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学者姓名：朱方捷
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Abstract ：
Paralogous transcription factors (TFs) frequently recognize highly similar DNA motifs. Homodimerization can help distinguish them according to their different dimeric configurations. Here, by studying R2R3-MYB TFs, we show that homodimerization can also directly change the recognized DNA motifs to distinguish between similar TFs. By high-throughput SELEX, we profiled the specificity landscape for 40 R2R3-MYBs of subfamily VIII and curated 833 motif models. The dimeric models show that homodimeric binding has evoked specificity changes for AtMYBs. Focusing on AtMYB2 as an example, we show that homodimerization has modified its specificity and allowed it to recognize additional cis-regulatory sequences that are different from the closely related CCWAA-box AtMYBs and are unique among all AtMYBs. Genomic sites described by the modified dimeric specificities of AtMYB2 are conserved in evolution and involved in AtMYB2-specific transcriptional activation. Collectively, this study provides rich data on sequence preferences of VIII R2R3-MYBs and suggests an alternative mechanism that guides closely related TFs to respective cis-regulatory sites.
Keyword ：
cis-elements cis-elements DNA binding specificity DNA binding specificity homodimerization homodimerization MYB family transcription factors MYB family transcription factors paralogs paralogs regulatory noncoding genome regulatory noncoding genome transcriptional regulation transcriptional regulation
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| GB/T 7714 | Li, Tian , Chen, Hao , Ma, Nana et al. Specificity landscapes of 40 R2R3-MYBs reveal how paralogs target different cis-elements by homodimeric binding [J]. | IMETA , 2025 , 4 (2) . |
| MLA | Li, Tian et al. "Specificity landscapes of 40 R2R3-MYBs reveal how paralogs target different cis-elements by homodimeric binding" . | IMETA 4 . 2 (2025) . |
| APA | Li, Tian , Chen, Hao , Ma, Nana , Jiang, Dingkun , Wu, Jiacheng , Zhang, Xinfeng et al. Specificity landscapes of 40 R2R3-MYBs reveal how paralogs target different cis-elements by homodimeric binding . | IMETA , 2025 , 4 (2) . |
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Pearl millet (Pennisetum glaucum) is a major staple food in arid and semi-arid regions of sub-Saharan Africa, India, and South Asia. However, how epigenetic mechanisms regulate tissue-specific gene expression in this crop remains poorly understood. In this study, we profiled multiple epigenetic features in the young panicles and roots of pearl millet using RNA-seq, ATAC-seq, whole-genome bisulfite sequencing, and ChIP-seq (H3K4me3 and H3K36me3). We identified thousands of genes that were differentially expressed between these two tissues. Root-specific genes were enriched for plant hormone signaling, oxidative phosphorylation, and stress responses. Analysis of chromatin accessibility revealed that root-specific accessible chromatin regions (ACRs) were enriched in binding motifs for stress-responsive transcription factors (e.g., NAC, WRKY), whereas ACRs in young panicles were enriched in motifs for developmental regulators (e.g., AP2/ERF). DNA methylation profiling revealed 25,141 tissue-specific differentially methylated regions, with CHH methylation—rather than CG or CHG methylation—showing the strongest tissue specificity. Promoters of root-specific genes had higher levels of CHH methylation compared to those of young panicle–specific genes, suggesting that the roles of CHH methylation in regulating transcription might be tissue dependent. Notably, promoter-associated H3K4me3 marked panicle-specific genes, whereas root-specific expression was primarily linked to chromatin accessibility, suggesting a transcription factor–mediated regulatory mechanism. Together, our findings highlight the distinct epigenetic frameworks governing tissue-specific gene expression in pearl millet and provide valuable insights for advancing the genetic improvement of this crop. © The Author(s) 2025.
Keyword ：
Alkylation Alkylation Arid regions Arid regions Gene expression regulation Gene expression regulation Methylation Methylation Plants (botany) Plants (botany) Tissue Tissue Tissue engineering Tissue engineering Transcription Transcription Transcription factors Transcription factors
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| GB/T 7714 | Luo, Lin , Qu, Qi , Cao, Mengxue et al. Epigenetic maps of pearl millet reveal a prominent role for CHH methylation in regulating tissue-specific gene expression [J]. | aBIOTECH , 2025 , 6 (3) : 394-410 . |
| MLA | Luo, Lin et al. "Epigenetic maps of pearl millet reveal a prominent role for CHH methylation in regulating tissue-specific gene expression" . | aBIOTECH 6 . 3 (2025) : 394-410 . |
| APA | Luo, Lin , Qu, Qi , Cao, Mengxue , Zhang, Yihui , Sun, Yuanchang , Mao, Fei et al. Epigenetic maps of pearl millet reveal a prominent role for CHH methylation in regulating tissue-specific gene expression . | aBIOTECH , 2025 , 6 (3) , 394-410 . |
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Cis-regulatory elements (CREs) are the genetic DNA fragments bound by transcription factors (TFs). CREs function as molecular switches that precisely modulate the dosage and spatiotemporal patterns of gene expression. The systematic identification of CREs not only facilitates the annotation of the functional non-coding genome but also provides essential insights into the architecture of gene regulatory networks and sheds light on an accurate selection of the target sites for genetic engineering of crops. In this review, we summarize the current high-throughput methodologies used for identifying CREs, illustrate the associations between CREs and agronomic traits in horticultural crops, and discuss how CREs can be exploited to facilitate crop breeding. © The Author(s) 2025.
