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8. The mammalian gene function resource: the International Knockout Mouse Consortium.

Author

Bradley, Allan, Anastassiadis, Konstantinos, Ayadi, Abdelkader, Battey, James F, Bell, Cindy, Birling, Marie-Christine, Bottomley, Joanna, Brown, Steve D, Bürger, Antje, Bult, Carol J, Bushell, Wendy, Collins, Francis S, Desaintes, Christian, Doe, Brendan, Economides, Aris, Eppig, Janan T, Finnell, Richard H, Fletcher, Colin, Fray, Martin, Frendewey, David, Friedel, Roland H, Grosveld, Frank G, Hansen, Jens, Hérault, Yann, Hicks, Geoffrey, Hörlein, Andreas, Houghton, Richard, Hrabé de Angelis, Martin, Huylebroeck, Danny, Iyer, Vivek, de Jong, Pieter J, Kadin, James A, Kaloff, Cornelia, Kennedy, Karen, Koutsourakis, Manousos, Lloyd, KC Kent, Marschall, Susan, Mason, Jeremy, McKerlie, Colin, McLeod, Michael P, von Melchner, Harald, Moore, Mark, Mujica, Alejandro O, Nagy, Andras, Nefedov, Mikhail, Nutter, Lauryl M, Pavlovic, Guillaume, Peterson, Jane L, Pollock, Jonathan, Ramirez-Solis, Ramiro, Rancourt, Derrick E, Raspa, Marcello, Remacle, Jacques E, Ringwald, Martin, Rosen, Barry, Rosenthal, Nadia, Rossant, Janet, Ruiz Noppinger, Patricia, Ryder, Ed, Schick, Joel Zupicich, Schnütgen, Frank, Schofield, Paul, Seisenberger, Claudia, Selloum, Mohammed, Simpson, Elizabeth M, Skarnes, William C, Smedley, Damian, Stanford, William L, Stewart, A Francis, Stone, Kevin, Swan, Kate, Tadepally, Hamsa, Teboul, Lydia, Tocchini-Valentini, Glauco P, Valenzuela, David, West, Anthony P, Yamamura, Ken-ichi, Yoshinaga, Yuko, and Wurst, Wolfgang

Subjects
Animals, Mice, Knockout, Mice, Internationality, Internet, Knockout, Genetics, Genetics & Heredity
Abstract

In 2007, the International Knockout Mouse Consortium (IKMC) made the ambitious promise to generate mutations in virtually every protein-coding gene of the mouse genome in a concerted worldwide action. Now, 5 years later, the IKMC members have developed high-throughput gene trapping and, in particular, gene-targeting pipelines and generated more than 17,400 mutant murine embryonic stem (ES) cell clones and more than 1,700 mutant mouse strains, most of them conditional. A common IKMC web portal (www.knockoutmouse.org) has been established, allowing easy access to this unparalleled biological resource. The IKMC materials considerably enhance functional gene annotation of the mammalian genome and will have a major impact on future biomedical research.

Published
2012

11. Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment

Author

Shevchenko, Anna, Roguev, Assen, Schaft, Daniel, Buchanan, Luke, Habermann, Bianca, Sakalar, Cagri, Thomas, Henrik, Krogan, Nevan J, Shevchenko, Andrej, and Stewart, A Francis

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Generic health relevance, Protein Interaction Mapping, Proteomics, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Schizosaccharomyces, Schizosaccharomyces pombe Proteins, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundUnderstanding the design logic of living systems requires the understanding and comparison of proteomes. Proteomes define the commonalities between organisms more precisely than genomic sequences. Because uncertainties remain regarding the accuracy of proteomic data, several issues need to be resolved before comparative proteomics can be fruitful.ResultsThe Saccharomyces cerevisiae proteome presents the highest quality proteomic data available. To evaluate the accuracy of these data, we intensively mapped a proteomic environment, termed 'Chromatin Central', which encompasses eight protein complexes, including the major histone acetyltransferases and deacetylases, interconnected by twelve proteomic hyperlinks. Using sequential tagging and a new method to eliminate background, we confirmed existing data but also uncovered new subunits and three new complexes, including ASTRA, which we suggest is a widely conserved aspect of telomeric maintenance, and two new variations of Rpd3 histone deacetylase complexes. We also examined the same environment in fission yeast and found a very similar architecture based on a scaffold of orthologues comprising about two-thirds of all proteins involved, whereas the remaining one-third is less constrained. Notably, most of the divergent hyperlinks were found to be due to gene duplications, hence providing a mechanism for the fixation of gene duplications in evolution.ConclusionsWe define several prerequisites for comparative proteomics and apply them to examine a proteomic environment in unprecedented detail. We suggest that high resolution mapping of proteomic environments will deliver the highest quality data for comparative proteomics.

