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For: Ricci WA, Lu Z, Ji L, Marand AP, Ethridge CL, Murphy NG, Noshay JM, Galli M, Mejía-Guerra MK, Colomé-Tatché M, Johannes F, Rowley MJ, Corces VG, Zhai J, Scanlon MJ, Buckler ES, Gallavotti A, Springer NM, Schmitz RJ, Zhang X. Widespread long-range cis-regulatory elements in the maize genome. Nat Plants 2019;5:1237-1249. [PMID: 31740773 PMCID: PMC6904520 DOI: 10.1038/s41477-019-0547-0] [Citation(s) in RCA: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/09/2019] [Indexed: 05/03/2023]
Number Cited by Other Article(s)
151
Crisp PA, Bhatnagar-Mathur P, Hundleby P, Godwin ID, Waterhouse PM, Hickey LT. Beyond the gene: epigenetic and cis-regulatory targets offer new breeding potential for the future. Curr Opin Biotechnol 2021;73:88-94. [PMID: 34348216 DOI: 10.1016/j.copbio.2021.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/06/2021] [Indexed: 12/20/2022]
152
Zhao H, Tu Z, Liu Y, Zong Z, Li J, Liu H, Xiong F, Zhan J, Hu X, Xie W. PlantDeepSEA, a deep learning-based web service to predict the regulatory effects of genomic variants in plants. Nucleic Acids Res 2021;49:W523-W529. [PMID: 34037796 PMCID: PMC8262748 DOI: 10.1093/nar/gkab383] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/09/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022]  Open
153
Meng F, Zhao H, Zhu B, Zhang T, Yang M, Li Y, Han Y, Jiang J. Genomic editing of intronic enhancers unveils their role in fine-tuning tissue-specific gene expression in Arabidopsis thaliana. THE PLANT CELL 2021;33:1997-2014. [PMID: 33764459 PMCID: PMC8290289 DOI: 10.1093/plcell/koab093] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 03/23/2021] [Indexed: 05/22/2023]
154
Wu D, Tanaka R, Li X, Ramstein GP, Cu S, Hamilton JP, Buell CR, Stangoulis J, Rocheford T, Gore MA. High-resolution genome-wide association study pinpoints metal transporter and chelator genes involved in the genetic control of element levels in maize grain. G3-GENES GENOMES GENETICS 2021;11:6156830. [PMID: 33677522 PMCID: PMC8759812 DOI: 10.1093/g3journal/jkab059] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/21/2021] [Indexed: 12/18/2022]
155
Huang Y, Sicar S, Ramirez-Prado JS, Manza-Mianza D, Antunez-Sanchez J, Brik-Chaouche R, Rodriguez-Granados NY, An J, Bergounioux C, Mahfouz MM, Hirt H, Crespi M, Concia L, Barneche F, Amiard S, Probst AV, Gutierrez-Marcos J, Ariel F, Raynaud C, Latrasse D, Benhamed M. Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis. Genome Res 2021;31:1230-1244. [PMID: 34083408 PMCID: PMC8256866 DOI: 10.1101/gr.273771.120] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 05/20/2021] [Indexed: 11/24/2022]
156
Song B, Buckler ES, Wang H, Wu Y, Rees E, Kellogg EA, Gates DJ, Khaipho-Burch M, Bradbury PJ, Ross-Ibarra J, Hufford MB, Romay MC. Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize. Genome Res 2021;31:1245-1257. [PMID: 34045362 PMCID: PMC8256870 DOI: 10.1101/gr.266528.120] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 05/21/2021] [Indexed: 01/16/2023]
157
Tripathi RK, Wilkins O. Single cell gene regulatory networks in plants: Opportunities for enhancing climate change stress resilience. PLANT, CELL & ENVIRONMENT 2021;44:2006-2017. [PMID: 33522607 PMCID: PMC8359182 DOI: 10.1111/pce.14012] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 05/05/2023]
158
DNA methylation-linked chromatin accessibility affects genomic architecture in Arabidopsis. Proc Natl Acad Sci U S A 2021;118:2023347118. [PMID: 33495321 PMCID: PMC7865151 DOI: 10.1073/pnas.2023347118] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
159
Jores T, Tonnies J, Wrightsman T, Buckler ES, Cuperus JT, Fields S, Queitsch C. Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters. NATURE PLANTS 2021;7:842-855. [PMID: 34083762 PMCID: PMC10246763 DOI: 10.1038/s41477-021-00932-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/27/2021] [Indexed: 05/24/2023]
160
Pei L, Li G, Lindsey K, Zhang X, Wang M. Plant 3D genomics: the exploration and application of chromatin organization. THE NEW PHYTOLOGIST 2021;230:1772-1786. [PMID: 33560539 PMCID: PMC8252774 DOI: 10.1111/nph.17262] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/01/2021] [Indexed: 05/29/2023]
161
