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Islam MK, Mummadi ST, Liu S, Wei H. Regulation of regeneration in Arabidopsis thaliana. ABIOTECH 2023; 4:332-351. [PMID: 38106435 PMCID: PMC10721781 DOI: 10.1007/s42994-023-00121-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/06/2023] [Indexed: 12/19/2023]
Abstract
We employed several algorithms with high efficacy to analyze the public transcriptomic data, aiming to identify key transcription factors (TFs) that regulate regeneration in Arabidopsis thaliana. Initially, we utilized CollaborativeNet, also known as TF-Cluster, to construct a collaborative network of all TFs, which was subsequently decomposed into many subnetworks using the Triple-Link and Compound Spring Embedder (CoSE) algorithms. Functional analysis of these subnetworks led to the identification of nine subnetworks closely associated with regeneration. We further applied principal component analysis and gene ontology (GO) enrichment analysis to reduce the subnetworks from nine to three, namely subnetworks 1, 12, and 17. Searching for TF-binding sites in the promoters of the co-expressed and co-regulated (CCGs) genes of all TFs in these three subnetworks and Triple-Gene Mutual Interaction analysis of TFs in these three subnetworks with the CCGs involved in regeneration enabled us to rank the TFs in each subnetwork. Finally, six potential candidate TFs-WOX9A, LEC2, PGA37, WIP5, PEI1, and AIL1 from subnetwork 1-were identified, and their roles in somatic embryogenesis (GO:0010262) and regeneration (GO:0031099) were discussed, so were the TFs in Subnetwork 12 and 17 associated with regeneration. The TFs identified were also assessed using the CIS-BP database and Expression Atlas. Our analyses suggest some novel TFs that may have regulatory roles in regeneration and embryogenesis and provide valuable data and insights into the regulatory mechanisms related to regeneration. The tools and the procedures used here are instrumental for analyzing high-throughput transcriptomic data and advancing our understanding of the regulation of various biological processes of interest. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-023-00121-9.
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Affiliation(s)
- Md Khairul Islam
- Computational Science and Engineering Program, Michigan Technological University, Houghton, MI 49931 USA
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931 USA
| | - Sai Teja Mummadi
- Computer Science, Michigan Technological University, Houghton, MI 49931 USA
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Hairong Wei
- Computational Science and Engineering Program, Michigan Technological University, Houghton, MI 49931 USA
- Computer Science, Michigan Technological University, Houghton, MI 49931 USA
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931 USA
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2
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Liu J, Huang T, Yao J, Zhao T, Zhang Y, Zhang R. Epitranscriptomic subtyping, visualization, and denoising by global motif visualization. Nat Commun 2023; 14:5944. [PMID: 37741827 PMCID: PMC10517956 DOI: 10.1038/s41467-023-41653-4] [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: 01/01/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023] Open
Abstract
Advances in sequencing technologies have empowered epitranscriptomic profiling at the single-base resolution. Putative RNA modification sites identified from a single high-throughput experiment may contain one type of modification deposited by different writers or different types of modifications, along with false positive results because of the challenge of distinguishing signals from noise. However, current tools are insufficient for subtyping, visualization, and denoising these signals. Here, we present iMVP, which is an interactive framework for epitranscriptomic analysis with a nonlinear dimension reduction technique and density-based partition. As exemplified by the analysis of mRNA m5C and ModTect variant data, we show that iMVP allows the identification of previously unknown RNA modification motifs and writers and the discovery of false positives that are undetectable by traditional methods. Using putative m6A/m6Am sites called from 8 profiling approaches, we illustrate that iMVP enables comprehensive comparison of different approaches and advances our understanding of the difference and pattern of true positives and artifacts in these methods. Finally, we demonstrate the ability of iMVP to analyze an extremely large human A-to-I editing dataset that was previously unmanageable. Our work provides a general framework for the visualization and interpretation of epitranscriptomic data.
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Affiliation(s)
- Jianheng Liu
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China.
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA.
| | - Tao Huang
- Department of Pathology and Pathophysiology, Shantou University Medical College, Shantou, 515041, P. R. China
| | - Jing Yao
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Tianxuan Zhao
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Yusen Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Rui Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China.
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3
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Evolutionary conservation of maternal RNA localization in fishes and amphibians revealed by TOMO-Seq. Dev Biol 2022; 489:146-160. [PMID: 35752299 DOI: 10.1016/j.ydbio.2022.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/18/2022] [Accepted: 06/19/2022] [Indexed: 11/24/2022]
Abstract
Asymmetrical localization of biomolecules inside the egg, results in uneven cell division and establishment of many biological processes, cell types and the body plan. However, our knowledge about evolutionary conservation of localized transcripts is still limited to a few models. Our goal was to compare localization profiles along the animal-vegetal axis of mature eggs from four vertebrate models, two amphibians (Xenopus laevis, Ambystoma mexicanum) and two fishes (Acipenser ruthenus, Danio rerio) using the spatial expression method called TOMO-Seq. We revealed that RNAs of many known important transcripts such as germ layer determinants, germ plasm factors and members of key signalling pathways, are localized in completely different profiles among the models. It was also observed that there was a poor correlation between the vegetally localized transcripts but a relatively good correlation between the animally localized transcripts. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model.
