1
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Sigeman H, Downing PA, Zhang H, Hansson B. The rate of W chromosome degeneration across multiple avian neo-sex chromosomes. Sci Rep 2024; 14:16548. [PMID: 39020011 PMCID: PMC11255319 DOI: 10.1038/s41598-024-66470-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 07/01/2024] [Indexed: 07/19/2024] Open
Abstract
When sex chromosomes evolve recombination suppression, the sex-limited chromosome (Y/W) commonly degenerate by losing functional genes. The rate of Y/W degeneration is believed to slow down over time as the most essential genes are maintained by purifying selection, but supporting data are scarce especially for ZW systems. Here, we study W degeneration in Sylvioidea songbirds where multiple autosomal translocations to the sex chromosomes, and multiple recombination suppression events causing separate evolutionary strata, have occurred during the last ~ 28.1-4.5 million years (Myr). We show that the translocated regions have maintained 68.3-97.7% of their original gene content, compared to only 4.2% on the much older ancestral W chromosome. By mapping W gene losses onto a dated phylogeny, we estimate an average gene loss rate of 1.0% per Myr, with only moderate variation between four independent lineages. Consistent with previous studies, evolutionarily constrained and haploinsufficient genes were preferentially maintained on W. However, the gene loss rate did not show any consistent association with strata age or with the number of W genes at strata formation. Our study provides a unique account on the pace of W gene loss and reinforces the significance of purifying selection in maintaining essential genes on sex chromosomes.
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Affiliation(s)
- Hanna Sigeman
- Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden.
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland.
| | - Philip A Downing
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Hongkai Zhang
- Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden
| | - Bengt Hansson
- Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden.
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2
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Mathur K, Singh B, Puria R, Nain V. In silico genome wide identification of long non-coding RNAs differentially expressed during Candida auris host pathogenesis. Arch Microbiol 2024; 206:253. [PMID: 38727738 DOI: 10.1007/s00203-024-03969-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 04/18/2024] [Indexed: 05/15/2024]
Abstract
Candida auris is an invasive fungal pathogen of high concern due to acquired drug tolerance against antifungals used in clinics. The prolonged persistence on biotic and abiotic surfaces can result in onset of hospital outbreaks causing serious health threat. An in depth understanding of pathology of C. auris is highly desirable for development of efficient therapeutics. Non-coding RNAs play crucial role in fungal pathology. However, the information about ncRNAs is scanty to be utilized. Herein our aim is to identify long noncoding RNAs with potent role in pathobiology of C. auris. Thereby, we analyzed the transcriptomics data of C. auris infection in blood for identification of potential lncRNAs with regulatory role in determining invasion, survival or drug tolerance under infection conditions. Interestingly, we found 275 lncRNAs, out of which 253 matched with lncRNAs reported in Candidamine, corroborating for our accurate data analysis pipeline. Nevertheless, we obtained 23 novel lncRNAs not reported earlier. Three lncRNAs were found to be under expressed throughout the course of infection, in the transcriptomics data. 16 of potent lncRNAs were found to be coexpressed with coding genes, emphasizing for their functional role. Noteworthy, these ncRNAs are expressed from intergenic regions of the genes associated with transporters, metabolism, cell wall biogenesis. This study recommends for possible association between lncRNA expression and C. auris pathogenesis.
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Affiliation(s)
- Kartavya Mathur
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Bharti Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Rekha Puria
- School of Biotechnology, Gautam Buddha University, Greater Noida, India.
| | - Vikrant Nain
- School of Biotechnology, Gautam Buddha University, Greater Noida, India.
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3
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Yan G, Song D, Li JJ. scReadSim: a single-cell RNA-seq and ATAC-seq read simulator. Nat Commun 2023; 14:7482. [PMID: 37980428 PMCID: PMC10657386 DOI: 10.1038/s41467-023-43162-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 11/02/2023] [Indexed: 11/20/2023] Open
Abstract
Benchmarking single-cell RNA-seq (scRNA-seq) and single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) computational tools demands simulators to generate realistic sequencing reads. However, none of the few read simulators aim to mimic real data. To fill this gap, we introduce scReadSim, a single-cell RNA-seq and ATAC-seq read simulator that allows user-specified ground truths and generates synthetic sequencing reads (in a FASTQ or BAM file) by mimicking real data. At both read-sequence and read-count levels, scReadSim mimics real scRNA-seq and scATAC-seq data. Moreover, scReadSim provides ground truths, including unique molecular identifier (UMI) counts for scRNA-seq and open chromatin regions for scATAC-seq. In particular, scReadSim allows users to design cell-type-specific ground-truth open chromatin regions for scATAC-seq data generation. In benchmark applications of scReadSim, we show that UMI-tools achieves the top accuracy in scRNA-seq UMI deduplication, and HMMRATAC and MACS3 achieve the top performance in scATAC-seq peak calling.
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Affiliation(s)
- Guanao Yan
- Department of Statistics, University of California, Los Angeles, CA 90095-1554, USA
| | - Dongyuan Song
- Bioinformatics Interdepartmental Ph.D. Program, University of California, Los Angeles, CA, 90095-7246, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, CA 90095-1554, USA.
- Bioinformatics Interdepartmental Ph.D. Program, University of California, Los Angeles, CA, 90095-7246, USA.
- Department of Human Genetics, University of California, Los Angeles, CA, 90095-7088, USA.
- Department of Computational Medicine, University of California, Los Angeles, CA, 90095-1766, USA.
- Department of Biostatistics, University of California, Los Angeles, CA, 90095-1772, USA.
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA, 02138, USA.
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4
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Bhin J, Yemelyanenko J, Chao X, Klarenbeek S, Opdam M, Malka Y, Hoekman L, Kruger D, Bleijerveld O, Brambillasca CS, Sprengers J, Siteur B, Annunziato S, van Haren MJ, Martin NI, van de Ven M, Peters D, Agami R, Linn SC, Boven E, Altelaar M, Jonkers J, Zingg D, Wessels LF. MYC is a clinically significant driver of mTOR inhibitor resistance in breast cancer. J Exp Med 2023; 220:e20211743. [PMID: 37642941 PMCID: PMC10465700 DOI: 10.1084/jem.20211743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 05/18/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023] Open
Abstract
Targeting the PI3K-AKT-mTOR pathway is a promising therapeutic strategy for breast cancer treatment. However, low response rates and development of resistance to PI3K-AKT-mTOR inhibitors remain major clinical challenges. Here, we show that MYC activation drives resistance to mTOR inhibitors (mTORi) in breast cancer. Multiomic profiling of mouse invasive lobular carcinoma (ILC) tumors revealed recurrent Myc amplifications in tumors that acquired resistance to the mTORi AZD8055. MYC activation was associated with biological processes linked to mTORi response and counteracted mTORi-induced translation inhibition by promoting translation of ribosomal proteins. In vitro and in vivo induction of MYC conferred mTORi resistance in mouse and human breast cancer models. Conversely, AZD8055-resistant ILC cells depended on MYC, as demonstrated by the synergistic effects of mTORi and MYCi combination treatment. Notably, MYC status was significantly associated with poor response to everolimus therapy in metastatic breast cancer patients. Thus, MYC is a clinically relevant driver of mTORi resistance that may stratify breast cancer patients for mTOR-targeted therapies.
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Affiliation(s)
- Jinhyuk Bhin
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, Netherlands
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
- Department of Biomedical System Informatics, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Julia Yemelyanenko
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Xue Chao
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Sjoerd Klarenbeek
- Experimental Animal Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Mark Opdam
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Yuval Malka
- Oncode Institute, Utrecht, Netherlands
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Dinja Kruger
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Medical Oncology, Amsterdam University Medical Center, Vrije Universiteit Amsterdam/Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Onno Bleijerveld
- Proteomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Chiara S. Brambillasca
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Justin Sprengers
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Bjørn Siteur
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Stefano Annunziato
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Matthijs J. van Haren
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Nathaniel I. Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Dennis Peters
- Core Facility Molecular Pathology and Biobanking, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Reuven Agami
- Oncode Institute, Utrecht, Netherlands
- Division of Oncogenomics, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sabine C. Linn
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Epie Boven
- Department of Medical Oncology, Amsterdam University Medical Center, Vrije Universiteit Amsterdam/Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Maarten Altelaar
- Proteomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
- Netherlands Proteomics Centre, Utrecht, Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Daniel Zingg
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Lodewyk F.A. Wessels
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
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5
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Law STS, Yu Y, Nong W, So WL, Li Y, Swale T, Ferrier DEK, Qiu J, Qian P, Hui JHL. The genome of the deep-sea anemone Actinernus sp. contains a mega-array of ANTP-class homeobox genes. Proc Biol Sci 2023; 290:20231563. [PMID: 37876192 PMCID: PMC10598428 DOI: 10.1098/rspb.2023.1563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
Members of the phylum Cnidaria include sea anemones, corals and jellyfish, and have successfully colonized both marine and freshwater habitats throughout the world. The understanding of how cnidarians adapt to extreme environments such as the dark, high-pressure deep-sea habitat has been hindered by the lack of genomic information. Here, we report the first chromosome-level deep-sea cnidarian genome, of the anemone Actinernus sp., which was 1.39 Gbp in length and contained 44 970 gene models including 14 806 tRNA genes and 30 164 protein-coding genes. Analyses of homeobox genes revealed the longest chromosome hosts a mega-array of Hox cluster, HoxL, NK cluster and NKL homeobox genes; until now, such an array has only been hypothesized to have existed in ancient ancestral genomes. In addition to this striking arrangement of homeobox genes, analyses of microRNAs revealed cnidarian-specific complements that are distinctive for nested clades of these animals, presumably reflecting the progressive evolution of the gene regulatory networks in which they are embedded. Also, compared with other sea anemones, circadian rhythm genes were lost in Actinernus sp., which likely reflects adaptation to living in the dark. This high-quality genome of a deep-sea cnidarian thus reveals some of the likely molecular adaptations of this ecologically important group of metazoans to the extreme deep-sea environment. It also deepens our understanding of the evolution of genome content and organization of animals in general and cnidarians in particular, specifically from the viewpoint of key developmental control genes like the homeobox-encoding genes, where we find an array of genes that until now has only been hypothesized to have existed in the ancient ancestor that pre-dated both the cnidarians and bilaterians.
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Affiliation(s)
- Sean Tsz Sum Law
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Yifei Yu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Wai Lok So
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Yiqian Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Thomas Swale
- Dovetail Genomics, LLC, Scotts Valley, CA 95066, USA
| | - David E. K. Ferrier
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St. Andrews, St. Andrews, UK
| | - Jianwen Qiu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People's Republic of China
- Department of Biology, Hong Kong Baptist University, Hong Kong, People's Republic of China
| | - Peiyuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People's Republic of China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, People's Republic of China
| | - Jerome Ho Lam Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
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6
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Xiang Y, Huang W, Tan L, Chen T, He Y, Irving PS, Weeks KM, Zhang QC, Dong X. Pervasive downstream RNA hairpins dynamically dictate start-codon selection. Nature 2023; 621:423-430. [PMID: 37674078 PMCID: PMC10499604 DOI: 10.1038/s41586-023-06500-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/31/2023] [Indexed: 09/08/2023]
Abstract
Translational reprogramming allows organisms to adapt to changing conditions. Upstream start codons (uAUGs), which are prevalently present in mRNAs, have crucial roles in regulating translation by providing alternative translation start sites1-4. However, what determines this selective initiation of translation between conditions remains unclear. Here, by integrating transcriptome-wide translational and structural analyses during pattern-triggered immunity in Arabidopsis, we found that transcripts with immune-induced translation are enriched with upstream open reading frames (uORFs). Without infection, these uORFs are selectively translated owing to hairpins immediately downstream of uAUGs, presumably by slowing and engaging the scanning preinitiation complex. Modelling using deep learning provides unbiased support for these recognizable double-stranded RNA structures downstream of uAUGs (which we term uAUG-ds) being responsible for the selective translation of uAUGs, and allows the prediction and rational design of translating uAUG-ds. We found that uAUG-ds-mediated regulation can be generalized to human cells. Moreover, uAUG-ds-mediated start-codon selection is dynamically regulated. After immune challenge in plants, induced RNA helicases that are homologous to Ded1p in yeast and DDX3X in humans resolve these structures, allowing ribosomes to bypass uAUGs to translate downstream defence proteins. This study shows that mRNA structures dynamically regulate start-codon selection. The prevalence of this RNA structural feature and the conservation of RNA helicases across kingdoms suggest that mRNA structural remodelling is a general feature of translational reprogramming.