Provart NJ, Brady SM, Parry G, Schmitz RJ, Queitsch C, Bonetta D, Waese J, Schneeberger K, Loraine AE. Anno genominis XX: 20 years of Arabidopsis genomics. THE PLANT CELL 2021;33:832-845. [PMID: 33793861 PMCID: PMC8226293 DOI: 10.1093/plcell/koaa038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/09/2020] [Indexed: 05/04/2023]
162
Wang M, Li Z, Zhang Y, Zhang Y, Xie Y, Ye L, Zhuang Y, Lin K, Zhao F, Guo J, Teng W, Zhang W, Tong Y, Xue Y, Zhang Y. An atlas of wheat epigenetic regulatory elements reveals subgenome divergence in the regulation of development and stress responses. THE PLANT CELL 2021;33:865-881. [PMID: 33594406 PMCID: PMC8226296 DOI: 10.1093/plcell/koab028] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 01/25/2021] [Indexed: 05/22/2023]
163
Marand AP, Chen Z, Gallavotti A, Schmitz RJ. A cis-regulatory atlas in maize at single-cell resolution. Cell 2021;184:3041-3055.e21. [PMID: 33964211 DOI: 10.1101/2020.09.27.315499] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/04/2021] [Accepted: 04/07/2021] [Indexed: 05/22/2023]
164
A cis-regulatory atlas in maize at single-cell resolution. Cell 2021;184:3041-3055.e21. [PMID: 33964211 DOI: 10.1016/j.cell.2021.04.014] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/04/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023]
165
Purugganan MD, Jackson SA. Advancing crop genomics from lab to field. Nat Genet 2021;53:595-601. [PMID: 33958781 DOI: 10.1038/s41588-021-00866-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/22/2021] [Indexed: 01/23/2023]
166
Lin Y, Zhao H, Kotlarz M, Jiang J. Enhancer-mediated reporter gene expression in Arabidopsis thaliana: a forward genetic screen. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021;106:661-671. [PMID: 33547831 DOI: 10.1111/tpj.15189] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
167
Liu A, Bergmann DC. How to build a crop plant: Defining the cis-regulatory landscape of maize. Cell 2021;184:2804-2806. [PMID: 34048703 DOI: 10.1016/j.cell.2021.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
168
Wang P, Jin S, Chen X, Wu L, Zheng Y, Yue C, Guo Y, Zhang X, Yang J, Ye N. Chromatin accessibility and translational landscapes of tea plants under chilling stress. HORTICULTURE RESEARCH 2021;8:96. [PMID: 33931606 PMCID: PMC8087716 DOI: 10.1038/s41438-021-00529-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 05/03/2023]
169
Li M, Noshay JM, Dong X, Springer NM, Li Q. A capture-based assay for detection and characterization of transposon polymorphisms in maize. G3-GENES GENOMES GENETICS 2021;11:6255745. [PMID: 33905487 PMCID: PMC8495914 DOI: 10.1093/g3journal/jkab138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 04/15/2021] [Indexed: 11/14/2022]
170
Huang MK, Zhang L, Zhou LM, Yung WS, Li MW, Lam HM. Genomic Features of Open Chromatin Regions (OCRs) in Wild Soybean and Their Effects on Gene Expressions. Genes (Basel) 2021;12:640. [PMID: 33923056 PMCID: PMC8146116 DOI: 10.3390/genes12050640] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 11/16/2022]  Open
171
Zhang TQ, Chen Y, Liu Y, Lin WH, Wang JW. Single-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root. Nat Commun 2021;12:2053. [PMID: 33824350 PMCID: PMC8024345 DOI: 10.1038/s41467-021-22352-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 03/08/2021] [Indexed: 12/26/2022]  Open
172
Zhang Q, Guan P, Zhao L, Ma M, Xie L, Li Y, Zheng R, Ouyang W, Wang S, Li H, Zhang Y, Peng Y, Cao Z, Zhang W, Xiao Q, Xiao Y, Fu T, Li G, Li X, Shen J. Asymmetric epigenome maps of subgenomes reveal imbalanced transcription and distinct evolutionary trends in Brassica napus. MOLECULAR PLANT 2021;14:604-619. [PMID: 33387675 DOI: 10.1016/j.molp.2020.12.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/28/2020] [Accepted: 12/28/2020] [Indexed: 05/20/2023]
173
Wang X, Aguirre L, Rodríguez-Leal D, Hendelman A, Benoit M, Lippman ZB. Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit. NATURE PLANTS 2021;7:419-427. [PMID: 33846596 DOI: 10.1038/s41477-021-00898-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/10/2021] [Indexed: 05/22/2023]
174
Technologies enabling rapid crop improvements for sustainable agriculture: example pennycress (Thlaspi arvense L.). Emerg Top Life Sci 2021;5:325-335. [DOI: 10.1042/etls20200330] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/17/2021] [Accepted: 03/04/2021] [Indexed: 11/17/2022]