Keyword ：
Crops Crops Genetic engineering Genetic engineering Transcription Transcription
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| GB/T 7714 | Li, Tian , Zeng, Wen , Zhu, Fangjie et al. Cis-regulatory elements: systematic identification and horticultural applications [J]. | aBIOTECH , 2025 , 6 (3) : 510-527 . |
| MLA | Li, Tian et al. "Cis-regulatory elements: systematic identification and horticultural applications" . | aBIOTECH 6 . 3 (2025) : 510-527 . |
| APA | Li, Tian , Zeng, Wen , Zhu, Fangjie , Lue, Peitao . Cis-regulatory elements: systematic identification and horticultural applications . | aBIOTECH , 2025 , 6 (3) , 510-527 . |
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Transcription factors (TFs) recognize specific bases within their DNA-binding motifs, with each base contributing nearly independently to total binding energy. However, the energetic contributions of particular dinucleotides can deviate strongly from the additive approximation, indicating that some TFs can specifically recognize DNA dinucleotides. Here we solved high-resolution (<1 & Aring;) structures of MYF5 and BARHL2 bound to DNAs containing sets of dinucleotides that have different affinities to the proteins. The dinucleotides were recognized either enthalpically, by an extensive water network that connects the adjacent bases to the TF, or entropically, by a hydrophobic patch that maintained interfacial water mobility. This mechanism confers differential temperature sensitivity to the optimal sites, with implications for thermal regulation of gene expression. Our results uncover the enigma of how TFs can recognize more complex local features than mononucleotides and demonstrate that water-mediated recognition is important for predicting affinities of macromolecules from their sequence.
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| GB/T 7714 | Morgunova, Ekaterina , Nagy, Gabor , Yin, Yimeng et al. Interfacial water confers transcription factors with dinucleotide specificity [J]. | NATURE STRUCTURAL & MOLECULAR BIOLOGY , 2025 , 32 (4) : 650-661 . |
| MLA | Morgunova, Ekaterina et al. "Interfacial water confers transcription factors with dinucleotide specificity" . | NATURE STRUCTURAL & MOLECULAR BIOLOGY 32 . 4 (2025) : 650-661 . |
| APA | Morgunova, Ekaterina , Nagy, Gabor , Yin, Yimeng , Zhu, Fangjie , Nayak, Sonali Priyadarshini , Xiao, Tianyi et al. Interfacial water confers transcription factors with dinucleotide specificity . | NATURE STRUCTURAL & MOLECULAR BIOLOGY , 2025 , 32 (4) , 650-661 . |
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The Arabidopsis transcription factor WUSCHEL-related homeobox 14 (AtWOX14) plays versatile roles in plant growth and development. However, its biochemical specificity of DNA binding, its genome-wide regulatory targets, and how these are affected by DNA methylation remain uncharacterized. To clarify the biochemistry underlying the regulatory function of AtWOX14, using the recently developed 5mC-incorporation strategy, this study performed SELEX and DAP-seq for AtWOX14 both in the presence and absence of cytosine methylation, systematically curated 65 motif models and identified 51,039 genomic binding sites for AtWOX14, and examined how 5mC affects DNA binding of AtWOX14 through bioinformatic analyses. Overall, 5mC represses the DNA binding of AtWOX14 monomers but facilitates the binding of its dimers, and the methylation effect on a cytosine's affinity to AtWOX14 is position-dependent. Notably, we found that the most preferred homodimeric configuration of AtWOX14 has changed from ER1 to ER0 upon methylation. This change has the potential to rewire the regulatory network downstream of AtWOX14, as suggested by the GO analyses and the strength changes in the DAP-seq peaks upon methylation. Therefore, this work comprehensively illustrates the specificity and targets of AtWOX14 and reports a previously unrecognized effect of DNA methylation on transcription factor binding.
