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title => protected'Modeling the immune regulation of clonal hematopoiesis' (54 chars)
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<p>Collaborating Supervisor: Dr. Linus Schumacher<br /> Group: <a href="https://www.ed.ac.uk/regenerative-medicine/research/linus-schumache r" target="_blank">Linus Schumacher Group</a><br /> Institute: University of Edinburgh, Centre for Regenerative Medicine</p>' (656 chars)
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<p>Akute leukemia is a blood cancer that usuall y starts displaying symptoms in a late stage, making its treatment difficult and often unsuccessful. The disease is caused by carcinogenic mutations in hematopoietic stem cells (HSCs). They cause the cells to proliferate instead of differentiating further towards mature blood cells. Recently, it has bee n observed that certain mutations are present in patients already a few deca des before the onset of leukemia, a property called clonal hematopoiesis of indeterminate potential (CHIP) [1,2].</p>
<p><br /> In the Marr Lab at Helm holtz Munich and at the Schumacher lab at the University of Edinburgh, we work on understanding hematopoiesis [3,4], the kinetics of CHIP [5], and the role of the immune system in the regulation of the CHIP mutated single c ells. This could help us prevent the development of leukemia, or lead to the development of less invasive treatments than chemotherapy and bone marrow t ransplantation.<br /> In the PhD project, the student will address the quest ion of how the immune system deals with CHIP from two different perspectives , using contemporary analytical tools. The first level will involve mathemat ical modeling of the kinetics of CHIP mutations and the blood production sys tem. The goal here is to use data from large cohorts to find phenotypic evid ence and properties of the immune system activity. This will include stochas tic modeling, ordinary differential equations and statistical inference to d escribe hematopoiesis. The second level will be understanding the molecular and epigenetic mechanisms of immune regulation of CHIP. The candidate will a nalyze data from blood and bone marrow smears, single cell RNA sequencing, s ingle cell ATAC sequencing, chromatin immunoprecipitation, and mass spectros copy with bioinformatic techniques and machine learnin models to understand the signaling pathways between CHIP cells and immune cells. The student will enter a 4 year program ...' (2691 chars)
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_versionedUid => protected15 (integer)modifiedpid => protected56624 (integer)000000000000116c0000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=16, pid=56624)bodytext => protected'<p>Relevant Literature:</p>
<ul> <li>Genovese G, Kähler AK, Handsaker RE, Lindberg J, Rose SA, Bakhoum SF, et al. Clonal hematopoiesis and blood-canc er risk inferred from blood DNA sequence. N Engl J Med. 2014;371: 2477–248 7</li> <li>Jaiswal S, Fontanillas P, Flannick J, Manning A, Grauman PV, Mar BG, et al. Age-related clonal hematopoiesis associated with adverse outcome s. N Engl J Med. 2014;371: 2488–2498</li> <li>Bast L, Buck MC, Hecker JS, Oostendorp RAJ, Götze KS, Marr C. Computational modeling of stem and proge nitor cell kinetics identifies plausible hematopoietic lineage hierarchies. iScience. 2021;24: 102120</li> <li>Buggenthin F, Buettner F, Hoppe PS, Ende le M, Kroiss M, Strasser M, et al. Prospective identification of hematopoiet ic lineage choice by deep learning. Nat Methods. 2017;14: 403–406</li> <l i>Robertson NA, Latorre-Crespo E, Terradas-Terradas M, Lemos-Portela J, Purc ell AC, Livesey BJ, et al. Longitudinal dynamics of clonal hematopoiesis ide ntifies gene-specific fitness effects. Nat Med. 2022;28: 1439–1446</li> </ ul>' (1067 chars)
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title => protected'Single-cell multiomic analysis of transposable elements with new Bayesian ma chine learning methods' (98 chars)
link => protected't3://page?uid=56934' (19 chars)
imageReference => protectedTYPO3\CMS\Extbase\Domain\Model\FileReferenceprototypepersistent entity (uid=157082, pid=56624)uidLocal => protected345666 (integer)
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_localizedUid => protected157082 (integer)modified_languageUid => protected0 (integer)modified_versionedUid => protected157082 (integer)modifiedpid => protected56624 (integer)image => protectedNULL
textItems => protectedTYPO3\CMS\Extbase\Persistence\ObjectStorageprototypeobject (3 items)000000000000111e0000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=17, pid=56624)bodytext => protected'<p>Main Supervisor: Dr. Antonio Scialdone<br /> Group: <a href="https:/ /www.helmholtz-munich.de/en/ies/research-groups/scialdone-lab" target="_blan k">Physics and Data-Based Modelling of Cellular Identity Changes</a><br /> I nstitute: <a href="https://www.helmholtz-munich.de/en/ies" target="_bla nk">Institute of Epigenetics and Stem Cells</a>, Helmholtz Center Munich</p>
