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Moyung K, Li Y, Hartemink AJ, MacAlpine DM. Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595391. [PMID: 38826400 PMCID: PMC11142231 DOI: 10.1101/2024.05.24.595391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Epigenetic mechanisms contribute to gene regulation by altering chromatin accessibility through changes in transcription factor (TF) and nucleosome occupancy throughout the genome. Despite numerous studies focusing on changes in gene expression, the intricate chromatin-mediated regulatory code remains largely unexplored on a comprehensive scale. We address this by employing a factor-agnostic, reverse-genetics approach that uses MNase-seq to capture genome-wide TF and nucleosome occupancies in response to the individual deletion of 201 transcriptional regulators in Saccharomyces cerevisiae, thereby assaying nearly one million mutant-gene interactions. We develop a principled approach to identify and quantify chromatin changes genome-wide, observing differences in TF and nucleosome occupancy that recapitulate well-established pathways identified by gene expression data. We also discover distinct chromatin signatures associated with the up- and downregulation of genes, and use these signatures to reveal regulatory mechanisms previously unexplored in expression-based studies. Finally, we demonstrate that chromatin features are predictive of transcriptional activity and leverage these features to reconstruct chromatin-based transcriptional regulatory networks. Overall, these results illustrate the power of an approach combining genetic perturbation with high-resolution epigenomic profiling; the latter enables a close examination of the interplay between TFs and nucleosomes genome-wide, providing a deeper, more mechanistic understanding of the complex relationship between chromatin organization and transcription.
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Affiliation(s)
- Kevin Moyung
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
| | - Yulong Li
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
- Department of Computer Science, Duke University, Durham, NC 27708
| | - Alexander J. Hartemink
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708
- Department of Computer Science, Duke University, Durham, NC 27708
| | - David M. MacAlpine
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
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2
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Obermeyer S, Kapoor H, Markusch H, Grasser KD. Transcript elongation by RNA polymerase II in plants: factors, regulation and impact on gene expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:645-656. [PMID: 36703573 DOI: 10.1111/tpj.16115] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Transcriptional elongation by RNA polymerase II (RNAPII) through chromatin is a dynamic and highly regulated step of eukaryotic gene expression. A combination of transcript elongation factors (TEFs) including modulators of RNAPII activity and histone chaperones facilitate efficient transcription on nucleosomal templates. Biochemical and genetic analyses, primarily performed in Arabidopsis, provided insight into the contribution of TEFs to establish gene expression patterns during plant growth and development. In addition to summarising the role of TEFs in plant gene expression, we emphasise in our review recent advances in the field. Thus, mechanisms are presented how aberrant intragenic transcript initiation is suppressed by repressing transcriptional start sites within coding sequences. We also discuss how transcriptional interference of ongoing transcription with neighbouring genes is prevented. Moreover, it appears that plants make no use of promoter-proximal RNAPII pausing in the way mammals do, but there are nucleosome-defined mechanism(s) that determine the efficiency of mRNA synthesis by RNAPII. Accordingly, a still growing number of processes related to plant growth, development and responses to changing environmental conditions prove to be regulated at the level of transcriptional elongation.
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Affiliation(s)
- Simon Obermeyer
- Cell Biology and Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Henna Kapoor
- Cell Biology and Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Hanna Markusch
- Cell Biology and Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Klaus D Grasser
- Cell Biology and Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
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3
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Tourdot E, Grob S. Three-dimensional chromatin architecture in plants - General features and novelties. Eur J Cell Biol 2023; 102:151344. [PMID: 37562220 DOI: 10.1016/j.ejcb.2023.151344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 07/21/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Research on the three-dimensional (3D) structure of the genome and its distribution within the nuclear space has made a big leap in the last two decades. Work in the animal field has led to significant advances in our general understanding on eukaryotic genome organization. This did not only bring along insights into how the 3D genome interacts with the epigenetic landscape and the transcriptional machinery but also how 3D genome architecture is relevant for fundamental developmental processes, such as cell differentiation. In parallel, the 3D organization of plant genomes have been extensively studied, which resulted in both congruent and novel findings, contributing to a more complete view on how eukaryotic genomes are organized in multiple dimensions. Plant genomes are remarkably diverse in size, composition, and ploidy. Furthermore, as intrinsically sessile organisms without the possibility to relocate to more favorable environments, plants have evolved an elaborate epigenetic repertoire to rapidly respond to environmental challenges. The diversity in genome organization and the complex epigenetic programs make plants ideal study subjects to acquire a better understanding on universal features and inherent constraints of genome organization. Furthermore, considering a wide range of species allows us to study the evolutionary crosstalk between the various levels of genome architecture. In this article, we aim at summarizing important findings on 3D genome architecture obtained in various plant species. These findings cover many aspects of 3D genome organization on a wide range of levels, from gene loops to topologically associated domains and to global 3D chromosome configurations. We present an overview on plant 3D genome organizational features that resemble those in animals and highlight facets that have only been observed in plants to date.
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Affiliation(s)
- Edouard Tourdot
- Department of Plant and Microbial Biology, University of Zurich, Switzerland.
| | - Stefan Grob
- Department of Plant and Microbial Biology, University of Zurich, Switzerland.
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4
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Obermeyer S, Schrettenbrunner L, Stöckl R, Schwartz U, Grasser K. Different elongation factors distinctly modulate RNA polymerase II transcription in Arabidopsis. Nucleic Acids Res 2023; 51:11518-11533. [PMID: 37819035 PMCID: PMC10681736 DOI: 10.1093/nar/gkad825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/24/2023] [Accepted: 09/21/2023] [Indexed: 10/13/2023] Open
Abstract
Various transcript elongation factors (TEFs) including modulators of RNA polymerase II (RNAPII) activity and histone chaperones tune the efficiency of transcription in the chromatin context. TEFs are involved in establishing gene expression patterns during growth and development in Arabidopsis, while little is known about the genomic distribution of the TEFs and the way they facilitate transcription. We have mapped the genome-wide occupancy of the elongation factors SPT4-SPT5, PAF1C and FACT, relative to that of elongating RNAPII phosphorylated at residues S2/S5 within the carboxyterminal domain. The distribution of SPT4-SPT5 along transcribed regions closely resembles that of RNAPII-S2P, while the occupancy of FACT and PAF1C is rather related to that of RNAPII-S5P. Under transcriptionally challenging heat stress conditions, mutant plants lacking the corresponding TEFs are differentially impaired in transcript synthesis. Strikingly, in plants deficient in PAF1C, defects in transcription across intron/exon borders are observed that are cumulative along transcribed regions. Upstream of transcriptional start sites, the presence of FACT correlates with nucleosomal occupancy. Under stress conditions FACT is particularly required for transcriptional upregulation and to promote RNAPII transcription through +1 nucleosomes. Thus, Arabidopsis TEFs are differently distributed along transcribed regions, and are distinctly required during transcript elongation especially upon transcriptional reprogramming.
