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Telzrow CL, Zwack PJ, Esher Righi S, Dietrich FS, Chan C, Owzar K, Alspaugh JA, Granek JA. Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries. G3 (Bethesda) 2021; 11:jkab301. [PMID: 34518880 PMCID: PMC8527493 DOI: 10.1093/g3journal/jkab301] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 08/19/2021] [Indexed: 11/13/2022]
Abstract
RNA sequencing (RNA-Seq) experiments focused on gene expression involve removal of ribosomal RNA (rRNA) because it is the major RNA constituent of cells. This process, called RNA enrichment, is done primarily to reduce cost: without rRNA removal, deeper sequencing must be performed to compensate for the sequencing reads wasted on rRNA. The ideal RNA enrichment method removes all rRNA without affecting other RNA in the sample. We tested the performance of three RNA enrichment methods on RNA isolated from Cryptococcus neoformans, a fungal pathogen of humans. We find that the RNase H depletion method is more efficient in depleting rRNA and more specific in recapitulating non-rRNA levels present in unenriched controls than the commonly-used Poly(A) isolation method. The RNase H depletion method is also more effective than the Ribo-Zero depletion method as measured by rRNA depletion efficiency and recapitulation of protein-coding RNA levels present in unenriched controls, while the Ribo-Zero depletion method more closely recapitulates annotated non-coding RNA (ncRNA) levels. Finally, we leverage these data to accurately map the C. neoformans mitochondrial rRNA genes, and also demonstrate that RNA-Seq data generated with the RNase H and Ribo-Zero depletion methods can be used to explore novel C. neoformans long non-coding RNA genes.
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Affiliation(s)
- Calla L Telzrow
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Paul J Zwack
- Department of Biology, Duke University, Durham, NC 27710, USA
| | - Shannon Esher Righi
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Fred S Dietrich
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Kouros Owzar
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
- Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - J Andrew Alspaugh
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joshua A Granek
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
- Duke Cancer Institute, Duke University, Durham, NC 27710, USA
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Zwack PJ, De Clercq I, Howton TC, Hallmark HT, Hurny A, Keshishian EA, Parish AM, Benkova E, Mukhtar MS, Van Breusegem F, Rashotte AM. Cytokinin Response Factor 6 Represses Cytokinin-Associated Genes during Oxidative Stress. Plant Physiol 2016; 172:1249-1258. [PMID: 27550996 PMCID: PMC5047073 DOI: 10.1104/pp.16.00415] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/18/2016] [Indexed: 05/04/2023]
Abstract
Cytokinin is a phytohormone that is well known for its roles in numerous plant growth and developmental processes, yet it has also been linked to abiotic stress response in a less defined manner. Arabidopsis (Arabidopsis thaliana) Cytokinin Response Factor 6 (CRF6) is a cytokinin-responsive AP2/ERF-family transcription factor that, through the cytokinin signaling pathway, plays a key role in the inhibition of dark-induced senescence. CRF6 expression is also induced by oxidative stress, and here we show a novel function for CRF6 in relation to oxidative stress and identify downstream transcriptional targets of CRF6 that are repressed in response to oxidative stress. Analysis of transcriptomic changes in wild-type and crf6 mutant plants treated with H2O2 identified CRF6-dependent differentially expressed transcripts, many of which were repressed rather than induced. Moreover, many repressed genes also show decreased expression in 35S:CRF6 overexpressing plants. Together, these findings suggest that CRF6 functions largely as a transcriptional repressor. Interestingly, among the H2O2 repressed CRF6-dependent transcripts was a set of five genes associated with cytokinin processes: (signaling) ARR6, ARR9, ARR11, (biosynthesis) LOG7, and (transport) ABCG14. We have examined mutants of these cytokinin-associated target genes to reveal novel connections to oxidative stress. Further examination of CRF6-DNA interactions indicated that CRF6 may regulate its targets both directly and indirectly. Together, this shows that CRF6 functions during oxidative stress as a negative regulator to control this cytokinin-associated module of CRF6-dependent genes and establishes a novel connection between cytokinin and oxidative stress response.