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Kyung J, Jeon M, Jeong G, Shin Y, Seo E, Yu J, Kim H, Park CM, Hwang D, Lee I. The two clock proteins CCA1 and LHY activate VIN3 transcription during vernalization through the vernalization-responsive cis-element. THE PLANT CELL 2022; 34:1020-1037. [PMID: 34931682 PMCID: PMC8894950 DOI: 10.1093/plcell/koab304] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 11/22/2021] [Indexed: 05/20/2023]
Abstract
Vernalization, a long-term cold-mediated acquisition of flowering competence, is critically regulated by VERNALIZATION INSENSITIVE 3 (VIN3), a gene induced by vernalization in Arabidopsis. Although the function of VIN3 has been extensively studied, how VIN3 expression itself is upregulated by long-term cold is not well understood. In this study, we identified a vernalization-responsive cis-element in the VIN3 promoter, VREVIN3, composed of a G-box and an evening element (EE). Mutations in either the G-box or the EE prevented VIN3 expression from being fully induced upon vernalization, leading to defects in the vernalization response. We determined that the core clock proteins CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) and LATE-ELONGATED HYPOCOTYL (LHY) associate with the EE of VREVIN3, both in vitro and in vivo. In a cca1 lhy double mutant background harboring a functional FRIGIDA allele, long-term cold-mediated VIN3 induction and acceleration of flowering were impaired, especially under mild cold conditions such as at 12°C. During prolonged cold exposure, oscillations of CCA1/LHY transcripts were altered, while CCA1 abundance increased at dusk, coinciding with the diurnal peak of VIN3 transcripts. We propose that modulation of the clock proteins CCA1 and LHY participates in the systems involved in sensing long-term cold for the activation of VIN3 transcription.
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Affiliation(s)
- Jinseul Kyung
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Myeongjune Jeon
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Goowon Jeong
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Yourae Shin
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Eunjoo Seo
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jihyeon Yu
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hoyeun Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Daehee Hwang
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Ilha Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul 08826, Korea
- Author for correspondence:
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de Medeiros Oliveira M, Bonadio I, Lie de Melo A, Mendes Souza G, Durham AM. TSSFinder-fast and accurate ab initio prediction of the core promoter in eukaryotic genomes. Brief Bioinform 2021; 22:bbab198. [PMID: 34050351 PMCID: PMC8574697 DOI: 10.1093/bib/bbab198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/14/2021] [Accepted: 02/23/2021] [Indexed: 12/02/2022] Open
Abstract
Promoter annotation is an important task in the analysis of a genome. One of the main challenges for this task is locating the border between the promoter region and the transcribing region of the gene, the transcription start site (TSS). The TSS is the reference point to delimit the DNA sequence responsible for the assembly of the transcribing complex. As the same gene can have more than one TSS, so to delimit the promoter region, it is important to locate the closest TSS to the site of the beginning of the translation. This paper presents TSSFinder, a new software for the prediction of the TSS signal of eukaryotic genes that is significantly more accurate than other available software. We currently are the only application to offer pre-trained models for six different eukaryotic organisms: Arabidopsis thaliana, Drosophila melanogaster, Gallus gallus, Homo sapiens, Oryza sativa and Saccharomyces cerevisiae. Additionally, our software can be easily customized for specific organisms using only 125 DNA sequences with a validated TSS signal and corresponding genomic locations as a training set. TSSFinder is a valuable new tool for the annotation of genomes. TSSFinder source code and docker container can be downloaded from http://tssfinder.github.io. Alternatively, TSSFinder is also available as a web service at http://sucest-fun.org/wsapp/tssfinder/.
