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Luan J, Xiang G, Gómez-García PA, Tome JM, Zhang Z, Vermunt MW, Zhang H, Huang A, Keller CA, Giardine BM, Zhang Y, Lan Y, Lis JT, Lakadamyali M, Hardison RC, Blobel GA. Distinct properties and functions of CTCF revealed by a rapidly inducible degron system. Cell Rep 2021; 34:108783. [PMID: 33626344 PMCID: PMC7999233 DOI: 10.1016/j.celrep.2021.108783] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 11/25/2020] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
CCCTC-binding factor (CTCF) is a conserved zinc finger transcription factor implicated in a wide range of functions, including genome organization, transcription activation, and elongation. To explore the basis for CTCF functional diversity, we coupled an auxin-induced degron system with precision nuclear run-on. Unexpectedly, oriented CTCF motifs in gene bodies are associated with transcriptional stalling in a manner independent of bound CTCF. Moreover, CTCF at different binding sites (CBSs) displays highly variable resistance to degradation. Motif sequence does not significantly predict degradation behavior, but location at chromatin boundaries and chromatin loop anchors, as well as co-occupancy with cohesin, are associated with delayed degradation. Single-molecule tracking experiments link chromatin residence time to CTCF degradation kinetics, which has ramifications regarding architectural CTCF functions. Our study highlights the heterogeneity of CBSs, uncovers properties specific to architecturally important CBSs, and provides insights into the basic processes of genome organization and transcription regulation.
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Affiliation(s)
- Jing Luan
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guanjue Xiang
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Pablo Aurelio Gómez-García
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jacob M Tome
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Zhe Zhang
- Department of Biomedical and Health Informatics, Children's Hospital of Pennsylvania, Philadelphia, PA, USA
| | - Marit W Vermunt
- Division of Hematology, The Children's Hospital of Pennsylvania, Philadelphia, PA, USA
| | - Haoyue Zhang
- Division of Hematology, The Children's Hospital of Pennsylvania, Philadelphia, PA, USA
| | - Anran Huang
- Division of Hematology, The Children's Hospital of Pennsylvania, Philadelphia, PA, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Belinda M Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Yu Zhang
- Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA
| | - Yemin Lan
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Pennsylvania, Philadelphia, PA, USA.
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Fang Q, Shi Y, Cao H, Tong Z, Xiao J, Liao M, Wu X, Hua R. Degradation Dynamics and Dietary Risk Assessments of Two Neonicotinoid Insecticides during Lonicera japonica Planting, Drying, and Tea Brewing Processes. J Agric Food Chem 2017; 65:1483-1488. [PMID: 28177236 DOI: 10.1021/acs.jafc.6b04658] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The degradation dynamics and dietary risk assessments of thiamethoxam and thiacloprid during Lonicera japonica planting, drying, and tea brewing processes were systematically investigated using high-performance liquid chromatography. The half-lives of thiamethoxam and thiacloprid were 1.0-4.1 d in the honeysuckle flowers and leaves, with degradation rate constants k ranging from -0.169 to -0.696. The safety interval time was 7 d. The sun- and oven-drying (70 °C) percent digestions were 59.4-81.0% for the residues, which were higher than the shade- and oven-drying percentages at lower temperatures (30, 40, 50, and 60 °C, which ranged from 37.7% to 57.0%). The percent transfers of thiamethoxam and thiacloprid were 0-48.4% and 0-25.2%, respectively, for the different tea brewing conditions. On the basis of the results of this study, abiding by the safety interval time is important, and using reasonable drying methods and tea brewing conditions can reduce the transfer of thiamethoxam and thiacloprid to humans.
