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Fujita T, Seist R, Kao SY, Soares V, Panano L, Khetani RS, Landegger LD, Batts S, Stankovic KM. miR-431 secreted by human vestibular schwannomas increases the mammalian inner ear's vulnerability to noise trauma. Front Neurol 2023; 14:1268359. [PMID: 37885485 PMCID: PMC10598552 DOI: 10.3389/fneur.2023.1268359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023] Open
Abstract
Introduction Vestibular schwannoma (VS) is an intracranial tumor that arises on the vestibular branch of cranial nerve VIII and typically presents with sensorineural hearing loss (SNHL). The mechanisms of this SNHL are postulated to involve alterations in the inner ear's microenvironment mediated by the genetic cargo of VS-secreted extracellular vesicles (EVs). We aimed to identify the EV cargo associated with poor hearing and determine whether its delivery caused hearing loss and cochlear damage in a mouse model in vivo. Methods VS tissue was collected from routinely resected tumors of patients with good (VS-GH) or poor (VS-PH) pre-surgical hearing measured via pure-tone average and word recognition scores. Next-generation sequencing was performed on RNA isolated from cultured primary human VS cells and EVs from VS-conditioned media, stratified by patients' hearing ability. microRNA expression levels were compared between VS-PH and VS-GH samples to identify differentially expressed candidates for packaging into a synthetic adeno-associated viral vector (Anc80L65). Viral vectors containing candidate microRNA were infused to the semicircular canals of mice to evaluate the effects on hearing, including after noise exposure. Results Differentially expressed microRNAs included hsa-miR-431-5p (enriched in VS-PH) and hsa-miR-192-5p (enriched in VS-GH). Newborn mice receiving intracochlear injection of viral vectors over-expressing hsa-miR-431-GFP, hsa-miR-192-GFP, or GFP only (control) had similar hearing 6 weeks post-injection. However, after acoustic trauma, the miR-431 group displayed significantly worse hearing, and greater loss of synaptic ribbons per inner hair cell in the acoustically traumatized cochlear region than the control group. Conclusion Our results suggest that miR-431 contributes to VS-associated hearing loss following cochlear stress. Further investigation is needed to determine whether miR-431 is a potential therapeutic target for SNHL.
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Affiliation(s)
- Takeshi Fujita
- Department of Otolaryngology – Head and Neck Surgery, Massachusetts Eye and Ear and Harvard Medical School, Boston, MA, United States
| | - Richard Seist
- Department of Otolaryngology – Head and Neck Surgery, Massachusetts Eye and Ear and Harvard Medical School, Boston, MA, United States
| | - Shyan-Yuan Kao
- Department of Otolaryngology – Head and Neck Surgery, Massachusetts Eye and Ear and Harvard Medical School, Boston, MA, United States
| | - Vitor Soares
- Department of Otolaryngology – Head and Neck Surgery, Massachusetts Eye and Ear and Harvard Medical School, Boston, MA, United States
| | - Lorena Panano
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Radhika S. Khetani
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Lukas D. Landegger
- Department of Otolaryngology – Head and Neck Surgery, Massachusetts Eye and Ear and Harvard Medical School, Boston, MA, United States
| | - Shelley Batts
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, United States
| | - Konstantina M. Stankovic
- Department of Otolaryngology – Head and Neck Surgery, Massachusetts Eye and Ear and Harvard Medical School, Boston, MA, United States
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, United States
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, United States
- Wu Tsai Neuroscience Institute, Stanford University, Stanford, CA, United States
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2
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O'Connell AE, Raveenthiraraj S, Adegboye C, Qi W, Khetani RS, Singh A, Sundaram N, Emeonye C, Lin J, Goldsmith JD, Thiagarajah JR, Carlone DL, Turner JR, Agrawal PB, Helmrath M, Breault DT. WNT2B Deficiency Causes Increased Susceptibility to Colitis in Mice and Impairs Intestinal Epithelial Development in Humans. bioRxiv 2023:2023.04.21.537894. [PMID: 37131772 PMCID: PMC10153278 DOI: 10.1101/2023.04.21.537894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Background and aims WNT2B is a canonical Wnt ligand previously thought to be fully redundant with other Wnts in the intestinal epithelium. However, humans with WNT2B deficiency have severe intestinal disease, highlighting a critical role for WNT2B. We sought to understand how WNT2B contributes to intestinal homeostasis. Methods We investigated the intestinal health of Wnt2b knock out (KO) mice. We assessed the impact of inflammatory challenge to the small intestine, using anti-CD3χ antibody, and to the colon, using dextran sodium sulfate (DSS). In addition, we generated human intestinal organoids (HIOs) from WNT2B-deficient human iPSCs for transcriptional and histological analyses. Results Mice with WNT2B deficiency had significantly decreased Lgr5 expression in the small intestine and profoundly decreased expression in the colon, but normal baseline histology. The small intestinal response to anti-CD3χ antibody was similar in Wnt2b KO and wild type (WT) mice. In contrast, the colonic response to DSS in Wnt2b KO mice showed an accelerated rate of injury, featuring earlier immune cell infiltration and loss of differentiated epithelium compared to WT. WNT2B-deficient HIOs showed abnormal epithelial organization and an increased mesenchymal gene signature. Conclusion WNT2B contributes to maintenance of the intestinal stem cell pool in mice and humans. WNT2B deficient mice, which do not have a developmental phenotype, show increased susceptibility to colonic injury but not small intestinal injury, potentially due to a higher reliance on WNT2B in the colon compared to the small intestine.WNT2B deficiency causes a developmental phenotype in human intestine with HIOs showing a decrease in their mesenchymal component and WNT2B-deficient patients showing epithelial disorganization. Data Transparency Statement All RNA-Seq data will be available through online repository as indicated in Transcript profiling. Any other data will be made available upon request by emailing the study authors.
