低温胁迫下组蛋白H3K18cr在水稻全基因组上的动态变化特征解析

doi:10.3724/SP.J.1006.2023.22059

Abstract

Abstract:

Histone modifications play an important role in response to abiotic stresses in rice. Crotonylation is a novel histone modification, and the changes of crotonylation in rice subjected to low temperature stress are rarely reported. In this study, RNA-seq and ChIP-seq were performed on normal-grown and cold-treated rice seedlings of rice variety ‘Nipponbare’, followed by combined analysis of the regulatory characteristics of the crotonylation modification at the histone H3 lysine 18-specific site (H3K18cr) on gene expression under cold stress. The results showed that H3K18cr was mainly enriched in the first exon and intergenic region and had positive correlation with gene expression and gene length. The global distribution of H3K18cr in rice genome did not change under cold stress, but WB and ChIP-seq results indicated that the overall modification level decreased. The differential modification analysis revealed that there were significant increase and decrease of 899 genes and 409 genes in the modification after cold stress, respectively. Association analysis with RNA-seq showed that a total of 199 genes had increased levels of H3K18cr modification and up-regulated expression levels. GO enrichment revealed that these genes were mainly involved in the processes such as the regulation of transcriptional activity. Further analysis indicated that histone H3K18cr was involved in the response process of cold stress by regulating the expression of transcription factors such as OsDREB1A, OsEATB, OsAP2-39, and OsNAC9 in rice. The results provide a theoretical basis for further understanding the epigenetic mechanisms of histone crotonylation in response to cold stress in plants.

Key words: rice, cold stress, H3K18cr, gene expression

LIU Kai, CHEN Ji-Jin, LIU Shuai, CHEN Xu, ZHAO Xin-Ru, SUN Shang, XUE Chao, GONG Zhi-Yun. Dynamic change profile of histone H3K18cr on rice whole genome under cold stress[J].Acta Agronomica Sinica, 2023, 49(9): 2398-2411.

Figures/Tables 9

Table 1

Fig. 1

Table 2

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Table 3

Fig. 3

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Fig. 5

Table 4

Transcription factor functional information"

TF 家族 TF family	基因 ID Gene ID	基因名字 Gene name	功能 Function	参考文献References
Dof	LOC_Os01g15900	RDD1; OsDof-2	产量相关 Yield-related	[45]
Dof	LOC_Os10g26620	OsDof-26; OsDof27	非生物逆境抗性 Abiotic stress tolerance	[46]
ERF	LOC_Os09g35030	OsDREB1A	非生物逆境抗性 Abiotic stress tolerance	[28]
	LOC_Os09g28440	OsEATB	株高发育; 非生物逆境抗性 Plant growth; Abiotic stress tolerance	[37-38]
	LOC_Os04g52090	OsAP2-39	非生物逆境抗性 Abiotic stress tolerance	[39]
ARF	LOC_Os04g36054	OsARF9	—	—
NAC	LOC_Os03g60080	SNAC1; OsNAC9	非生物逆境抗性 Abiotic stress tolerance	[41]
NAC	LOC_Os07g12340	OsNAC3	非生物逆境抗性 Abiotic stress tolerance	[40]
CO-like	LOC_Os09g06464	OsCO3	调控光周期 Regulate photoperiodic	[47]
CO-like	LOC_Os02g39710	OsCOL4	调控抽穗期 Regulate heading date	[48]
HD-ZIP	LOC_Os04g45810	Oshox22	非生物逆境抗性 Abiotic stress tolerance	[49]
bZIP	LOC_Os02g16680	RITA-1; OsbZIP20	非生物逆境抗性; 重金属胁迫 Abiotic stress tolerance; High metal stress	[50-51]
HSF	LOC_Os02g13800	OsHsfC2a	非生物逆境抗性 Abiotic stress tolerance	[52]
DBB	LOC_Os02g39360	OsBBX4; OsBBX25	非生物逆境抗性 Abiotic stress tolerance	[44]
	LOC_Os09g35880	OsBBX29	非生物逆境抗性 Abiotic stress tolerance	[43]
	LOC_Os04g41560	OsBBX11	非生物逆境抗性 Abiotic stress tolerance	[43]
bHLH	LOC_Os01g50940	OsMYL1	调控JA信号 Regulate JA signal	[53]
	LOC_Os04g41229	OsbHLH111	调控糖信号 Regulate sugar signal	[54]
	LOC_Os09g29930	OsbHLH032	调控BR信号 Regulate BR signal	[55]
GRAS	LOC_Os02g44360	SCL6-IIb; OsHAM1	非生物逆境抗性 Abiotic stress tolerance	[42]
	LOC_Os02g45760	OsGRAS-10	—	—
	LOC_Os01g62460	OsGRAS-2	—	—
MYB_related	LOC_Os04g49450	OsMYBR1	非生物逆境抗性 Abiotic stress tolerance	[56]
	LOC_Os02g46030	OsMYB1R	非生物逆境抗性 Abiotic stress tolerance	[57]
	LOC_Os02g45670	—	—	—
	LOC_Os01g41900	OsDLN13	—	—

