic alterations in kidney promote the expression of early markers of fibroblast activation.
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Affiliation(s)
- Faizan Rashid
- Biomedical Research Center in Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL, 61801, USA
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Anujaianthi Ramakrishnan
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Biomedical Research Center in Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL, 61801, USA
| | - Christopher Fields
- High Performance Computing in Biology – HPCBio, Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Joseph Irudayaraj
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Biomedical Research Center in Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL, 61801, USA
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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143
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Deyssenroth MA, Marsit CJ, Chen J, Lambertini L. In-depth characterization of the placental imprintome reveals novel differentially methylated regions across birth weight categories. Epigenetics 2020; 15:47-60. [PMID: 31403346 PMCID: PMC6961688 DOI: 10.1080/15592294.2019.1647945] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 06/11/2019] [Accepted: 06/18/2019] [Indexed: 01/05/2023] Open
Abstract
Imprinted genes play a pivotal role in placental processes underlying fetal development, and much interest centers on discerning whether these loci, via changes in DNA methylation and/or gene expression, inform disruptions in appropriate fetal growth. In this study, we comprehensively profiled DNA methylation across the placental imprintome and assessed the relationship with gene expression levels and aberrant fetal growth.Placental DNA methylation across 153 imprinted loci, including imprint control regions (ICR) and surrounding non-ICR regions, was surveyed using the Nimblegen TruSeq bisulfite sequencing platform among participants enrolled in the Rhode Island Child Health Study (RICHS, n = 163). Methylation and gene expression associations were assessed using eQTM analysis. Differential methylation analysis contrasting small (SGA) and large for gestational age (LGA) infants against appropriate for gestational age (AGA) infants was assessed using the DMRcate R package.We identified 34 SGA-related differentially methylated regions (DMRs) and 9 LGA-related DMRs (FDR<0.05), and these BW-DMRs predominated in promoter and intronic regions. We observed overall hypomethylation among SGA-DMRs overlapping maternally expressed (paternally imprinted) genes while no parent-of-origin effect was observed among LGA DMRs. Three BW-DMRs, mapping to GABRG3, IGF1R and MEST, were common to SGA and LGA placenta. We did not observe significant correlations between BW-DMR-associated CpG methylation and gene expression levels.We report the first in-depth characterization of the placental imprintome in a population-wide setting. Our findings reveal growth-related differences in methylation without concomitant expression differences in regions that extend beyond typically interrogated imprinted loci, highlighting potentially novel placental biomarkers of growth and development.
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Affiliation(s)
- Maya A. Deyssenroth
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carmen J. Marsit
- Environmental Health at Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Luca Lambertini
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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144
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Hernandez M, Recalde S, Garcia-Garcia L, Bezunartea J, Miskey C, Johnen S, Diarra S, Sebe A, Rodriguez-Madoz JR, Pouillot S, Marie C, Izsvák Z, Scherman D, Kropp M, Prosper F, Thumann G, Ivics Z, Garcia-Layana A, Fernandez-Robredo P. Preclinical Evaluation of a Cell-Based Gene Therapy Using the Sleeping Beauty Transposon System in Choroidal Neovascularization. Mol Ther Methods Clin Dev 2019; 15:403-417. [PMID: 31890733 PMCID: PMC6909167 DOI: 10.1016/j.omtm.2019.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 10/30/2019] [Indexed: 01/05/2023]
Abstract
Age-related macular degeneration (AMD) is a progressive retinal disorder characterized by imbalanced pro- and antiangiogenic signals. The aim of this study was to evaluate the effect of ex vivo cell-based gene therapy with stable expression of human pigment epithelium-derived factor (PEDF) release using the non-viral Sleeping Beauty (SB100X) transposon system delivered by miniplasmids free of antibiotic resistance markers (pFAR4). Retinal pigment epithelial (RPE) cells and iris pigment epithelial (IPE) cells were co-transfected with pFAR4-inverted terminal repeats (ITRs) CMV-PEDF-BGH and pFAR4-CMV-SB100X-SV40 plasmids. Laser-induced choroidal neovascularization (CNV) was performed in rats, and transfected primary cells (transfected RPE [tRPE] and transfected IPE [tIPE] cells) were injected into the subretinal space. The leakage and CNV areas, vascular endothelial growth factor (VEGF), PEDF protein expression, metalloproteinases 2 and 9 (MMP-2/9), and microglial/macrophage markers were measured. Injection with tRPE/IPE cells significantly reduced the leakage area at 7 and 14 days and the CNV area at 7 days. There was a significant increase in PEDF and the PEDF/VEGF ratio with tRPE cells and a reduction in the MMP-2 activity. Our data demonstrated that ex vivo non-viral gene therapy reduces CNV and could be an effective and safe therapeutic option for angiogenic retinal diseases.