175
Strable J. Developmental genetics of maize vegetative shoot architecture. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021;41:19. [PMID: 37309417 PMCID: PMC10236122 DOI: 10.1007/s11032-021-01208-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/25/2021] [Indexed: 06/13/2023]
176
Chen Z, Gallavotti A. Improving architectural traits of maize inflorescences. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021;41:21. [PMID: 37309422 PMCID: PMC10236070 DOI: 10.1007/s11032-021-01212-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/02/2021] [Indexed: 06/13/2023]
177
Brooks MD, Juang CL, Katari MS, Alvarez JM, Pasquino A, Shih HJ, Huang J, Shanks C, Cirrone J, Coruzzi GM. ConnecTF: A platform to integrate transcription factor-gene interactions and validate regulatory networks. PLANT PHYSIOLOGY 2021;185:49-66. [PMID: 33631799 PMCID: PMC8133578 DOI: 10.1093/plphys/kiaa012] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/27/2020] [Indexed: 05/08/2023]
178
Zhou L, Huang Y, Wang Q, Guo D. Chromatin Accessibility Is Associated with Artemisinin Biosynthesis Regulation in Artemisia annua. Molecules 2021;26:molecules26041194. [PMID: 33672342 PMCID: PMC7926469 DOI: 10.3390/molecules26041194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 11/21/2022]  Open
179
Yocca AE, Lu Z, Schmitz RJ, Freeling M, Edger PP. Evolution of Conserved Noncoding Sequences in Arabidopsis thaliana. Mol Biol Evol 2021;38:2692-2703. [PMID: 33565589 PMCID: PMC8233505 DOI: 10.1093/molbev/msab042] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
180
Ouyang W, Xiao Q, Li G, Li X. Technologies for Capturing 3D Genome Architecture in Plants. TRENDS IN PLANT SCIENCE 2021;26:196-197. [PMID: 33199261 DOI: 10.1016/j.tplants.2020.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
181
Lucero L, Ferrero L, Fonouni-Farde C, Ariel F. Functional classification of plant long noncoding RNAs: a transcript is known by the company it keeps. THE NEW PHYTOLOGIST 2021;229:1251-1260. [PMID: 32880949 DOI: 10.1111/nph.16903] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/05/2020] [Indexed: 05/27/2023]
182
Minnoye L, Marinov GK, Krausgruber T, Pan L, Marand AP, Secchia S, Greenleaf WJ, Furlong EEM, Zhao K, Schmitz RJ, Bock C, Aerts S. Chromatin accessibility profiling methods. NATURE REVIEWS. METHODS PRIMERS 2021;1:10. [PMID: 38410680 PMCID: PMC10895463 DOI: 10.1038/s43586-020-00008-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/01/2020] [Indexed: 02/06/2023]
183
Srikant T, Drost HG. How Stress Facilitates Phenotypic Innovation Through Epigenetic Diversity. FRONTIERS IN PLANT SCIENCE 2021;11:606800. [PMID: 33519857 PMCID: PMC7843580 DOI: 10.3389/fpls.2020.606800] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/16/2020] [Indexed: 05/14/2023]
184
Fagny M, Kuijjer ML, Stam M, Joets J, Turc O, Rozière J, Pateyron S, Venon A, Vitte C. Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks. Front Genet 2021;11:606285. [PMID: 33505431 PMCID: PMC7834273 DOI: 10.3389/fgene.2020.606285] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/03/2020] [Indexed: 12/27/2022]  Open
185
Zhou C, Yuan Z, Ma X, Yang H, Wang P, Zheng L, Zhang Y, Liu X. Accessible chromatin regions and their functional interrelations with gene transcription and epigenetic modifications in sorghum genome. PLANT COMMUNICATIONS 2021;2:100140. [PMID: 33511349 PMCID: PMC7816095 DOI: 10.1016/j.xplc.2020.100140] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/23/2020] [Accepted: 12/29/2020] [Indexed: 05/23/2023]
186
Deschamps S, Crow JA, Chaidir N, Peterson-Burch B, Kumar S, Lin H, Zastrow-Hayes G, May GD. Chromatin loop anchors contain core structural components of the gene expression machinery in maize. BMC Genomics 2021;22:23. [PMID: 33407087 PMCID: PMC7789236 DOI: 10.1186/s12864-020-07324-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/14/2020] [Indexed: 12/28/2022]  Open
187
Xu X, Crow M, Rice BR, Li F, Harris B, Liu L, Demesa-Arevalo E, Lu Z, Wang L, Fox N, Wang X, Drenkow J, Luo A, Char SN, Yang B, Sylvester AW, Gingeras TR, Schmitz RJ, Ware D, Lipka AE, Gillis J, Jackson D. Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery. Dev Cell 2021;56:557-568.e6. [PMID: 33400914 DOI: 10.1016/j.devcel.2020.12.015] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/31/2020] [Accepted: 12/15/2020] [Indexed: 12/30/2022]