Table 4

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引物名称 Primer name	引物序列 Primer sequence (5'-3')	引物名称 Primer name	引物序列 Primer sequence (5'-3')
OsDREB1A-F	GACGTCCTGAGTGACATGG	OsTPS1-F	CATCGTGTCAGAGTTTGTCG
OsDREB1A-R	CTAGTAGCTCCAGAGTGGGA	OsTPS1-R	TCACGTACCTGTAGTGCTTC
OsDREB1B-F	GTCCACACTTTTCAGTGCGAG	OsLEA5-F	CTCACCTACACCCTCAAGTG
OsDREB1B-R	AATCTCGCACTGAAAAGTGTGG	OsLEA5-R	CGAGATGAGGAAGTCGTAGG
OsMYBS3-F	CAAGAACCAGAGACCCAAGT	OsV5A-F	CTTCTGCTGAGAATGGACCT
OsMYBS3-R	AAGCTGGAACAATCACTGGA	OsV5A-R	GAGGGTGGGATGATGAATGT
OsMADS57-F	GTTCCAGCACTCCATACAGC	ONAC095-F	CAGGAGGAGAGGTGGAGG
OsMADS57-R	GGCAGATGAAGTCCCAGTTCT	ONAC095-R	GGGGATGATGTCGAACTTGA

样品名 Sample name	重复数 Replicate	总序列数 Total clean reads	比对序列数 Total aligned reads	唯一比对序列数 Total unique reads	Peak数 Total peaks	共有Peak数 Common peaks	相关性 Correlation coefficient
H3K18cr-CK	1	45,952,156	45,268,705 (98.51%)	30,248,490 (65.83%)	25,218	20,077	0.92
H3K18cr-CK	2	48,099,538	47,360,155 (98.46%)	32,023,294 (66.58%)	29,127	20,077	0.92
H3K18cr-Cold	1	47,721,602	46,868,242 (98.21%)	30,382,217 (63.67%)	23,544	17,944	0.92
H3K18cr-Cold	2	48,128,162	47,304,118 (98.29%)	30,250,892 (62.85%)	29,632	17,944	0.92

样品名 Sample	重复数 Replicate	总序列数 Total reads	比对序列数 Aligned reads	表达基因数 FPKM>0	相关性 Correlation coefficient
正常温度Control	1	51,702,548	49,740,100 (92.62%)	26,992	0.94
正常温度Control	2	54,410,846	50,622,035 (93.04%)	24,422	0.94
低温Cold	1	61,244,656	52,044,285 (84.98%)	25,474	0.95
低温Cold	2	72,466,862	67,205,195 (92.74%)	27,191	0.95

Dynamic change profile of histone H3K18cr on rice whole genome under cold stress

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