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Affiliation(s)
- Yezi Xiang
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | - Wenze Huang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Lianmei Tan
- Department of Pharmacology and Cancer Biology, Duke Medical Center, Duke University, Durham, NC, USA
| | - Tianyuan Chen
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | - Yang He
- Department of Biology, Duke University, Durham, NC, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | - Patrick S Irving
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xinnian Dong
- Department of Biology, Duke University, Durham, NC, USA.
- Howard Hughes Medical Institute, Duke University, Durham, NC, USA.
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7
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Ban H, Sato S, Yoshikawa S, Yamada K, Nakamura Y, Ichinomiya M, Sato N, Blanc-Mathieu R, Endo H, Kuwata A, Ogata H. Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs. Commun Biol 2023; 6:697. [PMID: 37420035 PMCID: PMC10328945 DOI: 10.1038/s42003-023-05002-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/31/2023] [Indexed: 07/09/2023] Open
Abstract
The order Parmales (class Bolidophyceae) is a minor group of pico-sized eukaryotic marine phytoplankton that contains species with cells surrounded by silica plates. Previous studies revealed that Parmales is a member of ochrophytes and sister to diatoms (phylum Bacillariophyta), the most successful phytoplankton group in the modern ocean. Therefore, parmalean genomes can serve as a reference to elucidate both the evolutionary events that differentiated these two lineages and the genomic basis for the ecological success of diatoms vs. the more cryptic lifestyle of parmaleans. Here, we compare the genomes of eight parmaleans and five diatoms to explore their physiological and evolutionary differences. Parmaleans are predicted to be phago-mixotrophs. By contrast, diatoms have lost genes related to phagocytosis, indicating the ecological specialization from phago-mixotrophy to photoautotrophy in their early evolution. Furthermore, diatoms show significant enrichment in gene sets involved in nutrient uptake and metabolism, including iron and silica, in comparison with parmaleans. Overall, our results suggest a strong evolutionary link between the loss of phago-mixotrophy and specialization to a silicified photoautotrophic life stage early in diatom evolution after diverging from the Parmales lineage.
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Affiliation(s)
- Hiroki Ban
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Shinya Sato
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Shinya Yoshikawa
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Kazumasa Yamada
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Yoji Nakamura
- Bioinformatics and Biosciences Division, Fisheries Stock Assessment Center, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fuku-ura, Kanazawa, Yokohama, Kanagawa, 236-8648, Japan
| | - Mutsuo Ichinomiya
- Prefectural University of Kumamoto, 3-1-100 Tsukide, Kumamoto, 862-8502, Japan
| | - Naoki Sato
- Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Romain Blanc-Mathieu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, IRIG, Grenoble, France
| | - Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Akira Kuwata
- Shiogama field station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 3-27-5 Shinhama-cho, Shiogama, Miyagi, Japan.
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
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Ilott NE, Neyazi M, Arancibia-Cárcamo CV, Powrie F, Geremia A. Tissue-dependent transcriptional and bacterial associations in primary sclerosing cholangitis-associated inflammatory bowel disease. Wellcome Open Res 2022; 6:199. [PMID: 36447600 PMCID: PMC9664024 DOI: 10.12688/wellcomeopenres.16901.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2022] [Indexed: 06/30/2024] Open
Abstract
Background: Patients with primary sclerosing cholangitis (PSC) frequently have co-ocurring ulcerative colitis (UC) and develop colorectal cancer. Colorectal cancer risk in patients with PSC-associated ulcerative colitis (PSC/UC) is elevated relative to patients with ulcerative colitis (UC) alone, reasons for which remain obscure. Understanding the molecular and microbial basis for differences between these two patient groups and how these vary across intestinal sites is important for the development of therapies to prevent colorectal cancer development in at-risk individuals. Methods: We employed ribonucleic acid sequencing (RNA-seq) analysis of biopsy samples across three intestinal tissue locations (ileum, caecum and rectum) in patients with PSC/UC (ileum n = 7, caecum n = 7, rectum n = 7), UC (ileum n = 9, caecum n = 10, rectum n = 10) and healthy controls (ileum n = 11, caecum n = 9, rectum n = 12) to determine tissue-dependent transcriptional alterations in PSC/UC. We also performed 16S ribosomal RNA (rRNA) amplicon sequencing to determine bacterial associations with PSC/UC. Results: Tissue-defining transcriptional signatures revealed that the ileum was enriched for genes involved in lipid and drug metabolism, the caecum for activated immune cells and the rectum for enteric neurogenesis. Transcriptional alterations relative to healthy control samples were largely shared between patients with PSC/UC or UC although were distinct across tissue locations. Nevertheless, we observed reduced expression of gamma-glutamyl transferase 1 ( GGT1) specifically in the ileum and caecum of patients with PSC/UC. Analysis of the bacterial component of the microbiome revealed high inter-individual variability of microbiome composition and little evidence for tissue-dependency. We observed a reduction in Parabacteroides relative abundance in the rectum of patients with PSC/UC. Conclusions: The role of gamma-glutamyl transferase in maintaining the redox environment through the glutathione salvage pathway makes our observed alterations a potential pathway to PSC-associated colorectal cancer.
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Affiliation(s)
- Nicholas E. Ilott
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7FY, UK
| | - Mastura Neyazi
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Oxford Translational Gastroenterology Unit Investigators
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7FY, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Carolina V. Arancibia-Cárcamo
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Fiona Powrie
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7FY, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Alessandra Geremia
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
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9
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Ray S, Abugable AA, Parker J, Liversidge K, Palminha NM, Liao C, Acosta-Martin AE, Souza CDS, Jurga M, Sudbery I, El-Khamisy SF. A mechanism for oxidative damage repair at gene regulatory elements. Nature 2022; 609:1038-1047. [PMID: 36171374 DOI: 10.1038/s41586-022-05217-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 08/09/2022] [Indexed: 11/09/2022]
Abstract
Oxidative genome damage is an unavoidable consequence of cellular metabolism. It arises at gene regulatory elements by epigenetic demethylation during transcriptional activation1,2. Here we show that promoters are protected from oxidative damage via a process mediated by the nuclear mitotic apparatus protein NuMA (also known as NUMA1). NuMA exhibits genomic occupancy approximately 100 bp around transcription start sites. It binds the initiating form of RNA polymerase II, pause-release factors and single-strand break repair (SSBR) components such as TDP1. The binding is increased on chromatin following oxidative damage, and TDP1 enrichment at damaged chromatin is facilitated by NuMA. Depletion of NuMA increases oxidative damage at promoters. NuMA promotes transcription by limiting the polyADP-ribosylation of RNA polymerase II, increasing its availability and release from pausing at promoters. Metabolic labelling of nascent RNA identifies genes that depend on NuMA for transcription including immediate-early response genes. Complementation of NuMA-deficient cells with a mutant that mediates binding to SSBR, or a mitotic separation-of-function mutant, restores SSBR defects. These findings underscore the importance of oxidative DNA damage repair at gene regulatory elements and describe a process that fulfils this function.
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Affiliation(s)
- Swagat Ray
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK.,School of Life and Environmental Sciences, Department of Life Sciences, University of Lincoln, Lincoln, UK
| | - Arwa A Abugable
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Jacob Parker
- School of Biosciences, University of Sheffield, Sheffield, UK.,Center for Advanced Parkinson Research, Harvard Medical School, Boston, MA, USA
| | | | - Nelma M Palminha
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Chunyan Liao
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Adelina E Acosta-Martin
- biOMICS Facility, Faculty of Science Mass Spectrometry Centre, University of Sheffield, Sheffield, UK
| | - Cleide D S Souza
- School of Biosciences, University of Sheffield, Sheffield, UK.,Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Mateusz Jurga
- Institute of Cancer Therapeutics, School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK
| | - Ian Sudbery
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Sherif F El-Khamisy
- School of Biosciences, University of Sheffield, Sheffield, UK. .,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK. .,Institute of Cancer Therapeutics, School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK.
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10
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Niu YN, Roberts EG, Denisko D, Hoffman MM. Assessing and assuring interoperability of a genomics file format. Bioinformatics 2022; 38:3327-3336. [PMID: 35575355 PMCID: PMC9237710 DOI: 10.1093/bioinformatics/btac327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/30/2022] [Accepted: 05/11/2022] [Indexed: 12/01/2022] Open
Abstract
Motivation Bioinformatics software tools operate largely through the use of specialized genomics file formats. Often these formats lack formal specification, making it difficult or impossible for the creators of these tools to robustly test them for correct handling of input and output. This causes problems in interoperability between different tools that, at best, wastes time and frustrates users. At worst, interoperability issues could lead to undetected errors in scientific results. Results We developed a new verification system, Acidbio, which tests for correct behavior in bioinformatics software packages. We crafted tests to unify correct behavior when tools encounter various edge cases—potentially unexpected inputs that exemplify the limits of the format. To analyze the performance of existing software, we tested the input validation of 80 Bioconda packages that parsed the Browser Extensible Data (BED) format. We also used a fuzzing approach to automatically perform additional testing. Of 80 software packages examined, 75 achieved less than 70% correctness on our test suite. We categorized multiple root causes for the poor performance of different types of software. Fuzzing detected other errors that the manually designed test suite could not. We also created a badge system that developers can use to indicate more precisely which BED variants their software accepts and to advertise the software’s performance on the test suite. Availability and implementation Acidbio is available at https://github.com/hoffmangroup/acidbio. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yi Nian Niu
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, M5G 2C1, Canada
| | - Eric G Roberts
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, M5G 2C1, Canada
| | - Danielle Denisko
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, M5G 2C1, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Michael M Hoffman
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, M5G 2C1, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, M5S 2E4, Canada.,Vector Institute, Toronto, ON, M5G 1M1, Canada
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11
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Kong BLH, Nong W, Wong KH, Law STS, So WL, Chan JJS, Zhang J, Lau TWD, Hui JHL, Shaw PC. Chromosomal level genome of Ilex asprella and insight into antiviral triterpenoid pathway. Genomics 2022; 114:110366. [PMID: 35413434 DOI: 10.1016/j.ygeno.2022.110366] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 01/14/2023]
Abstract
Ilex asprella is a widely used herbs in Traditional Chinese Medicine for treating viral infection and relieving inflammation. Due to the earlier fruiting period of I. asprella, it is the major food source for frugivores in summer. Despite its pharmacological and ecological importance, a reference genome for I. asprella is lacking. By using Illumina, stLFR and Omni-C sequencing data, we present the first chromosomal-level assembly for I. asprella. The genome assembly size is 804 Mbp, with Benchmarking Universal Single-Copy Orthologs (BUSCO) score 94.4% for eudicotyledon single copy genes. Transcriptomes of leaves, stems, flowers, premature fruits and roots were analyzed, providing 39,215 gene models. The complete set of genes involved in the triterpenoids production is disclosed for the first time. We have also found the oxidosqualene cyclases (OSCs), CYP716s and UDP-glycosyltransferases (UGTs), which are responsible for the modification of triterpenoid backbones, resulting in the high variety of triterpenoid saponins.
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Affiliation(s)
- Bobby Lim-Ho Kong
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, Institute of Chinese Medicine, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li, Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Kwan-Ho Wong
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Sean Tsz-Sum Law
- School of Life Sciences, Simon F.S. Li, Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai-Lok So
- School of Life Sciences, Simon F.S. Li, Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Johnson Jor-Shing Chan
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, Institute of Chinese Medicine, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Jordan Zhang
- Dovetail Genomics, Scotts Valley, CA, United States
| | - Tai-Wai David Lau
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Jerome Ho-Lam Hui
- School of Life Sciences, Simon F.S. Li, Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Pang-Chui Shaw
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, Institute of Chinese Medicine, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
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12
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The long non-coding RNA landscape of Candida yeast pathogens. Nat Commun 2021; 12:7317. [PMID: 34916523 PMCID: PMC8677757 DOI: 10.1038/s41467-021-27635-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/30/2021] [Indexed: 12/29/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) constitute a poorly studied class of transcripts with emerging roles in key cellular processes. Despite efforts to characterize lncRNAs across a wide range of species, these molecules remain largely unexplored in most eukaryotic microbes, including yeast pathogens of the Candida clade. Here, we analyze thousands of publicly available sequencing datasets to infer and characterize the lncRNA repertoires of five major Candida pathogens: Candida albicans, Candida tropicalis, Candida parapsilosis, Candida auris and Candida glabrata. Our results indicate that genomes of these species encode hundreds of lncRNAs that show levels of evolutionary constraint intermediate between those of intergenic genomic regions and protein-coding genes. Despite their low sequence conservation across the studied species, some lncRNAs are syntenic and are enriched in shared sequence motifs. We find co-expression of lncRNAs with certain protein-coding transcripts, hinting at potential functional associations. Finally, we identify lncRNAs that are differentially expressed during infection of human epithelial cells for four of the studied species. Our comprehensive bioinformatic analyses of Candida lncRNAs pave the way for future functional characterization of these transcripts. Long non-coding RNAs (lncRNAs) play roles in key cellular processes, but remain largely unexplored in fungal pathogens such as Candida. Here, Hovhannisyan and Gabaldón analyze thousands of sequencing datasets to infer and characterize the lncRNA repertoires of five Candida species, paving the way for their future functional characterization.