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3
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Theocharidis G, Baltzis D, Roustit M, Tellechea A, Dangwal S, Khetani RS, Shu B, Zhao W, Fu J, Bhasin S, Kafanas A, Hui D, Sui SH, Patsopoulos NA, Bhasin M, Veves A. Integrated Skin Transcriptomics and Serum Multiplex Assays Reveal Novel Mechanisms of Wound Healing in Diabetic Foot Ulcers. Diabetes 2020; 69:2157-2169. [PMID: 32763913 PMCID: PMC7506837 DOI: 10.2337/db20-0188] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/29/2020] [Indexed: 12/16/2022]
Abstract
Nonhealing diabetic foot ulcers (DFUs) are characterized by low-grade chronic inflammation, both locally and systemically. We prospectively followed a group of patients who either healed or developed nonhealing chronic DFUs. Serum and forearm skin analysis, both at the protein expression and the transcriptomic level, indicated that increased expression of factors such as interferon-γ (IFN-γ), vascular endothelial growth factor, and soluble vascular cell adhesion molecule-1 were associated with DFU healing. Furthermore, foot skin single-cell RNA sequencing analysis showed multiple fibroblast cell clusters and increased inflammation in the dorsal skin of patients with diabetes mellitus (DM) and DFU specimens compared with control subjects. In addition, in myeloid cell DM and DFU upstream regulator analysis, we observed inhibition of interleukin-13 and IFN-γ and dysregulation of biological processes that included cell movement of monocytes, migration of dendritic cells, and chemotaxis of antigen-presenting cells pointing to an impaired migratory profile of immune cells in DM skin. The SLCO2A1 and CYP1A1 genes, which were upregulated at the forearm of nonhealers, were mainly expressed by the vascular endothelial cell cluster almost exclusively in DFU, indicating a potential important role in wound healing. These results from integrated protein and transcriptome analyses identified individual genes and pathways that can potentially be targeted for enhancing DFU healing.
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Affiliation(s)
- Georgios Theocharidis
- Joslin-Beth Israel Deaconess Foot Center and The Rongxiang Xu, MD, Center for Regenerative Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Dimitrios Baltzis
- Joslin-Beth Israel Deaconess Foot Center and The Rongxiang Xu, MD, Center for Regenerative Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Matthieu Roustit
- Joslin-Beth Israel Deaconess Foot Center and The Rongxiang Xu, MD, Center for Regenerative Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Ana Tellechea
- Joslin-Beth Israel Deaconess Foot Center and The Rongxiang Xu, MD, Center for Regenerative Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Seema Dangwal
- Joslin-Beth Israel Deaconess Foot Center and The Rongxiang Xu, MD, Center for Regenerative Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Radhika S Khetani
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Bin Shu
- Joslin-Beth Israel Deaconess Foot Center and The Rongxiang Xu, MD, Center for Regenerative Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Wanni Zhao
- Joslin-Beth Israel Deaconess Foot Center and The Rongxiang Xu, MD, Center for Regenerative Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Jianfang Fu
- Joslin-Beth Israel Deaconess Foot Center and The Rongxiang Xu, MD, Center for Regenerative Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Swati Bhasin
- Department of Medicine, Division of Interdisciplinary Medicine and Biotechnology, and Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Antonios Kafanas
- Joslin-Beth Israel Deaconess Foot Center and The Rongxiang Xu, MD, Center for Regenerative Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Daniel Hui
- Systems Biology and Computer Science Program, Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
| | - Shannan Ho Sui
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Nikolaos A Patsopoulos
- Systems Biology and Computer Science Program, Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
| | - Manoj Bhasin
- Department of Medicine, Division of Interdisciplinary Medicine and Biotechnology, and Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Aristidis Veves
- Joslin-Beth Israel Deaconess Foot Center and The Rongxiang Xu, MD, Center for Regenerative Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
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4
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Leng S, Pignatti E, Khetani RS, Shah MS, Xu S, Miao J, Taketo MM, Beuschlein F, Barrett PQ, Carlone DL, Breault DT. β-Catenin and FGFR2 regulate postnatal rosette-based adrenocortical morphogenesis. Nat Commun 2020; 11:1680. [PMID: 32245949 PMCID: PMC7125176 DOI: 10.1038/s41467-020-15332-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 02/28/2020] [Indexed: 02/08/2023] Open
Abstract
Rosettes are widely used in epithelial morphogenesis during embryonic development and organogenesis. However, their role in postnatal development and adult tissue maintenance remains largely unknown. Here, we show zona glomerulosa cells in the adult adrenal cortex organize into rosettes through adherens junction-mediated constriction, and that rosette formation underlies the maturation of adrenal glomerular structure postnatally. Using genetic mouse models, we show loss of β-catenin results in disrupted adherens junctions, reduced rosette number, and dysmorphic glomeruli, whereas β-catenin stabilization leads to increased adherens junction abundance, more rosettes, and glomerular expansion. Furthermore, we uncover numerous known regulators of epithelial morphogenesis enriched in β-catenin-stabilized adrenals. Among these genes, we show Fgfr2 is required for adrenal rosette formation by regulating adherens junction abundance and aggregation. Together, our data provide an example of rosette-mediated postnatal tissue morphogenesis and a framework for studying the role of rosettes in adult zona glomerulosa tissue maintenance and function.
