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Li Y, Brooks M, Yeoh-Wang J, McCoy RM, Rock TM, Pasquino A, Moon CI, Patrick RM, Tanurdzic M, Ruffel S, Widhalm JR, McCombie WR, Coruzzi GM. SDG8-Mediated Histone Methylation and RNA Processing Function in the Response to Nitrate Signaling. Plant Physiol 2020; 182:215-227. [PMID: 31641075 PMCID: PMC6945839 DOI: 10.1104/pp.19.00682] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/09/2019] [Indexed: 05/04/2023]
Abstract
Chromatin modification has gained increased attention for its role in the regulation of plant responses to environmental changes, but the specific mechanisms and molecular players remain elusive. Here, we show that the Arabidopsis (Arabidopsis thaliana) histone methyltransferase SET DOMAIN GROUP8 (SDG8) mediates genome-wide changes in H3K36 methylation at specific genomic loci functionally relevant to nitrate treatments. Moreover, we show that the specific H3K36 methyltransferase encoded by SDG8 is required for canonical RNA processing, and that RNA isoform switching is more prominent in the sdg8-5 deletion mutant than in the wild type. To demonstrate that SDG8-mediated regulation of RNA isoform expression is functionally relevant, we examined a putative regulatory gene, CONSTANS, CO-like, and TOC1 101 (CCT101), whose nitrogen-responsive isoform-specific RNA expression is mediated by SDG8. We show by functional expression in shoot cells that the different RNA isoforms of CCT101 encode distinct regulatory proteins with different effects on genome-wide transcription. We conclude that SDG8 is involved in plant responses to environmental nitrogen supply, affecting multiple gene regulatory processes including genome-wide histone modification, transcriptional regulation, and RNA processing, and thereby mediating developmental and metabolic processes related to nitrogen use.
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Affiliation(s)
- Ying Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Matthew Brooks
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Jenny Yeoh-Wang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Rachel M McCoy
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Tara M Rock
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Angelo Pasquino
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
| | - Chang In Moon
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Ryan M Patrick
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Milos Tanurdzic
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Sandrine Ruffel
- Biochimie et Physiologie Moléculaire des Plantes, French National Institute for Agricultural Research, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier SupAgro, 34090 Montpellier, France
| | - Joshua R Widhalm
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | | | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003
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Maritz JM, Rogers KH, Rock TM, Liu N, Joseph S, Land KM, Carlton JM. An 18S rRNA Workflow for Characterizing Protists in Sewage, with a Focus on Zoonotic Trichomonads. Microb Ecol 2017; 74:923-936. [PMID: 28540488 PMCID: PMC5653731 DOI: 10.1007/s00248-017-0996-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/12/2017] [Indexed: 05/07/2023]
Abstract
Microbial eukaryotes (protists) are important components of terrestrial and aquatic environments, as well as animal and human microbiomes. Their relationships with metazoa range from mutualistic to parasitic and zoonotic (i.e., transmissible between humans and animals). Despite their ecological importance, our knowledge of protists in urban environments lags behind that of bacteria, largely due to a lack of experimentally validated high-throughput protocols that produce accurate estimates of protist diversity while minimizing non-protist DNA representation. We optimized protocols for detecting zoonotic protists in raw sewage samples, with a focus on trichomonad taxa. First, we investigated the utility of two commonly used variable regions of the 18S rRNA marker gene, V4 and V9, by amplifying and Sanger sequencing 23 different eukaryotic species, including 16 protist species such as Cryptosporidium parvum, Giardia intestinalis, Toxoplasma gondii, and species of trichomonad. Next, we optimized wet-lab methods for sample processing and Illumina sequencing of both regions from raw sewage collected from a private apartment building in New York City. Our results show that both regions are effective at identifying several zoonotic protists that may be present in sewage. A combination of small extractions (1 mL volumes) performed on the same day as sample collection, and the incorporation of a vertebrate blocking primer, is ideal to detect protist taxa of interest and combat the effects of metazoan DNA. We expect that the robust, standardized methods presented in our workflow will be applicable to investigations of protists in other environmental samples, and will help facilitate large-scale investigations of protistan diversity.
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Affiliation(s)
- Julia M Maritz
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Krysta H Rogers
- Wildlife Investigations Laboratory, California Department of Fish and Wildlife, Rancho Cordova, CA, 95670, USA
| | - Tara M Rock
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Nicole Liu
- Department of Biological Sciences, University of the Pacific, Stockton, CA, 95211, USA
| | - Susan Joseph
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Kirkwood M Land
- Department of Biological Sciences, University of the Pacific, Stockton, CA, 95211, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.