Published
2008

13. The BOD1L subunit of the mammalian SETD1A complex sustains the expression of DNA damage repair genes despite restraining H3K4 trimethylation

Author

Ciotta, Giovanni, primary, Singh, Sukhdeep, additional, Gupta, Ashish, additional, Torres, Davi Coe, additional, Fu, Jun, additional, Choudhury, Rupam, additional, Chu, Wai Kit, additional, Choudhary, Chuna, additional, Gahurova, Lenka, additional, Al-Fatlawi, Ali, additional, Schroeder, Michael, additional, Aasland, Rein, additional, Poetsch, Anna R., additional, Anastassiadis, Konstantinos, additional, and Stewart, A. Francis, additional

Published
2023
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14. Seamless site-directed mutagenesis in complex cloned DNA sequences using the RedEx method

Author

Luan, Ji, Song, Chaoyi, Liu, Yan, He, Ruoting, Guo, Ruofei, Cui, Qingwen, Jiang, Chanjuan, Li, Xiaochen, Hao, Kexin, Stewart, A. Francis, Fu, Jun, Zhang, Youming, and Wang, Hailong

Abstract

Seamless site-directed mutagenesis is an important technique for studying protein functions, tuning enzyme catalytic activities and modifying genetic elements in multiple rounds because it can insert, delete or substitute nucleotides, DNA segments or even entire genes at the target site without introducing any unwanted change. To facilitate seamless site-directed mutagenesis in large plasmids and bacterial artificial chromosomes (BACs) with repetitive sequences, we recently developed the RedEx strategy. Compared with previous methods, our approach achieves the recovery of correct recombinants with high accuracy by circumventing unwanted recombination between repetitive sequences. RedEx readily yields more than 80% accuracy in seamless DNA insertion and deletion in large multimodular polyketide synthase gene clusters, which are among the most difficult targets due to the large number of repetitive DNA sequences in modules encoding almost identical enzymes. Here we present the RedEx method by describing in detail the seamless site-directed mutagenesis in a BAC vector. Overall, the process includes three parts: (1) insertion of the RedEx cassette containing the desired mutation together with selection–counterselection markers flanked by unique restriction sites and 20-bp overlapping sequences into the target site by recombineering, (2) removal of the selection–counterselection markers in the BAC by restriction digestion and (3) circularization of the linear BAC by exonuclease-mediated in vitro DNA annealing. This protocol can be performed within 3 weeks and will enable researchers with DNA cloning experience to master seamless site-directed mutagenesis to accelerate their research.

Published
2024
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15. Deficiency and haploinsufficiency of histone macroH2A1.1 in mice recapitulate hematopoietic defects of human myelodysplastic syndrome

Author

Bereshchenko, Oxana, Lo Re, Oriana, Nikulenkov, Fedor, Flamini, Sara, Kotaskova, Jana, Mazza, Tommaso, Le Pannérer, Marguerite-Marie, Buschbeck, Marcus, Giallongo, Cesarina, Palumbo, Giuseppe, Li Volti, Giovanni, Pazienza, Valerio, Cervinek, Libor, Riccardi, Carlo, Krejci, Lumir, Pospisilova, Sarka, Stewart, A. Francis, and Vinciguerra, Manlio

Published
2019
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18. Analysis of combinatorial chemokine receptor expression dynamics using multi-receptor reporter mice

Author

Medina-Ruiz, Laura, Bartolini, Robin, Wilson, Gillian J., Dyer, Douglas P., Vidler, Francesca, Hughes, Catherine E., Schuette, Fabian, Love, Samantha, Fu, Jun, Stewart, Adrian Francis, and Graham, Gerard J.