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13
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Loss of mutual protection between human osteoclasts and chondrocytes in damaged joints initiates osteoclast-mediated cartilage degradation by MMPs. Sci Rep 2021; 11:22708. [PMID: 34811438 PMCID: PMC8608887 DOI: 10.1038/s41598-021-02246-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/09/2021] [Indexed: 01/09/2023] Open
Abstract
Osteoclasts are multinucleated, bone-resorbing cells. However, they also digest cartilage during skeletal maintenance, development and in degradative conditions including osteoarthritis, rheumatoid arthritis and primary bone sarcoma. This study explores the mechanisms behind the osteoclast–cartilage interaction. Human osteoclasts differentiated on acellular human cartilage expressed osteoclast marker genes (e.g. CTSK, MMP9) and proteins (TRAP, VNR), visibly damaged the cartilage surface and released glycosaminoglycan in a contact-dependent manner. Direct co-culture with chondrocytes during differentiation increased large osteoclast formation (p < 0.0001) except when co-cultured on dentine, when osteoclast formation was inhibited (p = 0.0002). Osteoclasts cultured on dentine inhibited basal cartilage degradation (p = 0.012). RNA-seq identified MMP8 overexpression in osteoclasts differentiated on cartilage versus dentine (8.89-fold, p = 0.0133), while MMP9 was the most highly expressed MMP. Both MMP8 and MMP9 were produced by osteoclasts in osteosarcoma tissue. This study suggests that bone-resident osteoclasts and chondrocytes exert mutually protective effects on their ‘native’ tissue. However, when osteoclasts contact non-native cartilage they cause degradation via MMPs. Understanding the role of osteoclasts in cartilage maintenance and degradation might identify new therapeutic approaches for pathologies characterized by cartilage degeneration.
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14
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Blanco E, González-Ramírez M, Di Croce L. Productive visualization of high-throughput sequencing data using the SeqCode open portable platform. Sci Rep 2021; 11:19545. [PMID: 34599234 PMCID: PMC8486768 DOI: 10.1038/s41598-021-98889-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 08/20/2021] [Indexed: 12/23/2022] Open
Abstract
Large-scale sequencing techniques to chart genomes are entirely consolidated. Stable computational methods to perform primary tasks such as quality control, read mapping, peak calling, and counting are likewise available. However, there is a lack of uniform standards for graphical data mining, which is also of central importance. To fill this gap, we developed SeqCode, an open suite of applications that analyzes sequencing data in an elegant but efficient manner. Our software is a portable resource written in ANSI C that can be expected to work for almost all genomes in any computational configuration. Furthermore, we offer a user-friendly front-end web server that integrates SeqCode functions with other graphical analysis tools. Our analysis and visualization toolkit represents a significant improvement in terms of performance and usability as compare to other existing programs. Thus, SeqCode has the potential to become a key multipurpose instrument for high-throughput professional analysis; further, it provides an extremely useful open educational platform for the world-wide scientific community. SeqCode website is hosted at http://ldicrocelab.crg.eu, and the source code is freely distributed at https://github.com/eblancoga/seqcode.
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Affiliation(s)
- Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
| | - Mar González-Ramírez
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,ICREA, Passeig Lluis Companys 23, 08010, Barcelona, Spain.
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15
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Ilott NE, Neyazi M, Arancibia-Cárcamo CV, Powrie F, Geremia A. Tissue-dependent transcriptional and bacterial associations in primary sclerosing cholangitis-associated inflammatory bowel disease. Wellcome Open Res 2021; 6:199. [PMID: 36447600 PMCID: PMC9664024 DOI: 10.12688/wellcomeopenres.16901.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2021] [Indexed: 06/30/2024] Open
Abstract
Background: Primary sclerosing cholangitis (PSC) is a disease of the bile duct and liver. However, patients frequently have co-morbidities including inflammatory bowel disease (IBD) and colorectal cancer. Colorectal cancer risk in patients with PSC-associated ulcerative colitis (PSC/UC) is elevated relative to patients with ulcerative colitis (UC) alone, reasons for which remain obscure. Further, clinical and immunological features, and involved intestinal sites differ between PSC/UC and UC. Understanding the molecular and microbial basis for differences in cancer risk between these two patient groups and how these differ across intestinal sites is important for the development of therapies to prevent colorectal cancer development in at-risk individuals. Methods: We employed ribonucleic acid sequencing (RNA-seq) analysis of biopsy samples across three intestinal tissue locations (ileum, caecum and rectum) in patients with PSC/UC (n = 8), UC (n = 10) and healthy controls (n = 12) to determine tissue-dependent transcriptional alterations in PSC/UC. We also performed 16S ribosomal RNA (rRNA) amplicon sequencing to determine bacterial associations with PSC/UC and host-microbiome associations. Results: Tissue-defining transcriptional signatures revealed that the ileum was enriched for genes involved in lipid and drug metabolism, the caecum for activated immune cells and the rectum for enteric neurogenesis. Transcriptional alterations relative to healthy control samples were largely shared between patients with PSC/UC or UC although were distinct across tissue locations. Nevertheless, we observed reduced expression of gamma-glutamyl transferase 1 ( GGT1) specifically in the ileum and caecum of patients with PSC/UC. Analysis of the bacterial component of the microbiome revealed high inter-individual variability of microbiome composition and little evidence for tissue-dependency. We observed a reduction in Parabacteroides relative abundance in the rectum of patients with PSC/UC. Conclusions: The role of gamma-glutamyl transferase in maintaining the redox environment through the glutathione salvage pathway makes our observed alterations a potential pathway to PSC-associated colorectal cancer.
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Affiliation(s)
- Nicholas E. Ilott
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7FY, UK
| | - Mastura Neyazi
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Oxford Translational Gastroenterology Unit Investigators
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7FY, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Carolina V. Arancibia-Cárcamo
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Fiona Powrie
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7FY, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Alessandra Geremia
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, and NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
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16
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Ninomiya K, Iwakiri J, Aly MK, Sakaguchi Y, Adachi S, Natsume T, Terai G, Asai K, Suzuki T, Hirose T. m 6 A modification of HSATIII lncRNAs regulates temperature-dependent splicing. EMBO J 2021; 40:e107976. [PMID: 34184765 DOI: 10.15252/embj.2021107976] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/24/2021] [Accepted: 05/28/2021] [Indexed: 12/21/2022] Open
Abstract
Nuclear stress bodies (nSBs) are nuclear membraneless organelles formed around stress-inducible HSATIII architectural long noncoding RNAs (lncRNAs). nSBs repress splicing of hundreds of introns during thermal stress recovery, which are partly regulated by CLK1 kinase phosphorylation of temperature-dependent Ser/Arg-rich splicing factors (SRSFs). Here, we report a distinct mechanism for this splicing repression through protein sequestration by nSBs. Comprehensive identification of RNA-binding proteins revealed HSATIII association with proteins related to N6 -methyladenosine (m6 A) RNA modification. 11% of the first adenosine in the repetitive HSATIII sequence were m6 A-modified. nSBs sequester the m6 A writer complex to methylate HSATIII, leading to subsequent sequestration of the nuclear m6 A reader, YTHDC1. Sequestration of these factors from the nucleoplasm represses m6 A modification of pre-mRNAs, leading to repression of m6 A-dependent splicing during stress recovery phase. Thus, nSBs serve as a common platform for regulation of temperature-dependent splicing through dual mechanisms employing two distinct ribonucleoprotein modules with partially m6 A-modified architectural lncRNAs.
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Affiliation(s)
- Kensuke Ninomiya
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Junichi Iwakiri
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Mahmoud Khamis Aly
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan.,Faculty of Biotechnology, Modern Sciences and Arts University, Giza, Egypt
| | - Yuriko Sakaguchi
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Shungo Adachi
- Cellular and Molecular Biotechnology Research Institute, National Institute for Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Tohru Natsume
- Cellular and Molecular Biotechnology Research Institute, National Institute for Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Goro Terai
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Kiyoshi Asai
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Tsutomu Suzuki
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
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17
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Sandoval DR, Clausen TM, Nora C, Cribbs AP, Denardo A, Clark AE, Garretson AF, Coker JKC, Narayanan A, Majowicz SA, Philpott M, Johansson C, Dunford JE, Spliid CB, Golden GJ, Payne NC, Tye MA, Nowell CJ, Griffis ER, Piermatteo A, Grunddal KV, Alle T, Magida JA, Hauser BM, Feldman J, Caradonna TM, Pu Y, Yin X, McVicar RN, Kwong EM, Weiss RJ, Downes M, Tsimikas S, Smidt AG, Ballatore C, Zengler K, Evans RM, Chanda SK, Croker BA, Leibel SL, Jose J, Mazitschek R, Oppermann U, Esko JD, Carlin AF, Gordts PLSM. The Prolyl-tRNA Synthetase Inhibitor Halofuginone Inhibits SARS-CoV-2 Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33791697 PMCID: PMC8010724 DOI: 10.1101/2021.03.22.436522] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We identify the prolyl-tRNA synthetase (PRS) inhibitor halofuginone 1 , a compound in clinical trials for anti-fibrotic and anti-inflammatory applications 2 , as a potent inhibitor of SARS-CoV-2 infection and replication. The interaction of SARS-CoV-2 spike protein with cell surface heparan sulfate (HS) promotes viral entry 3 . We find that halofuginone reduces HS biosynthesis, thereby reducing spike protein binding, SARS-CoV-2 pseudotyped virus, and authentic SARS-CoV-2 infection. Halofuginone also potently suppresses SARS-CoV-2 replication post-entry and is 1,000-fold more potent than Remdesivir 4 . Inhibition of HS biosynthesis and SARS-CoV-2 infection depends on specific inhibition of PRS, possibly due to translational suppression of proline-rich proteins. We find that pp1a and pp1ab polyproteins of SARS-CoV-2, as well as several HS proteoglycans, are proline-rich, which may make them particularly vulnerable to halofuginone's translational suppression. Halofuginone is orally bioavailable, has been evaluated in a phase I clinical trial in humans and distributes to SARS-CoV-2 target organs, including the lung, making it a near-term clinical trial candidate for the treatment of COVID-19.
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18
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Cribbs AP, Filippakopoulos P, Philpott M, Wells G, Penn H, Oerum H, Valge-Archer V, Feldmann M, Oppermann U. Dissecting the Role of BET Bromodomain Proteins BRD2 and BRD4 in Human NK Cell Function. Front Immunol 2021; 12:626255. [PMID: 33717143 PMCID: PMC7953504 DOI: 10.3389/fimmu.2021.626255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/13/2021] [Indexed: 12/19/2022] Open
Abstract
Natural killer (NK) cells are innate lymphocytes that play a pivotal role in the immune surveillance and elimination of transformed or virally infected cells. Using a chemo-genetic approach, we identify BET bromodomain containing proteins BRD2 and BRD4 as central regulators of NK cell functions, including direct cytokine secretion, NK cell contact-dependent inflammatory cytokine secretion from monocytes as well as NK cell cytolytic functions. We show that both BRD2 and BRD4 control inflammatory cytokine production in NK cells isolated from healthy volunteers and from rheumatoid arthritis patients. In contrast, knockdown of BRD4 but not of BRD2 impairs NK cell cytolytic responses, suggesting BRD4 as critical regulator of NK cell mediated tumor cell elimination. This is supported by pharmacological targeting where the first-generation pan-BET bromodomain inhibitor JQ1(+) displays anti-inflammatory effects and inhibit tumor cell eradication, while the novel bivalent BET bromodomain inhibitor AZD5153, which shows differential activity towards BET family members, does not. Given the important role of both cytokine-mediated inflammatory microenvironment and cytolytic NK cell activities in immune-oncology therapies, our findings present a compelling argument for further clinical investigation.