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Affiliation(s)
- Simon Obermeyer
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Lukas Schrettenbrunner
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Richard Stöckl
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Uwe Schwartz
- NGS Analysis Centre, Biology and Pre-Clinical Medicine, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Klaus D Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
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5
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Lee H, Seo P. Accessible gene borders establish a core structural unit for chromatin architecture in Arabidopsis. Nucleic Acids Res 2023; 51:10261-10277. [PMID: 37884483 PMCID: PMC10602878 DOI: 10.1093/nar/gkad710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 10/28/2023] Open
Abstract
Three-dimensional (3D) chromatin structure is linked to transcriptional regulation in multicellular eukaryotes including plants. Taking advantage of high-resolution Hi-C (high-throughput chromatin conformation capture), we detected a small structural unit with 3D chromatin architecture in the Arabidopsis genome, which lacks topologically associating domains, and also in the genomes of tomato, maize, and Marchantia polymorpha. The 3D folding domain unit was usually established around an individual gene and was dependent on chromatin accessibility at the transcription start site (TSS) and transcription end site (TES). We also observed larger contact domains containing two or more neighboring genes, which were dependent on accessible border regions. Binding of transcription factors to accessible TSS/TES regions formed these gene domains. We successfully simulated these Hi-C contact maps via computational modeling using chromatin accessibility as input. Our results demonstrate that gene domains establish basic 3D chromatin architecture units that likely contribute to higher-order 3D genome folding in plants.
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Affiliation(s)
- Hongwoo Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
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6
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Staunton PM, Peters AJ, Seoighe C. Somatic mutations inferred from RNA-seq data highlight the contribution of replication timing to mutation rate variation in a model plant. Genetics 2023; 225:iyad128. [PMID: 37450609 PMCID: PMC10550316 DOI: 10.1093/genetics/iyad128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 03/23/2023] [Accepted: 06/11/2023] [Indexed: 07/18/2023] Open
Abstract
Variation in the rates and characteristics of germline and somatic mutations across the genome of an organism is informative about DNA damage and repair processes and can also shed light on aspects of organism physiology and evolution. We adapted a recently developed method for inferring somatic mutations from bulk RNA-seq data and applied it to a large collection of Arabidopsis thaliana accessions. The wide range of genomic data types available for A. thaliana enabled us to investigate the relationships of multiple genomic features with the variation in the somatic mutation rate across the genome of this model plant. We observed that late replicated regions showed evidence of an elevated rate of somatic mutation compared to genomic regions that are replicated early. We identified transcriptional strand asymmetries, consistent with the effects of transcription-coupled damage and/or repair. We also observed a negative relationship between the inferred somatic mutation count and the H3K36me3 histone mark which is well documented in the literature of human systems. In addition, we were able to support previous reports of an inverse relationship between inferred somatic mutation count and guanine-cytosine content as well as a positive relationship between inferred somatic mutation count and DNA methylation for both cytosine and noncytosine mutations.
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Affiliation(s)
- Patrick M Staunton
- School of Mathematical and Statistical Sciences, University of Galway, Galway H91 TK33, Ireland
| | - Andrew J Peters
- School of Mathematical and Statistical Sciences, University of Galway, Galway H91 TK33, Ireland
| | - Cathal Seoighe
- School of Mathematical and Statistical Sciences, University of Galway, Galway H91 TK33, Ireland
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7
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Yang DL, Huang K, Deng D, Zeng Y, Wang Z, Zhang Y. DNA-dependent RNA polymerases in plants. THE PLANT CELL 2023; 35:3641-3661. [PMID: 37453082 PMCID: PMC10533338 DOI: 10.1093/plcell/koad195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 06/09/2023] [Accepted: 05/29/2023] [Indexed: 07/18/2023]
Abstract
DNA-dependent RNA polymerases (Pols) transfer the genetic information stored in genomic DNA to RNA in all organisms. In eukaryotes, the typical products of nuclear Pol I, Pol II, and Pol III are ribosomal RNAs, mRNAs, and transfer RNAs, respectively. Intriguingly, plants possess two additional Pols, Pol IV and Pol V, which produce small RNAs and long noncoding RNAs, respectively, mainly for silencing transposable elements. The five plant Pols share some subunits, but their distinct functions stem from unique subunits that interact with specific regulatory factors in their transcription cycles. Here, we summarize recent advances in our understanding of plant nucleus-localized Pols, including their evolution, function, structures, and transcription cycles.
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Affiliation(s)
- Dong-Lei Yang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Kun Huang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Deyin Deng
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Lin’an, Hangzhou 311300, China
| | - Yuan Zeng
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhenxing Wang
- College of Horticulture, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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8
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Zhou S, Zhao F, Zhu D, Zhang Q, Dai Z, Wu Z. Coupling of co-transcriptional splicing and 3' end Pol II pausing during termination in Arabidopsis. Genome Biol 2023; 24:206. [PMID: 37697420 PMCID: PMC10496290 DOI: 10.1186/s13059-023-03050-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/04/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND In Arabidopsis, RNA Polymerase II (Pol II) often pauses within a few hundred base pairs downstream of the polyadenylation site, reflecting efficient transcriptional termination, but how such pausing is regulated remains largely elusive. RESULT Here, we analyze Pol II dynamics at 3' ends by combining comprehensive experiments with mathematical modelling. We generate high-resolution serine 2 phosphorylated (Ser2P) Pol II positioning data specifically enriched at 3' ends and define a 3' end pause index (3'PI). The position but not the extent of the 3' end pause correlates with the termination window size. The 3'PI is not decreased but even mildly increased in the termination deficient mutant xrn3, indicating 3' end pause is a regulatory step early during the termination and before XRN3-mediated RNA decay that releases Pol II. Unexpectedly, 3'PI is closely associated with gene exon numbers and co-transcriptional splicing efficiency. Multiple exons genes often display stronger 3' end pauses and more efficient on-chromatin splicing than genes with fewer exons. Chemical inhibition of splicing strongly reduces the 3'PI and disrupts its correlation with exon numbers but does not globally impact 3' end readthrough levels. These results are further confirmed by fitting Pol II positioning data with a mathematical model, which enables the estimation of parameters that define Pol II dynamics. CONCLUSION Our work highlights that the number of exons via co-transcriptional splicing is a major determinant of Pol II pausing levels at the 3' end of genes in plants.