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Affiliation(s)
| | - Igor Bonadio
- Data Science, Elo7 Research Lab, São Paulo, Brazil
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Menzel M, Hurka S, Glasenhardt S, Gogol-Döring A. NoPeak: k-mer-based motif discovery in ChIP-Seq data without peak calling. Bioinformatics 2021; 37:596-602. [PMID: 32991679 DOI: 10.1093/bioinformatics/btaa845] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 09/14/2020] [Indexed: 01/30/2023] Open
Abstract
MOTIVATION The discovery of sequence motifs mediating DNA-protein binding usually implies the determination of binding sites using high-throughput sequencing and peak calling. The determination of peaks, however, depends strongly on data quality and is susceptible to noise. RESULTS Here, we present a novel approach to reliably identify transcription factor-binding motifs from ChIP-Seq data without peak detection. By evaluating the distributions of sequencing reads around the different k-mers in the genome, we are able to identify binding motifs in ChIP-Seq data that yield no results in traditional pipelines. AVAILABILITY AND IMPLEMENTATION NoPeak is published under the GNU General Public License and available as a standalone console-based Java application at https://github.com/menzel/nopeak. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Michael Menzel
- MNI, Technische Hochschule Mittelhessen, University of Applied Sciences, Giessen 35390, Germany
| | - Sabine Hurka
- Institute for Insect Biotechnology, Justus Liebig University, Giessen 35392, Germany
| | - Stefan Glasenhardt
- MNI, Technische Hochschule Mittelhessen, University of Applied Sciences, Giessen 35390, Germany
| | - Andreas Gogol-Döring
- MNI, Technische Hochschule Mittelhessen, University of Applied Sciences, Giessen 35390, Germany
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Luján MA, Soria-García Á, Claver A, Lorente P, Rubio MC, Picorel R, Alfonso M. Different Cis-Regulatory Elements Control the Tissue-Specific Contribution of Plastid ω-3 Desaturases to Wounding and Hormone Responses. FRONTIERS IN PLANT SCIENCE 2021; 12:727292. [PMID: 34777414 PMCID: PMC8578140 DOI: 10.3389/fpls.2021.727292] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/04/2021] [Indexed: 05/13/2023]
Abstract
Trienoic fatty acids are essential constituents of biomembranes and precursors of jasmonates involved in plant defense responses. Two ω-3 desaturases, AtFAD7 and AtFAD8, synthetize trienoic fatty acids in the plastid. Promoter:GUS and mutagenesis analysis was used to identify cis-elements controlling AtFAD7 and AtFAD8 basal expression and their response to hormones or wounding. AtFAD7 promoter GUS activity was much higher than that of AtFAD8 in leaves, with specific AtFAD7 expression in the flower stamen and pistil and root meristem and vasculature. This specific tissue and organ expression of AtFAD7 was controlled by different cis-elements. Thus, promoter deletion and mutagenesis analysis indicated that WRKY proteins might be essential for basal expression of AtFAD7 in leaves. Two MYB target sequences present in the AtFAD7 promoter might be responsible for its expression in the flower stamen and stigma of the pistil and in the root meristem, and for the AtFAD7 wound-specific response. Two MYB target sequences detected in the distal region of the AtFAD8 gene promoter seemed to negatively control AtFAD8 expression, particularly in true leaves and flowers, suggesting that MYB transcription factors act as repressors of AtFAD8 gene basal expression, modulating the different relative abundance of both plastid ω-3 desaturases at the transcriptional level. Our data showed that the two ABA repression sequences detected in the AtFAD7 promoter were functional, suggesting an ABA-dependent mechanism involved in the different regulation of both ω-3 plastid desaturases. These results reveal the implication of different signaling pathways for the concerted regulation of trienoic fatty acid content in Arabidopsis.
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Diniz AL, da Silva DIR, Lembke CG, Costa MDBL, ten-Caten F, Li F, Vilela RD, Menossi M, Ware D, Endres L, Souza GM. Amino Acid and Carbohydrate Metabolism Are Coordinated to Maintain Energetic Balance during Drought in Sugarcane. Int J Mol Sci 2020; 21:ijms21239124. [PMID: 33266228 PMCID: PMC7729667 DOI: 10.3390/ijms21239124] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 01/10/2023] Open
Abstract
The ability to expand crop plantations without irrigation is a major goal to increase agriculture sustainability. To achieve this end, we need to understand the mechanisms that govern plant growth responses under drought conditions. In this study, we combined physiological, transcriptomic, and genomic data to provide a comprehensive picture of drought and recovery responses in the leaves and roots of sugarcane. Transcriptomic profiling using oligoarrays and RNA-seq identified 2898 (out of 21,902) and 46,062 (out of 373,869) transcripts as differentially expressed, respectively. Co-expression analysis revealed modules enriched in photosynthesis, small molecule metabolism, alpha-amino acid metabolism, trehalose biosynthesis, serine family amino acid metabolism, and carbohydrate transport. Together, our findings reveal that carbohydrate metabolism is coordinated with the degradation of amino acids to provide carbon skeletons to the tricarboxylic acid cycle. This coordination may help to maintain energetic balance during drought stress adaptation, facilitating recovery after the stress is alleviated. Our results shed light on candidate regulatory elements and pave the way to biotechnology strategies towards the development of drought-tolerant sugarcane plants.