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Affiliation(s)
- Adam P Cribbs
- Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, United Kingdom
| | | | - Martin Philpott
- Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, United Kingdom
| | - Graham Wells
- Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, United Kingdom
| | - Henry Penn
- Arthritis Centre, Northwick Park Hospital, Harrow, United Kingdom
| | - Henrik Oerum
- Roche Innovation Center Copenhagen A/S, Hørsholm, Denmark
| | - Viia Valge-Archer
- Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Marc Feldmann
- Kennedy Institute of Rheumatology Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, Oxford, United Kingdom
| | - Udo Oppermann
- Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, United Kingdom.,Freiburg Institute of Advanced Studies, Freiburg, Germany.,Oxford Centre for Translational Myeloma Research, Oxford, United Kingdom
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19
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Tarazona E, Lucas-Lledó JI, Carmona MJ, García-Roger EM. Gene expression in diapausing rotifer eggs in response to divergent environmental predictability regimes. Sci Rep 2020; 10:21366. [PMID: 33288800 PMCID: PMC7721884 DOI: 10.1038/s41598-020-77727-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/17/2020] [Indexed: 12/02/2022] Open
Abstract
In unpredictable environments in which reliable cues for predicting environmental variation are lacking, a diversifying bet-hedging strategy for diapause exit is expected to evolve, whereby only a portion of diapausing forms will resume development at the first occurrence of suitable conditions. This study focused on diapause termination in the rotifer Brachionus plicatilis s.s., addressing the transcriptional profile of diapausing eggs from environments differing in the level of predictability and the relationship of such profiles with hatching patterns. RNA-Seq analyses revealed significant differences in gene expression between diapausing eggs produced in the laboratory under combinations of two contrasting selective regimes of environmental fluctuation (predictable vs unpredictable) and two different diapause conditions (passing or not passing through forced diapause). The results showed that the selective regime was more important than the diapause condition in driving differences in the transcriptome profile. Most of the differentially expressed genes were upregulated in the predictable regime and mostly associated with molecular functions involved in embryo morphological development and hatching readiness. This was in concordance with observations of earlier, higher, and more synchronous hatching in diapausing eggs produced under the predictable regime.
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Affiliation(s)
- Eva Tarazona
- Institut Cavanilles de Biodiversitat I Biologia Evolutiva, Universitat de València, Valencia, Spain
| | - J Ignacio Lucas-Lledó
- Institut Cavanilles de Biodiversitat I Biologia Evolutiva, Universitat de València, Valencia, Spain
| | - María José Carmona
- Institut Cavanilles de Biodiversitat I Biologia Evolutiva, Universitat de València, Valencia, Spain
| | - Eduardo M García-Roger
- Institut Cavanilles de Biodiversitat I Biologia Evolutiva, Universitat de València, Valencia, Spain.
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20
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Hotaling S, Shah AA, McGowan KL, Tronstad LM, Giersch JJ, Finn DS, Woods HA, Dillon ME, Kelley JL. Mountain stoneflies may tolerate warming streams: Evidence from organismal physiology and gene expression. GLOBAL CHANGE BIOLOGY 2020; 26:5524-5538. [PMID: 32698241 DOI: 10.1111/gcb.15294] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
Rapid glacier recession is altering the physical conditions of headwater streams. Stream temperatures are predicted to rise and become increasingly variable, putting entire meltwater-associated biological communities at risk of extinction. Thus, there is a pressing need to understand how thermal stress affects mountain stream insects, particularly where glaciers are likely to vanish on contemporary timescales. In this study, we measured the critical thermal maximum (CTMAX ) of stonefly nymphs representing multiple species and a range of thermal regimes in the high Rocky Mountains, USA. We then collected RNA-sequencing data to assess how organismal thermal stress translated to the cellular level. Our focal species included the meltwater stonefly, Lednia tumana, which was recently listed under the U.S. Endangered Species Act due to climate-induced habitat loss. For all study species, critical thermal maxima (CTMAX > 20°C) far exceeded the stream temperatures mountain stoneflies experience (<10°C). Moreover, while evidence for a cellular stress response was present, we also observed constitutive expression of genes encoding proteins known to underlie thermal stress (i.e., heat shock proteins) even at low temperatures that reflected natural conditions. We show that high-elevation aquatic insects may not be physiologically threatened by short-term exposure to warm temperatures and that longer-term physiological responses or biotic factors (e.g., competition) may better explain their extreme distributions.
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Affiliation(s)
- Scott Hotaling
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Alisha A Shah
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Kerry L McGowan
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Lusha M Tronstad
- Wyoming Natural Diversity Database, University of Wyoming, Laramie, WY, USA
| | - J Joseph Giersch
- U.S. Geological Survey, Northern Rocky Mountain Science Center, West Glacier, MT, USA
| | - Debra S Finn
- Department of Biology, Missouri State University, Springfield, MO, USA
| | - H Arthur Woods
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Michael E Dillon
- Department of Zoology and Physiology and Program in Ecology, University of Wyoming, Laramie, WY, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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21
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Ababneh NA, Scaber J, Flynn R, Douglas A, Barbagallo P, Candalija A, Turner MR, Sims D, Dafinca R, Cowley SA, Talbot K. Correction of amyotrophic lateral sclerosis related phenotypes in induced pluripotent stem cell-derived motor neurons carrying a hexanucleotide expansion mutation in C9orf72 by CRISPR/Cas9 genome editing using homology-directed repair. Hum Mol Genet 2020; 29:2200-2217. [PMID: 32504093 PMCID: PMC7399532 DOI: 10.1093/hmg/ddaa106] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/04/2020] [Accepted: 06/01/2020] [Indexed: 12/13/2022] Open
Abstract
The G4C2 hexanucleotide repeat expansion (HRE) in C9orf72 is the commonest cause of familial amyotrophic lateral sclerosis (ALS). A number of different methods have been used to generate isogenic control lines using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 and non-homologous end-joining by deleting the repeat region, with the risk of creating indels and genomic instability. In this study, we demonstrate complete correction of an induced pluripotent stem cell (iPSC) line derived from a C9orf72-HRE positive ALS/frontotemporal dementia patient using CRISPR/Cas9 genome editing and homology-directed repair (HDR), resulting in replacement of the excised region with a donor template carrying the wild-type repeat size to maintain the genetic architecture of the locus. The isogenic correction of the C9orf72 HRE restored normal gene expression and methylation at the C9orf72 locus, reduced intron retention in the edited lines and abolished pathological phenotypes associated with the C9orf72 HRE expansion in iPSC-derived motor neurons (iPSMNs). RNA sequencing of the mutant line identified 2220 differentially expressed genes compared with its isogenic control. Enrichment analysis demonstrated an over-representation of ALS relevant pathways, including calcium ion dependent exocytosis, synaptic transport and the Kyoto Encyclopedia of Genes and Genomes ALS pathway, as well as new targets of potential relevance to ALS pathophysiology. Complete correction of the C9orf72 HRE in iPSMNs by CRISPR/Cas9-mediated HDR provides an ideal model to study the earliest effects of the hexanucleotide expansion on cellular homeostasis and the key pathways implicated in ALS pathophysiology.
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Affiliation(s)
- Nidaa A Ababneh
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- Cell Therapy Center, University of Jordan, Queen Rania St, Amman 11942, Jordan
| | - Jakub Scaber
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Rowan Flynn
- James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Andrew Douglas
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
- Wessex Clinical Genetics Service, Level G, Mailpoint 627, Princess Anne Hospital, Coxford Road, Southampton SO16 5YA, UK
| | - Paola Barbagallo
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Ana Candalija
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - David Sims
- Weatherall Institute for Molecular Medicine, Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Ruxandra Dafinca
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Sally A Cowley
- James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
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22
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Gazanion E, Lacroix L, Alberti P, Gurung P, Wein S, Cheng M, Mergny JL, Gomes AR, Lopez-Rubio JJ. Genome wide distribution of G-quadruplexes and their impact on gene expression in malaria parasites. PLoS Genet 2020; 16:e1008917. [PMID: 32628663 PMCID: PMC7365481 DOI: 10.1371/journal.pgen.1008917] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 07/16/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022] Open
Abstract
Mechanisms of transcriptional control in malaria parasites are still not fully understood. The positioning patterns of G-quadruplex (G4) DNA motifs in the parasite's AT-rich genome, especially within the var gene family which encodes virulence factors, and in the vicinity of recombination hotspots, points towards a possible regulatory role of G4 in gene expression and genome stability. Here, we carried out the most comprehensive genome-wide survey, to date, of G4s in the Plasmodium falciparum genome using G4Hunter, which identifies G4 forming sequences (G4FS) considering their G-richness and G-skewness. We show an enrichment of G4FS in nucleosome-depleted regions and in the first exon of var genes, a pattern that is conserved within the closely related Laverania Plasmodium parasites. Under G4-stabilizing conditions, i.e., following treatment with pyridostatin (a high affinity G4 ligand), we show that a bona fide G4 found in the non-coding strand of var promoters modulates reporter gene expression. Furthermore, transcriptional profiling of pyridostatin-treated parasites, shows large scale perturbations, with deregulation affecting for instance the ApiAP2 family of transcription factors and genes involved in ribosome biogenesis. Overall, our study highlights G4s as important DNA secondary structures with a role in Plasmodium gene expression regulation, sub-telomeric recombination and var gene biology.
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Affiliation(s)
- Elodie Gazanion
- MIVEGEC UMR IRD 224, CNRS 5290, Montpellier University, Montpellier, France
| | - Laurent Lacroix
- IBENS, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Patrizia Alberti
- "Structure and Instability of Genomes" laboratory, Muséum National d'Histoire Naturelle (MNHN), Inserm U1154, CNRS UMR 7196, Paris, France
| | - Pratima Gurung
- Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, Montpellier, France
| | - Sharon Wein
- Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, Montpellier, France
| | - Mingpan Cheng
- ARNA Laboratory, IECB, CNRS UMR5320, INSERM U1212, Bordeaux University, Pessac, France
| | - Jean-Louis Mergny
- ARNA Laboratory, IECB, CNRS UMR5320, INSERM U1212, Bordeaux University, Pessac, France
- Institute of Biophysics of the Czech Academy of Sciences, Czech Republic
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, France
| | - Ana Rita Gomes
- Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, Montpellier, France
| | - Jose-Juan Lopez-Rubio
- MIVEGEC UMR IRD 224, CNRS 5290, Montpellier University, Montpellier, France
- Laboratory of Pathogen-Host Interactions (LPHI), UMR5235, CNRS, Montpellier University, Montpellier, France
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23
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Histone H3K27me3 demethylases regulate human Th17 cell development and effector functions by impacting on metabolism. Proc Natl Acad Sci U S A 2020; 117:6056-6066. [PMID: 32123118 PMCID: PMC7084125 DOI: 10.1073/pnas.1919893117] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
T cells control many immune functions, with Th17 cells critical in regulating inflammation. Following activation, T cells undergo metabolic reprogramming and utilize glycolysis to increase the ATP availability. Epigenetic mechanisms controlling metabolic functions in T cells are currently not well-defined. Here, we establish an epigenetic link between the histone H3K27me3 demethylases KDM6A/B and the coordination of a metabolic response. Inhibition of KDM6A/B leads to global increases in the repressive H3K27me3 histone mark, resulting in down-regulation of key transcription factors, followed by metabolic reprogramming and anergy. This work suggests a critical role of H3K27 demethylase enzymes in maintaining Th17 functions by controlling metabolic switches. Short-term treatment with KDM6 enzyme inhibitors may be useful in the therapy of chronic inflammatory diseases. T helper (Th) cells are CD4+ effector T cells that play a critical role in immunity by shaping the inflammatory cytokine environment in a variety of physiological and pathological situations. Using a combined chemico-genetic approach, we identify histone H3K27 demethylases KDM6A and KDM6B as central regulators of human Th subsets. The prototypic KDM6 inhibitor GSK-J4 increases genome-wide levels of the repressive H3K27me3 chromatin mark and leads to suppression of the key transcription factor RORγt during Th17 differentiation. In mature Th17 cells, GSK-J4 induces an altered transcriptional program with a profound metabolic reprogramming and concomitant suppression of IL-17 cytokine levels and reduced proliferation. Single-cell analysis reveals a specific shift from highly inflammatory cell subsets toward a resting state upon demethylase inhibition. The root cause of the observed antiinflammatory phenotype in stimulated Th17 cells is reduced expression of key metabolic transcription factors, such as PPRC1. Overall, this leads to reduced mitochondrial biogenesis, resulting in a metabolic switch with concomitant antiinflammatory effects. These data are consistent with an effect of GSK-J4 on Th17 T cell differentiation pathways directly related to proliferation and include regulation of effector cytokine profiles. This suggests that inhibiting KDM6 demethylases may be an effective, even in the short term, therapeutic target for autoimmune diseases, including ankylosing spondylitis.