Abstract

Inflammatory chemokines and their receptors are central to the development of inflammatory/immune pathologies. The apparent complexity of this system, coupled with lack of appropriate in vivo models, has limited our understanding of how chemokines orchestrate inflammatory responses and has hampered attempts at targeting this system in inflammatory disease. Novel approaches are therefore needed to provide crucial biological, and therapeutic, insights into the chemokine-chemokine receptor family. Here, we report the generation of transgenic multi-chemokine receptor reporter mice in which spectrally distinct fluorescent reporters mark expression of CCRs 1, 2, 3, and 5, key receptors for myeloid cell recruitment in inflammation. Analysis of these animals has allowed us to define, for the first time, individual and combinatorial receptor expression patterns on myeloid cells in resting and inflamed conditions. Our results demonstrate that chemokine receptor expression is highly specific, and more selective than previously anticipated.

Published
2022

20. The histone demethylase UTX regulates stem cell migration and hematopoiesis

Author

Thieme, Sebastian, Gyárfás, Tobias, Richter, Cornelia, Özhan, Günes, Fu, Jun, Alexopoulou, Dimitra, Muders, Michael H., Michalk, Irene, Jakob, Christiane, Dahl, Andreas, Klink, Barbara, Bandoła, Joanna, Bachmann, Michael, Schröck, Evelin, Buchholz, Frank, Stewart, A. Francis, Weidinger, Gilbert, Anastassiadis, Konstantinos, and Brenner, Sebastian

Published
2013
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23. RAP1-mediated MEK/ERK pathway defects in Kabuki syndrome

Author

Bogershausen, Nina, Tsai, I-Chun, Pohl, Esther, Kiper, Pelin Ozlem Simsek, Beleggia, Filippo, Percin, E. Ferda, Keupp, Katharina, Matchan, Angela, Milz, Esther, Alanay, Yasemin, Kayserili, Hulya, Liu, Yicheng, Banka, Siddharth, Kranz, Andrea, Zenker, Martin, Wieczorek, Dagmar, Elcioglu, Nursel, Prontera, Paolo, Lyonnet, Stanislas, Meitinger, Thomas, Stewart, A. Francis, Donnai, Dian, Strom, Tim M., Boduroglu, Koray, Yigit, Gokhan, Li, Yun, Katsanis, Nicholas, and Wollnik, Bernd

Subjects
Kabuki syndrome -- Risk factors -- Genetic aspects -- Research, Methyltransferases, Health care industry
Abstract

The genetic disorder Kabuki syndrome (KS) is characterized by developmental delay and congenital anomalies. Dominant mutations in the chromatin regulators lysine (K)-specific methyltransferase 2D (KMT2D) (also known as MLL2) and lysine (K)-specific demethylase 6A (KDM6A) underlie the majority of cases. Although the functions of these chromatin-modifying proteins have been studied extensively, the physiological systems regulated by them are largely unknown. Using whole-exome sequencing, we identified a mutation in RAP1A that was converted to homozygosity as the result of uniparental isodisomy (UPD) in a patient with KS and a de novo, dominant mutation in RAP1B in a second individual with a KS-like phenotype. We elucidated a genetic and functional interaction between the respective KS-associated genes and their products in zebrafish models and patient cell lines. Specifically, we determined that dysfunction of known KS genes and the genes identified in this study results in aberrant MEK/ERK signaling as well as disruption of F-actin polymerization and cell intercalation. Moreover, these phenotypes could be rescued in zebrafish models by rebalancing MEK/ERK signaling via administration of small molecule inhibitors of MEK. Taken together, our studies suggest that the KS pathophysiology overlaps with the RASopathies and provide a potential direction for treatment design., Introduction De novo dominant germline mutations in lysine (K)-specific methyltransferase 2D (KMT2D; formerly MLL2, ALR; ref. 1) or lysine (K)-specific demethylase 6A (KDM6A) cause Kabuki syndrome (KS; MIM 147920 and [...]