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Affiliation(s)
- Augusto Lima Diniz
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
| | - Danielle Izilda Rodrigues da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
- Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA
- Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Carolina Gimiliani Lembke
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
| | - Maximiller Dal-Bianco Lamas Costa
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Felipe ten-Caten
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
| | - Forrest Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; (F.L.); (D.W.)
| | - Romel Duarte Vilela
- Centro de Ciências Agrárias, Universidade Federal de Alagoas, Rio Largo, AL 57100-000, Brazil; (R.D.V.); (L.E.)
| | - Marcelo Menossi
- Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP 13083-862, Brazil;
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; (F.L.); (D.W.)
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Lauricio Endres
- Centro de Ciências Agrárias, Universidade Federal de Alagoas, Rio Largo, AL 57100-000, Brazil; (R.D.V.); (L.E.)
| | - Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
- Correspondence:
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10
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Souza GM, Van Sluys MA, Lembke CG, Lee H, Margarido GRA, Hotta CT, Gaiarsa JW, Diniz AL, Oliveira MDM, Ferreira SDS, Nishiyama MY, ten-Caten F, Ragagnin GT, Andrade PDM, de Souza RF, Nicastro GG, Pandya R, Kim C, Guo H, Durham AM, Carneiro MS, Zhang J, Zhang X, Zhang Q, Ming R, Schatz MC, Davidson B, Paterson AH, Heckerman D. Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. Gigascience 2019; 8:giz129. [PMID: 31782791 PMCID: PMC6884061 DOI: 10.1093/gigascience/giz129] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 05/23/2019] [Accepted: 10/08/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10-13 sets of chromosomes from 2 Saccharum species. The ploidy, hybridity, and size of the genome, estimated to have >10 Gb, pose a challenge for sequencing. RESULTS Here we present a gene space assembly of SP80-3280, including 373,869 putative genes and their potential regulatory regions. The alignment of single-copy genes in diploid grasses to the putative genes indicates that we could resolve 2-6 (up to 15) putative homo(eo)logs that are 99.1% identical within their coding sequences. Dissimilarities increase in their regulatory regions, and gene promoter analysis shows differences in regulatory elements within gene families that are expressed in a species-specific manner. We exemplify these differences for sucrose synthase (SuSy) and phenylalanine ammonia-lyase (PAL), 2 gene families central to carbon partitioning. SP80-3280 has particular regulatory elements involved in sucrose synthesis not found in the ancestor Saccharum spontaneum. PAL regulatory elements are found in co-expressed genes related to fiber synthesis within gene networks defined during plant growth and maturation. Comparison with sorghum reveals predominantly bi-allelic variations in sugarcane, consistent with the formation of 2 "subgenomes" after their divergence ∼3.8-4.6 million years ago and reveals single-nucleotide variants that may underlie their differences. CONCLUSIONS This assembly represents a large step towards a whole-genome assembly of a commercial sugarcane cultivar. It includes a rich diversity of genes and homo(eo)logous resolution for a representative fraction of the gene space, relevant to improve biomass and food production.
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Affiliation(s)
- Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
| | - Carolina Gimiliani Lembke
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Hayan Lee
- Cold Spring Harbor Laboratory, One Bungtown Road, Koch Building #1119, Cold Spring Harbor, NY11724, United States of America
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CACA94598, United States of America
| | - Gabriel Rodrigues Alves Margarido
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias, 11, Piracicaba, SP 13418-900, Brazil
| | - Carlos Takeshi Hotta
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Jonas Weissmann Gaiarsa
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
| | - Augusto Lima Diniz
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Mauro de Medeiros Oliveira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Sávio de Siqueira Ferreira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
| | - Milton Yutaka Nishiyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, Av. Vital Brasil, 1500, São Paulo, SP05503-900, Brazil
| | - Felipe ten-Caten
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Geovani Tolfo Ragagnin
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, São Paulo, SP 05508-090, Brazil
| | - Pablo de Morais Andrade
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, SP 05508-000, Brazil
| | - Robson Francisco de Souza
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av.Professor Lineu Prestes, 1734, São Paulo, SP 05508-900, Brazil
| | - Gianlucca Gonçalves Nicastro
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av.Professor Lineu Prestes, 1734, São Paulo, SP 05508-900, Brazil
| | - Ravi Pandya
- Microsoft Research, One Microsoft Way, Redmond, WA 98052, United States of America
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, 120 Green Street, Athens, GA 30602-7223,United States of America
- Department of Crop Science, Chungnam National University, 99 Daehak Ro Yuseong Gu, Deajeon,34134, South Korea
| | - Hui Guo
- Plant Genome Mapping Laboratory, University of Georgia, 120 Green Street, Athens, GA 30602-7223,United States of America
| | - Alan Mitchell Durham
- Departamento de Ciências da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo, Rua do Matão, 1010, São Paulo, SP 05508-090, Brazil
| | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Rodovia Washington Luis km 235, Araras, SP 13.565-905, Brazil
| | - Jisen Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
| | - Xingtan Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
| | - Qing Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Shangxiadian Road, Fuzhou 350002, Fujian, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 201 W. Gregory Dr. Urbana, Urbana, Illinois 61801, United States of America
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, One Bungtown Road, Koch Building #1119, Cold Spring Harbor, NY11724, United States of America
- Departments of Computer Science and Biology, Johns Hopkins University, 3400 North Charles Street,Baltimore, MD 21218-2608, United States of America
| | - Bob Davidson
- Microsoft Research, One Microsoft Way, Redmond, WA 98052, United States of America
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, 120 Green Street, Athens, GA 30602-7223,United States of America
| | - David Heckerman
- Microsoft Research, One Microsoft Way, Redmond, WA 98052, United States of America
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11
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Mijnendonckx K, Ali MM, Provoost A, Janssen P, Mergeay M, Leys N, Charlier D, Monsieurs P, Van Houdt R. Spontaneous mutation in the AgrRS two-component regulatory system ofCupriavidus metalliduransresults in enhanced silver resistance. Metallomics 2019; 11:1912-1924. [DOI: 10.1039/c9mt00123a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cupriavidus metalliduransis able to adapt to toxic silver concentrations and previously uncharacterized periplasmic proteins played a crucial role in this adaptation process.