Keyword ：
dimeric spacing dimeric spacing DNA binding specificity DNA binding specificity DNA methylation DNA methylation SELEX SELEX transcription factor transcription factor WUSCHEL-related homeobox 14 WUSCHEL-related homeobox 14
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| GB/T 7714 | Jiang, Dingkun , Zhang, Xinfeng , Luo, Lin et al. Cytosine Methylation Changes the Preferred Cis-Regulatory Configuration of Arabidopsis WUSCHEL-Related Homeobox 14 [J]. | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2025 , 26 (2) . |
| MLA | Jiang, Dingkun et al. "Cytosine Methylation Changes the Preferred Cis-Regulatory Configuration of Arabidopsis WUSCHEL-Related Homeobox 14" . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 26 . 2 (2025) . |
| APA | Jiang, Dingkun , Zhang, Xinfeng , Luo, Lin , Li, Tian , Chen, Hao , Ma, Nana et al. Cytosine Methylation Changes the Preferred Cis-Regulatory Configuration of Arabidopsis WUSCHEL-Related Homeobox 14 . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2025 , 26 (2) . |
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Among the regulatory factor X (RFX) transcription factor family, RFX5 is uniquely reported to bind nucleosomes and induce nucleosome remodeling in vivo. Dysfunctions in RFX5 have been implicated in various diseases. Here, we present the cryogenic electron microscopy (cryo-EM) structure of the RFX5-nucleosome complex, revealing that the extended DNA binding domain (eDBD) of RFX5 binds to the nucleosome at superhelical location +2. RFX5 eDBD engages not only with nucleosomal DNA but also with histones through extensive interactions. Compared to the structure of a free nucleosome, RFX5 eDBD induces localized distortion of the bound DNA gyre and detachment of the adjacent DNA gyre in the RFX5-nucleosome complex. This structural alteration could potentially increase DNA accessibility and enhance transcriptional activity in vivo. Overall, our study provides novel insights into the mechanisms by which RFX5 eDBD interacts with and destabilizes nucleosomes.
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| GB/T 7714 | Xue, Wanqiang , Han, Yaoyao , Tian, Ying et al. Structural basis of nucleosome binding and destabilization by the extended DNA binding domain of RFX5 [J]. | NUCLEIC ACIDS RESEARCH , 2025 , 53 (14) . |
| MLA | Xue, Wanqiang et al. "Structural basis of nucleosome binding and destabilization by the extended DNA binding domain of RFX5" . | NUCLEIC ACIDS RESEARCH 53 . 14 (2025) . |
| APA | Xue, Wanqiang , Han, Yaoyao , Tian, Ying , Wang, Junzheng , Xie, Zhiyuan , Zheng, Xin et al. Structural basis of nucleosome binding and destabilization by the extended DNA binding domain of RFX5 . | NUCLEIC ACIDS RESEARCH , 2025 , 53 (14) . |
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A distinct epigenetic feature of plants is the DNA methylation in non-CG contexts. Although the physiological roles of non-CG methylation have been elucidated, its direct impact on transcription factor (TF)-DNA interactions remains largely unexplored. Focusing on WRKY-family TFs, here we investigated how non-CG methylation influences their DNA binding specificity and genome-wide cis-regulatory elements (CREs). By generating 461 SELEX and DAP-seq libraries for 54 AtWRKYs, we show that DNA methylation alters both monomeric and dimeric binding specificities of WRKYs, leading to an overall increase in specificity divergence among family members. We curated 201 WRKY motifs and clustered them into 11 classes, 5 of which represent previously unreported specificities. Notably, the known WRKY cis-element PRE4 was found to be recognized only when methylated. The comprehensive dataset of accurate WRKY motifs also enabled the identification of the amino acid discriminants of W-box and WT-box. Expanding on prior knowledge, we demonstrate that methylation not only decreases but can also increase the affinity of WRKYs. This bidirectional effect has globally reshaped the genomic binding landscape of WRKYs upon methylation. Finally, we constructed the WRKY Regulatory Code Database (https://transysbio.cn/WRKYRCDB.php) to facilitate data access.
