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3. Concentration-dependent transcriptional switching through a collective action of cis-elements

Author

Rodriguez, Kevin, Do, Albert, Senay-Aras, Betul, Perales, Mariano, Alber, Mark, Chen, Weitao, and Reddy, G Venugopala

Subjects
Biochemistry and Cell Biology, Biological Sciences, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance
Abstract

Gene expression specificity of homeobox transcription factors has remained paradoxical. WUSCHEL activates and represses CLAVATA3 transcription at lower and higher concentrations, respectively. We use computational modeling and experimental analysis to investigate the properties of the cis-regulatory module. We find that intrinsically each cis-element can only activate CLAVATA3 at a higher WUSCHEL concentration. However, together, they repress CLAVATA3 at higher WUSCHEL and activate only at lower WUSCHEL, showing that the concentration-dependent interactions among cis-elements regulate both activation and repression. Biochemical experiments show that two adjacent functional cis-elements bind WUSCHEL with higher affinity and dimerize at relatively lower levels. Moreover, increasing the distance between cis-elements prolongs WUSCHEL monomer binding window, resulting in higher CLAVATA3 activation. Our work showing a constellation of optimally spaced cis-elements of defined affinities determining activation and repression thresholds in regulating CLAVATA3 transcription provides a previously unknown mechanism of cofactor-independent regulation of transcription factor binding in mediating gene expression specificity.

Published
2022

11. The Reply

Author

Yeoh, Aaron, primary, Cheung, Ramsey, additional, Ahmed, Aijaz, additional, Chitnis, Amit S., additional, Do, Albert, additional, and Wong, Robert J., additional

Published
2024
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12. Kinetics of Stem Cell Stasis and Transformation Through Transcription Factor WUSCHEL and its Interactors

Author

Do, Albert

Subjects
Genetics, Bioinformatics, Molecular biology, expression, genetics, molecular, plant, stem cell, WUSCHEL
Abstract

The process of growth in plants is driven by the shoot apical meristem (SAM) which is in turn driven by a signaling network centered around the transcription factor WUSCHEL (WUS). The interaction between WUS and its target genes has a key role in determining the structure of the SAM and fate of its stem cells, as well as how it responds and adapts to its environment. The interplay between WUS and a limited number of other targets such as the gene encoding the peptide CLAVATA3 (CLV3) has been outlined on a basic level through previous studies. However, much work remains to gather more detailed information, develop quantitative molecular explanations for the observed gene expression behaviors, generalize the biology to encompass the broad range of WUS targets, and potentially identify similar regulatory systems elsewhere in plants and other organisms. This study uses a multidisciplinary approach combining experimental and computational techniques to proceed toward these objectives through a number of different avenues. The nature of the cis-regulatory module (CRM) through which CLV3 interacts with WUS was examined showing that individual cis-elements of the CRM behave distinctly when they are working alone compared to when they are working together. This also provided molecular details about the concentration dependent mechanism where the CRM coordinated a nonlinear response to WUS. A computational simulation of the meristem network was tested and data is being gathered on how the resetting of the CLV3 expression gradient to the outer meristem occurs on a molecular level in CLV3 complementation assays. Surveying the CLV3 epigenome revealed a landscape of binding clusters and chromatin looping within the gene and at its ends. This and motif analysis, showed that other targets may share similar features. Imaging studies revealed tissue level dynamics, backing up previously hypothesized mechanisms relating expression to monomeric and multimeric WUS and how it not only regulates but is regulated in turn by a network of interactors.

Published
2022

28. Contributors

Author

Balogun, Oluwafemi O., Banini, Bubu A., Beier, Juliane I., Cheng, Katherine, Corey, Kathleen E., Crocombe, Dominic, Di Bartolomeo, Anna, Do, Albert, Fan, Jian-Gao, Fan, Weiguo, George, Jacob, Goens, Donald, Golabi, Pegah, Henry, Linda, Horn, Paul, Huang, Jee-Fu, Huang, Daniel Q., Ito, Takanori, Johnson-Mann, Crystal N., Jun, Dae Won, Kaya, Eda, Kim, Sun H., Kwo, Paul Y., Lam, Robert, Li, Guanlin, Lim, Joseph K., Lin, Huapeng, Medici, Valentina, Muthiah, Mark, Newsome, Philip N., Ng, Cheng Han, Nguyen, Mindie H., Oh, Joo Hyun, Patton, Heather, Rosenthal, Philip, Shaikh, Emad S., Spencer, Sean, Takahashi, Hirokazu, Teng, Margaret L.P., Tsochatzis, Emmanuel A., Török, Natalie J., Wong, Vincent Wai-Sun, Wong, Grace Lai-Hung, Yang, Rui-Xu, Yeh, Ming-Lun, Yeo, Yee Hui, Yilmaz, Yusuf, Younossi, Zobair M., Yu, Ming-Lung, Zarrinpar, Amir, and Zhang, Xinrong

Published
2024
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