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24
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Ninomiya K, Adachi S, Natsume T, Iwakiri J, Terai G, Asai K, Hirose T. LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation. EMBO J 2020; 39:e102729. [PMID: 31782550 PMCID: PMC6996502 DOI: 10.15252/embj.2019102729] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/17/2019] [Accepted: 10/29/2019] [Indexed: 12/19/2022] Open
Abstract
A number of long noncoding RNAs (lncRNAs) are induced in response to specific stresses to construct membrane-less nuclear bodies; however, their function remains poorly understood. Here, we report the role of nuclear stress bodies (nSBs) formed on highly repetitive satellite III (HSATIII) lncRNAs derived from primate-specific satellite III repeats upon thermal stress exposure. A transcriptomic analysis revealed that depletion of HSATIII lncRNAs, resulting in elimination of nSBs, promoted splicing of 533 retained introns during thermal stress recovery. A HSATIII-Comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS) analysis identified multiple splicing factors in nSBs, including serine and arginine-rich pre-mRNA splicing factors (SRSFs), the phosphorylation states of which affect splicing patterns. SRSFs are rapidly de-phosphorylated upon thermal stress exposure. During stress recovery, CDC like kinase 1 (CLK1) was recruited to nSBs and accelerated the re-phosphorylation of SRSF9, thereby promoting target intron retention. Our findings suggest that HSATIII-dependent nSBs serve as a conditional platform for phosphorylation of SRSFs by CLK1 to promote the rapid adaptation of gene expression through intron retention following thermal stress exposure.
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Grants
- JP26113002 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP16H06279 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP17H03630 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP17K19335 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP19K06478 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- Tokyo Biochemical Research Foundation (TBRF)
- Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- Tokyo Biochemical Research Foundation (TBRF)
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Affiliation(s)
| | - Shungo Adachi
- Molecular Profiling Research CenterNational Institute for Advanced Industrial Science and Technology (AIST)TokyoJapan
| | - Tohru Natsume
- Molecular Profiling Research CenterNational Institute for Advanced Industrial Science and Technology (AIST)TokyoJapan
| | - Junichi Iwakiri
- Graduate School of Frontier SciencesUniversity of TokyoKashiwaJapan
| | - Goro Terai
- Graduate School of Frontier SciencesUniversity of TokyoKashiwaJapan
| | - Kiyoshi Asai
- Graduate School of Frontier SciencesUniversity of TokyoKashiwaJapan
| | - Tetsuro Hirose
- Institute for Genetic MedicineHokkaido UniversitySapporoJapan
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25
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Coe EA, Tan JY, Shapiro M, Louphrasitthiphol P, Bassett AR, Marques AC, Goding CR, Vance KW. The MITF-SOX10 regulated long non-coding RNA DIRC3 is a melanoma tumour suppressor. PLoS Genet 2019; 15:e1008501. [PMID: 31881017 PMCID: PMC6934268 DOI: 10.1371/journal.pgen.1008501] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/30/2019] [Indexed: 01/14/2023] Open
Abstract
The MITF and SOX10 transcription factors regulate the expression of genes important for melanoma proliferation, invasion and metastasis. Despite growing evidence of the contribution of long noncoding RNAs (lncRNAs) in cancer, including melanoma, their functions within MITF-SOX10 transcriptional programmes remain poorly investigated. Here we identify 245 candidate melanoma associated lncRNAs whose loci are co-occupied by MITF-SOX10 and that are enriched at active enhancer-like regions. Our work suggests that one of these, Disrupted In Renal Carcinoma 3 (DIRC3), may be a clinically important MITF-SOX10 regulated tumour suppressor. DIRC3 depletion in human melanoma cells leads to increased anchorage-independent growth, a hallmark of malignant transformation, whilst melanoma patients classified by low DIRC3 expression have decreased survival. DIRC3 is a nuclear lncRNA that activates expression of its neighbouring IGFBP5 tumour suppressor through modulating chromatin structure and suppressing SOX10 binding to putative regulatory elements within the DIRC3 locus. In turn, DIRC3 dependent regulation of IGFBP5 impacts the expression of genes involved in cancer associated processes and is needed for DIRC3 control of anchorage-independent growth. Our work indicates that lncRNA components of MITF-SOX10 networks are an important new class of melanoma regulators and candidate therapeutic targets that can act not only as downstream mediators of MITF-SOX10 function but as feedback regulators of MITF-SOX10 activity.
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Affiliation(s)
- Elizabeth A. Coe
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Jennifer Y. Tan
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Michael Shapiro
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | | | - Andrew R. Bassett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Ana C. Marques
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Colin R. Goding
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Keith W. Vance
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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26
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Transcriptome-wide dynamics of extensive m 6A mRNA methylation during Plasmodium falciparum blood-stage development. Nat Microbiol 2019; 4:2246-2259. [PMID: 31384004 DOI: 10.1038/s41564-019-0521-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 06/20/2019] [Indexed: 01/17/2023]
Abstract
Malaria pathogenesis results from the asexual replication of Plasmodium falciparum within human red blood cells, which relies on a precisely timed cascade of gene expression over a 48-h life cycle. Although substantial post-transcriptional regulation of this hardwired program has been observed, it remains unclear how these processes are mediated on a transcriptome-wide level. To this end, we identified mRNA modifications in the P. falciparum transcriptome and performed a comprehensive characterization of N6-methyladenosine (m6A) over the course of blood-stage development. Using mass spectrometry and m6A RNA sequencing, we demonstrate that m6A is highly developmentally regulated, exceeding m6A levels known in any other eukaryote. We characterize a distinct m6A writer complex and show that knockdown of the putative m6A methyltransferase, PfMT-A70, by CRISPR interference leads to increased levels of transcripts that normally contain m6A. In accordance, we find an inverse correlation between m6A methylation and mRNA stability or translational efficiency. We further identify two putative m6A-binding YTH proteins that are likely to be involved in the regulation of these processes across the parasite's life cycle. Our data demonstrate unique features of an extensive m6A mRNA methylation programme in malaria parasites and reveal its crucial role in dynamically fine-tuning the transcriptional cascade of a unicellular eukaryote.
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27
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Bromodomain inhibition of the coactivators CBP/EP300 facilitate cellular reprogramming. Nat Chem Biol 2019; 15:519-528. [PMID: 30962627 DOI: 10.1038/s41589-019-0264-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/27/2019] [Indexed: 01/09/2023]
Abstract
Silencing of the somatic cell type-specific genes is a critical yet poorly understood step in reprogramming. To uncover pathways that maintain cell identity, we performed a reprogramming screen using inhibitors of chromatin factors. Here, we identify acetyl-lysine competitive inhibitors targeting the bromodomains of coactivators CREB (cyclic-AMP response element binding protein) binding protein (CBP) and E1A binding protein of 300 kDa (EP300) as potent enhancers of reprogramming. These inhibitors accelerate reprogramming, are critical during its early stages and, when combined with DOT1L inhibition, enable efficient derivation of human induced pluripotent stem cells (iPSCs) with OCT4 and SOX2. In contrast, catalytic inhibition of CBP/EP300 prevents iPSC formation, suggesting distinct functions for different coactivator domains in reprogramming. CBP/EP300 bromodomain inhibition decreases somatic-specific gene expression, histone H3 lysine 27 acetylation (H3K27Ac) and chromatin accessibility at target promoters and enhancers. The master mesenchymal transcription factor PRRX1 is one such functionally important target of CBP/EP300 bromodomain inhibition. Collectively, these results show that CBP/EP300 bromodomains sustain cell-type-specific gene expression and maintain cell identity.
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28
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Anzilotti C, Swan DJ, Boisson B, Deobagkar-Lele M, Oliveira C, Chabosseau P, Engelhardt KR, Xu X, Chen R, Alvarez L, Berlinguer-Palmini R, Bull KR, Cawthorne E, Cribbs AP, Crockford TL, Dang TS, Fearn A, Fenech EJ, de Jong SJ, Lagerholm BC, Ma CS, Sims D, van den Berg B, Xu Y, Cant AJ, Kleiner G, Leahy TR, de la Morena MT, Puck JM, Shapiro RS, van der Burg M, Chapman JR, Christianson JC, Davies B, McGrath JA, Przyborski S, Santibanez Koref M, Tangye SG, Werner A, Rutter GA, Padilla-Parra S, Casanova JL, Cornall RJ, Conley ME, Hambleton S. An essential role for the Zn 2+ transporter ZIP7 in B cell development. Nat Immunol 2019; 20:350-361. [PMID: 30718914 PMCID: PMC6561116 DOI: 10.1038/s41590-018-0295-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 12/05/2018] [Indexed: 12/20/2022]
Abstract
Despite the known importance of zinc for human immunity, molecular insights into its roles have remained limited. Here we report a novel autosomal recessive disease characterized by absent B cells, agammaglobulinemia and early onset infections in five unrelated families. The immunodeficiency results from hypomorphic mutations of SLC39A7, which encodes the endoplasmic reticulum-to-cytoplasm zinc transporter ZIP7. Using CRISPR-Cas9 mutagenesis we have precisely modeled ZIP7 deficiency in mice. Homozygosity for a null allele caused embryonic death, but hypomorphic alleles reproduced the block in B cell development seen in patients. B cells from mutant mice exhibited a diminished concentration of cytoplasmic free zinc, increased phosphatase activity and decreased phosphorylation of signaling molecules downstream of the pre-B cell and B cell receptors. Our findings highlight a specific role for cytosolic Zn2+ in modulating B cell receptor signal strength and positive selection.
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Affiliation(s)
- Consuelo Anzilotti
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - David J Swan
- Primary Immunodeficiency Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Bertrand Boisson
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163 Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
| | - Mukta Deobagkar-Lele
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Catarina Oliveira
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Pauline Chabosseau
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Imperial College, London, UK
| | - Karin R Engelhardt
- Primary Immunodeficiency Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Xijin Xu
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rui Chen
- Primary Immunodeficiency Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Luis Alvarez
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Katherine R Bull
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Eleanor Cawthorne
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Adam P Cribbs
- MRC WIMM Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Tanya L Crockford
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Tarana Singh Dang
- Primary Immunodeficiency Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Amy Fearn
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Emma J Fenech
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Sarah J de Jong
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - B Christoffer Lagerholm
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Cindy S Ma
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of NSW, Darlinghurst, New South Wales, Australia
| | - David Sims
- MRC WIMM Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Bert van den Berg
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Yaobo Xu
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew J Cant
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Gary Kleiner
- Pediatric Allergy and Immunology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - T Ronan Leahy
- Paediatric Immunology and Infectious Diseases, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - M Teresa de la Morena
- Division of Immunology, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Jennifer M Puck
- Department of Pediatrics, Division of Allergy, Immunology, and Blood and Bone Marrow Transplantation, University of California, San Francisco, CA, USA
- UCSF Benioff Children's Hospital, San Francisco, CA, USA
| | | | - Mirjam van der Burg
- Department of Immunology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - J Ross Chapman
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Benjamin Davies
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - John A McGrath
- St John's Institute of Dermatology, King's College London, London, UK
| | | | | | - Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of NSW, Darlinghurst, New South Wales, Australia
| | - Andreas Werner
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Imperial College, London, UK
| | - Sergi Padilla-Parra
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Dynamic Structural Virology Group, Biocruces Health Research Institute, Barakaldo, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163 Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Imagine Institute, Paris, France
- Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Richard J Cornall
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | - Mary Ellen Conley
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
| | - Sophie Hambleton
- Primary Immunodeficiency Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK.