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Tighe S, Afshinnekoo E, Rock TM, McGrath K, Alexander N, McIntyre A, Ahsanuddin S, Bezdan D, Green SJ, Joye S, Stewart Johnson S, Baldwin DA, Bivens N, Ajami N, Carmical JR, Herriott IC, Colwell R, Donia M, Foox J, Greenfield N, Hunter T, Hoffman J, Hyman J, Jorgensen E, Krawczyk D, Lee J, Levy S, Garcia-Reyero N, Settles M, Thomas K, Gómez F, Schriml L, Kyrpides N, Zaikova E, Penterman J, Mason CE. Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP). J Biomol Tech 2017; 28:31-39. [PMID: 28337070 DOI: 10.7171/jbt.17-2801-004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines. Here, we highlight the different ongoing projects that we have been working on, as well as details on the various methods we use to characterize the microbiome and metagenome of these complex samples. In particular, we present data of a novel multienzyme extraction protocol that we developed, called Polyzyme or MetaPolyZyme. Presently, the XMP is characterizing sample sites around the world with the intent of discovering new species, genes, and gene clusters. Once a project site is complete, the resulting data will be publically available. Sites include Lake Hillier in Western Australia, the "Door to Hell" crater in Turkmenistan, deep ocean brine lakes of the Gulf of Mexico, deep ocean sediments from Greenland, permafrost tunnels in Alaska, ancient microbial biofilms from Antarctica, Blue Lagoon Iceland, Ethiopian toxic hot springs, and the acidic hypersaline ponds in Western Australia.
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Affiliation(s)
- Scott Tighe
- Advanced Genomics Lab, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA; School of Medicine, New York Medical College, Valhalla, New York, USA
| | - Tara M Rock
- Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - Ken McGrath
- Australian Genome Research Facility, Gehrmann Labs, University of Queensland, St Lucia, QLD, Australia
| | - Noah Alexander
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Alexa McIntyre
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Sofia Ahsanuddin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Daniela Bezdan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Stefan J Green
- DNA Services Facility, Research Resources Center, University of Illinois, Chicago, Illinois, USA
| | - Samantha Joye
- Marine Sciences, The University of Georgia, Athens, Georgia, USA
| | | | - Don A Baldwin
- Signal Biology Inc., Philadelphia, Pennsylvania, USA
| | - Nathan Bivens
- DNA Core Facility, University of Missouri, Columbia, Missouri, USA
| | - Nadim Ajami
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Joseph R Carmical
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Ian Charold Herriott
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Rita Colwell
- Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, College Park, Maryland, USA
| | - Mohamed Donia
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA; Department of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | | | - Tim Hunter
- Advanced Genomics Lab, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, USA
| | - Jessica Hoffman
- Advanced Genomics Lab, University of Vermont Cancer Center, University of Vermont, Burlington, Vermont, USA
| | - Joshua Hyman
- UW Biotechnology Center, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | | | - Diana Krawczyk
- Greenland Institute of Natural Resources, Greenland Climate Research Centre, Nuuk, Greenland
| | - Jodie Lee
- Molecular Diagnostics, Qiagen, Germantown, Maryland, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Natàlia Garcia-Reyero
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, US Army Engineer Research & Development Center, Vicksburg, Mississippi, USA
| | - Matthew Settles
- Genome Center, University of California-Davis, Davis, California, USA
| | - Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Felipe Gómez
- Department of Planetology and Habitability, Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir, Torrejon de Ardoz, Madrid, Spain
| | - Lynn Schriml
- Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Nikos Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Elena Zaikova
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Jon Penterman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA; The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York, USA
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Cheng Z, Teo G, Krueger S, Rock TM, Koh HWL, Choi H, Vogel C. Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress. Mol Syst Biol 2016; 12:855. [PMID: 26792871 PMCID: PMC4731011 DOI: 10.15252/msb.20156423] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The relative importance of regulation at the mRNA versus protein level is subject to ongoing debate. To address this question in a dynamic system, we mapped proteomic and transcriptomic changes in mammalian cells responding to stress induced by dithiothreitol over 30 h. Specifically, we estimated the kinetic parameters for the synthesis and degradation of RNA and proteins, and deconvoluted the response patterns into common and unique to each regulatory level using a new statistical tool. Overall, the two regulatory levels were equally important, but differed in their impact on molecule concentrations. Both mRNA and protein changes peaked between two and eight hours, but mRNA expression fold changes were much smaller than those of the proteins. mRNA concentrations shifted in a transient, pulse‐like pattern and returned to values close to pre‐treatment levels by the end of the experiment. In contrast, protein concentrations switched only once and established a new steady state, consistent with the dominant role of protein regulation during misfolding stress. Finally, we generated hypotheses on specific regulatory modes for some genes.
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Affiliation(s)
- Zhe Cheng
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Guoshou Teo
- Saw Swee Hock School of Public Health, National University Singapore, Singapore National University Health System, Singapore
| | - Sabrina Krueger
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Tara M Rock
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Hiromi W L Koh
- Saw Swee Hock School of Public Health, National University Singapore, Singapore National University Health System, Singapore
| | - Hyungwon Choi
- Saw Swee Hock School of Public Health, National University Singapore, Singapore National University Health System, Singapore
| | - Christine Vogel
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
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