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Affiliation(s)
- Sixian Zhou
- Harbin Institute of Technology, Harbin, 150001, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Fengli Zhao
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Danling Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Qiqi Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ziwei Dai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Zhe Wu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
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9
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Markusch H, Michl-Holzinger P, Obermeyer S, Thorbecke C, Bruckmann A, Babl S, Längst G, Osakabe A, Berger F, Grasser KD. Elongation factor 1 is a component of the Arabidopsis RNA polymerase II elongation complex and associates with a subset of transcribed genes. THE NEW PHYTOLOGIST 2023; 238:113-124. [PMID: 36627730 DOI: 10.1111/nph.18724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Elongation factors modulate the efficiency of mRNA synthesis by RNA polymerase II (RNAPII) in the context of chromatin, thus contributing to implement proper gene expression programmes. The zinc-finger protein elongation factor 1 (ELF1) is a conserved transcript elongation factor (TEF), whose molecular function so far has not been studied in plants. Using biochemical approaches, we examined the interaction of Arabidopsis ELF1 with DNA and histones in vitro and with the RNAPII elongation complex in vivo. In addition, cytological assays demonstrated the nuclear localisation of the protein, and by means of double-mutant analyses, interplay with genes encoding other elongation factors was explored. The genome-wide distribution of ELF1 was addressed by chromatin immunoprecipitation. ELF1 isolated from Arabidopsis cells robustly copurified with RNAPII and various other elongation factors including SPT4-SPT5, SPT6, IWS1, FACT and PAF1C. Analysis of a CRISPR-Cas9-mediated gene editing mutant of ELF1 revealed distinct genetic interactions with mutants deficient in other elongation factors. Moreover, ELF1 associated with genomic regions actively transcribed by RNAPII. However, ELF1 occupied only c. 33% of the RNAPII transcribed loci with preference for inducible rather than constitutively expressed genes. Collectively, these results establish that Arabidopsis ELF1 shares several characteristic attributes with RNAPII TEFs.
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Affiliation(s)
- Hanna Markusch
- Cell Biology & Plant Biochemistry, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Philipp Michl-Holzinger
- Cell Biology & Plant Biochemistry, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Simon Obermeyer
- Cell Biology & Plant Biochemistry, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Claudia Thorbecke
- Cell Biology & Plant Biochemistry, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Astrid Bruckmann
- Institute for Biochemistry I, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Sabrina Babl
- Institute for Biochemistry III, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Gernot Längst
- Institute for Biochemistry III, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Akihisa Osakabe
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Klaus D Grasser
- Cell Biology & Plant Biochemistry, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
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Appel LM, Benedum J, Engl M, Platzer S, Schleiffer A, Strobl X, Slade D. SPOC domain proteins in health and disease. Genes Dev 2023; 37:140-170. [PMID: 36927757 PMCID: PMC10111866 DOI: 10.1101/gad.350314.122] [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] [Indexed: 03/18/2023]
Abstract
Since it was first described >20 yr ago, the SPOC domain (Spen paralog and ortholog C-terminal domain) has been identified in many proteins all across eukaryotic species. SPOC-containing proteins regulate gene expression on various levels ranging from transcription to RNA processing, modification, export, and stability, as well as X-chromosome inactivation. Their manifold roles in controlling transcriptional output implicate them in a plethora of developmental processes, and their misregulation is often associated with cancer. Here, we provide an overview of the biophysical properties of the SPOC domain and its interaction with phosphorylated binding partners, the phylogenetic origin of SPOC domain proteins, the diverse functions of mammalian SPOC proteins and their homologs, the mechanisms by which they regulate differentiation and development, and their roles in cancer.
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Affiliation(s)
- Lisa-Marie Appel
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
| | - Johannes Benedum
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Magdalena Engl
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Sebastian Platzer
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Xué Strobl
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Dea Slade
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria;
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
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11
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Lin J, Li QQ. Coupling epigenetics and RNA polyadenylation: missing links. TRENDS IN PLANT SCIENCE 2023; 28:223-234. [PMID: 36175275 DOI: 10.1016/j.tplants.2022.08.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Precise regulation of gene expression is crucial for plant survival. As a cotranscriptional regulatory mechanism, pre-mRNA polyadenylation is essential for fine-tuning gene expression. Polyadenylation can be alternatively projected at various sites of a transcript, which contributes to transcriptome diversity. Epigenetic modification is another mechanism of transcriptional control. Recent studies have uncovered crosstalk between cotranscriptional polyadenylation processes and both epigenomic and epitranscriptomic markers. Genetic analyses have demonstrated that DNA methylation, histone modifications, and epitranscriptomic modification are involved in regulating polyadenylation in plants. Here we summarize current understanding of the links between epigenetics and polyadenylation and their novel biological efficacy for plant development and environmental responses. Unresolved issues and future directions are discussed to shed light on the field.
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Affiliation(s)
- Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China; FAFU-UCR Joint Center, Horticulture Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Qingshun Quinn Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China; Biomedical Science Division, College of Dental Medicine, Western University of Health Sciences, Pomona, CA 91766, USA.
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12
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Qin Y, Long Y, Zhai J. Genome-wide characterization of nascent RNA processing in plants. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102294. [PMID: 36063636 DOI: 10.1016/j.pbi.2022.102294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Following transcription initiation, RNA polymerase II (Pol II) elongates through the genic region and terminates after the polyadenylation signal. This process is accompanied by splicing, 3' cleavage, and polyadenylation, to eventually form a mature mRNA. Recent advances in short-read and long-read high-throughput sequencing methods have shed light on the global landscape of these co-transcriptional events at nucleotide resolution. In this mini review, we summarize recent developments in genome-wide approaches that broadened our understanding of nascent RNA processing in plants.
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Affiliation(s)
- Yuwei Qin
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Yanping Long
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Jixian Zhai
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China.