Published
2015
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24. Author response: Analysis of combinatorial chemokine receptor expression dynamics using multi-receptor reporter mice

Author

Medina-Ruiz, Laura, primary, Bartolini, Robin, additional, Wilson, Gillian J, additional, Dyer, Douglas P, additional, Vidler, Francesca, additional, Hughes, Catherine E, additional, Schuette, Fabian, additional, Love, Samantha, additional, Pingen, Marieke, additional, Hayes, Alan James, additional, Fu, Jun, additional, Stewart, Adrian Francis, additional, and Graham, Gerard J, additional

Published
2022
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28. MLL1 is required for maintenance of intestinal stem cells

Author

Goveas, Neha, primary, Waskow, Claudia, additional, Arndt, Kathrin, additional, Heuberger, Julian, additional, Zhang, Qinyu, additional, Alexopoulou, Dimitra, additional, Dahl, Andreas, additional, Birchmeier, Walter, additional, Anastassiadis, Konstantinos, additional, Stewart, A. Francis, additional, and Kranz, Andrea, additional

Published
2021
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29. Postnatal expression of the lysine methyltransferase SETD1B is essential for learning and the regulation of neuron‐enriched genes

Author

Michurina, Alexandra, primary, Sakib, M Sadman, additional, Kerimoglu, Cemil, additional, Krüger, Dennis Manfred, additional, Kaurani, Lalit, additional, Islam, Md Rezaul, additional, Joshi, Parth Devesh, additional, Schröder, Sophie, additional, Centeno, Tonatiuh Pena, additional, Zhou, Jiayin, additional, Pradhan, Ranjit, additional, Cha, Julia, additional, Xu, Xingbo, additional, Eichele, Gregor, additional, Zeisberg, Elisabeth M, additional, Kranz, Andrea, additional, Stewart, A Francis, additional, and Fischer, André, additional

Published
2021
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34. Postnatal SETD1B is essential for learning and the regulation of neuronal plasticity genes

Author

Michurina, Alexandra, primary, Sakib, M Sadman, additional, Kerimoglu, Cemil, additional, Krüger, Dennis Manfred, additional, Kaurani, Lalit, additional, Islam, Md Rezaul, additional, Devesh, Joshi Parth, additional, Schröder, Sophie, additional, Centeno, Tonatiuh Pena, additional, Zhou, Jiayin, additional, Pradhan, Ranjit, additional, Cha, Julia, additional, Xu, Xingbo, additional, Eichele, Gregor, additional, Zeisberg, Elisabeth M., additional, Kranz, Andrea, additional, Stewart, A. Francis, additional, and Fischer, Andre, additional

Published
2021
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37. Immune checkpoint inhibitors (ICI) in advanced upper tract and lower tract urothelial carcinoma (UC): A comparison of outcomes

Author

Esagian, Stepan M. Khaki, Ali Raza Carril-Ajuria, Lucia and Park, Joseph J. Bilen, Mehmet Asim Stewart, Tyler Francis and Santos, Victor Sacristan Jain, Jayanshu Morales-Barrera, Rafael and Devitt, Michael Edward Hoimes, Christopher J. Shreck, Evana and Tripathi, Abhishek Zakopoulou, Roubini Rodriguez-Vida, Alejo and Drakaki, Alexandra Kumar, Vivek Msaouel, Pavlos Koshkin, Vadim S. Petros, Grivas

Published
2021

38. Cooperative genetic networks drive embryonic stem cell transition from naive to formative pluripotency

Author

Lackner, Andreas, Sehlke, Robert, Garmhausen, Marius, Giuseppe Stirparo, Giuliano, Huth, Michelle, Titz-Teixeira, Fabian, van Der Lelij, Petra, Ramesmayer, Julia, Thomas, Henry F., Ralser, Meryem, Santini, Laura, Galimberti, Elena, Sarov, Mihail, Stewart, A. Francis, Smith, Austin, Beyer, Andreas, Leeb, Martin, Lackner, Andreas, Sehlke, Robert, Garmhausen, Marius, Giuseppe Stirparo, Giuliano, Huth, Michelle, Titz-Teixeira, Fabian, van Der Lelij, Petra, Ramesmayer, Julia, Thomas, Henry F., Ralser, Meryem, Santini, Laura, Galimberti, Elena, Sarov, Mihail, Stewart, A. Francis, Smith, Austin, Beyer, Andreas, and Leeb, Martin