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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29
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Queiroz RML, Smith T, Villanueva E, Marti-Solano M, Monti M, Pizzinga M, Mirea DM, Ramakrishna M, Harvey RF, Dezi V, Thomas GH, Willis AE, Lilley KS. Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS). Nat Biotechnol 2019; 37:169-178. [PMID: 30607034 DOI: 10.1038/s41587-018-0001-2] [Citation(s) in RCA: 199] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/19/2018] [Indexed: 12/31/2022]
Abstract
Existing high-throughput methods to identify RNA-binding proteins (RBPs) are based on capture of polyadenylated RNAs and cannot recover proteins that interact with nonadenylated RNAs, including long noncoding RNA, pre-mRNAs and bacterial RNAs. We present orthogonal organic phase separation (OOPS), which does not require molecular tagging or capture of polyadenylated RNA, and apply it to recover cross-linked protein-RNA and free protein, or protein-bound RNA and free RNA, in an unbiased way. We validated OOPS in HEK293, U2OS and MCF10A human cell lines, and show that 96% of proteins recovered were bound to RNA. We show that all long RNAs can be cross-linked to proteins, and recovered 1,838 RBPs, including 926 putative novel RBPs. OOPS is approximately 100-fold more efficient than existing methods and can enable analyses of dynamic RNA-protein interactions. We also characterize dynamic changes in RNA-protein interactions in mammalian cells following nocodazole arrest, and present a bacterial RNA-interactome for Escherichia coli. OOPS is compatible with downstream proteomics and RNA sequencing, and can be applied in any organism.
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Affiliation(s)
- Rayner M L Queiroz
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tom Smith
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Eneko Villanueva
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | | | - Mie Monti
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Dan-Mircea Mirea
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | | | - Veronica Dezi
- MRC Toxicology Unit, University of Cambridge, Leicester, UK
| | | | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Leicester, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.
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30
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Lesbirel S, Viphakone N, Parker M, Parker J, Heath C, Sudbery I, Wilson SA. The m 6A-methylase complex recruits TREX and regulates mRNA export. Sci Rep 2018; 8:13827. [PMID: 30218090 PMCID: PMC6138711 DOI: 10.1038/s41598-018-32310-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/04/2018] [Indexed: 11/09/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification of eukaryotic mRNA. This modification has previously been shown to alter the export kinetics for mRNAs though the molecular details surrounding this phenomenon remain poorly understood. Recruitment of the TREX mRNA export complex to mRNA is driven by transcription, 5' capping and pre-mRNA splicing. Here we identify a fourth mechanism in human cells driving the association of TREX with mRNA involving the m6A methylase complex. We show that the m6A complex recruits TREX to m6A modified mRNAs and this process is essential for their efficient export. TREX also stimulates recruitment of the m6A reader protein YTHDC1 to the mRNA and the m6A complex influences the interaction of TREX with YTHDC1. Together our studies reveal a key role for TREX in the export of m6A modified mRNAs.
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Affiliation(s)
- Simon Lesbirel
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK
| | - Nicolas Viphakone
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK
| | - Matthew Parker
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK
| | - Jacob Parker
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK
| | - Catherine Heath
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK
| | - Ian Sudbery
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK
| | - Stuart A Wilson
- Sheffield Institute For Nucleic Acids (SInFoNiA), Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court Western Bank, Sheffield, S10 2TN, UK.
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31
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Stockenhuber K, Hegazy AN, West NR, Ilott NE, Stockenhuber A, Bullers SJ, Thornton EE, Arnold IC, Tucci A, Waldmann H, Ogg GS, Powrie F. Foxp3 + T reg cells control psoriasiform inflammation by restraining an IFN-I-driven CD8 + T cell response. J Exp Med 2018; 215:1987-1998. [PMID: 29980582 PMCID: PMC6080913 DOI: 10.1084/jem.20172094] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/29/2018] [Accepted: 06/11/2018] [Indexed: 12/15/2022] Open
Abstract
Psoriasis is a complex inflammatory skin disease affecting ∼3% of the population worldwide. Although type I interferons (IFN-I) are thought to be involved in its pathogenesis, the details of this relationship remain elusive. Here we show that in a murine model of imiquimod-driven psoriatic skin inflammation, Foxp3+ regulatory T cells (T reg cells) control inflammation severity by restraining IFN-I. Depletion of T reg cells induces IFN-I and IFN-stimulated gene expression, and leads to accumulation of CD8+ T cells in lesional skin. Mononuclear phagocytes (MNPs) were the source of IFN-I, and their depletion reversed the effect of T reg cell depletion. Blockade of IFN-I signaling abolished CD8+ T cell infiltration and excess inflammation in the skin of T reg cell-depleted mice. Depletion of CD8+ T cells attenuated pathology, confirming their role as critical effector cells downstream of IFN-I. Our results describe an unexpected role for T reg cells in restraint of an MNP-IFN-I-driven CD8+ T cell response during psoriasiform skin inflammation. These findings highlight a pathway with potential relevance for the treatment of early-stage disease.
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Affiliation(s)
- Krista Stockenhuber
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ahmed N Hegazy
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Nathaniel R West
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Nicholas E Ilott
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Alexander Stockenhuber
- Wellcome Trust Centre for Human Genetics, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Samuel J Bullers
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Emily E Thornton
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Isabelle C Arnold
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Andrea Tucci
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Herman Waldmann
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Graham S Ogg
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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32
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Morgan MD, Marioni JC. CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness. Genome Biol 2018; 19:81. [PMID: 29945659 PMCID: PMC6020341 DOI: 10.1186/s13059-018-1461-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/04/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Population phenotypic variation can arise from genetic differences between individuals, or from cellular heterogeneity in an isogenic group of cells or organisms. The emergence of gene expression differences between genetically identical cells is referred to as gene expression noise, the sources of which are not well understood. RESULTS In this work, by studying gene expression noise between multiple cell lineages and mammalian species, we find consistent evidence of a role for CpG islands as sources of gene expression noise. Variation in noise among CpG island promoters can be partially attributed to differences in island size, in which short islands have noisier gene expression. Building on these findings, we investigate the potential for short CpG islands to act as fast response elements to environmental stimuli. Specifically, we find that these islands are enriched amongst primary response genes in SWI/SNF-independent stimuli, suggesting that expression noise is an indicator of promoter responsiveness. CONCLUSIONS Thus, through the integration of single-cell RNA expression profiling, chromatin landscape and temporal gene expression dynamics, we have uncovered a role for short CpG island promoters as fast response elements.
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Affiliation(s)
- Michael D Morgan
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - John C Marioni
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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Stamatopoulos B, Smith T, Crompot E, Pieters K, Clifford R, Mraz M, Robbe P, Burns A, Timbs A, Bruce D, Hillmen P, Meuleman N, Mineur P, Firescu R, Maerevoet M, De Wilde V, Efira A, Philippé J, Verhasselt B, Offner F, Sims D, Heger A, Dreau H, Schuh A. The Light Chain IgLV3-21 Defines a New Poor Prognostic Subgroup in Chronic Lymphocytic Leukemia: Results of a Multicenter Study. Clin Cancer Res 2018; 24:5048-5057. [PMID: 29945996 DOI: 10.1158/1078-0432.ccr-18-0133] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/07/2018] [Accepted: 06/22/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Unmutated (UM) immunoglobulin heavy chain variable region (IgHV) status or IgHV3-21 gene usage is associated with poor prognosis in chronic lymphocytic leukemia (CLL) patients. Interestingly, IgHV3-21 is often co-expressed with light chain IgLV3-21, which is potentially able to trigger cell-autonomous BCR-mediated signaling. However, this light chain has never been characterized independently of the heavy chain IgHV3-21.Experimental Design: We performed total RNA sequencing in 32 patients and investigated IgLV3-21 prognostic impact in terms of treatment-free survival (TFS) and overall survival (OS) in 3 other independent cohorts for a total of 813 patients. IgLV3-21 presence was tested by real-time PCR and confirmed by Sanger sequencing.Results: Using total RNA sequencing to characterize 32 patients with high-risk CLL, we found a high frequency (28%) of IgLV3-21 rearrangements. Gene set enrichment analysis revealed that these patients express higher levels of genes responsible for ribosome biogenesis and translation initiation (P < 0.0001) as well as MYC target genes (P = 0.0003). Patients with IgLV3-21 rearrangements displayed a significantly shorter TFS and OS (P < 0.05), particularly those with IgHV mutation. In each of the three independent validation cohorts, we showed that IgLV3-21 rearrangements-similar to UM IgHV status-conferred poor prognosis compared with mutated IgHV (P < 0.0001). Importantly, we confirmed by multivariate analysis that this was independent of IgHV mutational status or subset #2 stereotyped receptor (P < 0.0001).Conclusions: We have demonstrated for the first time that a light chain can affect CLL prognosis and that IgLV3-21 light chain usage defines a new subgroup of CLL patients with poor prognosis. Clin Cancer Res; 24(20); 5048-57. ©2018 AACR.
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Affiliation(s)
- Basile Stamatopoulos
- Laboratory of Clinical Cell Therapy, Jules Bordet Institute, ULB-Research Cancer Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium. .,Molecular Diagnostic Centre, Oxford University Hospitals, Oxford, United Kingdom.,Nuffield Department of Laboratory Sciences, University of Oxford, Oxford, United Kingdom
| | - Thomas Smith
- Computational Genomics Analysis and Training Program, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Emerence Crompot
- Laboratory of Clinical Cell Therapy, Jules Bordet Institute, ULB-Research Cancer Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Karlien Pieters
- Laboratory of Clinical Cell Therapy, Jules Bordet Institute, ULB-Research Cancer Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ruth Clifford
- Molecular Diagnostic Centre, Oxford University Hospitals, Oxford, United Kingdom.,Nuffield Department of Laboratory Sciences, University of Oxford, Oxford, United Kingdom
| | - Marek Mraz
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pauline Robbe
- Molecular Diagnostic Centre, Oxford University Hospitals, Oxford, United Kingdom.,Nuffield Department of Laboratory Sciences, University of Oxford, Oxford, United Kingdom
| | - Adam Burns
- Molecular Diagnostic Centre, Oxford University Hospitals, Oxford, United Kingdom.,Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Adele Timbs
- Molecular Diagnostic Centre, Oxford University Hospitals, Oxford, United Kingdom
| | - David Bruce
- Molecular Diagnostic Centre, Oxford University Hospitals, Oxford, United Kingdom.,Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Peter Hillmen
- St. James' Institute of Oncology, St James' University Hospital, Leeds, United Kingdom
| | | | - Philippe Mineur
- Department of Hemato-Oncology, Grand Hôpital de Charleroi, Charleroi, Belgium
| | - Radu Firescu
- Hematology Department, CHU Ambroise Paré, Mons, Belgium
| | - Marie Maerevoet
- Hematology Department, Jules Bordet Institute, Brussels, Belgium.,Hematology Department, Hôpital Erasme (ULB), Brussels, Belgium
| | | | - André Efira
- Department of Hemato-oncology, Centre Hospitalier Universitaire Brugmann, Brussels, Belgium
| | - Jan Philippé
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Bruno Verhasselt
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Fritz Offner
- Department of Internal Medicine, Hematology, Ghent University Hospital, Ghent, Belgium
| | - David Sims
- Computational Genomics Analysis and Training Program, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Andreas Heger
- Computational Genomics Analysis and Training Program, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Hélène Dreau
- Molecular Diagnostic Centre, Oxford University Hospitals, Oxford, United Kingdom
| | - Anna Schuh
- Molecular Diagnostic Centre, Oxford University Hospitals, Oxford, United Kingdom.,Department of Oncology, University of Oxford, Oxford, United Kingdom
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34
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Cartier J, Smith T, Thomson JP, Rose CM, Khulan B, Heger A, Meehan RR, Drake AJ. Investigation into the role of the germline epigenome in the transmission of glucocorticoid-programmed effects across generations. Genome Biol 2018; 19:50. [PMID: 29636086 PMCID: PMC5891941 DOI: 10.1186/s13059-018-1422-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/16/2018] [Indexed: 12/13/2022] Open
Abstract
Background Early life exposure to adverse environments affects cardiovascular and metabolic systems in the offspring. These programmed effects are transmissible to a second generation through both male and female lines, suggesting germline transmission. We have previously shown that prenatal overexposure to the synthetic glucocorticoid dexamethasone (Dex) in rats reduces birth weight in the first generation (F1), a phenotype which is transmitted to a second generation (F2), particularly through the male line. We hypothesize that Dex exposure affects developing germ cells, resulting in transmissible alterations in DNA methylation, histone marks and/or small RNA in the male germline. Results We profile epigenetic marks in sperm from F1 Sprague Dawley rats expressing a germ cell-specific GFP transgene following Dex or vehicle treatment of the mothers, using methylated DNA immunoprecipitation sequencing, small RNA sequencing and chromatin immunoprecipitation sequencing for H3K4me3, H3K4me1, H3K27me3 and H3K9me3. Although effects on birth weight are transmitted to the F2 generation through the male line, no differences in DNA methylation, histone modifications or small RNA were detected between germ cells and sperm from Dex-exposed animals and controls. Conclusions Although the phenotype is transmitted to a second generation, we are unable to detect specific changes in DNA methylation, common histone modifications or small RNA profiles in sperm. Dex exposure is associated with more variable 5mC levels, particularly at non-promoter loci. Although this could be one mechanism contributing to the observed phenotype, other germline epigenetic modifications or non-epigenetic mechanisms may be responsible for the transmission of programmed effects across generations in this model. Electronic supplementary material The online version of this article (10.1186/s13059-018-1422-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jessy Cartier
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, The Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Thomas Smith
- MRC Computational Genomics Analysis and Training Programme, University of Oxford, MRC WIMM Centre for Computational Biology, The Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DS, UK
| | - John P Thomson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Catherine M Rose
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, The Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Batbayar Khulan
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, The Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Andreas Heger
- MRC Computational Genomics Analysis and Training Programme, University of Oxford, MRC WIMM Centre for Computational Biology, The Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DS, UK
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Amanda J Drake
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, The Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK.