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13
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Velay F, Méteignier LV, Laloi C. You shall not pass! A Chromatin barrier story in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:888102. [PMID: 36212303 PMCID: PMC9540200 DOI: 10.3389/fpls.2022.888102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
As in other eukaryotes, the plant genome is functionally organized in two mutually exclusive chromatin fractions, a gene-rich and transcriptionally active euchromatin, and a gene-poor, repeat-rich, and transcriptionally silent heterochromatin. In Drosophila and humans, the molecular mechanisms by which euchromatin is preserved from heterochromatin spreading have been extensively studied, leading to the identification of insulator DNA elements and associated chromatin factors (insulator proteins), which form boundaries between chromatin domains with antagonistic features. In contrast, the identity of factors assuring such a barrier function remains largely elusive in plants. Nevertheless, several genomic elements and associated protein factors have recently been shown to regulate the spreading of chromatin marks across their natural boundaries in plants. In this minireview, we focus on recent findings that describe the spreading of chromatin and propose avenues to improve the understanding of how plant chromatin architecture and transitions between different chromatin domains are defined.
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Affiliation(s)
- Florent Velay
- Aix Marseille Université, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille (BIAM), Equipe de Luminy de Génétique et Biophysique des Plantes, Marseille, F-13009, France
| | - Louis-Valentin Méteignier
- Aix Marseille Université, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille (BIAM), Equipe de Luminy de Génétique et Biophysique des Plantes, Marseille, F-13009, France
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Christophe Laloi
- Aix Marseille Université, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille (BIAM), Equipe de Luminy de Génétique et Biophysique des Plantes, Marseille, F-13009, France
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14
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Kyung J, Jeon M, Lee I. Recent advances in the chromatin-based mechanism of FLOWERING LOCUS C repression through autonomous pathway genes. FRONTIERS IN PLANT SCIENCE 2022; 13:964931. [PMID: 36035698 PMCID: PMC9411803 DOI: 10.3389/fpls.2022.964931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Proper timing of flowering, a phase transition from vegetative to reproductive development, is crucial for plant fitness. The floral repressor FLOWERING LOCUS C (FLC) is the major determinant of flowering in Arabidopsis thaliana. In rapid-cycling A. thaliana accessions, which bloom rapidly, FLC is constitutively repressed by autonomous pathway (AP) genes, regardless of photoperiod. Diverse AP genes have been identified over the past two decades, and most of them repress FLC through histone modifications. However, the detailed mechanism underlying such modifications remains unclear. Several recent studies have revealed novel mechanisms to control FLC repression in concert with histone modifications. This review summarizes the latest advances in understanding the novel mechanisms by which AP proteins regulate FLC repression, including changes in chromatin architecture, RNA polymerase pausing, and liquid-liquid phase separation- and ncRNA-mediated gene silencing. Furthermore, we discuss how each mechanism is coupled with histone modifications in FLC chromatin.
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Affiliation(s)
- Jinseul Kyung
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, South Korea
| | - Myeongjune Jeon
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, South Korea
| | - Ilha Lee
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, South Korea
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15
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Zhang Y, Tang M, Huang M, Xie J, Cheng J, Fu Y, Jiang D, Yu X, Li B. Dynamic enhancer transcription associates with reprogramming of immune genes during pattern triggered immunity in Arabidopsis. BMC Biol 2022; 20:165. [PMID: 35864475 PMCID: PMC9301868 DOI: 10.1186/s12915-022-01362-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 06/24/2022] [Indexed: 11/25/2022] Open
Abstract
Background Enhancers are cis-regulatory elements present in eukaryote genomes, which constitute indispensable determinants of gene regulation by governing the spatiotemporal and quantitative expression dynamics of target genes, and are involved in multiple life processes, for instance during development and disease states. The importance of enhancer activity has additionally been highlighted for immune responses in animals and plants; however, the dynamics of enhancer activities and molecular functions in plant innate immunity are largely unknown. Here, we investigated the involvement of distal enhancers in early innate immunity in Arabidopsis thaliana. Results A group of putative distal enhancers producing low-abundance transcripts either unidirectionally or bidirectionally are identified. We show that enhancer transcripts are dynamically modulated in plant immunity triggered by microbe-associated molecular patterns and are strongly correlated with open chromatin, low levels of methylated DNA, and increases in RNA polymerase II targeting and acetylated histone marks. Dynamic enhancer transcription is correlated with target early immune gene expression patterns. Cis motifs that are bound by immune-related transcription factors, such as WRKYs and SARD1, are highly enriched within upregulated enhancers. Moreover, a subset of core pattern-induced enhancers are upregulated by multiple patterns from diverse pathogens. The expression dynamics of putative immunity-related enhancers and the importance of WRKY binding motifs for enhancer function were also validated. Conclusions Our study demonstrates the general occurrence of enhancer transcription in plants and provides novel information on the distal regulatory landscape during early plant innate immunity, providing new insights into immune gene regulation and ultimately improving the mechanistic understanding of the plant immune system. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01362-8.
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Affiliation(s)
- Ying Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
| | - Meng Tang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
| | - Mengling Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yanping Fu
- Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
| | - Xiao Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. .,Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. .,Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China.
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16
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Chen Z, Huang X, Fu R, Zhan A. Neighbours matter: Effects of genomic organization on gene expression plasticity in response to environmental stresses during biological invasions. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100992. [PMID: 35504120 DOI: 10.1016/j.cbd.2022.100992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/07/2022] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
Gene expression regulation has been widely recognized as an important molecular mechanism underlying phenotypic plasticity in environmental adaptation. However, it remains largely unexplored on the effects of genomic organization on gene expression plasticity under environmental stresses during biological invasions. Here, we use an invasive model ascidian, Ciona robusta, to investigate how genomic organization affects gene expression in response to salinity stresses during range expansions. Our study showed that neighboring genes were co-expressed and approximately 30% of stress responsive genes were physically clustered on chromosomes. Such coordinated expression was substantially affected by the physical distance and orientation of genes. Interestingly, the overall expression correlation of neighboring genes was significantly decreased under high salinity stresses, illustrating that the co-expression regulation could be disrupted by salinity challenges. Furthermore, the clustering of genes was associated with their function constraints and expression patterns - operon genes enriched in gene expression machinery had the highest transcriptional activity and expression stability. Notably, our analyses showed that the tail-to-tail genes, mainly involved in biological functions related to phosphorylation, homeostatic process, and ion transport, exhibited higher intrinsic expression variability and greater response to salinity challenges. Altogether, the results obtained here provide new insights into the effects of gene organization on gene expression plasticity under environmental challenges, hence improving our knowledge on mechanisms of rapid environmental adaptation during biological invasions.
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Affiliation(s)
- Zaohuang Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China
| | - Ruiying Fu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China.
