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Bromodomain-containing proteins interact with a non-canonical RNA polymerase II kinase to maintain gene expression upon heat stress

Nature Plants volume 11, pages 1416–1428 (2025)Cite this article

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Abstract

Phosphorylation at the carboxy-terminal domain of the largest subunit of RNA polymerase II plays a critical role in transcription, and histone acetylation is correlated with active transcription. However, the regulatory mechanisms by which histone acetylation modulates RNA polymerase II phosphorylation in plants remain unclear. Here we show that two functionally redundant bromodomain-containing proteins, global transcription factor group E2 (GTE2) and GTE7, can bind to acetylated histone H4. Both GTE2 and GTE7 interact with cyclin-dependent kinase-like 9 (CDKL9), which belongs to a plant-specific CDKL group. Unlike canonical CDKs, CDKL9 functions in a cyclin- and CDK-activating-kinase-independent manner and can phosphorylate at least the serine 2 and serine 5 residues of the carboxy-terminal domain in vitro. The GTE2/GTE7–CDKL9 complex is required to maintain serine 2 and serine 5 phosphorylation under heat stress. Consistently, loss-of-function gte2/gte7 and cdkl9 mutants show similar heat-sensitive phenotypes. We also demonstrate that the acetylated-histone-binding activity of GTE7 is essential for the association of CDKL9 with chromatin and for plant heat tolerance. Together, these findings provide mechanistic insight into transcriptional regulation via histone acetylation in response to heat stress and suggest that plants might have evolved a unique group of carboxy-terminal domain kinases for stress tolerance.

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Fig. 1: GTE2 and GTE7 interact with CDKL9.
Fig. 2: CDKL9 is a Pol II CTD kinase.
Fig. 3: The GTE2/GTE7–CDKL9 complex maintains Pol II phosphorylation under heat stress.
Fig. 4: The kinase activity of CDKL9 is enhanced by heat to maintain heat-responsive gene expression.
Fig. 5: GTE2/GTE7–CDKL9 associates with stress-responsive genes and maintains their Pol II phosphorylation and expression.
Fig. 6: GTE2 and GTE7 bind to acetylated H4 to promote plant heat tolerance.
Fig. 7: GTE2 and GTE7 recruit CDKL9 to chromatin through binding to acetylated H4.

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Data availability

High-throughput sequencing of ChIP and transcriptome data are available on the China National Center for Bioinformation (https://ngdc.cncb.ac.cn/) with the accession number CRA019323. Source data are provided with this paper.

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Acknowledgements

We thank X. Zhong from Washington University in St Louis and D.-X. Zhou from University Paris-Saclay for their valuable suggestions for this study. We also thank Q. Lu from the Core Facility of the State Key Laboratory of Hybrid Rice at Wuhan University for technical support. This work was supported by the National Key Technologies R&D Program of China (grant no. 2023YFF1002400), the Hubei Provincial Natural Science Foundation (grant nos 2024AFA062 and 2022CFA025) and the National Natural Science Foundation of China (grant no. 32470618).

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Authors and Affiliations

  1. State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China

    Xinjing Zheng, Zhihao Zuo, Peng Yao, Xiaojing Li, Qingche Zhang & Xiangsong Chen

  2. Hubei Hongshan Laboratory, Wuhan, China

    Xinjing Zheng, Zhihao Zuo, Peng Yao, Xiaojing Li, Qingche Zhang & Xiangsong Chen

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  1. Xinjing Zheng
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  3. Peng Yao
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  4. Xiaojing Li
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Contributions

X.Z. and X.C. designed the experiments. X.Z. performed most of the experiments. Z.Z. performed all bioinformatic analysis. P.Y., Q.Z. and X.L. provided technical assistance. X.Z. and X.C. analysed the data and wrote the paper. X.C. conceived of and supervised the project. All authors discussed the results and commented on the paper.

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Correspondence to Xiangsong Chen.

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Extended data

Extended Data Fig. 1 Phylogenetic analysis of GTE proteins.

a. Phylogenetic tree of bromodomain-containing proteins from Arabidopsis thaliana, Oryza sativa and Homo sapiens. The phylogenetic tree was constructed using MEGA11. b. Phylogenetic tree of Arabidopsis thaliana GTE family members. Diagrams at the right represent the protein structures for each member.

Extended Data Fig. 2 Phylogenetic analysis of CDKs and CDKLs in Arabidopsis thaliana and Homo sapiens.

Phylogenetic tree of CDKs and CDKLs from Arabidopsis thaliana and Homo sapiens. The names with green background are Arabidopsis thaliana CDKLs and yellow background are Homo sapiens CDKLs. The red colored names show Homo sapiens CDKs and CDKLs, and the black colored names show Arabidopsis thaliana CDKs and CDKLs.

Extended Data Fig. 3 In vitro kinase activity assays of CDKL9 and GTE7.

a. The protein structure of CDKL9 was predicted by AlphaFold3. Potential ATP binding sites (196-205) were zoomed in by dashed box. b. In vitro kinase assay of CDKL9 on GTE7. c. In vitro kinase assay of GTE7 on Pol II CTD. The experiments in b and c were repeated independently two times and showed similar results.