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Affiliation(s)
| | - Md Muntasir Ali
- Unit of Microbiology
- Belgian Nuclear Research Centre SCK·CEN
- 2400 Mol
- Belgium
- Research Group of Microbiology
| | - Ann Provoost
- Unit of Microbiology
- Belgian Nuclear Research Centre SCK·CEN
- 2400 Mol
- Belgium
| | - Paul Janssen
- Unit of Microbiology
- Belgian Nuclear Research Centre SCK·CEN
- 2400 Mol
- Belgium
| | - Max Mergeay
- Unit of Microbiology
- Belgian Nuclear Research Centre SCK·CEN
- 2400 Mol
- Belgium
| | - Natalie Leys
- Unit of Microbiology
- Belgian Nuclear Research Centre SCK·CEN
- 2400 Mol
- Belgium
| | - Daniël Charlier
- Research Group of Microbiology
- Department of Bioengineering Sciences
- Vrije Universiteit Brussel
- B-1050 Brussel
- Belgium
| | - Pieter Monsieurs
- Unit of Microbiology
- Belgian Nuclear Research Centre SCK·CEN
- 2400 Mol
- Belgium
| | - Rob Van Houdt
- Unit of Microbiology
- Belgian Nuclear Research Centre SCK·CEN
- 2400 Mol
- Belgium
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12
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Gan KA, Carrasco Pro S, Sewell JA, Fuxman Bass JI. Identification of Single Nucleotide Non-coding Driver Mutations in Cancer. Front Genet 2018; 9:16. [PMID: 29456552 PMCID: PMC5801294 DOI: 10.3389/fgene.2018.00016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/12/2018] [Indexed: 12/14/2022] Open
Abstract
Recent whole-genome sequencing studies have identified millions of somatic variants present in tumor samples. Most of these variants reside in non-coding regions of the genome potentially affecting transcriptional and post-transcriptional gene regulation. Although a few hallmark examples of driver mutations in non-coding regions have been reported, the functional role of the vast majority of somatic non-coding variants remains to be determined. This is because the few driver variants in each sample must be distinguished from the thousands of passenger variants and because the logic of regulatory element function has not yet been fully elucidated. Thus, variants prioritized based on mutational burden and location within regulatory elements need to be validated experimentally. This is generally achieved by combining assays that measure physical binding, such as chromatin immunoprecipitation, with those that determine regulatory activity, such as luciferase reporter assays. Here, we present an overview of in silico approaches used to prioritize somatic non-coding variants and the experimental methods used for functional validation and characterization.