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Affiliation(s)
- Sining Leng
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, 02115, USA
- Division of Medical Sciences, Harvard Medical School, Boston, MA, 02115, USA
| | - Emanuele Pignatti
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Radhika S Khetani
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Manasvi S Shah
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Simiao Xu
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Ji Miao
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Makoto M Taketo
- Division of Experimental Therapeutics, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-Cho, Sakyo, Kyoto, 606-8506, Japan
| | - Felix Beuschlein
- Department of Endocrinology, Diabetology and Clinical Nutrition, UniversitätsSpital Zürich, Zurich, Switzerland
- Medizinische Klinik und Poliklinik IV, Klinikum der Ludwig-Maximilians-Universität München, Munich, Germany
| | - Paula Q Barrett
- Departments of Pharmacology, University of Virginia, Charlottesville, VA, 22947, USA
| | - Diana L Carlone
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - David T Breault
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
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5
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Dong Y, Sanford RA, Inskeep WP, Srivastava V, Bulone V, Fields CJ, Yau PM, Sivaguru M, Ahrén D, Fouke KW, Weber J, Werth CR, Cann IK, Keating KM, Khetani RS, Hernandez AG, Wright C, Band M, Imai BS, Fried GA, Fouke BW. Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats. Astrobiology 2019; 19:1442-1458. [PMID: 31038352 PMCID: PMC6918859 DOI: 10.1089/ast.2018.1965] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
The evolutionarily ancient Aquificales bacterium Sulfurihydrogenibium spp. dominates filamentous microbial mat communities in shallow, fast-flowing, and dysoxic hot-spring drainage systems around the world. In the present study, field observations of these fettuccini-like microbial mats at Mammoth Hot Springs in Yellowstone National Park are integrated with geology, geochemistry, hydrology, microscopy, and multi-omic molecular biology analyses. Strategic sampling of living filamentous mats along with the hot-spring CaCO3 (travertine) in which they are actively being entombed and fossilized has permitted the first direct linkage of Sulfurihydrogenibium spp. physiology and metabolism with the formation of distinct travertine streamer microbial biomarkers. Results indicate that, during chemoautotrophy and CO2 carbon fixation, the 87-98% Sulfurihydrogenibium-dominated mats utilize chaperons to facilitate enzyme stability and function. High-abundance transcripts and proteins for type IV pili and extracellular polymeric substances (EPSs) are consistent with their strong mucus-rich filaments tens of centimeters long that withstand hydrodynamic shear as they become encrusted by more than 5 mm of travertine per day. Their primary energy source is the oxidation of reduced sulfur (e.g., sulfide, sulfur, or thiosulfate) and the simultaneous uptake of extremely low concentrations of dissolved O2 facilitated by bd-type cytochromes. The formation of elevated travertine ridges permits the Sulfurihydrogenibium-dominated mats to create a shallow platform from which to access low levels of dissolved oxygen at the virtual exclusion of other microorganisms. These ridged travertine streamer microbial biomarkers are well preserved and create a robust fossil record of microbial physiological and metabolic activities in modern and ancient hot-spring ecosystems.
