Effects of Histone Deacetylase Inhibitor TSA Treatment on the Stem Development of Poplar

doi:10.13560/j.cnki.biotech.bull.1985.2024-0469

Abstract

Abstract:

【Objective】To investigate the molecular mechanism of histone acetylation modification on the development of stem in poplar trees.【Method】In this study, we treated 84K poplar（Populus alba × P. glandulosa）with the histone deacetylase inhibitor trichostatin A（TSA）for different duration, and then detected the alteration of histone acetylation level using Western blot, analyzed the gene expressions using RNA-Seq technology, and observed the stem phenotype using paraffin section and scanning electron microscopy.【Result】Western blot results showed that histone H3 acetylation levels increased in the stems with 2 μmol/L TSA treatment for 2 h. The acetylation level of histone H3 further increased as the TSA treatment time prolonged. The transcriptome results show that TSA treatment at 2 h and 12 h led to a total of 5 625 differentially expressed genes, with 2 158 up-regulated genes and 1 556 down-regulated genes at 2 h; 905 up-regulated genes and 1 006 down-regulated genes at 12 h. GO functional analysis showed that differentially up-regulated genes were enriched on cell wall components and DNA-binding transcription factors; while differentially down-regulated genes were enriched on photosynthesis and response to abiotic stimulus. KEGG pathway analysis showed that the differentially up-regulated genes were significant enriched in the lignin synthesis pathway. Compared to untreated group, the plant height decreased by 9.03% in the TSA treatment group of poplar, but the diameter of stem and the thickness of xylem was not affected significantly.【Conclusion】The increasing of histone acetylation levels might participate in the development of stem in poplar tree by enhancing the expression of genes related to transcriptional activity or cell wall components, which affects plant height.

Key words: transcriptome, histone acetylation, TSA, cell wall, 84K poplar

KOU Bei-sen, CHENG Meng-meng, GUO Xue-qin, GE Bin, LIU Di, LU Hai, LI Hui. Effects of Histone Deacetylase Inhibitor TSA Treatment on the Stem Development of Poplar[J]. Biotechnology Bulletin, 2025, 41(1): 240-251.

Figures/Tables 11

References 31

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样品 Simple	原始数据Raw reads(×10⁶)	高质量数据Clean reads(×10⁶)	Q20/%	Q30/%	比对到参考基因组 Alignment to reference genome /%	唯一参考序列数 Number of unique reference sequences/%	比对到参考基因组 Alignment to reference genome/%	唯一参考序列数 Number of unique reference sequences/%
WT0	47.77	42.32	97.2	91.3	96.69	84.51	96.69	84.51
CL2	48.93	42.84	97.3	91.8	96.44	84.38	96.44	84.38
CL12	46.02	42.46	97.1	91.4	96.98	85.22	96.98	85.22

样品 Simple	原始数据Raw reads(×10⁶)	高质量数据Clean reads(×10⁶)	Q20/%	Q30/%	比对到参考基因组 Alignment to reference genome /%	唯一参考序列数 Number of unique reference sequences/%	比对到参考基因组 Alignment to reference genome/%	唯一参考序列数 Number of unique reference sequences/%
WT0	47.77	42.32	97.2	91.3	96.69	84.51	96.69	84.51
CL2	48.93	42.84	97.3	91.8	96.44	84.38	96.44	84.38
CL12	46.02	42.46	97.1	91.4	96.98	85.22	96.98	85.22