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Affiliation(s)
- Kok A Gan
- Department of Biology, Boston University, Boston, MA, United States
| | | | - Jared A Sewell
- Department of Biology, Boston University, Boston, MA, United States
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13
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Nakaoka H, Gurumurthy A, Hayano T, Ahmadloo S, Omer WH, Yoshihara K, Yamamoto A, Kurose K, Enomoto T, Akira S, Hosomichi K, Inoue I. Allelic Imbalance in Regulation of ANRIL through Chromatin Interaction at 9p21 Endometriosis Risk Locus. PLoS Genet 2016; 12:e1005893. [PMID: 27055116 PMCID: PMC4824487 DOI: 10.1371/journal.pgen.1005893] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 02/02/2016] [Indexed: 12/19/2022] Open
Abstract
Genome-wide association studies (GWASs) have discovered numerous single nucleotide polymorphisms (SNPs) associated with human complex disorders. However, functional characterization of the disease-associated SNPs remains a formidable challenge. Here we explored regulatory mechanism of a SNP on chromosome 9p21 associated with endometriosis by leveraging “allele-specific” functional genomic approaches. By re-sequencing 1.29 Mb of 9p21 region and scrutinizing DNase-seq data from the ENCODE project, we prioritized rs17761446 as a candidate functional variant that was in perfect linkage disequilibrium with the original GWAS SNP (rs10965235) and located on DNase I hypersensitive site. Chromosome conformation capture followed by high-throughput sequencing revealed that the protective G allele of rs17761446 exerted stronger chromatin interaction with ANRIL promoter. We demonstrated that the protective allele exhibited preferential binding affinities to TCF7L2 and EP300 by bioinformatics and chromatin immunoprecipitation (ChIP) analyses. ChIP assays for histone H3 lysine 27 acetylation and RNA polymerase II reinforced the enhancer activity of the SNP site. The allele specific expression analysis for eutopic endometrial tissues and endometrial carcinoma cell lines showed that rs17761446 was a cis-regulatory variant where G allele was associated with increased ANRIL expression. Our work illuminates the allelic imbalances in a series of transcriptional regulation from factor binding to gene expression mediated by chromatin interaction underlie the molecular mechanism of 9p21 endometriosis risk locus. Functional genomics on common disease will unlock functional aspect of genotype-phenotype correlations in the post-GWAS stage. A large number of variants associated with human complex diseases have been discovered by genome-wide association studies (GWASs). These discoveries have been anticipated to be translated into the definitive understanding of disease pathogeneses; however, functional characterization of the disease-associated SNPs remains a formidable challenge. Here we explored regulatory mechanism of a variant on chromosome 9p21 associated with endometriosis, a common gynecological disorder. By scrutinizing linkage disequilibrium structure and DNase I hypersensitive sites across the risk locus, we prioritized rs17761446 as a candidate causal variant. The results of our “allele-specific” functional genomic approaches sheds light on regulatory mechanisms underlying 9p21 endometriosis risk locus, in which preferential bindings of TCF7L2 and its coactivator EP300 to the protective G allele of rs17761446 lead to stronger chromatin interaction with the promoter of ANRIL, which in turn activate transcription of the non-coding RNA. Motivated by the fact that TCF7L2 was a key transcription factor of Wnt signaling pathway, we postulated that the induction of Wnt signaling activated expression levels of ANRIL and cell cycle inhibitors, CDKN2A/2B. Functional genomics on common disease will unlock functional aspect of genotype-phenotype correlations in the post-GWAS stage.
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Affiliation(s)
- Hirofumi Nakaoka
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Aishwarya Gurumurthy
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Takahide Hayano
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Somayeh Ahmadloo
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Waleed H Omer
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Akihito Yamamoto
- Department of Obstetrics and Gynecology, Nippon Medical School, Bunkyo-ku, Tokyo, Japan
| | - Keisuke Kurose
- Department of Obstetrics and Gynecology, Nippon Medical School, Bunkyo-ku, Tokyo, Japan
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Shigeo Akira
- Department of Obstetrics and Gynecology, Nippon Medical School, Bunkyo-ku, Tokyo, Japan
| | - Kazuyoshi Hosomichi
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Ituro Inoue
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
- * E-mail:
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14
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Grassi E, Zapparoli E, Molineris I, Provero P. Total Binding Affinity Profiles of Regulatory Regions Predict Transcription Factor Binding and Gene Expression in Human Cells. PLoS One 2015; 10:e0143627. [PMID: 26599758 PMCID: PMC4658012 DOI: 10.1371/journal.pone.0143627] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 11/07/2015] [Indexed: 11/29/2022] Open
Abstract
Transcription factors regulate gene expression by binding regulatory DNA. Understanding the rules governing such binding is an essential step in describing the network of regulatory interactions, and its pathological alterations. We show that describing regulatory regions in terms of their profile of total binding affinities for transcription factors leads to increased predictive power compared to methods based on the identification of discrete binding sites. This applies both to the prediction of transcription factor binding as revealed by ChIP-seq experiments and to the prediction of gene expression through RNA-seq. Further significant improvements in predictive power are obtained when regulatory regions are defined based on chromatin states inferred from histone modification data.