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Affiliation(s)
- Yiran Dong
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Robert A. Sanford
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - William P. Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
- Thermal Biology Institute, Montana State University, Bozeman, Montana, USA
| | - Vaibhav Srivastava
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Vincent Bulone
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden
- Division School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia
| | - Christopher J. Fields
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Peter M. Yau
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Mayandi Sivaguru
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carl Zeiss Labs @ Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Dag Ahrén
- Microbial Ecology Group, Bioinformatics Infrastructure for Life Sciences, Department of Biology, Lund University, Lund, Sweden
- Pufendorf Institute for Advanced Sciences, Lund University, Lund, Sweden
| | - Kyle W. Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Geology and Environmental Sciences, Bucknell University, Lewisburg, Pennsylvania, USA
| | - Joseph Weber
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Charles R. Werth
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Civil, Architectural and Environmental Engineering, University of Texas Austin, Texas, USA
| | - Isaac K. Cann
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kathleen M. Keating
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Radhika S. Khetani
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Alvaro G. Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Chris Wright
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Mark Band
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Brian S. Imai
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Glenn A. Fried
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carl Zeiss Labs @ Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Bruce W. Fouke
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Geology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Thermal Biology Institute, Montana State University, Bozeman, Montana, USA
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carl Zeiss Labs @ Location Partner, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Pufendorf Institute for Advanced Sciences, Lund University, Lund, Sweden
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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6
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Spadafora R, Lu J, Khetani RS, Zhang C, Iberg A, Li H, Shi Y, Lerou PH. Lung-Resident Mesenchymal Stromal Cells Reveal Transcriptional Dynamics of Lung Development in Preterm Infants. Am J Respir Crit Care Med 2019; 198:961-964. [PMID: 29757681 DOI: 10.1164/rccm.201801-0024le] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
| | - Junjie Lu
- 2 Massachusetts General Hospital Boston, Massachusetts
| | | | | | - Aimee Iberg
- 5 Boston Children's Hospital Boston, Massachusetts
| | - Hu Li
- 4 Mayo Clinic Rochester, Minnesota and
| | - Yang Shi
- 5 Boston Children's Hospital Boston, Massachusetts
| | - Paul H Lerou
- 2 Massachusetts General Hospital Boston, Massachusetts
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7
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Hancock ML, Meyer RC, Mistry M, Khetani RS, Wagschal A, Shin T, Ho Sui SJ, Näär AM, Flanagan JG. Insulin Receptor Associates with Promoters Genome-wide and Regulates Gene Expression. Cell 2019; 177:722-736.e22. [PMID: 30955890 PMCID: PMC6478446 DOI: 10.1016/j.cell.2019.02.030] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/07/2019] [Accepted: 02/19/2019] [Indexed: 02/08/2023]
Abstract
Insulin receptor (IR) signaling is central to normal metabolic control and dysregulated in prevalent chronic diseases. IR binds insulin at the cell surface and transduces rapid signaling via cytoplasmic kinases. However, mechanisms mediating long-term effects of insulin remain unclear. Here, we show that IR associates with RNA polymerase II in the nucleus, with striking enrichment at promoters genome-wide. The target genes were highly enriched for insulin-related functions including lipid metabolism and protein synthesis and diseases including diabetes, neurodegeneration, and cancer. IR chromatin binding was increased by insulin and impaired in an insulin-resistant disease model. Promoter binding by IR was mediated by coregulator host cell factor-1 (HCF-1) and transcription factors, revealing an HCF-1-dependent pathway for gene regulation by insulin. These results show that IR interacts with transcriptional machinery at promoters and identify a pathway regulating genes linked to insulin's effects in physiology and disease.
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Affiliation(s)
- Melissa L. Hancock
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA,Present address: John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge,
MA, USA
| | - Rebecca C. Meyer
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA,These authors contributed equally
| | - Meeta Mistry
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA,These authors contributed equally
| | - Radhika S. Khetani
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA,These authors contributed equally
| | - Alexandre Wagschal
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA,Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA,Present address: Exonics Therapeutics, Cambridge, MA, USA
| | - Taehwan Shin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Shannan J. Ho Sui
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Anders M. Näär
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA,Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA,Present address: Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA
94720, USA
| | - John G. Flanagan
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA,Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA,Lead Contact,Correspondence:
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8
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Doğramacı M, Foley ME, Horvath DP, Hernandez AG, Khetani RS, Fields CJ, Keating KM, Mikel MA, Anderson JV. Glyphosate's impact on vegetative growth in leafy spurge identifies molecular processes and hormone cross-talk associated with increased branching. BMC Genomics 2015; 16:395. [PMID: 25986459 PMCID: PMC4437557 DOI: 10.1186/s12864-015-1627-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 05/11/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Leafy spurge (Euphorbia esula) is a perennial weed that is considered glyphosate tolerant, which is partially attributed to escape through establishment of new vegetative shoots from an abundance of underground adventitious buds. Leafy spurge plants treated with sub-lethal concentrations of foliar-applied glyphosate produce new vegetative shoots with reduced main stem elongation and increased branching. Processes associated with the glyphosate-induced phenotype were determined by RNAseq using aerial shoots derived from crown buds of glyphosate-treated and -untreated plants. Comparison between transcript abundance and accumulation of shikimate or phytohormones (abscisic acid, auxin, cytokinins, and gibberellins) from these same samples was also done to reveal correlations. RESULTS Transcriptome assembly and analyses confirmed differential abundance among 12,918 transcripts (FDR ≤ 0.05) and highlighted numerous processes associated with shoot apical meristem maintenance and stem growth, which is consistent with the increased number of actively growing meristems in response to glyphosate. Foliar applied glyphosate increased shikimate abundance in crown buds prior to decapitation of aboveground shoots, which induces growth from these buds, indicating that 5-enolpyruvylshikimate 3-phosphate (EPSPS) the target site of glyphosate was inhibited. However, abundance of shikimate was similar in a subsequent generation of aerial shoots derived from crown buds of treated and untreated plants, suggesting EPSPS is no longer inhibited or abundance of shikimate initially observed in crown buds dissipated over time. Overall, auxins, gibberellins (precursors and catabolites of bioactive gibberellins), and cytokinins (precursors and bioactive cytokinins) were more abundant in the aboveground shoots derived from glyphosate-treated plants. CONCLUSION Based on the overall data, we propose that the glyphosate-induced phenotype resulted from complex interactions involving shoot apical meristem maintenance, hormone biosynthesis and signaling (auxin, cytokinins, gibberellins, and strigolactones), cellular transport, and detoxification mechanisms.