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Affiliation(s)
- Maria Hernandez
- Experimental Ophthalmology Laboratory, Ophthalmology, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Red Temática de Investigación Cooperativa Sanitaria en Enfermedades Oculares, Oftared, ISCIII, Madrid, Spain
| | - Sergio Recalde
- Experimental Ophthalmology Laboratory, Ophthalmology, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Red Temática de Investigación Cooperativa Sanitaria en Enfermedades Oculares, Oftared, ISCIII, Madrid, Spain
| | - Laura Garcia-Garcia
- Experimental Ophthalmology Laboratory, Ophthalmology, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Red Temática de Investigación Cooperativa Sanitaria en Enfermedades Oculares, Oftared, ISCIII, Madrid, Spain
| | - Jaione Bezunartea
- Experimental Ophthalmology Laboratory, Ophthalmology, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich-Institut, 63225 Langen, Germany
| | - Sandra Johnen
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Sabine Diarra
- Department of Ophthalmology, University Hospital RWTH Aachen, 52074 Aachen, Germany
| | - Attila Sebe
- Division of Medical Biotechnology, Paul Ehrlich-Institut, 63225 Langen, Germany
| | - Juan Roberto Rodriguez-Madoz
- Regenerative Medicine Program, Center for Applied Medical Research (CIMA), University of Navarra, IdiSNA, Pamplona 31008, Spain
| | | | - Corinne Marie
- Université de Paris, UTCBS, CNRS, INSERM, F-75006 Paris, France
- Chimie ParisTech, PSL Research University, F-75005 Paris, France
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Daniel Scherman
- Université de Paris, UTCBS, CNRS, INSERM, F-75006 Paris, France
| | - Martina Kropp
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Felipe Prosper
- Regenerative Medicine Program, Center for Applied Medical Research (CIMA), University of Navarra, IdiSNA, Pamplona 31008, Spain
- Area of Cell Therapy, Clínica Universidad de Navarra, University of Navarra, IdiSNA, Pamplona 31008, Spain
| | - Gabriele Thumann
- Experimental Ophthalmology, University of Geneva, 1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich-Institut, 63225 Langen, Germany
| | - Alfredo Garcia-Layana
- Experimental Ophthalmology Laboratory, Ophthalmology, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Red Temática de Investigación Cooperativa Sanitaria en Enfermedades Oculares, Oftared, ISCIII, Madrid, Spain
| | - Patricia Fernandez-Robredo
- Experimental Ophthalmology Laboratory, Ophthalmology, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
- Red Temática de Investigación Cooperativa Sanitaria en Enfermedades Oculares, Oftared, ISCIII, Madrid, Spain
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145
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Wogan GOU, Yuan ML, Mahler DL, Wang IJ. Genome-wide epigenetic isolation by environment in a widespread Anolis lizard. Mol Ecol 2019; 29:40-55. [PMID: 31710739 DOI: 10.1111/mec.15301] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 10/26/2019] [Accepted: 11/08/2019] [Indexed: 12/12/2022]
Abstract
Epigenetic changes can provide a pathway for organisms to respond to local environmental conditions by influencing gene expression. However, we still know little about the spatial distribution of epigenetic variation in natural systems, how it relates to the distribution of genetic variation and the environmental structure of the landscape, and the processes that generate and maintain it. Studies examining spatial patterns of genetic and epigenetic variation can provide valuable insights into how ecological and population processes contribute to epigenetic divergence across heterogeneous landscapes. Here, we perform a comparative analysis of spatial genetic and epigenetic variation based on 8,459 single nucleotide polymorphisms (SNPs) and 8,580 single methylation variants (SMVs) from eight populations of the Puerto Rican crested anole, Anolis cristatellus, an abundant lizard in the adaptive radiations of anoles on the Greater Antilles that occupies a diverse range of habitats. Using generalized dissimilarity modelling and multiple matrix regression, we found that genome-wide epigenetic differentiation is strongly correlated with environmental divergence, even after controlling for the underlying genetic structure. We also detected significant associations between key environmental variables and 96 SMVs, including 42 located in promoter regions or gene bodies. Our results suggest an environmental basis for population-level epigenetic differentiation in this system and contribute to better understanding how environmental gradients structure epigenetic variation in nature.