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35
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Punctuated evolution of canonical genomic aberrations in uveal melanoma. Nat Commun 2018; 9:116. [PMID: 29317634 PMCID: PMC5760704 DOI: 10.1038/s41467-017-02428-w] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 11/29/2017] [Indexed: 12/27/2022] Open
Abstract
Cancer is thought to arise through the accumulation of genomic aberrations evolving under Darwinian selection. However, it remains unclear when the aberrations associated with metastasis emerge during tumor evolution. Uveal melanoma (UM) is the most common primary eye cancer and frequently leads to metastatic death, which is strongly linked to BAP1 mutations. Accordingly, UM is ideally suited for studying the clonal evolution of metastatic competence. Here we analyze sequencing data from 151 primary UM samples using a customized bioinformatic pipeline, to improve detection of BAP1 mutations and infer the clonal relationships among genomic aberrations. Strikingly, we find BAP1 mutations and other canonical genomic aberrations usually arise in an early punctuated burst, followed by neutral evolution extending to the time of clinical detection. This implies that the metastatic proclivity of UM is "set in stone" early in tumor evolution and may explain why advances in primary treatment have not improved survival.
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36
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Cribbs A, Hookway ES, Wells G, Lindow M, Obad S, Oerum H, Prinjha RK, Athanasou N, Sowman A, Philpott M, Penn H, Soderstrom K, Feldmann M, Oppermann U. Inhibition of histone H3K27 demethylases selectively modulates inflammatory phenotypes of natural killer cells. J Biol Chem 2018; 293:2422-2437. [PMID: 29301935 PMCID: PMC5818173 DOI: 10.1074/jbc.ra117.000698] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/21/2017] [Indexed: 01/12/2023] Open
Abstract
Natural killer (NK) cells are innate lymphocytes, important in immune surveillance and elimination of stressed, transformed, or virus-infected cells. They critically shape the inflammatory cytokine environment to orchestrate interactions of cells of the innate and adaptive immune systems. Some studies have reported that NK cell activation and cytokine secretion are controlled epigenetically but have yielded only limited insight into the mechanisms. Using chemical screening with small-molecule inhibitors of chromatin methylation and acetylation, further validated by knockdown approaches, we here identified Jumonji-type histone H3K27 demethylases as key regulators of cytokine production in human NK cell subsets. The prototypic JMJD3/UTX (Jumonji domain–containing protein 3) H3K27 demethylase inhibitor GSK-J4 increased global levels of the repressive H3K27me3 mark around transcription start sites of effector cytokine genes. Moreover, GSK-J4 reduced IFN-γ, TNFα, granulocyte–macrophage colony-stimulating factor (GM-CSF), and interleukin-10 levels in cytokine-stimulated NK cells while sparing their cytotoxic killing activity against cancer cells. The anti-inflammatory effect of GSK-J4 in NK cell subsets, isolated from peripheral blood or tissue from individuals with rheumatoid arthritis (RA), coupled with an inhibitory effect on formation of bone-resorbing osteoclasts, suggested that histone demethylase inhibition has broad utility for modulating immune and inflammatory responses. Overall, our results indicate that H3K27me3 is a dynamic and important epigenetic modification during NK cell activation and that JMJD3/UTX-driven H3K27 demethylation is critical for NK cell function.
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Affiliation(s)
- Adam Cribbs
- From the Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford OX3 7DQ, United Kingdom, .,the Kennedy Institute of Rheumatology Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford BRU and
| | - Edward S Hookway
- From the Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Graham Wells
- From the Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Morten Lindow
- the Roche Innovation Center Copenhagen A/S, DK 2970 Hørsholm, Denmark
| | - Susanna Obad
- the Roche Innovation Center Copenhagen A/S, DK 2970 Hørsholm, Denmark
| | - Henrik Oerum
- the Roche Innovation Center Copenhagen A/S, DK 2970 Hørsholm, Denmark
| | - Rab K Prinjha
- the Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage SG1 2NY, United Kingdom
| | - Nick Athanasou
- From the Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Aneka Sowman
- From the Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Martin Philpott
- From the Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Henry Penn
- the Arthritis Centre, Northwick Park Hospital, Harrow, HA13UJ, United Kingdom
| | - Kalle Soderstrom
- From the Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Marc Feldmann
- From the Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford OX3 7DQ, United Kingdom.,the Kennedy Institute of Rheumatology Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford BRU and
| | - Udo Oppermann
- From the Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford OX3 7DQ, United Kingdom, .,the Structural Genomics Consortium, University of Oxford, Oxford OX3 7LD, United Kingdom.,the Freiburg Institute of Advanced Studies, 79104 Freiburg, Germany, and.,the Oxford Centre for Translational Myeloma Research Oxford, Oxford OX3 7DQ, United Kingdom
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37
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Bartosovic M, Molares HC, Gregorova P, Hrossova D, Kudla G, Vanacova S. N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3'-end processing. Nucleic Acids Res 2017; 45:11356-11370. [PMID: 28977517 PMCID: PMC5737695 DOI: 10.1093/nar/gkx778] [Citation(s) in RCA: 288] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 08/26/2017] [Indexed: 12/16/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant base modification found in messenger RNAs (mRNAs). The discovery of FTO as the first m6A mRNA demethylase established the concept of reversible RNA modification. Here, we present a comprehensive transcriptome-wide analysis of RNA demethylation and uncover FTO as a potent regulator of nuclear mRNA processing events such as alternative splicing and 3΄ end mRNA processing. We show that FTO binds preferentially to pre-mRNAs in intronic regions, in the proximity of alternatively spliced (AS) exons and poly(A) sites. FTO knockout (KO) results in substantial changes in pre-mRNA splicing with prevalence of exon skipping events. The alternative splicing effects of FTO KO anti-correlate with METTL3 knockdown suggesting the involvement of m6A. Besides, deletion of intronic region that contains m6A-linked DRACH motifs partially rescues the FTO KO phenotype in a reporter system. All together, we demonstrate that the splicing effects of FTO are dependent on the catalytic activity in vivo and are mediated by m6A. Our results reveal for the first time the dynamic connection between FTO RNA binding and demethylation activity that influences several mRNA processing events.
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Affiliation(s)
- Marek Bartosovic
- CEITEC-Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
| | - Helena Covelo Molares
- CEITEC-Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
| | - Pavlina Gregorova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
| | - Dominika Hrossova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
| | - Grzegorz Kudla
- MRC Human Genetics Unit MRC IGMM, University of Edinburgh Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Stepanka Vanacova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
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U1 snRNP telescripting regulates a size-function-stratified human genome. Nat Struct Mol Biol 2017; 24:993-999. [PMID: 28967884 DOI: 10.1038/nsmb.3473] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 08/28/2017] [Indexed: 12/16/2022]
Abstract
U1 snRNP (U1) functions in splicing introns and telescripting, which suppresses premature cleavage and polyadenylation (PCPA). Using U1 inhibition in human cells, we show that U1 telescripting is selectively required for sustaining long-distance transcription elongation in introns of large genes (median 39 kb). Evidence of widespread PCPA in the same locations in normal tissues reveals that large genes incur natural transcription attrition. Underscoring the importance of U1 telescripting as a gene-size-based mRNA-regulation mechanism, small genes were not sensitive to PCPA, and the spliced-mRNA productivity of ∼1,000 small genes (median 6.8 kb) increased upon U1 inhibition. Notably, these small, upregulated genes were enriched in functions related to acute stimuli and cell-survival response, whereas genes subject to PCPA were enriched in cell-cycle progression and developmental functions. This gene size-function polarization increased in metazoan evolution by enormous intron expansion. We propose that telescripting adds an overarching layer of regulation to size-function-stratified genomes, leveraged by selective intron expansion to rapidly shift gene expression priorities.
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Yin D, Ritchie ME, Jabbari JS, Beck T, Blewitt ME, Keniry A. High concordance between Illumina HiSeq2500 and NextSeq500 for reduced representation bisulfite sequencing (RRBS). GENOMICS DATA 2016; 10:97-100. [PMID: 27766205 PMCID: PMC5065634 DOI: 10.1016/j.gdata.2016.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 09/29/2016] [Accepted: 10/05/2016] [Indexed: 11/25/2022]
Abstract
Reduced representation bisulfite sequencing (RRBS) provides an efficient method for measuring DNA methylation at single base resolution in regions of high CpG density. This technique has been extensively tested on the HiSeq2500, which uses a 4-colour detection method, however it is unclear if the method will also work on the NextSeq500 platform, which employs a 2-colour detection system. We created an RRBS library and sequenced it on both the HiSeq2500 and NextSeq500, and found no significant difference in the base composition of reads derived from either machine. Moreover, the methylation calls made from the data of each instrument were highly concordant, with methylation patterns across the genome appearing as expected. Therefore, RRBS can be sequenced on the Nextseq500 with comparable quality to that of the HiSeq2500. All sequencing data are deposited in the GEO database under accession number GSE87097.
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Affiliation(s)
- Danqing Yin
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Matthew E Ritchie
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, Parkville, Victoria 3010, Australia; School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jafar S Jabbari
- The Australian Genome Research Facility, Melbourne, Parkville, Victoria 3052, Australia
| | - Tamara Beck
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Marnie E Blewitt
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, Parkville, Victoria 3010, Australia
| | - Andrew Keniry
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, Parkville, Victoria 3010, Australia
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Chan MC, Ilott NE, Schödel J, Sims D, Tumber A, Lippl K, Mole DR, Pugh CW, Ratcliffe PJ, Ponting CP, Schofield CJ. Tuning the Transcriptional Response to Hypoxia by Inhibiting Hypoxia-inducible Factor (HIF) Prolyl and Asparaginyl Hydroxylases. J Biol Chem 2016; 291:20661-73. [PMID: 27502280 PMCID: PMC5034057 DOI: 10.1074/jbc.m116.749291] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/05/2016] [Indexed: 01/08/2023] Open
Abstract
The hypoxia-inducible factor (HIF) system orchestrates cellular responses to hypoxia in animals. HIF is an α/β-heterodimeric transcription factor that regulates the expression of hundreds of genes in a tissue context-dependent manner. The major hypoxia-sensing component of the HIF system involves oxygen-dependent catalysis by the HIF hydroxylases; in humans there are three HIF prolyl hydroxylases (PHD1-3) and an asparaginyl hydroxylase (factor-inhibiting HIF (FIH)). PHD catalysis regulates HIFα levels, and FIH catalysis regulates HIF activity. How differences in HIFα hydroxylation status relate to variations in the induction of specific HIF target gene transcription is unknown. We report studies using small molecule HIF hydroxylase inhibitors that investigate the extent to which HIF target gene expression is induced by PHD or FIH inhibition. The results reveal substantial differences in the role of prolyl and asparaginyl hydroxylation in regulating hypoxia-responsive genes in cells. PHD inhibitors with different structural scaffolds behave similarly. Under the tested conditions, a broad-spectrum 2-oxoglutarate dioxygenase inhibitor is a better mimic of the overall transcriptional response to hypoxia than the selective PHD inhibitors, consistent with an important role for FIH in the hypoxic transcriptional response. Indeed, combined application of selective PHD and FIH inhibitors resulted in the transcriptional induction of a subset of genes not fully responsive to PHD inhibition alone. Thus, for the therapeutic regulation of HIF target genes, it is important to consider both PHD and FIH activity, and in the case of some sets of target genes, simultaneous inhibition of the PHDs and FIH catalysis may be preferable.