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Affiliation(s)
- Münevver Doğramacı
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - Michael E Foley
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - David P Horvath
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - Alvaro G Hernandez
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Radhika S Khetani
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Christopher J Fields
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Kathleen M Keating
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Mark A Mikel
- Department of Crop Sciences, 2608 Institute for Genomic Biology, and Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL, 61801, USA.
| | - James V Anderson
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
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Doğramacı M, Foley ME, Horvath DP, Hernandez AG, Khetani RS, Fields CJ, Keating KM, Mikel MA, Anderson JV. Glyphosate's impact on vegetative growth in leafy spurge identifies molecular processes and hormone cross-talk associated with increased branching. BMC Genomics 2015. [PMID: 25986459 DOI: 10.1186/s12864‐015‐1627‐9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Leafy spurge (Euphorbia esula) is a perennial weed that is considered glyphosate tolerant, which is partially attributed to escape through establishment of new vegetative shoots from an abundance of underground adventitious buds. Leafy spurge plants treated with sub-lethal concentrations of foliar-applied glyphosate produce new vegetative shoots with reduced main stem elongation and increased branching. Processes associated with the glyphosate-induced phenotype were determined by RNAseq using aerial shoots derived from crown buds of glyphosate-treated and -untreated plants. Comparison between transcript abundance and accumulation of shikimate or phytohormones (abscisic acid, auxin, cytokinins, and gibberellins) from these same samples was also done to reveal correlations. RESULTS Transcriptome assembly and analyses confirmed differential abundance among 12,918 transcripts (FDR ≤ 0.05) and highlighted numerous processes associated with shoot apical meristem maintenance and stem growth, which is consistent with the increased number of actively growing meristems in response to glyphosate. Foliar applied glyphosate increased shikimate abundance in crown buds prior to decapitation of aboveground shoots, which induces growth from these buds, indicating that 5-enolpyruvylshikimate 3-phosphate (EPSPS) the target site of glyphosate was inhibited. However, abundance of shikimate was similar in a subsequent generation of aerial shoots derived from crown buds of treated and untreated plants, suggesting EPSPS is no longer inhibited or abundance of shikimate initially observed in crown buds dissipated over time. Overall, auxins, gibberellins (precursors and catabolites of bioactive gibberellins), and cytokinins (precursors and bioactive cytokinins) were more abundant in the aboveground shoots derived from glyphosate-treated plants. CONCLUSION Based on the overall data, we propose that the glyphosate-induced phenotype resulted from complex interactions involving shoot apical meristem maintenance, hormone biosynthesis and signaling (auxin, cytokinins, gibberellins, and strigolactones), cellular transport, and detoxification mechanisms.
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Affiliation(s)
- Münevver Doğramacı
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - Michael E Foley
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - David P Horvath
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
| | - Alvaro G Hernandez
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Radhika S Khetani
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Christopher J Fields
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Kathleen M Keating
- University of Illinois, W.M. Keck Center for Comparative and Functional Genomics, Urbana, IL, 61801, USA.
| | - Mark A Mikel
- Department of Crop Sciences, 2608 Institute for Genomic Biology, and Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL, 61801, USA.
| | - James V Anderson
- United States Department of Agriculture, Agricultural Research Service, Sunflower and Plant Biology Research, Fargo, ND, 58102, USA.