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Affiliation(s)
- Guinevere O U Wogan
- Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley, CA, USA
| | - Michael L Yuan
- Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley, CA, USA
| | - D Luke Mahler
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley, CA, USA
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146
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Wreczycka K, Franke V, Uyar B, Wurmus R, Bulut S, Tursun B, Akalin A. HOT or not: examining the basis of high-occupancy target regions. Nucleic Acids Res 2019; 47:5735-5745. [PMID: 31114922 PMCID: PMC6582337 DOI: 10.1093/nar/gkz460] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 05/02/2019] [Accepted: 05/13/2019] [Indexed: 01/16/2023] Open
Abstract
High-occupancy target (HOT) regions are segments of the genome with unusually high number of transcription factor binding sites. These regions are observed in multiple species and thought to have biological importance due to high transcription factor occupancy. Furthermore, they coincide with house-keeping gene promoters and consequently associated genes are stably expressed across multiple cell types. Despite these features, HOT regions are solely defined using ChIP-seq experiments and shown to lack canonical motifs for transcription factors that are thought to be bound there. Although, ChIP-seq experiments are the golden standard for finding genome-wide binding sites of a protein, they are not noise free. Here, we show that HOT regions are likely to be ChIP-seq artifacts and they are similar to previously proposed ‘hyper-ChIPable’ regions. Using ChIP-seq data sets for knocked-out transcription factors, we demonstrate presence of false positive signals on HOT regions. We observe sequence characteristics and genomic features that are discriminatory of HOT regions, such as GC/CpG-rich k-mers, enrichment of RNA–DNA hybrids (R-loops) and DNA tertiary structures (G-quadruplex DNA). The artificial ChIP-seq enrichment on HOT regions could be associated to these discriminatory features. Furthermore, we propose strategies to deal with such artifacts for the future ChIP-seq studies.
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Affiliation(s)
- Katarzyna Wreczycka
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Vedran Franke
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Bora Uyar
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ricardo Wurmus
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Selman Bulut
- Gene Regulation and Cell Fate Decision in C. elegans, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Baris Tursun
- Gene Regulation and Cell Fate Decision in C. elegans, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
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147
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Gkountela S, Castro-Giner F, Szczerba BM, Vetter M, Landin J, Scherrer R, Krol I, Scheidmann MC, Beisel C, Stirnimann CU, Kurzeder C, Heinzelmann-Schwarz V, Rochlitz C, Weber WP, Aceto N. Circulating Tumor Cell Clustering Shapes DNA Methylation to Enable Metastasis Seeding. Cell 2019; 176:98-112.e14. [PMID: 30633912 PMCID: PMC6363966 DOI: 10.1016/j.cell.2018.11.046] [Citation(s) in RCA: 532] [Impact Index Per Article: 106.4] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/31/2018] [Accepted: 11/28/2018] [Indexed: 01/01/2023]
Abstract
The ability of circulating tumor cells (CTCs) to form clusters has been linked to increased metastatic potential. Yet biological features and vulnerabilities of CTC clusters remain largely unknown. Here, we profile the DNA methylation landscape of single CTCs and CTC clusters from breast cancer patients and mouse models on a genome-wide scale. We find that binding sites for stemness- and proliferation-associated transcription factors are specifically hypomethylated in CTC clusters, including binding sites for OCT4, NANOG, SOX2, and SIN3A, paralleling embryonic stem cell biology. Among 2,486 FDA-approved compounds, we identify Na+/K+ ATPase inhibitors that enable the dissociation of CTC clusters into single cells, leading to DNA methylation remodeling at critical sites and metastasis suppression. Thus, our results link CTC clustering to specific changes in DNA methylation that promote stemness and metastasis and point to cluster-targeting compounds to suppress the spread of cancer.
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Affiliation(s)
- Sofia Gkountela
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland
| | - Francesc Castro-Giner
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Barbara Maria Szczerba
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland
| | - Marcus Vetter
- Gynecologic Cancer Center, University Hospital Basel, 4056 Basel, Switzerland; Department of Medical Oncology, University Hospital Basel, 4056 Basel, Switzerland
| | - Julia Landin
- Department of Medical Oncology, University Hospital Basel, 4056 Basel, Switzerland; Breast Center, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Ramona Scherrer
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland
| | - Ilona Krol
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland
| | - Manuel C Scheidmann
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | | | - Christian Kurzeder
- Gynecologic Cancer Center, University Hospital Basel, 4056 Basel, Switzerland; Breast Center, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | | | - Christoph Rochlitz
- Department of Medical Oncology, University Hospital Basel, 4056 Basel, Switzerland
| | - Walter Paul Weber
- Breast Center, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Nicola Aceto
- Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 4058 Basel, Switzerland.
