UNBRANCHED3 Expression and Inflorescence Development is Mediated by UNBRANCHED2 and the Distal Enhancer, KRN4, in Maize

Autoři: Yanfang Du aff001;  Lei Liu aff001;  Yong Peng aff001;  Manfei Li aff001;  Yunfu Li aff001;  Dan Liu aff001;  Xingwang Li aff001;  Zuxin Zhang aff001
Působiště autorů: National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China aff001
Vyšlo v časopise: UNBRANCHED3 Expression and Inflorescence Development is Mediated by UNBRANCHED2 and the Distal Enhancer, KRN4, in Maize. PLoS Genet 16(4): e32767. doi:10.1371/journal.pgen.1008764
Kategorie: Research Article
doi: 10.1371/journal.pgen.1008764


Enhancers are cis-acting DNA segments with the ability to increase target gene expression. They show high sensitivity to DNase and contain specific DNA elements in an open chromatin state that allows the binding of transcription factors (TFs). While numerous enhancers are annotated in the maize genome, few have been characterized genetically. KERNEL ROW NUMBER4 (KRN4), an intergenic quantitative trait locus for kernel row number, is assumed to be a cis-regulatory element of UNBRANCHED3 (UB3), a key inflorescence gene. However, the mechanism by which KRN4 controls UB3 expression remains unclear. Here, we found that KRN4 exhibits an open chromatin state, harboring sequences that showed high enhancer activity toward the 35S and UB3 promoters. KRN4 is bound by UB2-centered transcription complexes and interacts with the UB3 promoter by three duplex interactions to affect UB3 expression. Sequence variation at KRN4 enhances ub2 and ub3 mutant ear fasciation. Therefore, we suggest that KRN4 functions as a distal enhancer of the UB3 promoter via chromatin interactions and recruitment of UB2-centered transcription complexes for the fine-tuning of UB3 expression in meristems of ear inflorescences. These results provide evidence that an intergenic region helps to finely tune gene expression, providing a new perspective on the genetic control of quantitative traits.

Klíčová slova:

Ears – Gene expression – Gene regulation – Chromatin – Inflorescences – Luciferase – Maize – Plant genomics


1. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, et al. The B73 maize genome: complexity, diversity, and dynamics. Science. 2009; 326(5956):1112–5. doi: 10.1126/science.1178534 19965430

2. Springer NM, Anderson SN, Andorf CM, Ahern KR, Bai F, Barad O, et al. The maize W22 genome provides a foundation for functional genomics and transposon biology. Nat Genet. 2018; 50(9):1282–1288. doi: 10.1038/s41588-018-0158-0 30061736

3. Michael T.P., VanBuren R. Progress, challenges and the future of crop genomes. Curr Opin Plant Biol. 2015; 24:71–81. doi: 10.1016/j.pbi.2015.02.002 25703261

4. Castillo-Davis C.I. The evolution of noncoding DNA: how much junk, how much func? Trends Genet. 2005; 21(10):533–6. doi: 10.1016/j.tig.2005.08.001 16098630

5. Alexander R.P., Fang G., Rozowsky J., Snyder M., Gerstein M.B. Annotating non-coding regions of the genome. Nat Rev Genet. 11,559–571 (2010). doi: 10.1038/nrg2814 20628352

6. Zhang X., Bernatavichute Y.V., Cokus S., Pellegrini M., Jacobsen S.E. Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol. 2009; 10(6):R62. doi: 10.1186/gb-2009-10-6-r62 19508735

7. Du Z, Li H, Wei Q, Zhao X, Wang C, Zhu Q, et al. Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica. Mol Plant. 2013; 6(5):1463–72. doi: 10.1093/mp/sst018 23355544

8. Rodgers-Melnick E., Vera D.L., Bass H.W., Buckler E.S. Open chromatin reveals the functional maize genome. Proc Natl Acad Sci USA 2016; 113(22):E3177–84. doi: 10.1073/pnas.1525244113 27185945

9. Liu J, Chen J, Zheng X, Wu F, Lin Q, Heng Y, et al. GW5 acts in the brassinosteroid signalling pathway to regulate grain width and weight in rice. Nat Plants. 2017; 3:17043. doi: 10.1038/nplants.2017.43 28394310

10. Stam M., Belele C., Dorweiler J.E., Chandler V.L. Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation. Genes Dev. 2002; 16(15):1906–18. doi: 10.1101/gad.1006702 12154122

11. Arteaga-Vazquez M.A., Chandler V.L. Paramutation in maize: RNA mediated trans-generational gene silencing. Curr Opin Genet Dev. 2010; 20(2):156–63. doi: 10.1016/j.gde.2010.01.008 20153628

12. Castelletti S., Tuberosa R., Pindo M., Salvi S. A MITE transposon insertion is associated with differential methylation at the maize flowering time QTL Vgt1. G3 (Bethesda). 2014; 4(5):805–12.