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10
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Kenny PJ, Zhou H, Kim M, Skariah G, Khetani RS, Drnevich J, Arcila ML, Kosik KS, Ceman S. MOV10 and FMRP regulate AGO2 association with microRNA recognition elements. Cell Rep 2014; 9:1729-1741. [PMID: 25464849 DOI: 10.1016/j.celrep.2014.10.054] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 10/09/2014] [Accepted: 10/18/2014] [Indexed: 10/24/2022] Open
Abstract
The fragile X mental retardation protein FMRP regulates translation of its bound mRNAs through incompletely defined mechanisms. FMRP has been linked to the microRNA pathway, and we show here that it associates with the RNA helicase MOV10, also associated with the microRNA pathway. FMRP associates with MOV10 directly and in an RNA-dependent manner and facilitates MOV10's association with RNAs in brain and cells, suggesting a cooperative interaction. We identified the RNAs recognized by MOV10 using RNA immunoprecipitation and iCLIP. Examination of the fate of MOV10 on RNAs revealed a dual function for MOV10 in regulating translation: it facilitates microRNA-mediated translation of some RNAs, but it also increases expression of other RNAs by preventing AGO2 function. The latter subset was also bound by FMRP in close proximity to the MOV10 binding site, suggesting that FMRP prevents MOV10-mediated microRNA suppression. We have identified a mechanism for FMRP-mediated translational regulation through its association with MOV10.
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Affiliation(s)
- Phillip J Kenny
- Cell and Developmental Biology, Roy J. Carver Biotechnology Center, University of Illinois-Urbana Champaign, Urbana, IL 61801, USA
| | - Hongjun Zhou
- Neuroscience Research Institute and Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Miri Kim
- College of Medicine, Roy J. Carver Biotechnology Center, University of Illinois-Urbana Champaign, Urbana, IL 61801, USA; Neuroscience Program, Roy J. Carver Biotechnology Center, University of Illinois-Urbana Champaign, Urbana, IL 61801, USA
| | - Geena Skariah
- Neuroscience Program, Roy J. Carver Biotechnology Center, University of Illinois-Urbana Champaign, Urbana, IL 61801, USA
| | - Radhika S Khetani
- High-Performance Biological Computing, Roy J. Carver Biotechnology Center, University of Illinois-Urbana Champaign, Urbana, IL 61801, USA
| | - Jenny Drnevich
- High-Performance Biological Computing, Roy J. Carver Biotechnology Center, University of Illinois-Urbana Champaign, Urbana, IL 61801, USA
| | - Mary Luz Arcila
- Neuroscience Research Institute and Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Kenneth S Kosik
- Neuroscience Research Institute and Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Stephanie Ceman
- Cell and Developmental Biology, Roy J. Carver Biotechnology Center, University of Illinois-Urbana Champaign, Urbana, IL 61801, USA; College of Medicine, Roy J. Carver Biotechnology Center, University of Illinois-Urbana Champaign, Urbana, IL 61801, USA; Neuroscience Program, Roy J. Carver Biotechnology Center, University of Illinois-Urbana Champaign, Urbana, IL 61801, USA.
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11
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Elsik CG, Worley KC, Bennett AK, Beye M, Camara F, Childers CP, de Graaf DC, Debyser G, Deng J, Devreese B, Elhaik E, Evans JD, Foster LJ, Graur D, Guigo R, Hoff KJ, Holder ME, Hudson ME, Hunt GJ, Jiang H, Joshi V, Khetani RS, Kosarev P, Kovar CL, Ma J, Maleszka R, Moritz RFA, Munoz-Torres MC, Murphy TD, Muzny DM, Newsham IF, Reese JT, Robertson HM, Robinson GE, Rueppell O, Solovyev V, Stanke M, Stolle E, Tsuruda JM, Vaerenbergh MV, Waterhouse RM, Weaver DB, Whitfield CW, Wu Y, Zdobnov EM, Zhang L, Zhu D, Gibbs RA. Finding the missing honey bee genes: lessons learned from a genome upgrade. BMC Genomics 2014; 15:86. [PMID: 24479613 PMCID: PMC4028053 DOI: 10.1186/1471-2164-15-86] [Citation(s) in RCA: 280] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 01/27/2014] [Indexed: 11/21/2022] Open
Abstract
Background The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. Results Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. Conclusions Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.
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Affiliation(s)
- Christine G Elsik
- Division of Animal Sciences, Division of Plant Sciences, and MU Informatics Institute, University of Missouri, Columbia, MO 65211, USA.