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148
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Huang J, Wang L. Cell-Free DNA Methylation Profiling Analysis-Technologies and Bioinformatics. Cancers (Basel) 2019; 11:cancers11111741. [PMID: 31698791 PMCID: PMC6896050 DOI: 10.3390/cancers11111741] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 12/24/2022] Open
Abstract
Analysis of circulating nucleic acids in bodily fluids, referred to as “liquid biopsies”, is rapidly gaining prominence. Studies have shown that cell-free DNA (cfDNA) has great potential in characterizing tumor status and heterogeneity, as well as the response to therapy and tumor recurrence. DNA methylation is an epigenetic modification that plays an important role in a broad range of biological processes and diseases. It is well known that aberrant DNA methylation is generalizable across various samples and occurs early during the pathogenesis of cancer. Methylation patterns of cfDNA are also consistent with their originated cells or tissues. Systemic analysis of cfDNA methylation profiles has emerged as a promising approach for cancer detection and origin determination. In this review, we will summarize the technologies for DNA methylation analysis and discuss their feasibility for liquid biopsy applications. We will also provide a brief overview of the bioinformatic approaches for analysis of DNA methylation sequencing data. Overall, this review provides informative guidance for the selection of experimental and computational methods in cfDNA methylation-based studies.
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149
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Sepulveda JL. Using R and Bioconductor in Clinical Genomics and Transcriptomics. J Mol Diagn 2019; 22:3-20. [PMID: 31605800 DOI: 10.1016/j.jmoldx.2019.08.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 05/02/2019] [Accepted: 08/08/2019] [Indexed: 02/08/2023] Open
Abstract
Bioinformatics pipelines are essential in the analysis of genomic and transcriptomic data generated by next-generation sequencing (NGS). Recent guidelines emphasize the need for rigorous validation and assessment of robustness, reproducibility, and quality of NGS analytic pipelines intended for clinical use. Software tools written in the R statistical language and, in particular, the set of tools available in the Bioconductor repository are widely used in research bioinformatics; and these frameworks offer several advantages for use in clinical bioinformatics, including the breath of available tools, modular nature of software packages, ease of installation, enforcement of interoperability, version control, and short learning curve. This review provides an introduction to R and Bioconductor software, its advantages and limitations for clinical bioinformatics, and illustrative examples of tools that can be used in various steps of NGS analysis.
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Affiliation(s)
- Jorge L Sepulveda
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York; Informatics Subdivision Leadership, Association for Molecular Pathology, Bethesda, Maryland.
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150
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Wang X, Kadarmideen HN. Genome-wide DNA methylation analysis using next-generation sequencing to reveal candidate genes responsible for boar taint in pigs. Anim Genet 2019; 50:644-659. [PMID: 31515844 DOI: 10.1111/age.12842] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2019] [Indexed: 01/23/2023]
Abstract
Boar taint (BT) is an offensive flavor observed in non-castrated male pigs that reduces the carcass price. Surgical castration effectively avoids the taint but is associated with animal welfare concerns. The functional annotation of farm animal genomes for understanding the biology of complex traits can be used in the selection of breeding animals to achieve favorable phenotypic outcomes. The characterization of pig epigenomes/methylation changes between animals with high and low BT and genome-wide epigenetic markers that can predict BT are lacking. Reduced representation bisulfite sequencing of DNA methylation patterns based on next-generation sequencing is an efficient technology to identify candidate epigenetic biomarkers associated with BT. Three different BT levels were analyzed using reduced representation bisulfite sequencing data to calculate the methylation levels of cytosine and guanine dinucleotide (CpG) sites. The co-analysis of differentially methylated CpG sites identified by this study and differentially expressed genes identified by a previous study found 32 significant co-located genes. The joint analysis of GO terms and pathways revealed that methylation and gene expression of seven candidate genes were associated with BT; in particular, FASN plays a key role in fatty acid biosynthesis, and PEMT might be involved in estrogen regulation and the development of BT. This study is the first to report the genome-wide DNA methylation profiles of BT in pigs using next-generation sequencing and summarize candidate genes associated with epigenetic markers of BT, which could contribute to the understanding of the functional biology of BT traits and selective breeding of pigs against BT based on epigenetic biomarkers.
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Affiliation(s)
- X Wang
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Richard Petersens Plads, Building 324, Kongens Lyngby, 2800, Denmark
| | - H N Kadarmideen
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Richard Petersens Plads, Building 324, Kongens Lyngby, 2800, Denmark
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