13. Salvi S, Sponza G, Morgante M, Tomes D, Niu X, Fengler KA, et al. Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc Natl Acad Sci USA. 2007; 104(27):11376–81. doi: 10.1073/pnas.0704145104 17595297

14. Clark R.M., Wagler T.N., Quijada P., Doebley J. A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nat Genet. 2006; 38(5):594–7. doi: 10.1038/ng1784 16642024

15. Studer A., Zhao Q., Ross-Ibarra J., Doebley J. Identification of a functional transposon insertion in the maize domestication gene tb1. Nat Genet. 2011; 43(11):1160–3. doi: 10.1038/ng.942 21946354

16. Bird C.P., Stranger B.E., Dermitzakis E.T. Functional variation and evolution of non-coding DNA. Curr Opin Genet Dev. 2006; 16(6):559–64. doi: 10.1016/j.gde.2006.10.003 17055246

17. Wei J.W., Huang K., Yang C., Kang C.S. Non-coding RNAs as regulators in epigenetics. Oncol Rep. 2017; 37(1):3–9. doi: 10.3892/or.2016.5236 27841002

18. McCue A.D., Nuthikattu S., Slotkin R.K. Genome-wide identification of genes regulated in trans by transposable element small interfering RNAs. RNA Biol. 2013; 10(8):1379–95. doi: 10.4161/rna.25555 23863322

19. Denker A., de Laat W. A long-distance chromatin affair. Cell. 2015; 162(5):942–3. doi: 10.1016/j.cell.2015.08.022 26317462

20. Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012; 148(1–2):84–98. doi: 10.1016/j.cell.2011.12.014 22265404

21. Weber B., Zicola J., Oka R., Stam M. Plant enhancers: A call for discovery. Trends Plant Sci. 2016; 21(11):974–987. doi: 10.1016/j.tplants.2016.07.013 27593567

22. Zhu B., Zhang W., Zhang T., Liu B., Jiang J. Genome-wide prediction and validation of intergenic enhancers in Arabidopsis using open chromatin signatures. Plant Cell. 2015; 27(9):2415–26. doi: 10.1105/tpc.15.00537 26373455

23. Oka R, Zicola J, Weber B, Anderson SN, Hodgman C, Gent JI, et al. Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biol. 2017; 18(1):137. doi: 10.1186/s13059-017-1273-4 28732548

24. Li E, Liu H, Huang L, Zhang X, Dong X, Song W, et al. Long-range interactions between proximal and distal regulatory regions in maize. Nat Commun. 2019; 10(1):2633. doi: 10.1038/s41467-019-10603-4 31201330

25. Peng Y, Xiong D, Zhao L, Ouyang W, Wang S, Sun J, et al. Chromatin interaction maps reveal genetic regulation for quantitative traits in maize. Nat Commun. 2019; 10(1):2632. doi: 10.1038/s41467-019-10602-5 31201335

26. Chuck G.S., Brown P.J., Meeley R., Hake S. Maize SBP-box transcription factors unbranched2 and unbranched3 affect yield traits by regulating the rate of lateral primordia initiation. Proc Natl Acad Sci USA. 2014; 111(52):18775–80. doi: 10.1073/pnas.1407401112 25512525

27. Liu L, Du Y, Shen X, Li M, Sun W, Huang J, et al. KRN4 controls quantitative variation in maize kernel row number. PLoS Genet. 2015; 1(11):e1005670.

28. Du Y, Liu L, Li M, Fang S, Shen X, Chu, et al. UNBRANCHED3 regulates branching by modulating cytokinin biosynthesis and signaling in maize and rice. New Phytol. 2017; 214(2):721–733. doi: 10.1111/nph.14391 28040882

29. Bommert P, Nagasawa NS, Jackson D. Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus. Nat Genet. 2013; 45(3):334–7. doi: 10.1038/ng.2534 23377180

30. Birkenbihl R.P., Jach G., Saedler H., Huijser P. Functional dissection of the plant-specific SBP-domain: overlap of the DNA-binding and nuclear localization domains. J Mol Biol. 2005; 352(3):585–96. doi: 10.1016/j.jmb.2005.07.013 16095614

31. Rowley MJ, Nichols MH, Lyu X, Ando-Kuri M, Rivera ISM, Hermetz K, et al. Evolutionarily conserved principles predict 3D chromatin organization. Mol Cell. 2017; 67(5):837–852.e7. doi: 10.1016/j.molcel.2017.07.022 28826674

32. Li X, Luo OJ, Wang P, Zheng M, Wang D, Piecuch E, et al. Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions. Nat Protoc. 2017; 12(5):899–915. doi: 10.1038/nprot.2017.012 28358394

33. Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA 2010; 107(50):21931–6. doi: 10.1073/pnas.1016071107 21106759

34. Pekowska A, Benoukraf T, Zacarias-Cabeza J, Belhocine M, Koch F, Holota H, et al. H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J. 2011; 30(20):4198–210. doi: 10.1038/emboj.2011.295 21847099

35. McPherson C.E., Shim E.Y., Friedman D.S., Zaret K.S. An active tissue-specific enhancer and bound transcription factors existing in a precisely positioned nucleosomal array. Cell. 1993; 75(2):387–98. doi: 10.1016/0092-8674(93)80079-t 8402920

