Dynamic modulation of enhancer responsiveness by core promoter elements in living Drosophila embryos

Grant-in-Aid for Transformative Research Areas (A) (Research in a ProposedResearch Area) [21H05742]; Grant-inAid for Scientific Research on Innovative Areas (Research in a Proposed Research Area) [20H05357]; Grant-in-Aid for Scientific Research (B) [19H03154]; Grant-in-Aid for Challenging Research (Exploratory) [19K22378]; Grant-inAid for Research Activity Start-up [18H06040] from the Japan Society for the Promotion of Science; Grant-in-Aid for Leading Initiative for ExcellentYoungResearchers from the Ministry of Education, Culture, Sports, Science and Technology in Japan; Tomizawa Jun-ichi & Keiko Fund of Molecular Biology Society of Japan for Young Scientist; research grants from the Mochida Memorial Foundation for Medical and Pharmaceutical Research; Nakajima Foundation; Inamori Foundation; Takeda Science Foundation; Sumitomo Foundation; Senri Life Science Foundation; Mitsubishi Foundation; M.Y. is supported by the Grant-in-Aid for Early-Career Scientists [20K15710] from the Japan Society for the Promotion of Science; Employment Stability Support for Young Researchers from the University of Tokyo; JST, ACT-X [JPMJAX211J]; K.K. is supported by the Grant-in-Aid for Research Activity Start-up [21K20627] from the Japan Society for the Promotion of Science; M.C. is supported by the FPI research grant [FPI2015/074837] from the MINECO-Feder; FisyMat PhD Student Research program from University of Granada. Funding for open access charge: Japan Society for the Promotion of Science.Regulatory interactions between enhancers and core promoters are fundamental for the temporal and spatial specificity of gene expression in development. The central role of core promoters is to initiate productive transcription in response to enhancer’s activation cues. However, it has not been systematically assessed how individual core promoter elements affect the induction of transcriptional bursting by enhancers. Here, we provide evidence that each core promoter element differentially modulates functional parameters of transcriptional bursting in developing Drosophila embryos. Quantitative live imaging analysis revealed that the timing and the continuity of burst induction are common regulatory steps on which core promoter elements impact. We further show that the upstream TATA also affects the burst amplitude. On the other hand, Inr, MTE and DPE mainly contribute to the regulation of the burst frequency. Genome editing analysis of the pair-rule gene fushi tarazu revealed that the endogenous TATA and DPE are both essential for its correct expression and function during the establishment of body segments in early embryos. We suggest that core promoter elements serve as a key regulatory module in converting enhancer activity into transcription dynamics during animal development.Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT)Japan Society for the Promotion of Science 18H06040 20K15710 21K20627Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT)Tomizawa Jun-ichi & Keiko Fund of Molecular Biology Society of Japan for Young ScientistMochida Memorial Foundation for Medical and Pharmaceutical ResearchNakajima FoundationInamori FoundationTakeda Science Foundation (TSF)Sumitomo FoundationSenri Life Science FoundationMitsubishi FoundationUniversity of TokyoJST, ACT-X JPMJAX211JSpanish Government FPI2015/074837University of Granada 21H05742 20H05357 19H03154 19K2237

Predictive model for cytoneme guidance in Hedgehog signaling based on Ihog- Glypicans interaction

Additional information Supplementary information The online version contains supplementary material available at https://doi.org/10.1038/s41467-022-33262-4.Acknowledgements We are grateful to and Pedro Ripoll and Ana-Citlali Gradilla for comments on the manuscript. We also thank to Laura González-Méndez, Carlos Jiménez-Jiménez, David Sánchez-Hernández and Eléanor Simon in I.G laboratory for their help with some experiments, the Confocal Facilities of the CBMSO and Bloomington and Vienna stock centers for fly stocks. This work was supported by grants BFU2017-83789-P, PID2020-114533GB-C21 and TENTACLES consortium RED2018-102411-T to I.G from the Spanish Ministry of Science, Innovation and Universities and by institutional grants from the Fundación Areces and Banco de Santander to the CBMSO. FPI fellowship from the Spanish Ministry of Science, Innovation and Universities supported A.A-T (BFU2017-83789- P). This work was also supported by grants RTI2018-098850-B-I00 to J.S from the MINECO-Feder (Spain), PY18-RT-2422 & A-FQM-311-UGR18 to M.C, D.P and J.S from the Junta de Andalucia (Spain), MECD (Spain) research grant FPI2015/074837 to M.C, and partially supported by the MECD (Spain) research grant FPU14/06304 and the European Research Council (Europe) Project ERC-COG-2019 WACONDY (grant agreement No 865711) to D.P.MINECO-Feder A-FQM-311-UGR18, PY18-RT-2422Banco Santander RTI2018-098850-B-I00Ministerio de Ciencia, Innovación y Universidades MCIUEuropean Research Council 865711, ERC-COG-2019 ERCMinisterio de Educación, Cultura y Deporte FPI2015/074837, FPU14/06304Junta de Andalucí