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17
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Nissani N, Ulitsky I. Unique features of transcription termination and initiation at closely spaced tandem human genes. Mol Syst Biol 2022; 18:e10682. [PMID: 35362230 PMCID: PMC8972054 DOI: 10.15252/msb.202110682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 11/09/2022] Open
Abstract
The synthesis of RNA polymerase II (Pol2) products, which include messenger RNAs or long noncoding RNAs, culminates in transcription termination. How the transcriptional termination of a gene impacts the activity of promoters found immediately downstream of it, and which can be subject to potential transcriptional interference, remains largely unknown. We examined in an unbiased manner the features of the intergenic regions between pairs of 'tandem genes'-closely spaced (< 2 kb) human genes found on the same strand. Intergenic regions separating tandem genes are enriched with guanines and are characterized by binding of several proteins, including AGO1 and AGO2 of the RNA interference pathway. Additionally, we found that Pol2 is particularly enriched in this region, and it is lost upon perturbations affecting splicing or transcriptional elongation. Perturbations of genes involved in Pol2 pausing and R loop biology preferentially affect expression of downstream genes in tandem gene pairs. Overall, we find that features associated with Pol2 pausing and accumulation rather than those associated with avoidance of transcriptional interference are the predominant driving force shaping short tandem intergenic regions.
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Affiliation(s)
- Noa Nissani
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
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18
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Liu H, Jiang L, Wen Z, Yang Y, Singer SD, Bennett D, Xu W, Su Z, Yu Z, Cohn J, Chae H, Que Q, Liu Y, Liu C, Liu Z. Rice RS2-9, which is bound by transcription factor OSH1, blocks enhancer-promoter interactions in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:541-554. [PMID: 34773305 PMCID: PMC9303810 DOI: 10.1111/tpj.15574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/02/2021] [Indexed: 05/13/2023]
Abstract
Insulators characterized in Drosophila and mammals have been shown to play a key role in the restriction of promiscuous enhancer-promoter interactions, as well as reshaping the topological landscape of chromosomes. Yet the role of insulators in plants remains poorly understood, in large part because of a lack of well-characterized insulators and binding factor(s). In this study, we isolated a 1.2-kb RS2-9 insulator from the Oryza sativa (rice) genome that can, when interposed between an enhancer and promoter, efficiently block the activation function of both constitutive and floral organ-specific enhancers in transgenic Arabidopsis and Nicotiana tabacum (tobacco). In the rice genome, the genes flanking RS2-9 exhibit an absence of mutual transcriptional interactions, as well as a lack of histone modification spread. We further determined that O. sativa Homeobox 1 (OSH1) bound two regions of RS2-9, as well as over 50 000 additional sites in the rice genome, the majority of which resided in intergenic regions. Mutation of one of the two OSH1-binding sites in RS2-9 impaired insulation activity by up to 60%, whereas the mutation of both binding sites virtually abolished insulator function. We also demonstrated that OSH1 binding sites were associated with 72% of the boundaries of topologically associated domains (TADs) identified in the rice genome, which is comparable to the 77% of TAD boundaries bound by the insulator CCCTC-binding factor (CTCF) in mammals. Taken together, our findings indicate that OSH1-RS2-9 acts as a true insulator in plants, and highlight a potential role for OSH1 in gene insulation and topological organization in plant genomes.
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Affiliation(s)
- Huawei Liu
- USDA‐ARS, Appalachian Fruit Research StationKearneysvilleWest Virginia25430USA
- College of Food Science and TechnologyNanjing Agricultural UniversityNanjing210095China
| | - Li Jiang
- USDA‐ARS, Appalachian Fruit Research StationKearneysvilleWest Virginia25430USA
- College of Food Science and TechnologyNanjing Agricultural UniversityNanjing210095China
| | - Zhifeng Wen
- USDA‐ARS, Appalachian Fruit Research StationKearneysvilleWest Virginia25430USA
- College of HorticultureFujian Agriculture and Forestry UniversityFuzhou350002China
| | - Yingjun Yang
- USDA‐ARS, Appalachian Fruit Research StationKearneysvilleWest Virginia25430USA
- Forestry CollegeHenan University of Science and TechnologyLuoyang471023China
| | - Stacy D. Singer
- Agriculture and Agri‐Food CanadaLethbridge Research and Development CentreLethbridgeAlbertaT1J 4B1Canada
| | - Dennis Bennett
- USDA‐ARS, Appalachian Fruit Research StationKearneysvilleWest Virginia25430USA
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
| | - Zhifang Yu
- College of Food Science and TechnologyNanjing Agricultural UniversityNanjing210095China
| | - Jonathan Cohn
- Syngenta Crop ProtectionLLCResearch Triangle ParkNorth Carolina27709USA
| | - Hyunsook Chae
- Syngenta Crop ProtectionLLCResearch Triangle ParkNorth Carolina27709USA
| | - Qiudeng Que
- Syngenta Crop ProtectionLLCResearch Triangle ParkNorth Carolina27709USA
| | - Yue Liu
- College of HorticultureQingdao Agricultural UniversityQingdao266109China
| | - Chang Liu
- Department of EpigeneticsUniversity of HohenheimStuttgart70599Germany
| | - Zongrang Liu
- USDA‐ARS, Appalachian Fruit Research StationKearneysvilleWest Virginia25430USA
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19
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Mo W, Liu B, Zhang H, Jin X, Lu D, Yu Y, Liu Y, Jia J, Long Y, Deng X, Cao X, Guo H, Zhai J. Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing. Genome Biol 2021; 22:322. [PMID: 34823554 PMCID: PMC8613925 DOI: 10.1186/s13059-021-02543-4] [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] [Received: 07/24/2021] [Accepted: 11/01/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The dynamic process of transcription termination produces transient RNA intermediates that are difficult to distinguish from each other via short-read sequencing methods. RESULTS Here, we use single-molecule nascent RNA sequencing to characterize the various forms of transient RNAs during termination at genome-wide scale in wildtype Arabidopsis and in atxrn3, fpa, and met1 mutants. Our data reveal a wide range of termination windows among genes, ranging from ~ 50 nt to over 1000 nt. We also observe efficient termination before downstream tRNA genes, suggesting that chromatin structure around the promoter region of tRNA genes may block pol II elongation. 5' Cleaved readthrough transcription in atxrn3 with delayed termination can run into downstream genes to produce normally spliced and polyadenylated mRNAs in the absence of their own transcription initiation. Consistent with previous reports, we also observe long chimeric transcripts with cryptic splicing in fpa mutant; but loss of CG DNA methylation has no obvious impact on termination in the met1 mutant. CONCLUSIONS Our method is applicable to establish a comprehensive termination landscape in a broad range of species.