36. Foley RC, Grossman C, Ellis JG, Llewellyn DJ, Dennis ES, Peacock WJ, et al. Isolation of a maize bZIP protein subfamily: candidates for the ocs-element transcription factor. Plant J. 1993; 3(5):669–79. 8374617

37. Singh K, Dennis ES, Ellis JG, Llewellyn DJ, Tokuhisa JG, Wahleithner JA, et al. OCSBF-1, a maize ocs enhancer binding factor: isolation and expression during development. Plant Cell. 1990; 2(9):891–90. doi: 10.1105/tpc.2.9.891 2152133

38. Zhang B., Foley R.C., Singh K.B. Isolation and characterization of two related Arabidopsis ocs-element bZIP binding proteins. Plant J. 1993; 4(4):711–6. doi: 10.1046/j.1365-313x.1993.04040711.x 8252072

39. Hood K.R., Baasiri R.A., Fritz S.E., Hood E.E. Biochemical and tissue print analyses of hydroxyproline-rich glycoproteins in cell walls of sporophytic maize tissues. Plant Physiol. 1991; 96(4):1214–9. doi: 10.1104/pp.96.4.1214 16668322

40. Sidorenko L., Li X., Tagliani L., Bowen B., Peterson T. Characterization of the regulatory elements of the maize P-rr gene by transient expression assays. Plant Mol Biol. 1999; 39(1):11–9. doi: 10.1023/a:1006172815663 10080705

41. Zheng L, McMullen MD, Bauer E, Schön CC, Gierl A, Frey M, et al. Prolonged expression of the BX1 signature enzyme is associated with a recombination hotspot in the benzoxazinoid gene cluster in Zea mays. J Exp Bot. 2015; 66(13):3917–30. doi: 10.1093/jxb/erv192 25969552

42. Wallace JG, Bradbury PJ, Zhang N, Gibon Y, Stitt M4, Buckler ES, et al. Association mapping across numerous traits reveals patterns of functional variation in maize. PLoS Genet. 2014; 10(12):e1004845. doi: 10.1371/journal.pgen.1004845 25474422

43. Bulger M., Groudine M. Functional and mechanistic diversity of distal transcription enhancers. Cell. 2011; 144(3):327–39. doi: 10.1016/j.cell.2011.01.024 21295696

44. Ong C.T., Corces V.G. Enhancer function: new insights into the regulation of tissue-specific gene expression. Nat Rev Genet. 2011; 12(4):283–93. doi: 10.1038/nrg2957 21358745

45. Krivega I., Dean A. Enhancer and promoter interactions-long distance calls. Curr Opin Genet Dev. 2012; 22(2):79–85. doi: 10.1016/j.gde.2011.11.001 22169023

46. Vernimmen D., Bickmore W.A. The hierarchy of transcriptional activation: from enhancer to promoter. Trends Genet. 2015; 31(12):696–708. doi: 10.1016/j.tig.2015.10.004 26599498

47. Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-André V, Sigova AA, et al. Super-enhancers in the control of cell identity and disease. Cell. 2013; 155(4):934–47. doi: 10.1016/j.cell.2013.09.053 24119843

48. Hnisz D., Shrinivas K., Young R.A., Chakraborty A.K., Sharp P.A. A phase separation model for transcriptional control. Cell. 2017; 169(1):13–23. doi: 10.1016/j.cell.2017.02.007 28340338

49. Boeynaems S, Alberti S, Fawzi NL, Mittag T, Polymenidou M, Rousseau F, et al. Protein phase separation: A new phase in cell biology. Trends Cell Biol. 2018; 28(6):420–435. doi: 10.1016/j.tcb.2018.02.004 29602697

50. Sabari BR, Dall'Agnese A, Boija A, Klein IA, Coffey EL, Shrinivas K, et al. Coactivator condensation at super-enhancers links phase separation and gene control. Science. 2018; 361(6400).

51. Jackson, D. P. In-situ hybridization in plants. pp. 1991; 163–174.

52. Yoo S.D., Cho Y.H., Sheen J. Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat Protoc. 2007; 2(7):1565–72. doi: 10.1038/nprot.2007.199 17585298

53. Wingett S.W., Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control. Version 2. F1000Res. 2018; 7:1338. doi: 10.12688/f1000research.15931.2 30254741

54. Kim D., Langmead B., Salzberg S.L. HISAT: a fast spliced aligner with low 716 memory requirements. Nat Methods. 2015; 12(4):357–60. doi: 10.1038/nmeth.3317 25751142

55. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008; 9(9):R137. doi: 10.1186/gb-2008-9-9-r137 18798982

56. Thorvaldsdóttir H., Robinson J.T., Mesirov J.P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013; 14(2):178–92. doi: 10.1093/bib/bbs017 22517427

57. Chen H, Zou Y, Shang Y, Lin H, Wang Y, Cai R, et al. Firefly luciferase complementation imaging assay for protein-protein interactions in plants. Plant Physiol. 2008; 146(2):368–76. doi: 10.1104/pp.107.111740 18065554

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