Abstract

In the mammalian embryo, epiblast cells must exit the naive state and acquire formative pluripotency. This cell state transition is recapitulated by mouse embryonic stem cells (ESCs), which undergo pluripotency progression in defined conditions in vitro. However, our understanding of the molecular cascades and gene networks involved in the exit from naive pluripotency remains fragmentary. Here, we employed a combination of genetic screens in haploid ESCs, CRISPR/Cas9 gene disruption, large-scale transcriptomics and computational systems biology to delineate the regulatory circuits governing naive state exit. Transcriptome profiles for 73 ESC lines deficient for regulators of the exit from naive pluripotency predominantly manifest delays on the trajectory from naive to formative epiblast. We find that gene networks operative in ESCs are also active during transition from pre- to post-implantation epiblast in utero. We identified 496 naive state-associated genes tightly connected to the in vivo epiblast state transition and largely conserved in primate embryos. Integrated analysis of mutant transcriptomes revealed funnelling of multiple gene activities into discrete regulatory modules. Finally, we delineate how intersections with signalling pathways direct this pivotal mammalian cell state transition.

Published
2021

39. Building synthetic multicellular systems from the bottom-up

Author

Stewart, A. Francis, Danelon, Christophe, Technische Universität Dresden, Gonzales, David T., Stewart, A. Francis, Danelon, Christophe, Technische Universität Dresden, and Gonzales, David T.

Abstract

Biological cell populations, such as in tissues or microbial communities, are constantly subject to different sources of noise and variability. Despite this, multicellular systems are still able to function properly because cells coordinate with each other by communication. Using biological model systems to study this multiscalar process can be challenging because of their innate complexity. In this thesis, we address this challenge by building a synthetic multicellular system using bottom-up in vitro assembly approaches. Using this platform, we aim to study the effect of cell-to-cell communication to population variability in a minimal and simplified context. To achieve this, we require a synthetic cell population with (i) quantifiable gene expression dynamics, (ii) customizable population variability, and (iii) intercellular communication. Having these characteristics will allow us to test different initial configurations of population variability and monitor population gene expression dynamics with and without cell-to-cell communication. To generate these synthetic cell populations, reconstituted cell-free expression systems (CFES) are encapsulated into monodisperse-sized liposomes using double-emulsion microfluidics. Both transcription and translation levels are simultaneously monitored and quantified to develop models of cell-free gene expression dynamics and differentiate between bulk and encapsulated formats. Population variability was then incorporated by combining different batches of cells to create distinct subpopulations or by using a two-inlet double-emulsion microfluidic device to generate single populations with a large dispersion of encapsulated DNA template. Lastly, genetic circuits based on the quorum sensing system of Vibrio fischeri are used to implement diffusion-mediated intercellular signalling. Quorum sensing gene circuits in Escherichia coli extract-based CFES were tested in bulk and phase transfer-generated synthetic cells. Together with th, Biologische Zellpopulationen, z.B. in Geweben oder mikrobiellen Gemeinschaften, sind ständig verschiedenen Quellen von Rauschen und Variabilität ausgesetzt. Trotzdem sind multizelluläre Systeme in der Lage, ordnungsgemäß zu funktionieren, weil sich die Zellen durch Kommunikation miteinander abstimmen. Die Verwendung biologischer Modellsysteme zur Untersuchung dieses multiskalaren Prozesses kann aufgrund ihrer angeborenen Komplexität eine Herausforderung darstellen. In dieser Arbeit gehen wir diese Herausforderung an, indem wir ein synthetisches multizelluläres System mit Hilfe von Bottom-up-in vitro-Assembly-Ansätzen aufbauen. Mit Hilfe dieser Plattform wollen wir die Auswirkungen der Kommunikation von Zelle zu Zelle auf die Populationsvariabilität in einem minimalen und vereinfachten Kontext untersuchen. Um dies zu erreichen, benötigen wir eine synthetische Zellpopulation mit (i) quantifizierbarer Genexpressionsdynamik, (ii) anpassbarer Populationsvariabilität und (iii) interzellulärer Kommunikation. Mit diesen Eigenschaften können wir verschiedene Ausgangskonfigurationen der Populationsvariabilität testen und die Genexpressionsdynamik der Population mit und ohne Zell-zu-Zell-Kommunikation beobachten. Um diese synthetischen Zellpopulationen zu erzeugen, werden rekonstituierte zellfreie Expressionssysteme (CFES) mit Hilfe der Doppelemulsions-Mikrofluidik in monodisperse Liposomen eingekapselt. Sowohl die Transkriptions- als auch die Translationsraten werden gleichzeitig überwacht und quantifiziert, um Modelle für die Dynamik der zellfreien Genexpression zu entwickeln und zwischen Bulk- und verkapselten Formaten zu unterscheiden. Die Variabilität der Populationen wurde dann durch die Kombination verschiedener Zellchargen zur Bildung unterschiedlicher Subpopulationen oder durch die Verwendung einer mikrofluidischen Doppelemulsionsvorrichtung mit zwei Einlässen zur Erzeugung einzelner Populationen mit einer großen Streuung der eingekapselten DNA-Vorlage einbezogen. Sch