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Affiliation(s)
- Weipeng Mo
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Bo Liu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hong Zhang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xianhao Jin
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Dongdong Lu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yiming Yu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuelin Liu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jinbu Jia
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yanping Long
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hongwei Guo
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jixian Zhai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China.
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, 518055, China.
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20
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Appel LM, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nat Commun 2021; 12:6078. [PMID: 34667177 PMCID: PMC8526623 DOI: 10.1038/s41467-021-26360-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/29/2021] [Indexed: 12/16/2022] Open
Abstract
The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay.
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Affiliation(s)
- Lisa-Marie Appel
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Vedran Franke
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany
| | - Melania Bruno
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Irina Grishkovskaya
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Aiste Kasiliauskaite
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tanja Kaufmann
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Ursula E Schoeberl
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martin G Puchinger
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Sebastian Kostrhon
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Carmen Ebenwaldner
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Marek Sebesta
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Etienne Beltzung
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Gen Lin
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Anna Vlasova
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Martin Leeb
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna Biocenter (VBC), Vienna, Austria
| | - Altuna Akalin
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany
| | - Richard Stefl
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Carrie Bernecky
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, Klosterneuburg, Austria
| | - Kristina Djinovic-Carugo
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
- Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Dea Slade
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria.
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
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21
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Yu X, Martin PGP, Zhang Y, Trinidad JC, Xu F, Huang J, Thum KE, Li K, Zhao S, Gu Y, Wang X, Michaels SD. The BORDER family of negative transcription elongation factors regulates flowering time in Arabidopsis. Curr Biol 2021; 31:5377-5384.e5. [PMID: 34666004 DOI: 10.1016/j.cub.2021.09.074] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/20/2021] [Accepted: 09/27/2021] [Indexed: 11/27/2022]
Abstract
Transcription initiation has long been considered a primary regulatory step in gene expression. Recent work, however, shows that downstream events, such as transcription elongation, can also play important roles.1-3 A well-characterized example from animals is promoter-proximal pausing, where transcriptionally engaged Pol II accumulates 30-50 bp downstream of the transcription start site (TSS) and is thought to enable rapid gene activation.2 Plants do not make widespread use of promoter-proximal pausing; however, in a phenomenon known as 3' pausing, a significant increase in Pol II is observed near the transcript end site (TES) of many genes.4-6 Previous work has shown that 3' pausing is promoted by the BORDER (BDR) family of negative transcription elongation factors. Here we show that BDR proteins play key roles in gene repression. Consistent with BDR proteins acting to slow or pause elongating Pol II, BDR-repressed genes are characterized by high levels of Pol II occupancy, yet low levels of mRNA. The BDR proteins physically interact with FPA,7 one of approximately two dozen genes collectively referred to as the autonomous floral-promotion pathway,8 which are necessary for the repression of the flowering time gene FLOWERING LOCUS C (FLC).9-11 In early-flowering strains, FLC expression is repressed by repressive histone modifications, such as histone H3 lysine 27 trimethylation (H3K27me3), thereby allowing the plants to flower early. These results suggest that the repression of transcription elongation by BDR proteins may allow for the temporary pausing of transcription or facilitate the long-term repression of genes by repressive histone modifications.
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Affiliation(s)
- Xuhong Yu
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA.
| | - Pascal G P Martin
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
| | - Yixiang Zhang
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Jonathan C Trinidad
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Laboratory for Biological Mass Spectrometry, Department of Chemistry, Indiana University Bloomington, Bloomington, IN, USA
| | - Feifei Xu
- Institute of Nuclear Agricultural Sciences, Key Laboratory for Nuclear Agricultural Sciences of Zhejiang Province and Ministry of Agriculture and Rural Affairs, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Jie Huang
- Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
| | - Karen E Thum
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
| | - Ke Li
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
| | - ShuZhen Zhao
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xingjun Wang
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Scott D Michaels
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA.
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22
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Kurbidaeva A, Purugganan M. Insulators in Plants: Progress and Open Questions. Genes (Basel) 2021; 12:genes12091422. [PMID: 34573404 PMCID: PMC8470105 DOI: 10.3390/genes12091422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
The genomes of higher eukaryotes are partitioned into topologically associated domains or TADs, and insulators (also known as boundary elements) are the key elements responsible for their formation and maintenance. Insulators were first identified and extensively studied in Drosophila as well as mammalian genomes, and have also been described in yeast and plants. In addition, many insulator proteins are known in Drosophila, and some have been investigated in mammals. However, much less is known about this important class of non-coding DNA elements in plant genomes. In this review, we take a detailed look at known plant insulators across different species and provide an overview of potential determinants of plant insulator functions, including cis-elements and boundary proteins. We also discuss methods previously used in attempts to identify plant insulators, provide a perspective on their importance for research and biotechnology, and discuss areas of potential future research.
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23
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Fütterer A, Talavera-Gutiérrez A, Pons T, de Celis J, Gutiérrez J, Domínguez Plaza V, Martínez-A C. Impaired stem cell differentiation and somatic cell reprogramming in DIDO3 mutants with altered RNA processing and increased R-loop levels. Cell Death Dis 2021; 12:637. [PMID: 34155199 PMCID: PMC8217545 DOI: 10.1038/s41419-021-03906-2] [Citation(s) in RCA: 7] [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: 05/17/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 02/08/2023]
Abstract
Embryonic stem cell (ESC) differentiation and somatic cell reprogramming are biological processes governed by antagonistic expression or repression of a largely common set of genes. Accurate regulation of gene expression is thus essential for both processes, and alterations in RNA processing are predicted to negatively affect both. We show that truncation of the DIDO gene alters RNA splicing and transcription termination in ESC and mouse embryo fibroblasts (MEF), which affects genes involved in both differentiation and reprogramming. We combined transcriptomic, protein interaction, and cellular studies to identify the underlying molecular mechanism. We found that DIDO3 interacts with the helicase DHX9, which is involved in R-loop processing and transcription termination, and that DIDO3-exon16 deletion increases nuclear R-loop content and causes DNA replication stress. Overall, these defects result in failure of ESC to differentiate and of MEF to be reprogrammed. MEF immortalization restored impaired reprogramming capacity. We conclude that DIDO3 has essential functions in ESC differentiation and somatic cell reprogramming by supporting accurate RNA metabolism, with its exon16-encoded domain playing the main role.