Numerical simulations and modelling in biological species development

La presente tesis se centra en el desarrollo de modelos aplicados a distintos ámbitos de la morfogénesis. Dichos ámbitos se dan en diferentes etapas del desarrollo del ser vivo. Por ello, los modelos presentados han de ser capaces de trabajar en distintas escalas tanto espaciales, como temporales. Esto da lugar un trabajo de modelado donde, dependiendo del problema a tratar, se han de utilizar herramientas matemáticas particulares para cada uno. Entrando en detalle, podemos resumir en dos las escalas biológicas que tratan la presente tesis: la escala tisular, y la escala molecular. Por un lado, la escala tisular recoge eventos biológicos globales, que se dan en una amplia zona del tejido en desarrollo. En esta escala la importancia del problema a modelar reside no en un elemento en particular del problema, sino en un conjunto de elementos. Generalmente suele atribuirse con el concepto matemático de escala macroscópica, donde se tiende a plantear modelos continuos de nidos por ecuaciones en derivadas parciales. Un ejemplo claro de estos modelos es la difusión de proteínas (señales) en un tejido. En este tipo de problemas se suele modelar la evolución temporal de las concentraciones de proteínas mediante ecuaciones usualmente tipo parabólicas, como la ecuación del difusión. Sin embargo, en la presente tesis se ha optado por estudiar el problema de señalización desde una perspectiva más centrada en el funcionamiento biológico en sí. De esta manera, si bien sigue siendo un problema a escala tisular, la forma de abordarlo y modelarlo matemáticamente dependerá mucho de la maquinaria biológica que hay detrás: en este caso, los citonemas. Los citonemas son componentes biológicas de las que, a día de depósito de este documento, aún se conoce poco tanto a nivel biológico como matemático. Aplicando técnicas de minimización de funcionales, y en constante convenio entre la experimentación tanto biológica como numérica, la presente tesis propone novedosas técnicas de modelado para analizar mejor estos elementos. Por otro lado está la escala molecular. Ésta se centra en unidades individuales, con un funcionamiento propio, tales como son los núcleos de las células que componen un tejido. Éstas, dependiendo de la información externa que reciben, se comportan de una manera u otra. A su vez, el comportamiento de una célula está codi cado en los genes que conforman su ADN. Por ello, comprender de forma adecuada cómo funciona la transcripción (copiado) de genes es una base fundamental para poder entender mejor los entresijos de la morfogénesis. En esta escala, la presente tesis trata da abordar el problema de la transcripción génica mediante modelados termoestadísticos.This thesis focuses on the development of models applied to di erent areas of morphogenesis. These areas refer to di erent stages of the development of the living being. For this reason, the models presented must be able of working at di erent scales, both spatial and temporal. This gives rise to a modeling work where, depending on the problem to be dealt with, particular mathematical tools have to be used for each one. Going into more particular details, we can summarize the biological scales covered by this thesis into two: the tissular scale and the molecular scale. On the one hand, the tissular scale collects global biological events, which occur in a wide area of the developing tissue. At this scale, the importance of the problem to be modeled resides not in a sole element, but in a set of elements. Generally it is usually related with the mathematical concept of macroscopic scale, where it tends to pose continuous models de ned by partial derivative equations. A clear example of these models is the di usion of proteins (signals) in a tissue. In this type of problem, the temporal evolution of protein concentrations is modeled using equations, usually parabolic, such as the di usion equation. However, in this thesis we study the signaling problem from a perspective more focused on the biological elements itself. In this way, although it is still a problem on a tissular scale, the way to approach it and model it mathematically will depend basically on the biological machinery behind it: in this case, the cytonemes. Cytonemes are biological components of which, at the time of deposit of this document, little is still known both at the biological and mathematical levels. Applying functional minimization techniques, and in constant agreement between both biological and numerical experimentation, the present thesis proposes novel modeling techniques to better analyze these elements. On the other hand there exists the molecular scale. This focuses on individual units, with their own functioning, such as the nucleus of cells that make up a tissue. These, depending on the external information they receive, behave in one way or another. In turn, the behavior of a cell is encoded in the genes in its DNA. Therefore, a proper understanding of how gene transcription (copying) works is a fundamental basis to better understand the ins and outs of morphogenesis. At this scale, the present thesis tries to address the problem of gene transcription through thermostatistic modeling.Tesis Univ. Granada.MINECO-Feder (Gobierno de España) números FPI2015/074837 y RTI2018- 098850-B-100Consejería de Economía, Innovación, Ciencia y Empleo, Proyecto PY18-RT-2422 de la Junta de Andalucía (Gobierno de Andalucía)Universidad de Granada-Feder A-FQM-311-UGR1