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Affiliation(s)
- Paul J Zwack
- Department of Biological Sciences, Auburn University, Auburn, AL 36849 (P.J.Z., H.T.H., E.A.K., A.M.P., A.M.R.); Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (I.D.C., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium (I.D.C., F.V.B.);Department of Biology, University of Alabama, Birmingham, AL 35294 (T.C.H., M.S.M.); and Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria (A.H., E.B.)
| | - Inge De Clercq
- Department of Biological Sciences, Auburn University, Auburn, AL 36849 (P.J.Z., H.T.H., E.A.K., A.M.P., A.M.R.); Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (I.D.C., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium (I.D.C., F.V.B.);Department of Biology, University of Alabama, Birmingham, AL 35294 (T.C.H., M.S.M.); and Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria (A.H., E.B.)
| | - Timothy C Howton
- Department of Biological Sciences, Auburn University, Auburn, AL 36849 (P.J.Z., H.T.H., E.A.K., A.M.P., A.M.R.); Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (I.D.C., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium (I.D.C., F.V.B.);Department of Biology, University of Alabama, Birmingham, AL 35294 (T.C.H., M.S.M.); and Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria (A.H., E.B.)
| | - H Tucker Hallmark
- Department of Biological Sciences, Auburn University, Auburn, AL 36849 (P.J.Z., H.T.H., E.A.K., A.M.P., A.M.R.); Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (I.D.C., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium (I.D.C., F.V.B.);Department of Biology, University of Alabama, Birmingham, AL 35294 (T.C.H., M.S.M.); and Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria (A.H., E.B.)
| | - Andrej Hurny
- Department of Biological Sciences, Auburn University, Auburn, AL 36849 (P.J.Z., H.T.H., E.A.K., A.M.P., A.M.R.); Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (I.D.C., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium (I.D.C., F.V.B.);Department of Biology, University of Alabama, Birmingham, AL 35294 (T.C.H., M.S.M.); and Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria (A.H., E.B.)
| | - Erika A Keshishian
- Department of Biological Sciences, Auburn University, Auburn, AL 36849 (P.J.Z., H.T.H., E.A.K., A.M.P., A.M.R.); Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (I.D.C., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium (I.D.C., F.V.B.);Department of Biology, University of Alabama, Birmingham, AL 35294 (T.C.H., M.S.M.); and Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria (A.H., E.B.)
| | - Alyssa M Parish
- Department of Biological Sciences, Auburn University, Auburn, AL 36849 (P.J.Z., H.T.H., E.A.K., A.M.P., A.M.R.); Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (I.D.C., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium (I.D.C., F.V.B.);Department of Biology, University of Alabama, Birmingham, AL 35294 (T.C.H., M.S.M.); and Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria (A.H., E.B.)
| | - Eva Benkova
- Department of Biological Sciences, Auburn University, Auburn, AL 36849 (P.J.Z., H.T.H., E.A.K., A.M.P., A.M.R.); Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (I.D.C., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium (I.D.C., F.V.B.);Department of Biology, University of Alabama, Birmingham, AL 35294 (T.C.H., M.S.M.); and Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria (A.H., E.B.)
| | - M Shahid Mukhtar
- Department of Biological Sciences, Auburn University, Auburn, AL 36849 (P.J.Z., H.T.H., E.A.K., A.M.P., A.M.R.); Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (I.D.C., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium (I.D.C., F.V.B.);Department of Biology, University of Alabama, Birmingham, AL 35294 (T.C.H., M.S.M.); and Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria (A.H., E.B.)
| | - Frank Van Breusegem
- Department of Biological Sciences, Auburn University, Auburn, AL 36849 (P.J.Z., H.T.H., E.A.K., A.M.P., A.M.R.); Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (I.D.C., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium (I.D.C., F.V.B.);Department of Biology, University of Alabama, Birmingham, AL 35294 (T.C.H., M.S.M.); and Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria (A.H., E.B.)
| | - Aaron M Rashotte
- Department of Biological Sciences, Auburn University, Auburn, AL 36849 (P.J.Z., H.T.H., E.A.K., A.M.P., A.M.R.); Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (I.D.C., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium (I.D.C., F.V.B.);Department of Biology, University of Alabama, Birmingham, AL 35294 (T.C.H., M.S.M.); and Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria (A.H., E.B.)
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