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Affiliation(s)
- Mun Chiang Chan
- From the Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, the Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN
| | - Nicholas E Ilott
- the Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, and
| | - Johannes Schödel
- the Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN
| | - David Sims
- the Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, and
| | - Anthony Tumber
- the Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Kerstin Lippl
- From the Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA
| | - David R Mole
- the Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN
| | - Christopher W Pugh
- the Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN
| | - Peter J Ratcliffe
- the Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN
| | - Chris P Ponting
- the Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, and
| | - Christopher J Schofield
- From the Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA,
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High-fat diet disrupts metabolism in two generations of rats in a parent-of-origin specific manner. Sci Rep 2016; 6:31857. [PMID: 27550193 PMCID: PMC4994008 DOI: 10.1038/srep31857] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/28/2016] [Indexed: 01/24/2023] Open
Abstract
Experimental and epidemiological evidence demonstrate that ancestral diet might contribute towards offspring health. This suggests that nutrition may be able to modify genetic or epigenetic information carried by germ cells (GCs). To examine if a parental high fat diet (HFD) influences metabolic health in two generations of offspring, GC-eGFP Sprague Dawley rats were weaned onto HFD (45% fat) or Control Diet (CD; 10% fat). At 19 weeks, founders (F0) were bred with controls, establishing the F1 generation. HFD resulted in 9.7% and 14.7% increased weight gain in male and female F0 respectively. F1 offspring of HFD mothers and F1 daughters of HFD-fed fathers had increased weight gain compared to controls. F1 rats were bred with controls at 19 weeks to generate F2 offspring. F2 male offspring derived from HFD-fed maternal grandfathers exhibited increased adiposity, plasma leptin and luteinising hormone to testosterone ratio. Despite transmission via the founding male germline, we did not find significant changes in the F0 intra-testicular GC transcriptome. Thus, HFD consumption by maternal grandfathers results in a disrupted metabolic and reproductive hormone phenotype in grandsons in the absence of detectable changes in the intra-testicular GC transcriptome.
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Ilott NE, Bollrath J, Danne C, Schiering C, Shale M, Adelmann K, Krausgruber T, Heger A, Sims D, Powrie F. Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling. ISME JOURNAL 2016; 10:2389-404. [PMID: 27003245 PMCID: PMC5030693 DOI: 10.1038/ismej.2016.40] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 02/06/2016] [Accepted: 02/10/2016] [Indexed: 12/23/2022]
Abstract
The gut microbiome is significantly altered in inflammatory bowel diseases, but the basis of these changes is not well understood. We have combined metagenomic and metatranscriptomic profiling of the gut microbiome to assess modifications to both bacterial community structure and transcriptional activity in a mouse model of colitis. By using transcriptomic analysis of colonic tissue and luminal RNA derived from the host, we have also characterised how host transcription relates to the microbial transcriptional response in inflammation. In colitis, increased abundance and transcription of diverse microbial gene families involved in responses to nutrient deprivation, antimicrobial peptide production and oxidative stress support an adaptation of multiple commensal genera to withstand a diverse set of environmental stressors in the inflammatory environment. These data are supported by a transcriptional signature of activated macrophages and granulocytes in the gut lumen during colitis, a signature that includes the transcription of the key antimicrobial genes S100a8 and S100a9 (calprotectin). Genes involved in microbial resistance to oxidative stress, including Dps/ferritin, Fe-dependent peroxidase and glutathione S-transferase were identified as changing to a greater extent at the level of transcription than would be predicted by DNA abundance changes, implicating a role for increased oxygen tension and/or host-derived reactive oxygen species in driving transcriptional changes in commensal microbes.
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Affiliation(s)
| | - Julia Bollrath
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.,Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Camille Danne
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Chris Schiering
- The Francis Crick Institute, Mill Hill Laboratory, London, UK
| | - Matthew Shale
- Translational Gastroenterology Unit, Experimental Medicine, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, UK
| | - Krista Adelmann
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andreas Heger
- Computational Genomics Analysis and Training (CGAT), MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - David Sims
- Computational Genomics Analysis and Training (CGAT), MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
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Pembroke WG, Babbs A, Davies KE, Ponting CP, Oliver PL. Temporal transcriptomics suggest that twin-peaking genes reset the clock. eLife 2015; 4. [PMID: 26523393 PMCID: PMC4718813 DOI: 10.7554/elife.10518] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/01/2015] [Indexed: 01/08/2023] Open
Abstract
The mammalian suprachiasmatic nucleus (SCN) drives daily rhythmic behavior and physiology, yet a detailed understanding of its coordinated transcriptional programmes is lacking. To reveal the finer details of circadian variation in the mammalian SCN transcriptome we combined laser-capture microdissection (LCM) and RNA-seq over a 24 hr light / dark cycle. We show that 7-times more genes exhibited a classic sinusoidal expression signature than previously observed in the SCN. Another group of 766 genes unexpectedly peaked twice, near both the start and end of the dark phase; this twin-peaking group is significantly enriched for synaptic transmission genes that are crucial for light-induced phase shifting of the circadian clock. 341 intergenic non-coding RNAs, together with novel exons of annotated protein-coding genes, including Cry1, also show specific circadian expression variation. Overall, our data provide an important chronobiological resource (www.wgpembroke.com/shiny/SCNseq/) and allow us to propose that transcriptional timing in the SCN is gating clock resetting mechanisms. DOI:http://dx.doi.org/10.7554/eLife.10518.001 The daily cycles of life in mammals are driven by a small region of the brain called the suprachiasmatic nucleus (or SCN). The SCN receives signals from sunlight and other environmental factors to help coordinate most aspects of daily biological activity and behaviour. To work correctly, it is essential that the SCN switches certain genes on and off at exactly the right time. However, many questions remain over the identity of these genes and how their levels of activity change during a 24-hour period. When a gene is active (or “being expressed”), it is used as a template to build the molecules of RNA that are needed to make proteins and to help to control how cells work. Pembroke et al. have now sequenced the RNA molecules made in the SCN of mice (which plays the same role as the equivalent human brain region) over a 24-hour period. The mice spent half of each day in the light, and half in the dark. This revealed that the expression levels of over a quarter of all the genes that are found in the SCN fluctuate over a 24-hour period. One particular group of genes peak in activity twice a day; Pembroke et al. suggest that these genes are important for controlling how an animal can adjust its body clock to light. Further research is now needed to find out which of the newly discovered fluctuating genes play the most important roles in daily activity rhythms, and which might play a part in disease. DOI:http://dx.doi.org/10.7554/eLife.10518.002
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Affiliation(s)
- William G Pembroke
- MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Arran Babbs
- MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Kay E Davies
- MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Chris P Ponting
- MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Peter L Oliver
- MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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Maehara K, Ohkawa Y. agplus: a rapid and flexible tool for aggregation plots: Fig. 1. Bioinformatics 2015; 31:3046-7. [DOI: 10.1093/bioinformatics/btv322] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/17/2015] [Indexed: 11/15/2022] Open
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Sims D, Ponting CP, Heger A. CGAT: a model for immersive personalized training in computational genomics. Brief Funct Genomics 2015; 15:32-7. [PMID: 25981124 PMCID: PMC4812590 DOI: 10.1093/bfgp/elv021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
How should the next generation of genomics scientists be trained while simultaneously pursuing high quality and diverse research? CGAT, the Computational Genomics Analysis and Training programme, was set up in 2010 by the UK Medical Research Council to complement its investment in next-generation sequencing capacity. CGAT was conceived around the twin goals of training future leaders in genome biology and medicine, and providing much needed capacity to UK science for analysing genome scale data sets. Here we outline the training programme employed by CGAT and describe how it dovetails with collaborative research projects to launch scientists on the road towards independent research careers in genomics.
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Sansom SN, Shikama-Dorn N, Zhanybekova S, Nusspaumer G, Macaulay IC, Deadman ME, Heger A, Ponting CP, Holländer GA. Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia. Genome Res 2014; 24:1918-31. [PMID: 25224068 PMCID: PMC4248310 DOI: 10.1101/gr.171645.113] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Accepted: 09/12/2014] [Indexed: 12/18/2022]
Abstract
Promiscuous gene expression (PGE) by thymic epithelial cells (TEC) is essential for generating a diverse T cell antigen receptor repertoire tolerant to self-antigens, and thus for avoiding autoimmunity. Nevertheless, the extent and nature of this unusual expression program within TEC populations and single cells are unknown. Using deep transcriptome sequencing of carefully identified mouse TEC subpopulations, we discovered a program of PGE that is common between medullary (m) and cortical TEC, further elaborated in mTEC, and completed in mature mTEC expressing the autoimmune regulator gene (Aire). TEC populations are capable of expressing up to 19,293 protein-coding genes, the highest number of genes known to be expressed in any cell type. Remarkably, in mouse mTEC, Aire expression alone positively regulates 3980 tissue-restricted genes. Notably, the tissue specificities of these genes include known targets of autoimmunity in human AIRE deficiency. Led by the observation that genes induced by Aire expression are generally characterized by a repressive chromatin state in somatic tissues, we found these genes to be strongly associated with H3K27me3 marks in mTEC. Our findings are consistent with AIRE targeting and inducing the promiscuous expression of genes previously epigenetically silenced by Polycomb group proteins. Comparison of the transcriptomes of 174 single mTEC indicates that genes induced by Aire expression are transcribed stochastically at low cell frequency. Furthermore, when present, Aire expression-dependent transcript levels were 16-fold higher, on average, in individual TEC than in the mTEC population.
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Affiliation(s)
- Stephen N Sansom
- MRC Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom;
| | - Noriko Shikama-Dorn
- Paediatric Immunology, Department of Biomedicine, University of Basel, and The Basel University Children's Hospital, Basel, 4058, Switzerland
| | - Saule Zhanybekova
- Paediatric Immunology, Department of Biomedicine, University of Basel, and The Basel University Children's Hospital, Basel, 4058, Switzerland
| | - Gretel Nusspaumer
- Paediatric Immunology, Department of Biomedicine, University of Basel, and The Basel University Children's Hospital, Basel, 4058, Switzerland
| | - Iain C Macaulay
- Wellcome Trust Sanger Institute-EBI Single Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Mary E Deadman
- Developmental Immunology, Department of Paediatrics, and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Andreas Heger
- MRC Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom
| | - Chris P Ponting
- MRC Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom; Wellcome Trust Sanger Institute-EBI Single Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Georg A Holländer
- Paediatric Immunology, Department of Biomedicine, University of Basel, and The Basel University Children's Hospital, Basel, 4058, Switzerland; Developmental Immunology, Department of Paediatrics, and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
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Abstract
Personalized medicine is the cornerstone of medical practice. It tailors treatments for specific conditions of an affected individual. The borders of personalized medicine are defined by limitations in technology and our understanding of biology, physiology and pathology of various conditions. Current advances in technology have provided physicians with the tools to investigate the molecular makeup of the disease. Translating these molecular make-ups to actionable targets has led to the development of small molecular inhibitors. Also, detailed understanding of genetic makeup has allowed us to develop prognostic markers, better known as companion diagnostics. Current attempts in the development of drug delivery systems offer the opportunity of delivering specific inhibitors to affected cells in an attempt to reduce the unwanted side effects of drugs.
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Affiliation(s)
- Gayane Badalian-Very
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, 450 Brookline ave, Boston, MA 02115, United States. Tel.: + 1 617 513 7940; fax: + 1 617 632 5998.
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