Published
2021

42. Cooperative genetic networks drive embryonic stem cell transition from naïve to formative pluripotency

Author

Lackner, Andreas, primary, Sehlke, Robert, additional, Garmhausen, Marius, additional, Giuseppe Stirparo, Giuliano, additional, Huth, Michelle, additional, Titz‐Teixeira, Fabian, additional, van der Lelij, Petra, additional, Ramesmayer, Julia, additional, Thomas, Henry F, additional, Ralser, Meryem, additional, Santini, Laura, additional, Galimberti, Elena, additional, Sarov, Mihail, additional, Stewart, A Francis, additional, Smith, Austin, additional, Beyer, Andreas, additional, and Leeb, Martin, additional

Published
2021
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43. Association between sites of metastases (mets) and outcomes with immune checkpoint inhibitor (ICI) therapy for advanced urothelial carcinoma (aUC).

Author

Makrakis, Dimitrios, primary, Diamantopoulos, Leonidas Nikolaos, additional, Koshkin, Vadim S, additional, Alva, Ajjai Shivaram, additional, Bilen, Mehmet Asim, additional, Stewart, Tyler Francis, additional, Santos, Victor Sacristan, additional, Jain, Jayanshu, additional, Morales-Barrera, Rafael, additional, Devitt, Michael E., additional, Carril-Ajuria, Lucia, additional, Nelson, Ariel Ann, additional, Sankin, Alexander, additional, Zakopoulou, Roubini, additional, Pinato, David James, additional, Fröbe, Ana, additional, Joshi, Monika, additional, Sonpavde, Guru, additional, Grivas, Petros, additional, and Khaki, Ali Raza, additional

Published
2021
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46. Immune checkpoint inhibitors (ICI) in advanced upper tract and lower tract urothelial carcinoma (UC): A comparison of outcomes.

Author

Esagian, Stepan M., primary, Khaki, Ali Raza, additional, Carril-Ajuria, Lucia, additional, Park, Joseph J., additional, Bilen, Mehmet Asim, additional, Stewart, Tyler Francis, additional, Santos, Victor Sacristan, additional, Jain, Jayanshu, additional, Morales-Barrera, Rafael, additional, Devitt, Michael Edward, additional, Hoimes, Christopher J., additional, Shreck, Evan, additional, Tripathi, Abhishek, additional, Zakopoulou, Roubini, additional, Rodriguez-Vida, Alejo, additional, Drakaki, Alexandra, additional, Kumar, Vivek, additional, Msaouel, Pavlos, additional, Koshkin, Vadim S, additional, and Grivas, Petros, additional

Published
2021
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48. Cooperative molecular networks drive a mammalian cell state transition