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12
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Cingolani P, Cao X, Khetani RS, Chen CC, Coon M, Sammak A, Bollig-Fischer A, Land S, Huang Y, Hudson ME, Garfinkel MD, Zhong S, Robinson GE, Ruden DM. Intronic non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees. BMC Genomics 2013; 14:666. [PMID: 24079845 PMCID: PMC3850688 DOI: 10.1186/1471-2164-14-666] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 09/22/2013] [Indexed: 11/20/2022] Open
Abstract
Background Previous whole-genome shotgun bisulfite sequencing experiments showed that DNA cytosine methylation in the honey bee (Apis mellifera) is almost exclusively at CG dinucleotides in exons. However, the most commonly used method, bisulfite sequencing, cannot distinguish 5-methylcytosine from 5-hydroxymethylcytosine, an oxidized form of 5-methylcytosine that is catalyzed by the TET family of dioxygenases. Furthermore, some analysis software programs under-represent non-CG DNA methylation and hydryoxymethylation for a variety of reasons. Therefore, we used an unbiased analysis of bisulfite sequencing data combined with molecular and bioinformatics approaches to distinguish 5-methylcytosine from 5-hydroxymethylcytosine. By doing this, we have performed the first whole genome analyses of DNA modifications at non-CG sites in honey bees and correlated the effects of these DNA modifications on gene expression and alternative mRNA splicing. Results We confirmed, using unbiased analyses of whole-genome shotgun bisulfite sequencing (BS-seq) data, with both new data and published data, the previous finding that CG DNA methylation is enriched in exons in honey bees. However, we also found evidence that cytosine methylation and hydroxymethylation at non-CG sites is enriched in introns. Using antibodies against 5-hydroxmethylcytosine, we confirmed that DNA hydroxymethylation at non-CG sites is enriched in introns. Additionally, using a new technique, Pvu-seq (which employs the enzyme PvuRts1l to digest DNA at 5-hydroxymethylcytosine sites followed by next-generation DNA sequencing), we further confirmed that hydroxymethylation is enriched in introns at non-CG sites. Conclusions Cytosine hydroxymethylation at non-CG sites might have more functional significance than previously appreciated, and in honey bees these modifications might be related to the regulation of alternative mRNA splicing by defining the locations of the introns.
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Affiliation(s)
- Pablo Cingolani
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA.
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13
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Sen Sarma M, Arcoleo D, Khetani RS, Chee B, Ling X, He X, Jiang J, Mei Q, Zhai C, Schatz B. BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature. Nucleic Acids Res 2011; 39:W462-9. [PMID: 21558175 PMCID: PMC3125736 DOI: 10.1093/nar/gkr285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
With the rapid decrease in cost of genome sequencing, the classification of gene function is becoming a primary problem. Such classification has been performed by human curators who read biological literature to extract evidence. BeeSpace Navigator is a prototype software for exploratory analysis of gene function using biological literature. The software supports an automatic analogue of the curator process to extract functions, with a simple interface intended for all biologists. Since extraction is done on selected collections that are semantically indexed into conceptual spaces, the curation can be task specific. Biological literature containing references to gene lists from expression experiments can be analyzed to extract concepts that are computational equivalents of a classification such as Gene Ontology, yielding discriminating concepts that differentiate gene mentions from other mentions. The functions of individual genes can be summarized from sentences in biological literature, to produce results resembling a model organism database entry that is automatically computed. Statistical frequency analysis based on literature phrase extraction generates offline semantic indexes to support these gene function services. The website with BeeSpace Navigator is free and open to all; there is no login requirement at www.beespace.illinois.edu for version 4. Materials from the 2010 BeeSpace Software Training Workshop are available at www.beespace.illinois.edu/bstwmaterials.php.
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Affiliation(s)
- Moushumi Sen Sarma
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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14
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Page SL, Khetani RS, Lake CM, Nielsen RJ, Jeffress JK, Warren WD, Bickel SE, Hawley RS. Corona is required for higher-order assembly of transverse filaments into full-length synaptonemal complex in Drosophila oocytes. PLoS Genet 2008; 4:e1000194. [PMID: 18802461 PMCID: PMC2529403 DOI: 10.1371/journal.pgen.1000194] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Accepted: 08/07/2008] [Indexed: 11/19/2022] Open
Abstract
The synaptonemal complex (SC) is an intricate structure that forms between homologous chromosomes early during the meiotic prophase, where it mediates homolog pairing interactions and promotes the formation of genetic exchanges. In Drosophila melanogaster, C(3)G protein forms the transverse filaments (TFs) of the SC. The N termini of C(3)G homodimers localize to the Central Element (CE) of the SC, while the C-termini of C(3)G connect the TFs to the chromosomes via associations with the axial elements/lateral elements (AEs/LEs) of the SC. Here, we show that the Drosophila protein Corona (CONA) co-localizes with C(3)G in a mutually dependent fashion and is required for the polymerization of C(3)G into mature thread-like structures, in the context both of paired homologous chromosomes and of C(3)G polycomplexes that lack AEs/LEs. Although AEs assemble in cona oocytes, they exhibit defects that are characteristic of c(3)G mutant oocytes, including failure of AE alignment and synapsis. These results demonstrate that CONA, which does not contain a coiled coil domain, is required for the stable 'zippering' of TFs to form the central region of the Drosophila SC. We speculate that CONA's role in SC formation may be similar to that of the mammalian CE proteins SYCE2 and TEX12. However, the observation that AE alignment and pairing occurs in Tex12 and Syce2 mutant meiocytes but not in cona oocytes suggests that the SC plays a more critical role in the stable association of homologs in Drosophila than it does in mammalian cells.
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Affiliation(s)
- Scott L Page
- Comparative Genomics Centre, School of Pharmacy and Molecular Sciences, James Cook University, Townsville, Australia.