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Affiliation(s)
- Qingkui Fang
- School of Plant Protection, Provincial Key Laboratory for Agri-Food Safety, and ‡School of Resource & Environment, Provincial Key Laboratory for Agri-Food Safety, Anhui Agricultural University , Hefei 230036, China
| | - Yanhong Shi
- School of Plant Protection, Provincial Key Laboratory for Agri-Food Safety, and ‡School of Resource & Environment, Provincial Key Laboratory for Agri-Food Safety, Anhui Agricultural University , Hefei 230036, China
| | - Haiqun Cao
- School of Plant Protection, Provincial Key Laboratory for Agri-Food Safety, and ‡School of Resource & Environment, Provincial Key Laboratory for Agri-Food Safety, Anhui Agricultural University , Hefei 230036, China
| | - Zhou Tong
- School of Plant Protection, Provincial Key Laboratory for Agri-Food Safety, and ‡School of Resource & Environment, Provincial Key Laboratory for Agri-Food Safety, Anhui Agricultural University , Hefei 230036, China
| | - Jinjing Xiao
- School of Plant Protection, Provincial Key Laboratory for Agri-Food Safety, and ‡School of Resource & Environment, Provincial Key Laboratory for Agri-Food Safety, Anhui Agricultural University , Hefei 230036, China
| | - Min Liao
- School of Plant Protection, Provincial Key Laboratory for Agri-Food Safety, and ‡School of Resource & Environment, Provincial Key Laboratory for Agri-Food Safety, Anhui Agricultural University , Hefei 230036, China
| | - Xiangwei Wu
- School of Plant Protection, Provincial Key Laboratory for Agri-Food Safety, and ‡School of Resource & Environment, Provincial Key Laboratory for Agri-Food Safety, Anhui Agricultural University , Hefei 230036, China
| | - Rimao Hua
- School of Plant Protection, Provincial Key Laboratory for Agri-Food Safety, and ‡School of Resource & Environment, Provincial Key Laboratory for Agri-Food Safety, Anhui Agricultural University , Hefei 230036, China
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Zhang C, Hu X, Luo J, Wu Z, Wang L, Li B, Wang Y, Sun G. Degradation dynamics of glyphosate in different types of citrus orchard soils in China. Molecules 2015; 20:1161-75. [PMID: 25587790 PMCID: PMC6272633 DOI: 10.3390/molecules20011161] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 01/06/2015] [Indexed: 12/02/2022] Open
Abstract
Glyphosate formulations that are used as a broad-spectrum systemic herbicide have been widely applied in agriculture, causing increasing concerns about residues in soils. In this study, the degradation dynamics of glyphosate in different types of citrus orchard soils in China were evaluated under field conditions. Glyphosate soluble powder and aqueous solution were applied at 3000 and 5040 g active ingredient/hm2, respectively, in citrus orchard soils, and periodically drawn soil samples were analyzed by high performance liquid chromatography. The results showed that the amount of glyphosate and its degradation product aminomethylphosphonic acid (AMPA) in soils was reduced with the increase of time after application of glyphosate formulations. Indeed, the amount of glyphosate in red soil from Hunan and Zhejiang Province, and clay soil from Guangxi Province varied from 0.13 to 0.91 µg/g at 42 days after application of aqueous solution. Furthermore, the amount of glyphosate in medium loam from Zhejiang and Guangdong Province, and brown loam from Guizhou Province varied from less than 0.10 to 0.14 µg/g, while the amount of AMPA varied from less than 0.10 to 0.99 µg/g at 42 days after application of soluble powder. Overall, these findings demonstrated that the degradation dynamics of glyphosate aqueous solution and soluble powder as well as AMPA depend on the physicochemical properties of the applied soils, in particular soil pH, which should be carefully considered in the application of glyphosate herbicide.
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Affiliation(s)
- Changpeng Zhang
- MOA Key Lab for Pesticide Residue Detection, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Xiuqing Hu
- MOA Key Lab for Pesticide Residue Detection, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Jinyan Luo
- Shanghai Extension and Service Center of Agriculture Technical, Shanghai 201103, China.
| | - Zhiyi Wu
- Zhejiang Entry-Exit Inspection and Quarantine Bureau, Hangzhou 310012, China.
| | - Li Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Bin Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Yanli Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Plant Pest and Disease Control, Key Laboratory of Detection for Pesticide Residues, Ministry of Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Guochang Sun
- State Key Laboratory Breeding Base for Zhejiang Sustainable Plant Pest and Disease Control, Key Laboratory of Detection for Pesticide Residues, Ministry of Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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