Author

Lackner, Andreas, Sehlke, Robert, Garmhausen, Marius, Stirparo, Giuliano Giuseppe, Huth, Michelle, Titz-Teixeira, Fabian, van der Lelij, Petra, Ramesmayer, Julia, Thomas, Henry Fabian, Ralser, Meryem, Santini, Laura, Sarov, Mihail, Stewart, A. Francis, Smith, Austin, Beyer, Andreas, and Leeb, Martin

Subjects
embryonic structures
Abstract

In the mammalian embryo, epiblast cells must exit their naïve state and acquire formative pluripotency. This cell state transition is recapitulated by mouse embryonic stem cells (ESCs), which undergo pluripotency progression in defined conditions in vitro . Here we employed a combination of genetic screens in haploid ESCs, CRISPR/Cas9 gene disruption, large-scale transcriptomics and computational systems-biology to delineate the regulatory circuits governing naïve state exit. Transcriptome profiles for 73 knockouts (KOs) predominantly manifest delays on the trajectory from naive to formative epiblast. We identified 374 naïve-associated genes (NAGs), which are tightly connected to the epiblast state and largely conserved in human stem cells and primate embryos. Integrated analysis of mutant transcriptomes revealed that the activity of multiple genes promoting pluripotency progression is funneled into discrete regulatory modules. We demonstrate that these modules are under control of five signaling pathways that operate in parallel to direct this pivotal mammalian cell state transition.

Published
2020
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50. KMT2B Is Selectively Required for Neuronal Transdifferentiation, and Its Loss Exposes Dystonia Candidate Genes

Author

Barbagiovanni, Giulia, Germain, Pierre Luc, Zech, Michael, Atashpaz, Sina, Lo Riso, Pietro, D'Antonio-Chronowska, Agnieszka, Tenderini, Erika, Caiazzo, Massimiliano, Boesch, Sylvia, Jech, Robert, Haslinger, Bernhard, Broccoli, Vania, Stewart, Adrian Francis, Winkelmann, Juliane, Testa, Giuseppe, Afd Pharmaceutics, Pharmaceutics, Barbagiovanni, Giulia, Germain, Pierre-Luc, Zech, Michael, Atashpaz, Sina, Lo Riso, Pietro, D'Antonio-Chronowska, Agnieszka, Tenderini, Erika, Caiazzo, Massimiliano, Boesch, Sylvia, Jech, Robert, Haslinger, Bernhard, Broccoli, Vania, Stewart, Adrian Franci, Winkelmann, Juliane, Testa, Giuseppe, Afd Pharmaceutics, and Pharmaceutics

Subjects
0301 basic medicine, Candidate gene, Histone H3 Lysine 4, mouse embryonic fibroblasts, transdifferentiation, Biochemistry, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, medicine, lcsh:QH301-705.5, Transcription factor, myocyte, Dystonia, induced neuronal cells, epigenetics, biology, Biochemistry, Genetics and Molecular Biology(all), Transdifferentiation, KMT2B, Epigenome, myocytes, medicine.disease, histone H3 lysine 4 methylation, Cell biology, induced neuronal cell, cell fate conversion, mouse embryonic fibroblast, ASCL1, 030104 developmental biology, KMT2A, lcsh:Biology (General), biology.protein, MLL2, dystonia, epigenetic, Genetics and Molecular Biology(all)
Abstract

Transdifferentiation of fibroblasts into induced neuronal cells (iNs) by the neuron-specific transcription factors Brn2, Myt1l, and Ascl1 is a paradigmatic example of inter-lineage conversion across epigenetically distant cells. Despite tremendous progress regarding the transcriptional hierarchy underlying transdifferentiation, the enablers of the concomitant epigenome resetting remain to be elucidated. Here, we investigated the role of KMT2A and KMT2B, two histone H3 lysine 4 methylases with cardinal roles in development, through individual and combined inactivation. We found that Kmt2b, whose human homolog’s mutations cause dystonia, is selectively required for iN conversion through suppression of the alternative myocyte program and induction of neuronal maturation genes. The identification of KMT2B-vulnerable targets allowed us, in turn, to expose, in a cohort of 225 patients, 45 unique variants in 39 KMT2B targets, which represent promising candidates to dissect the molecular bases of dystonia., Cell Reports, 25 (4), ISSN:2666-3864, ISSN:2211-1247

Published
2018

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