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Affiliation(s)
- Elena Grassi
- Dept. of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Ettore Zapparoli
- Dept. of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Ivan Molineris
- Dept. of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Paolo Provero
- Dept. of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
- Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy
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15
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Hogan GJ, Brown PO, Herschlag D. Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets. PLoS Biol 2015; 13:e1002307. [PMID: 26587879 PMCID: PMC4654594 DOI: 10.1371/journal.pbio.1002307] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 10/23/2015] [Indexed: 12/31/2022] Open
Abstract
Reprogramming of a gene’s expression pattern by acquisition and loss of sequences recognized by specific regulatory RNA binding proteins may be a major mechanism in the evolution of biological regulatory programs. We identified that RNA targets of Puf3 orthologs have been conserved over 100–500 million years of evolution in five eukaryotic lineages. Focusing on Puf proteins and their targets across 80 fungi, we constructed a parsimonious model for their evolutionary history. This model entails extensive and coordinated changes in the Puf targets as well as changes in the number of Puf genes and alterations of RNA binding specificity including that: 1) Binding of Puf3 to more than 200 RNAs whose protein products are predominantly involved in the production and organization of mitochondrial complexes predates the origin of budding yeasts and filamentous fungi and was maintained for 500 million years, throughout the evolution of budding yeast. 2) In filamentous fungi, remarkably, more than 150 of the ancestral Puf3 targets were gained by Puf4, with one lineage maintaining both Puf3 and Puf4 as regulators and a sister lineage losing Puf3 as a regulator of these RNAs. The decrease in gene expression of these mRNAs upon deletion of Puf4 in filamentous fungi (N. crassa) in contrast to the increase upon Puf3 deletion in budding yeast (S. cerevisiae) suggests that the output of the RNA regulatory network is different with Puf4 in filamentous fungi than with Puf3 in budding yeast. 3) The coregulated Puf4 target set in filamentous fungi expanded to include mitochondrial genes involved in the tricarboxylic acid (TCA) cycle and other nuclear-encoded RNAs with mitochondrial function not bound by Puf3 in budding yeast, observations that provide additional evidence for substantial rewiring of post-transcriptional regulation. 4) Puf3 also expanded and diversified its targets in filamentous fungi, gaining interactions with the mRNAs encoding the mitochondrial electron transport chain (ETC) complex I as well as hundreds of other mRNAs with nonmitochondrial functions. The many concerted and conserved changes in the RNA targets of Puf proteins strongly support an extensive role of RNA binding proteins in coordinating gene expression, as originally proposed by Keene. Rewiring of Puf-coordinated mRNA targets and transcriptional control of the same genes occurred at different points in evolution, suggesting that there have been distinct adaptations via RNA binding proteins and transcription factors. The changes in Puf targets and in the Puf proteins indicate an integral involvement of RNA binding proteins and their RNA targets in the adaptation, reprogramming, and function of gene expression. A map of the evolutionary history of Puf proteins and their RNA targets shows that reprogramming of global gene expression programs via adaptive mutations that affect protein-RNA interactions is an important source of biological diversity. We set out to trace the evolutionary history of an RNA binding protein and how its interactions with targets change over evolution. Identifying this natural history is a step toward understanding the critical differences between organisms and how gene expression programs are rewired during evolution. Using bioinformatics and experimental approaches, we broadly surveyed the evolution of binding targets of a particular family of RNA binding proteins—the Puf proteins, whose protein sequences and target RNA sequences are relatively well-characterized—across 99 eukaryotic species. We found five groups of species in which targets have been conserved for at least 100 million years and then took advantage of genome sequences from a large number of fungal species to deeply investigate the conservation and changes in Puf proteins and their RNA targets. Our analyses identified multiple and extensive reconfigurations during the natural history of fungi and suggest that RNA binding proteins and their RNA targets are profoundly involved in evolutionary reprogramming of gene expression and help define distinct programs unique to each organism. Continuing to uncover the natural history of RNA binding proteins and their interactions will provide a unique window into the gene expression programs of present day species and point to new ways to engineer gene expression programs.
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Affiliation(s)
- Gregory J. Hogan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Patrick O. Brown
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (POB); (DH)
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Chemistry, Stanford University, Stanford, California, United States of America
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
- ChEM-H Institute, Stanford University, Stanford, California, United States of America
- * E-mail: (POB); (DH)
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16
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Harr JC, Luperchio TR, Wong X, Cohen E, Wheelan SJ, Reddy KL. Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins. ACTA ACUST UNITED AC 2015; 208:33-52. [PMID: 25559185 PMCID: PMC4284222 DOI: 10.1083/jcb.201405110] [Citation(s) in RCA: 211] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nuclear organization has been implicated in regulating gene activity. Recently, large developmentally regulated regions of the genome dynamically associated with the nuclear lamina have been identified. However, little is known about how these lamina-associated domains (LADs) are directed to the nuclear lamina. We use our tagged chromosomal insertion site system to identify small sequences from borders of fibroblast-specific variable LADs that are sufficient to target these ectopic sites to the nuclear periphery. We identify YY1 (Ying-Yang1) binding sites as enriched in relocating sequences. Knockdown of YY1 or lamin A/C, but not lamin A, led to a loss of lamina association. In addition, targeted recruitment of YY1 proteins facilitated ectopic LAD formation dependent on histone H3 lysine 27 trimethylation and histone H3 lysine di- and trimethylation. Our results also reveal that endogenous loci appear to be dependent on lamin A/C, YY1, H3K27me3, and H3K9me2/3 for maintenance of lamina-proximal positioning.