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15
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Abstract
During meiosis, cohesion between sister chromatids is required for normal levels of homologous recombination, maintenance of chiasmata and accurate chromosome segregation during both divisions. In Drosophila, null mutations in the ord gene abolish meiotic cohesion, although how ORD protein promotes cohesion has remained elusive. We show that SMC subunits of the cohesin complex colocalize with ORD at centromeres of ovarian germ-line cells. In addition, cohesin SMCs and ORD are visible along the length of meiotic chromosomes during pachytene and remain associated with chromosome cores following DNase I digestion. In flies lacking ORD activity, cohesin SMCs fail to accumulate at oocyte centromeres. Although SMC1 and SMC3 localization along chromosome cores appears normal during early pachytene in ord mutant oocytes, the cores disassemble as meiosis progresses. These data suggest that cohesin loading and/or accumulation at centromeres versus arms is under differential control during Drosophila meiosis. Our experiments also reveal that the alpha-kleisin C(2)M is required for the assembly of chromosome cores during pachytene but is not involved in recruitment of cohesin SMCs to the centromeres. We present a model for how chromosome cores are assembled during Drosophila meiosis and the role of ORD in meiotic cohesion, chromosome core maintenance and homologous recombination.
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Affiliation(s)
- Radhika S Khetani
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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16
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Chakravarty A, Carlson JM, Khetani RS, DeZiel CE, Gross RH. SPACER: identification of cis-regulatory elements with non-contiguous critical residues. ACTA ACUST UNITED AC 2007; 23:1029-31. [PMID: 17470480 DOI: 10.1093/bioinformatics/btm041] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
MOTIVATION Many transcription factors bind to sites that are long and loosely related to each other. De novo identification of such motifs is computationally challenging. In this article, we propose a novel semi-greedy algorithm over the space of all IUPAC degenerate strings to identify the most over-represented highly degenerate motifs. RESULTS We present an implementation of this algorithm, named SPACER (Separated Pattern-based Algorithm for cis-Element Recognition) and demonstrate its effectiveness in identifying 'gapped' and highly degenerate motifs. We compare SPACER's performance against ten motif finders on 42 experimentally defined regulons from Bacillus subtilis, Escherichia coli and Saccharomyces cerevisiae. These motif finders cover a wide range of both enumerative and statistical approaches, including programs specifically designed for prokaryotic and 'gapped' motifs. AVAILABILITY A Java 1.4 implementation is freely available on the Web at http://genie.Dartmouth.edu/SPACER/
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Affiliation(s)
- Arijit Chakravarty
- Department of Cancer Pharmacology, Millennium Pharmaceuticals Inc., Cambridge, MA, USA
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17
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Carlson JM, Chakravarty A, Khetani RS, Gross RH. Bounded search for de novo identification of degenerate cis-regulatory elements. BMC Bioinformatics 2006; 7:254. [PMID: 16700920 PMCID: PMC1481619 DOI: 10.1186/1471-2105-7-254] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Accepted: 05/15/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The identification of statistically overrepresented sequences in the upstream regions of coregulated genes should theoretically permit the identification of potential cis-regulatory elements. However, in practice many cis-regulatory elements are highly degenerate, precluding the use of an exhaustive word-counting strategy for their identification. While numerous methods exist for inferring base distributions using a position weight matrix, recent studies suggest that the independence assumptions inherent in the model, as well as the inability to reach a global optimum, limit this approach. RESULTS In this paper, we report PRISM, a degenerate motif finder that leverages the relationship between the statistical significance of a set of binding sites and that of the individual binding sites. PRISM first identifies overrepresented, non-degenerate consensus motifs, then iteratively relaxes each one into a high-scoring degenerate motif. This approach requires no tunable parameters, thereby lending itself to unbiased performance comparisons. We therefore compare PRISM's performance against nine popular motif finders on 28 well-characterized S. cerevisiae regulons. PRISM consistently outperforms all other programs. Finally, we use PRISM to predict the binding sites of uncharacterized regulons. Our results support a proposed mechanism of action for the yeast cell-cycle transcription factor Stb1, whose binding site has not been determined experimentally. CONCLUSION The relationship between statistical measures of the binding sites and the set as a whole leads to a simple means of identifying the diverse range of cis-regulatory elements to which a protein binds. This approach leverages the advantages of word-counting, in that position dependencies are implicitly accounted for and local optima are more easily avoided. While we sacrifice guaranteed optimality to prevent the exponential blowup of exhaustive search, we prove that the error is bounded and experimentally show that the performance is superior to other methods. A Java implementation of this algorithm can be downloaded from our web server at http://genie.dartmouth.edu/prism.
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Affiliation(s)
- Jonathan M Carlson
- Department of Computer Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Arijit Chakravarty
- Department of Cancer Pharmacology, Millennium Pharmaceuticals Inc., Cambridge, MA 02138, USA
| | | | - Robert H Gross
- Department of Biology, Dartmouth College, Hanover, NH 03755, USA
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