188
Huang M, Zhang L, Zhou L, Wang M, Yung WS, Wang Z, Duan S, Xiao Z, Wang Q, Wang X, Li MW, Lam HM. An expedient survey and characterization of the soybean JAGGED 1 (GmJAG1) transcription factor binding preference in the soybean genome by modified ChIPmentation on soybean protoplasts. Genomics 2021;113:344-355. [PMID: 33338631 DOI: 10.1016/j.ygeno.2020.12.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/11/2020] [Accepted: 12/13/2020] [Indexed: 12/21/2022]
189
DNA methylation mutants in Physcomitrella patens elucidate individual roles of CG and non-CG methylation in genome regulation. Proc Natl Acad Sci U S A 2020;117:33700-33710. [PMID: 33376225 DOI: 10.1073/pnas.2011361117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
190
Ouyang W, Xiong D, Li G, Li X. Unraveling the 3D Genome Architecture in Plants: Present and Future. MOLECULAR PLANT 2020;13:1676-1693. [PMID: 33065269 DOI: 10.1016/j.molp.2020.10.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 08/09/2020] [Accepted: 10/08/2020] [Indexed: 05/02/2023]
191
Cai YM, Kallam K, Tidd H, Gendarini G, Salzman A, Patron NJ. Rational design of minimal synthetic promoters for plants. Nucleic Acids Res 2020;48:11845-11856. [PMID: 32856047 DOI: 10.1101/2020.05.14.095406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/03/2020] [Accepted: 08/04/2020] [Indexed: 05/20/2023]  Open
192
Cai YM, Kallam K, Tidd H, Gendarini G, Salzman A, Patron N. Rational design of minimal synthetic promoters for plants. Nucleic Acids Res 2020;48:11845-11856. [PMID: 32856047 PMCID: PMC7708054 DOI: 10.1093/nar/gkaa682] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/03/2020] [Accepted: 08/04/2020] [Indexed: 12/12/2022]  Open
193
Numaguchi K, Akagi T, Kitamura Y, Ishikawa R, Ishii T. Interspecific introgression and natural selection in the evolution of Japanese apricot (Prunus mume). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020;104:1551-1567. [PMID: 33048374 DOI: 10.1111/tpj.15020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/09/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
194
Xu G, Lyu J, Li Q, Liu H, Wang D, Zhang M, Springer NM, Ross-Ibarra J, Yang J. Evolutionary and functional genomics of DNA methylation in maize domestication and improvement. Nat Commun 2020;11:5539. [PMID: 33139747 PMCID: PMC7606521 DOI: 10.1038/s41467-020-19333-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 10/08/2020] [Indexed: 12/23/2022]  Open
195
Galli M, Feng F, Gallavotti A. Mapping Regulatory Determinants in Plants. Front Genet 2020;11:591194. [PMID: 33193733 PMCID: PMC7655918 DOI: 10.3389/fgene.2020.591194] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/28/2020] [Indexed: 12/24/2022]  Open
196
Cis-regulatory units of grass genomes identified by their DNA methylation. Proc Natl Acad Sci U S A 2020;117:25198-25199. [PMID: 33008886 DOI: 10.1073/pnas.2017729117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
197
Ouyang W, Cao Z, Xiong D, Li G, Li X. Decoding the plant genome: From epigenome to 3D organization. J Genet Genomics 2020;47:425-435. [PMID: 33023833 DOI: 10.1016/j.jgg.2020.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 12/25/2022]
198
Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes. Proc Natl Acad Sci U S A 2020;117:23991-24000. [PMID: 32879011 DOI: 10.1073/pnas.2010250117] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
199
Huang Y, Rodriguez-Granados NY, Latrasse D, Raynaud C, Benhamed M, Ramirez-Prado JS. The matrix revolutions: towards the decoding of the plant chromatin three-dimensional reality. JOURNAL OF EXPERIMENTAL BOTANY 2020;71:5129-5147. [PMID: 32639553 DOI: 10.1093/jxb/eraa322] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
200
Dong P, Tu X, Liang Z, Kang BH, Zhong S. Plant and animal chromatin three-dimensional organization: similar structures but different functions. JOURNAL OF EXPERIMENTAL BOTANY 2020;71:5119-5128. [PMID: 32374833 DOI: 10.1093/jxb/eraa220] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
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