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Affiliation(s)
- Agnes Fütterer
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), 28049, Madrid, Spain
| | - Amaia Talavera-Gutiérrez
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), 28049, Madrid, Spain
| | - Tirso Pons
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), 28049, Madrid, Spain
| | - Jesús de Celis
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), 28049, Madrid, Spain
| | - Julio Gutiérrez
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), 28049, Madrid, Spain
| | - Verónica Domínguez Plaza
- Transgenesis Unit, CNB & Centro de Biología Molecular Severo Ochoa, CSIC-Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Carlos Martínez-A
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), 28049, Madrid, Spain.
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24
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Abstract
Plants have an extraordinary diversity of transcription machineries, including five nuclear DNA-dependent RNA polymerases. Four of these enzymes are dedicated to the production of long noncoding RNAs (lncRNAs), which are ribonucleic acids with functions independent of their protein-coding potential. lncRNAs display a broad range of lengths and structures, but they are distinct from the small RNA guides of RNA interference (RNAi) pathways. lncRNAs frequently serve as structural, catalytic, or regulatory molecules for gene expression. They can affect all elements of genes, including promoters, untranslated regions, exons, introns, and terminators, controlling gene expression at various levels, including modifying chromatin accessibility, transcription, splicing, and translation. Certain lncRNAs protect genome integrity, while others respond to environmental cues like temperature, drought, nutrients, and pathogens. In this review, we explain the challenge of defining lncRNAs, introduce the machineries responsible for their production, and organize this knowledge by viewing the functions of lncRNAs throughout the structure of a typical plant gene.
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Affiliation(s)
- Andrzej T Wierzbicki
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Todd Blevins
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, F-67084 Strasbourg, France;
| | - Szymon Swiezewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland;
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25
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Parker MT, Knop K, Zacharaki V, Sherwood AV, Tomé D, Yu X, Martin PGP, Beynon J, Michaels SD, Barton GJ, Simpson GG. Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA. eLife 2021; 10:e65537. [PMID: 33904405 PMCID: PMC8116057 DOI: 10.7554/elife.65537] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
Genes involved in disease resistance are some of the fastest evolving and most diverse components of genomes. Large numbers of nucleotide-binding, leucine-rich repeat (NLR) genes are found in plant genomes and are required for disease resistance. However, NLRs can trigger autoimmunity, disrupt beneficial microbiota or reduce fitness. It is therefore crucial to understand how NLRs are controlled. Here, we show that the RNA-binding protein FPA mediates widespread premature cleavage and polyadenylation of NLR transcripts, thereby controlling their functional expression and impacting immunity. Using long-read Nanopore direct RNA sequencing, we resolved the complexity of NLR transcript processing and gene annotation. Our results uncover a co-transcriptional layer of NLR control with implications for understanding the regulatory and evolutionary dynamics of NLRs in the immune responses of plants.
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Affiliation(s)
- Matthew T Parker
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Katarzyna Knop
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | | | - Anna V Sherwood
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Daniel Tomé
- School of Life Sciences, University of WarwickCoventryUnited Kingdom
| | - Xuhong Yu
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Pascal GP Martin
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Jim Beynon
- School of Life Sciences, University of WarwickCoventryUnited Kingdom
| | - Scott D Michaels
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | | | - Gordon G Simpson
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
- The James Hutton InstituteInvergowrieUnited Kingdom
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26
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Liu M, Zhu J, Dong Z. Immediate transcriptional responses of Arabidopsis leaves to heat shock. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:468-483. [PMID: 32644278 DOI: 10.1111/jipb.12990] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/08/2020] [Indexed: 05/26/2023]
Abstract
Plants have evolved efficient mechanisms for adapting to temperature fluctuations, known as heat stress response and heat stress memory. Although the transcriptional regulatory network of plant heat stress response has been established, little is known about the genome-wide transcriptional changes occurring within the first several minutes after heat shock. Here, we investigated the nascent RNA and mature messenger RNA (mRNA) from plant leaf tissues exposed to 5 min of heat shock treatment using global run-on sequencing and RNA sequencing methods. Only a small group of genes were up- or downregulated at both the nascent RNA and mRNA levels. Primed plants that were already exposed to mild heat stress exhibited a more drastic alteration at multiple transcriptional steps than naïve plants that had not experienced heat stress. Upon heat shock, we also observed the following: (i) engaged RNA polymerase II accumulated downstream of transcription start sites; (ii) 5' pausing release was a rate-limiting step for the induction of some heat shock protein genes; (iii) numerous genes switched transcription modes; (iv) pervasive read-through was induced at terminators; and (v) heat stress memory occurs at multiple steps of the transcription cycle, such as at Pol II recruitment, 5' pausing, elongation, and termination.
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Affiliation(s)
- Min Liu
- Innovative Center of Molecular Genetics and Evolution, Guangzhou Higher Education Mega Center, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Jiafu Zhu
- Innovative Center of Molecular Genetics and Evolution, Guangzhou Higher Education Mega Center, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhicheng Dong
- Innovative Center of Molecular Genetics and Evolution, Guangzhou Higher Education Mega Center, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
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27
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Inagaki S, Takahashi M, Takashima K, Oya S, Kakutani T. Chromatin-based mechanisms to coordinate convergent overlapping transcription. NATURE PLANTS 2021; 7:295-302. [PMID: 33649596 DOI: 10.1038/s41477-021-00868-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
In eukaryotic genomes, the transcription units of genes often overlap with other protein-coding and/or noncoding transcription units1,2. In such intertwined genomes, the coordinated transcription of nearby or overlapping genes would be important to ensure the integrity of genome function3-6; however, the mechanisms underlying this coordination are largely unknown. Here, we show in Arabidopsis thaliana that genes with convergent orientation of transcription are major sources of antisense transcripts and that these genes transcribed on both strands are regulated by a putative Lysine-Specific Demethylase 1 family histone demethylase, FLOWERING LOCUS D (FLD)7,8. Our genome-wide chromatin profiling revealed that FLD, as well as its associating factor LUMINIDEPENDENS9, downregulates histone H3K4me1 in regions with convergent overlapping transcription. FLD localizes to actively transcribed genes, where it colocalizes with elongating RNA polymerase II phosphorylated at the Ser2 or Ser5 sites. Genome-wide transcription analyses suggest that FLD-mediated H3K4me1 removal negatively regulates the transcription of genes with high levels of antisense transcription. Furthermore, the effect of FLD on transcription dynamics is antagonized by DNA topoisomerase I. Our study reveals chromatin-based mechanisms to cope with overlapping transcription, which may occur by modulating DNA topology. This global mechanism to cope with overlapping transcription could be co-opted for specific epigenetic processes, such as cellular memory of responses to the environment10.
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Affiliation(s)
- Soichi Inagaki
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, Tokyo, Japan.