基因ID Gene ID	log₂ （CL2/WT0）	Q value （WT0-vs-CL2）	描述 Description
Pop_A01G003964	5.769956725	1.32E-41	ERF1A
Pop_A01G032260	5.649644852	1.26E-05	ERF21
Pop_A01G059811	5.539774145	5.91E-07	ERF61
Pop_A01G060003	7.0861912	1.99E-09	DREB1E
Pop_A04G018519	3.029867059	3.13E-06	bHLH162
Pop_A06G061940	2.433933971	0.032353534	ORG2
Pop_A14G044066	2.36624488	0.001496264	bZip53
Pop_A08G063663	2.588359391	4.82E-13	CDF2
Pop_G19G009429	2.356323627	6.09E-16	CDF3
Pop_G09G015087	2.033526993	0.003029387	ZAT10
Pop_A16G090138	3.342912788	3.50E-13	PHL7
Pop_G10G047973	6.429548834	0.001027136	ORR25
Pop_A09G014447	2.372666749	6.59E-06	SCR3
Pop_A06G062082	6.325653816	0.001158459	HSF4b
Pop_A16G055308	2.667183627	5.18E-06	HSF3
Pop_A02G066179	5.110284639	8.26E-05	MYB73
Pop_A07G011878	2.013444428	1.37E-12	MYB44
Pop_A08G063813	2.04957107	0.013470953	MYB108
Pop_A14G000372	3.81186488	1.23E-08	MYB44
Pop_A15G064557	4.679506153	1.94E-16	MYB62
Pop_A04G019588	2.206753814	6.93E-06	NAC73
Pop_A04G026457	3.711825186	0.000111049	TCP13
Pop_A01G059075	3.408636654	6.29E-05	WRKY28
Pop_A01G080041	3.413796772	6.86E-30	WRKY40
Pop_A02G012299	2.225001206	0.013563496	WRKY22
Pop_A03G019779	2.390109471	0.001165373	WRKY75

基因ID Gene ID	log₂ （CL2/WT0）	Q value （WT0-vs-CL2）	描述 Description
Pop_A01G003964	5.769956725	1.32E-41	ERF1A
Pop_A01G032260	5.649644852	1.26E-05	ERF21
Pop_A01G059811	5.539774145	5.91E-07	ERF61
Pop_A01G060003	7.0861912	1.99E-09	DREB1E
Pop_A04G018519	3.029867059	3.13E-06	bHLH162
Pop_A06G061940	2.433933971	0.032353534	ORG2
Pop_A14G044066	2.36624488	0.001496264	bZip53
Pop_A08G063663	2.588359391	4.82E-13	CDF2
Pop_G19G009429	2.356323627	6.09E-16	CDF3
Pop_G09G015087	2.033526993	0.003029387	ZAT10
Pop_A16G090138	3.342912788	3.50E-13	PHL7
Pop_G10G047973	6.429548834	0.001027136	ORR25
Pop_A09G014447	2.372666749	6.59E-06	SCR3
Pop_A06G062082	6.325653816	0.001158459	HSF4b
Pop_A16G055308	2.667183627	5.18E-06	HSF3
Pop_A02G066179	5.110284639	8.26E-05	MYB73
Pop_A07G011878	2.013444428	1.37E-12	MYB44
Pop_A08G063813	2.04957107	0.013470953	MYB108
Pop_A14G000372	3.81186488	1.23E-08	MYB44
Pop_A15G064557	4.679506153	1.94E-16	MYB62
Pop_A04G019588	2.206753814	6.93E-06	NAC73
Pop_A04G026457	3.711825186	0.000111049	TCP13
Pop_A01G059075	3.408636654	6.29E-05	WRKY28
Pop_A01G080041	3.413796772	6.86E-30	WRKY40
Pop_A02G012299	2.225001206	0.013563496	WRKY22
Pop_A03G019779	2.390109471	0.001165373	WRKY75

基因ID Gene ID	log₂（CL12/WT0）	Q value	描述 Description
Pop_A02G023792	1.224720934	1.09E-10	GAUT8
Pop_G02G015804	1.084322434	1.96E-08	GAUT8
Pop_G18G078711	1.659192116	3.08E-11	CesA1
Pop_A18G012937	1.547823248	7.46E-12	CesA1
Pop_A03G049677	2.0312488	1.97E-08	PAE7
Pop_A05G016925	1.624518546	3.92E-06	PAE12
Pop_G03G021316	1.771860445	3.93E-08	PAE7
Pop_G05G032831	1.404050162	4.41E-07	PAE12
Pop_G03G011242	1.373107821	4.15E-14	PT
Pop_A02G023780	2.640491502	1.58E-21	XTH2
Pop_A19G055144	0.555458286	0.19872077	XTH9
Pop_G01G002830	2.869514357	0.070436159	XTH27
Pop_G02G015923	3.12618234	4.66E-63	XTH21
Pop_A01G074711	2.335379968	0.044535379	XTHA
Pop_G19G084027	0.768927412	0.025571895	XTH9
Pop_G06G075982	1.258093365	0.194655673	XTH6/TCH4