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Affiliation(s)
- Jennifer C Harr
- Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205 Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205
| | - Teresa Romeo Luperchio
- Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205 Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205
| | - Xianrong Wong
- Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205 Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205
| | - Erez Cohen
- Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205 Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205
| | - Sarah J Wheelan
- Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205
| | - Karen L Reddy
- Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205 Department of Biological Chemistry, Center for Epigenetics, and Department of Oncology Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21205
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17
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Balazadeh S, Schildhauer J, Araújo WL, Munné-Bosch S, Fernie AR, Proost S, Humbeck K, Mueller-Roeber B. Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: transcriptomic and metabolomic consequences. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:3975-92. [PMID: 24692653 PMCID: PMC4106441 DOI: 10.1093/jxb/eru119] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Leaf senescence is a developmentally controlled process, which is additionally modulated by a number of adverse environmental conditions. Nitrogen shortage is a well-known trigger of precocious senescence in many plant species including crops, generally limiting biomass and seed yield. However, leaf senescence induced by nitrogen starvation may be reversed when nitrogen is resupplied at the onset of senescence. Here, the transcriptomic, hormonal, and global metabolic rearrangements occurring during nitrogen resupply-induced reversal of senescence in Arabidopsis thaliana were analysed. The changes induced by senescence were essentially in keeping with those previously described; however, these could, by and large, be reversed. The data thus indicate that plants undergoing senescence retain the capacity to sense and respond to the availability of nitrogen nutrition. The combined data are discussed in the context of the reversibility of the senescence programme and the evolutionary benefit afforded thereby. Future prospects for understanding and manipulating this process in both Arabidopsis and crop plants are postulated.
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Affiliation(s)
- Salma Balazadeh
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, D-14476 Potsdam-Golm, Germany Max-Planck Institute of Molecular Plant Physiology, Plant Signalling Group, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Jörg Schildhauer
- Martin-Luther-University Halle-Wittenberg, Institute of Biology, Weinbergweg 10, D-06120 Halle, Germany
| | - Wagner L Araújo
- Max-Planck Institute of Molecular Plant Physiology, Central Metabolism Group, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-000 Viçosa, MG, Brasil
| | - Sergi Munné-Bosch
- Departament de Biologia Vegetal, Universitat de Barcelona, Facultat de Biologia, 08028 Barcelona, Spain
| | - Alisdair R Fernie
- Max-Planck Institute of Molecular Plant Physiology, Central Metabolism Group, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Sebastian Proost
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, D-14476 Potsdam-Golm, Germany Max-Planck Institute of Molecular Plant Physiology, Plant Signalling Group, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Klaus Humbeck
- Martin-Luther-University Halle-Wittenberg, Institute of Biology, Weinbergweg 10, D-06120 Halle, Germany
| | - Bernd Mueller-Roeber
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, D-14476 Potsdam-Golm, Germany Max-Planck Institute of Molecular Plant Physiology, Plant Signalling Group, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany
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18
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Biswas A, Brown CM. Scan for Motifs: a webserver for the analysis of post-transcriptional regulatory elements in the 3' untranslated regions (3' UTRs) of mRNAs. BMC Bioinformatics 2014; 15:174. [PMID: 24909639 PMCID: PMC4067372 DOI: 10.1186/1471-2105-15-174] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/16/2014] [Indexed: 11/21/2022] Open
Abstract
Background Gene expression in vertebrate cells may be controlled post-transcriptionally through regulatory elements in mRNAs. These are usually located in the untranslated regions (UTRs) of mRNA sequences, particularly the 3′UTRs. Results Scan for Motifs (SFM) simplifies the process of identifying a wide range of regulatory elements on alignments of vertebrate 3′UTRs. SFM includes identification of both RNA Binding Protein (RBP) sites and targets of miRNAs. In addition to searching pre-computed alignments, the tool provides users the flexibility to search their own sequences or alignments. The regulatory elements may be filtered by expected value cutoffs and are cross-referenced back to their respective sources and literature. The output is an interactive graphical representation, highlighting potential regulatory elements and overlaps between them. The output also provides simple statistics and links to related resources for complementary analyses. The overall process is intuitive and fast. As SFM is a free web-application, the user does not need to install any software or databases. Conclusions Visualisation of the binding sites of different classes of effectors that bind to 3′UTRs will facilitate the study of regulatory elements in 3′ UTRs.
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Affiliation(s)
| | - Chris M Brown
- Department of Biochemistry, Genetics Otago, University of Otago, Dunedin, New Zealand.
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