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| GB/T 7714 | Ma, Nana , Jiang, Dingkun , Li, Tian et al. The specificity landscape of WRKY transcription factors reveals the bidirectional influence of non-CG methylation [J]. | NUCLEIC ACIDS RESEARCH , 2025 , 53 (21) . |
| MLA | Ma, Nana et al. "The specificity landscape of WRKY transcription factors reveals the bidirectional influence of non-CG methylation" . | NUCLEIC ACIDS RESEARCH 53 . 21 (2025) . |
| APA | Ma, Nana , Jiang, Dingkun , Li, Tian , Luo, Lin , Chen, Hao , Zhang, Xinfeng et al. The specificity landscape of WRKY transcription factors reveals the bidirectional influence of non-CG methylation . | NUCLEIC ACIDS RESEARCH , 2025 , 53 (21) . |
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Pearl millet is a major cereal crop that feeds more than 90 million people worldwide in arid and semi-arid regions. The stalk phenotypes of Poaceous grasses are critical for their productivity and stress tolerance; however, the molecular mechanisms governing stalk development in pearl millet remain to be deciphered. In this study, we spatiotemporally measured 19 transcriptomes for stalk internodes of four different early developmental stages. Data analysis of the transcriptomes defined four developmental zones on the stalks and identified 12 specific gene sets with specific expression patterns across the zones. Using weighted gene co-expression network analysis (WGCNA), we found that two co-expression modules together with candidate genes were involved in stalk elongation and the thickening of pearl millet. Among the elongation-related candidate genes, we established by SELEX that a MYB-family transcription factor PMF7G02448 can bind to the promoters of three cell wall synthases genes (CesAs). In summary, these findings provide insights into stalk development and offer potential targets for future genetic improvement in pearl millet.
Keyword ：
gene expression gene expression genetic improvement genetic improvement pearl millet pearl millet stalk development stalk development transcriptome analysis transcriptome analysis
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| GB/T 7714 | Mao, Fei , Luo, Lin , Ma, Nana et al. A Spatiotemporal Transcriptome Reveals Stalk Development in Pearl Millet [J]. | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2024 , 25 (18) . |
| MLA | Mao, Fei et al. "A Spatiotemporal Transcriptome Reveals Stalk Development in Pearl Millet" . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 25 . 18 (2024) . |
| APA | Mao, Fei , Luo, Lin , Ma, Nana , Qu, Qi , Chen, Hao , Yi, Chao et al. A Spatiotemporal Transcriptome Reveals Stalk Development in Pearl Millet . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2024 , 25 (18) . |
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Enhancers play a critical role in dynamically regulating spatial-temporal gene expression and establishing cell identity, underscoring the significance of designing them with specific properties for applications in biosynthetic engineering and gene therapy. Despite numerous high-throughput methods facilitating genome-wide enhancer identification, deciphering the sequence determinants of their activity remains challenging. Here, we present the DREAM (DNA cis-Regulatory Elements with controllable Activity design platforM) framework, a novel deep learning-based approach for synthetic enhancer design. Proficient in uncovering subtle and intricate patterns within extensive enhancer screening data, DREAM achieves cutting-edge sequence-based enhancer activity prediction and highlights critical sequence features implicating strong enhancer activity. Leveraging DREAM, we have engineered enhancers that surpass the potency of the strongest enhancer within the Drosophila genome by approximately 3.6-fold. Remarkably, these synthetic enhancers exhibited conserved functionality across species that have diverged more than billion years, indicating that DREAM was able to learn highly conserved enhancer regulatory grammar. Additionally, we designed silencers and cell line-specific enhancers using DREAM, demonstrating its versatility. Overall, our study not only introduces an interpretable approach for enhancer design but also lays out a general framework applicable to the design of other types of cis-regulatory elements. Graphical Abstract
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| GB/T 7714 | Li, Zhaohong , Zhang, Yuanyuan , Peng, Bo et al. A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity [J]. | NUCLEIC ACIDS RESEARCH , 2024 , 52 (21) : 13447-13468 . |
| MLA | Li, Zhaohong et al. "A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity" . | NUCLEIC ACIDS RESEARCH 52 . 21 (2024) : 13447-13468 . |
| APA | Li, Zhaohong , Zhang, Yuanyuan , Peng, Bo , Qin, Shenghua , Zhang, Qian , Chen, Yun et al. A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity . | NUCLEIC ACIDS RESEARCH , 2024 , 52 (21) , 13447-13468 . |
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| GB/T 7714 | Luo, Lin , Lin, Dongmei , Li, Jinhui et al. EGDB: A comprehensive multi-omics database for energy grasses and the epigenomic atlas of pearl millet [J]. | IMETA , 2024 , 4 (1) . |
| MLA | Luo, Lin et al. "EGDB: A comprehensive multi-omics database for energy grasses and the epigenomic atlas of pearl millet" . | IMETA 4 . 1 (2024) . |
| APA | Luo, Lin , Lin, Dongmei , Li, Jinhui , Chen, Hao , Qu, Qi , Zhang, Lin et al. EGDB: A comprehensive multi-omics database for energy grasses and the epigenomic atlas of pearl millet . | IMETA , 2024 , 4 (1) . |
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