Source data

Extended Data Fig. 4 Generation and phenotypic analysis of gte2, gte7 and cdkl9 mutants.

a. Diagram of GTE2 and GTE7 genes show the positions of T-DNA insertions. b, c. Confirmation of the gte2 (b) and gte7 (c) T-DNA insertion lines by RT-PCR, MON1 served as internal control. The experiments in b and c were repeated independently two times and showed similar results. d. Diagram of cdkl9 mutant generated by CRISPR-Cas9. e. Confirmation of the cdkl9 mutant by PCR. F and R primers position are shown in (d). The experiments were repeated independently two times and showed similar results. f. Fresh weights of rosette leaves of WT, gte2, gte7, gte2/7 and GTE7/gte2gte7 plants. Each circle represents an individual plant. Data are presented as mean ± s.e.m. Significance was evaluated by a one-way analysis of variance. Different letters indicate significant differences tested by Tukey’s multiple range test (P < 0.05). F represents the ratio of between-group variance to within-group variance, df indicates degrees of freedom between groups, and P denotes the probability of observing the effect under the null hypothesis. g. Fresh weights of rosette leaves of cdkl9, gte2/7 and cdkl9 gte2/7 mutants. Each circle represents an individual plant. Data are presented as mean ± s.e.m. Significance was evaluated in the same way as in (f).

Source data

Extended Data Fig. 5 Phenotypic and protein level analysis of gte2/7, cdkl9 mutants and rescued plants.

a-d. Vann diagrams show the overlapped genes with decreased Ser2P (a) or Ser5P (c) and increased Ser2P (b) or Ser5P (d) in gte2/7 or cdkl9 under normal condition. e. The seed germination rate of WT, gte2/7 and GTE7/gte2gte7 on CK, 200 mM NaCl, 350 mM Mannitol and 4°C. Data are presented as mean ± s.e.m. (n = 3 biological replicates). f. The seed germination phenotypes of WT, gte2/7 and GTE7/gte2gte7 under heat stress. g. Quantifications of the relative germination rate for each genotype presented in (f) after heat stress. Data are presented as mean ± s.e.m. (n = 12 biological replicates). P values are calculated by two-tailed Student’s t test. h, i. Vann diagrams show the overlapped genes with increased Ser2P (h) or Ser5P (i) in gte2/7 or cdkl9 under heat condition. j. Protein levels of GTE2-HA, GTE7-HA and CDKL9-HA under normal and Heat conditions. ACTIN served as control. The experiments were repeated independently two times and showed similar results.

Source data

Extended Data Fig. 6 Transcriptomic analysis of WT, gte2/7 and cdkl9 mutants under normal and heat conditions.

a. Principal component analysis (PCA) of RNA-seq data in WT, gte2/7 and cdkl9 under normal condition. b. Volcano plots showing differentially expressed genes in gte2/7 or cdkl9 compared with WT under normal condition. P values are calculated using two-tailed Wald tests under negative binomial generalized linear models, with 95% confidence intervals derived from normal approximation. c. Principal component analysis (PCA) of RNA-seq data in WT, gte2/7 and cdkl9 under heat condition. d. Volcano plots showing differentially expressed genes in gte2/7 or cdkl9 compared with WT under heat condition. P values are calculated using two-tailed Wald tests under negative binomial generalized linear models, with 95% confidence intervals derived from normal approximation. e. Expression levels of the 95 genes overlapped (Fig. 4c) in WT, gte2/7 and cdkl9 under normal and heat condition. P values were calculated by two-tailed Student’s t test. Each plotting panel, from left to right, displays the frequency distribution of the data, the boxplot, and the raw data points. In the boxplot, the central horizontal line within the box represents the median of the data. The upper edge of the box corresponds to the upper quartile, while the lower edge indicates the lower quartile. The whiskers extend to the minimum and maximum values within 1.5 times the interquartile range.

Extended Data Fig. 7 Chromatin associations of GTE2, GTE7 and CDKL9.

a, b. Chromosomal views of GTE2 and GTE7 under normal (a) and heat (b) condition distribution on five chromosomes. The Y-axis represents the log2 value of GTE2-HA and GTE7-HA ChIP-seq reads relative to untagged WT control. Chr1, Chr2, Chr3, Chr4 and Chr5 represent chromosomes 1 to 5, respectively. Black triangles indicate the location of centromeric regions. c. Metaplots and heatmaps show the distribution patterns of GTE2 and GTE7 protein on all genes. TSS, transcription start site; TES, transcription end site; −2 and 2 kb represent 2 kb upstream of TSS and 2 kb downstream TES, respectively. d. Additional biological replicate for Fig. 5p showing ChIP-quantitative PCR (ChIP-qPCR) analysis for CDKL9 enrichment under normal and heat condition on representative genes (n = 2 technical replicates). e, f. ChIP-quantitative PCR (ChIP-qPCR) analysis of CDKL9 enrichment under normal and heat condition on representative genes chosen from the GTE2 and GTE7 bound genes (n = 2 technical replicates). e and f represent two biological replicates.

Extended Data Fig. 8 Sequence and functional analysis of histone acetylation-binding activity of GTE7.

a. Sequence alignment of bromodomains of GTE2, GTE7, BRD4, CBP, P300 and PCAF. Two conserved residues of Tyr and Asn are shown in red box. b. Metaplots show the GTE7 and GTE72A enrichment level on GTE2/7-enriched genes under heat condition. c. Additional biological replicate for Fig. 7a showing ChIP-qPCR analysis of CDKL9 enrichment on genes in wild-type and gte2/7 mutant backgrounds (n = 2 technical replicates). d. Additional biological replicate for Fig. 7b showing ChIP-qPCR analysis of CDKL9 enrichment on genes in wild-type and GTE72A-rescued gte2/7 mutant backgrounds (n = 2 technical replicates).

Extended Data Table 1 List of proteins co-purified with GTE7. Immunoprecipitation followed by mass spectrometry assay show that transcription factors are co-purified with GTE7. Unique peptides represent the number of identified unique peptides that are mapped to an individual protein. WT as a negative control
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Zheng, X., Zuo, Z., Yao, P. et al. Bromodomain-containing proteins interact with a non-canonical RNA polymerase II kinase to maintain gene expression upon heat stress. Nat. Plants 11, 1416–1428 (2025). https://doi.org/10.1038/s41477-025-02044-3

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