Genome-Wide Identification of NAP1 and Function Analysis in Moso Bamboo ()

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2022 Jun 24

PMID 35742936

Authors

Yaxing Zhang

Jun Zhang

Deming Yang

Yandong Jin

Xuqing Liu

Zeyu Zhang

Lianfeng Gu

Hangxiao Zhang

Affiliations

Soon will be listed here.

Abstract

The nucleosome assembly protein 1 (NAP1) family is the main histone chaperone of histone H2A-H2B. To explore the function of NAP1 family genes in moso bamboo (), characterized by extremely rapid growth and a long flowering cycle, we originally conducted a genome-wide analysis of the PheNAP1 gene. The phylogenetic relationship, gene expression pattern, DNA methylation, and histone modification were analyzed. Eventually, 12 PheNAP1 genes were recognized from the genome, divided into two sorts: the NRP subfamily (four members) and the NAP subfamily (eight members). Highly conserved motifs exist in each subfamily, which are distinct between subfamilies. PheNAP1 was distributed homogeneously on 10 out of 24 chromosomes, and gene duplication contributed significantly to the enhancement of the PheNAP1 gene in the genome. -acting element analysis showed that PheNAP1 family genes are involved in light, hormone, and abiotic stress responses and may play an important role in the rapid growth and flowering. PheNAP1 exhibited the highest expression level in fast-growing shoots, indicating it is closely associated with the rapid growth of moso bamboo. Besides, PheNAP1 can rescue the early-flowering phenotype of , and it affected the expression of genes related to the flowering pathway, like , suggesting the vital role that PheNAP1 may take in the flowering process of moso bamboo. In addition, histone modification results showed that PheNAP1 could bind to phosphorylation-, acetylation-, and methylation-modified histones to further regulate gene expression. A sketch appears: that PheNAP1 can accompany histones to regulate fast-growth- and flowering-related genes in moso bamboo. The consequences of this study enrich the understanding of the epigenetic regulation mechanism of bamboo plants and lays a foundation for further studies on the role of the NAP1 gene in and the function of chromatin regulation in forest growth and development.

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References

Ratcliffe O, Nadzan G, Reuber T, Riechmann J . Regulation of flowering in Arabidopsis by an FLC homologue. Plant Physiol. 2001; 126(1):122-32. PMC: 102287. DOI: 10.1104/pp.126.1.122. View

Chen C, Chen H, Zhang Y, Thomas H, Frank M, He Y . TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Mol Plant. 2020; 13(8):1194-1202. DOI: 10.1016/j.molp.2020.06.009. View

Zhao H, Gao Z, Wang L, Wang J, Wang S, Fei B . Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis). Gigascience. 2018; 7(10). PMC: 6204424. DOI: 10.1093/gigascience/giy115. View

Wang Y, Zhong Z, Zhang Y, Xu L, Feng S, Rayatpisheh S . NAP1-RELATED PROTEIN1 and 2 negatively regulate H2A.Z abundance in chromatin in Arabidopsis. Nat Commun. 2020; 11(1):2887. PMC: 7280298. DOI: 10.1038/s41467-020-16691-x. View

Pertea M, Pertea G, Antonescu C, Chang T, Mendell J, Salzberg S . StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015; 33(3):290-5. PMC: 4643835. DOI: 10.1038/nbt.3122. View

Wang Y, Gao Y, Zhang H, Wang H, Liu X, Xu X . Genome-Wide Profiling of Circular RNAs in the Rapidly Growing Shoots of Moso Bamboo (Phyllostachys edulis). Plant Cell Physiol. 2019; 60(6):1354-1373. DOI: 10.1093/pcp/pcz043. View

Liu Z, Zhu Y, Gao J, Yu F, Dong A, Shen W . Molecular and reverse genetic characterization of NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) genes unravels their function in transcription and nucleotide excision repair in Arabidopsis thaliana. Plant J. 2009; 59(1):27-38. DOI: 10.1111/j.1365-313X.2009.03844.x. View

Lin X, Chow T, Chen H, Liu C, Chou S, Huang B . Understanding bamboo flowering based on large-scale analysis of expressed sequence tags. Genet Mol Res. 2010; 9(2):1085-93. DOI: 10.4238/vol9-2gmr804. View

Galichet A, Gruissem W . Developmentally controlled farnesylation modulates AtNAP1;1 function in cell proliferation and cell expansion during Arabidopsis leaf development. Plant Physiol. 2006; 142(4):1412-26. PMC: 1676069. DOI: 10.1104/pp.106.088344. View

10.

Gurley L, DANNA J, Barham S, Deaven L, Tobey R . Histone phosphorylation and chromatin structure during mitosis in Chinese hamster cells. Eur J Biochem. 1978; 84(1):1-15. DOI: 10.1111/j.1432-1033.1978.tb12135.x. View

11.

Zhu Y, Dong A, Meyer D, Pichon O, Renou J, Cao K . Arabidopsis NRP1 and NRP2 encode histone chaperones and are required for maintaining postembryonic root growth. Plant Cell. 2006; 18(11):2879-92. PMC: 1693930. DOI: 10.1105/tpc.106.046490. View

12.

Zhang W, Lee H, Koo D, Jiang J . Epigenetic modification of centromeric chromatin: hypomethylation of DNA sequences in the CENH3-associated chromatin in Arabidopsis thaliana and maize. Plant Cell. 2008; 20(1):25-34. PMC: 2254920. DOI: 10.1105/tpc.107.057083. View

13.

Yoon H, Kim M, Lee S, Hwang I, Bahk J, Hong J . Molecular cloning and functional characterization of a cDNA encoding nucleosome assembly protein 1 (NAP-1) from soybean. Mol Gen Genet. 1995; 249(5):465-73. DOI: 10.1007/BF00290572. View

14.

Howe G, Yoshida Y . Evolutionary Origin of JAZ Proteins and Jasmonate Signaling. Mol Plant. 2019; 12(2):153-155. DOI: 10.1016/j.molp.2019.01.015. View

15.

Pertea M, Kim D, Pertea G, Leek J, Salzberg S . Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016; 11(9):1650-67. PMC: 5032908. DOI: 10.1038/nprot.2016.095. View

16.

Kumar S, Stecher G, Li M, Knyaz C, Tamura K . MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 2018; 35(6):1547-1549. PMC: 5967553. DOI: 10.1093/molbev/msy096. View

17.

Wang Y, Tang H, DeBarry J, Tan X, Li J, Wang X . MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012; 40(7):e49. PMC: 3326336. DOI: 10.1093/nar/gkr1293. View

18.

Prakash A, Jeffryes M, Bateman A, Finn R . The HMMER Web Server for Protein Sequence Similarity Search. Curr Protoc Bioinformatics. 2017; 60:3.15.1-3.15.23. DOI: 10.1002/cpbi.40. View

19.

Wang D, Wan H, Zhang S, Yu J . Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates. Biol Direct. 2009; 4:20. PMC: 2702329. DOI: 10.1186/1745-6150-4-20. View

20.

Zhou W, Zhu Y, Dong A, Shen W . Histone H2A/H2B chaperones: from molecules to chromatin-based functions in plant growth and development. Plant J. 2015; 83(1):78-95. DOI: 10.1111/tpj.12830. View