- National Institute of Genetics, Mishima, Japan.
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Shonankokusaimura, Hayama, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.
| | | | | | - Satoyo Oya
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, Tokyo, Japan
| | - Tetsuji Kakutani
- Department of Biological Sciences, Faculty of Science, The University of Tokyo, Tokyo, Japan
- National Institute of Genetics, Mishima, Japan
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Shonankokusaimura, Hayama, Japan
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28
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Wang HH, Qiu Y, Yu Q, Zhang Q, Li X, Wang J, Li X, Zhang Y, Yang Y. Close arrangement of CARK3 and PMEIL affects ABA-mediated pollen sterility in Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2020; 43:2699-2711. [PMID: 32816352 DOI: 10.1111/pce.13871] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
Abscisic acid (ABA) signaling is a vital plant signaling pathway for plant responses to stress conditions. ABA treatment can alter global gene expression patterns and cause significant phenotypic changes. We investigated the responses to ABA treatment during flowering in Arabidopsis thaliana. Dipping the flowers of CARK3 T-DNA mutants in ABA solution, led to less reduction of pollen fertility than in the wild type plants (Col-0). We demonstrated that PMEIL, a gene located downstream of CARK3, directly affects pollen fertility. Due to the close arrangement of CARK3 and PMEIL, CARK3 expression represses transcription of PMEIL in an ABA-dependent manner through transcriptional interference. Our study uncovers a molecular mechanism underlying ABA-mediated pollen sterility and provides an example of how transcriptional interference caused by close arrangement of genes may mediate stress responses during plant reproduction.
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Affiliation(s)
- Hsi-Hua Wang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Yao Qiu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Qin Yu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Qian Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Xiaoyi Li
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Jianmei Wang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Xufeng Li
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Yang Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Yi Yang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
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29
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Bäurle I, Trindade I. Chromatin regulation of somatic abiotic stress memory. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5269-5279. [PMID: 32076719 DOI: 10.1093/jxb/eraa098] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/19/2020] [Indexed: 05/20/2023]
Abstract
In nature, plants are often subjected to periods of recurrent environmental stress that can strongly affect their development and productivity. To cope with these conditions, plants can remember a previous stress, which allows them to respond more efficiently to a subsequent stress, a phenomenon known as priming. This ability can be maintained at the somatic level for a few days or weeks after the stress is perceived, suggesting that plants can store information of a past stress during this recovery phase. While the immediate responses to a single stress event have been extensively studied, knowledge on priming effects and how stress memory is stored is still scarce. At the molecular level, memory of a past condition often involves changes in chromatin structure and organization, which may be maintained independently from transcription. In this review, we will summarize the most recent developments in the field and discuss how different levels of chromatin regulation contribute to priming and plant abiotic stress memory.
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Affiliation(s)
- Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Inês Trindade
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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30
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Leng X, Thomas Q, Rasmussen SH, Marquardt S. A G(enomic)P(ositioning)S(ystem) for Plant RNAPII Transcription. TRENDS IN PLANT SCIENCE 2020; 25:744-764. [PMID: 32673579 DOI: 10.1016/j.tplants.2020.03.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/24/2020] [Accepted: 03/10/2020] [Indexed: 06/11/2023]
Abstract
Post-translational modifications (PTMs) of histone residues shape the landscape of gene expression by modulating the dynamic process of RNA polymerase II (RNAPII) transcription. The contribution of particular histone modifications to the definition of distinct RNAPII transcription stages remains poorly characterized in plants. Chromatin immunoprecipitation combined with next-generation sequencing (ChIP-seq) resolves the genomic distribution of histone modifications. Here, we review histone PTM ChIP-seq data in Arabidopsis thaliana and find support for a Genomic Positioning System (GPS) that guides RNAPII transcription. We review the roles of histone PTM 'readers', 'writers', and 'erasers', with a focus on the regulation of gene expression and biological functions in plants. The distinct functions of RNAPII transcription during the plant transcription cycle may rely, in part, on the characteristic histone PTM profiles that distinguish transcription stages.
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Affiliation(s)
- Xueyuan Leng
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark
| | - Quentin Thomas
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark
| | - Simon Horskjær Rasmussen
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark
| | - Sebastian Marquardt
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark.
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31
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Guo Q, Wang T, Yang Y, Gao L, Zhao Q, Zhang W, Xi T, Zheng L. Transcriptional Factor Yin Yang 1 Promotes the Stemness of Breast Cancer Cells by Suppressing miR-873-5p Transcriptional Activity. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:527-541. [PMID: 32711380 PMCID: PMC7381513 DOI: 10.1016/j.omtn.2020.06.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/20/2020] [Accepted: 06/22/2020] [Indexed: 01/01/2023]
Abstract
Transcription factor Yin Yang 1 (YY1) is upregulated in multiple tumors and plays essential roles in tumor proliferation and metastasis. However, the function of YY1 in breast cancer stemness remains unclear. Herein, we found that YY1 expression was negatively correlated with the overall survival and relapse-free survival of breast cancer patients and positively correlated with the expression of stemness markers in breast cancer. Overexpression of YY1 increased the expression of stemness markers, elevated CD44+CD24− cell sub-population, and enhanced the capacity of cell spheroid formation and tumor-initiation. In contrast, YY1 knockdown exhibited the opposite effects. Mechanistically, YY1 decreased microRNA-873-5p (miR-873-5p) level by recruiting histone deacetylase 4 (HDAC4) and HDAC9 to miR-873-5p promoter and thus increasing the deacetylation level of miR-873-5p promoter. Sequentially, YY1 activated the downstream PI3K/AKT and ERK1/2 pathways, which have been confirmed to be suppressed by miR-873-5p in our recent work. Moreover, the suppressed effect of YY1/miR-873-5p axis on the stemness of breast cancer cells was partially dependent on PI3K/AKT and ERK1/2 pathways. Finally, it was found that the YY1/miR-873-5p axis is involved in the chemoresistance of breast cancer cells. Our study defines a novel YY1/miR-873-5p axis responsible for the stemness of breast cancer cells.
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Affiliation(s)
- Qianqian Guo
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, 127 Dongming Road, Zhengzhou 450003, People's Republic of China
| | - Ting Wang
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Yue Yang
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Lanlan Gao
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Qiong Zhao
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China
| | - Wenzhou Zhang
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, 127 Dongming Road, Zhengzhou 450003, People's Republic of China
| | - Tao Xi
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China.
| | - Lufeng Zheng
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People's Republic of China.
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