<p>Collaborating Supervisor: Dr. Catalina Vallejos<br /> Group: <a hr ef="https://www.ed.ac.uk/mrc-human-genetics-unit/research/vallejos-group" ta rget="_blank">Biomedical Data Science</a><br /> Institute: MRC Human Genetic s Unit, Institute of Genetics & Molecular Medicine, University of Edinbu rgh</p>' (691 chars)
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_versionedUid => protected17 (integer)modifiedpid => protected56624 (integer)000000000000117d0000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=18, pid=56624)bodytext => protected'<p>Project Description:</p>
<p>Transposable elements (TEs) are mobile DNA s equences that constitute large fractions of many eukaryotic genomes. They ha ve an increasingly recognized role in regulating cellular identity changes i n many different contexts, like embryonic development and the onset of many diseases, including neurodegenerative diseases and cancer (Bourque et al. 20 18). However, we still know little about how they are regulated. The current availability of a large number of single-cell omic datasets provides a grea t opportunity to map the transcriptional activity and the chromatin state of these elements at a single-cell resolution genome-wide. However, there are fundamental computational challenges that remain to be solved. The main chal lenge comes from the repetitive nature of TEs, which hinders the mapping of reads originating from them. The currently available computational tools des igned to address this challenge either profile TEs at a sub-family level, lo sing any information on the TE genomic location; or exploit mutations to pin point the location of TEs, a strategy that fails with “young” intact TEs having a low substitution rate.</p>
<p><br /> This project has two main ai ms: (i) devise new computational methods to characterize the transcriptional and chromatin state of TEs from single-cell sequencing datasets; (ii) use t hese methods to characterize TEs regulation during human embryonic developme nt and in stem-cell-based models of human embryos.</p>
<p><br /> For the fi rst aim, we will develop a novel algorithm based on Bayesian Machine Learnin g starting from existing approaches to analyze single-cell RNA-seq datasets (Eling et al. 2018), which will be extended to explicitly model ambiguous re ads in scRNA-seq data as well as other types of sequencing data, like single -cell ATAC-seq and bisulfite sequencing (Kapourani et al. 2021). This will e nable us to also analyze single-cell multi-omic datasets and investigate the regulation of TEs in va...' (2751 chars)
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_versionedUid => protected18 (integer)modifiedpid => protected56624 (integer)00000000000011800000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=19, pid=56624)bodytext => protected'<p>Relevant Literature:</p>
<ul> <li>Bourque, Guillaume, Kathleen H. Burns , Mary Gehring, Vera Gorbunova, Andrei Seluanov, Molly Hammell, Michaël Imb eault, et al. 2018. “Ten Things You Should Know about Transposable Element s.” Genome Biology 19 (1): 199</li> <li>Eling, Nils, Arianne C. Richard, Sylvia Richardson, John C. Marioni, and Catalina A. Vallejos. 2018. “Corre cting the Mean-Variance Dependency for Differential Variability Testing Usin g Single-Cell RNA Sequencing Data.” Cell Systems 7 (3): 284–94.e12</li> <li>Kapourani, Chantriolnt-Andreas, Ricard Argelaguet, Guido Sanguinetti, a nd Catalina A. Vallejos. 2021. “scMET: Bayesian Modeling of DNA Methylatio n Heterogeneity at Single-Cell Resolution.” Genome Biology 22 (1): 114</li > <li>Scialdone, Antonio, and Nicolas Rivron. 2022. “In Preprints: Improv ing and Interrogating Embryo Models.” Development 149 (23). <a href=" https://doi.org/10.1242/dev.201404" target="_blank">doi.org/10.1242/dev.2014 04</a></li> <li>Tyser, Richard C. V., Elmir Mahammadov, Shota Nakanoh, Ludo vic Vallier, Antonio Scialdone, and Shankar Srinivas. 2021. “Single-Cell T ranscriptomic Characterization of a Gastrulating Human Embryo.” Nature 600 (November): 285</li> </ul>' (1243 chars)
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uid => protected28 (integer)
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title => protected'Single cell epigenomic study of the frequency, dynamics and origin of resist ant epimutations in response to external insults' (124 chars)
link => protected't3://page?uid=56936' (19 chars)
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uid => protected157083 (integer)
_localizedUid => protected157083 (integer)modified_languageUid => protected0 (integer)modified_versionedUid => protected157083 (integer)modifiedpid => protected56624 (integer)image => protectedNULL
textItems => protectedTYPO3\CMS\Extbase\Persistence\ObjectStorageprototypeobject (3 items)000000000000115e0000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=21, pid=56624)bodytext => protected'<p>Main Supervisor: Dr. Maria Colomé-Tatché<br /> Group: <a href="htt ps://www.helmholtz-munich.de/en/icb/research-groups/colome-tatche-lab" targe t="_blank">Computational Epigenomics</a><br /> Institute: <a href="http s://www.helmholtz-munich.de/en/computational-health-center" target="_blank"> Institute of Computational Biology</a>, Helmholtz Center Munich</p>
<p>Co llaborating Supervisor: Dr. Robin Allshire<br /> Group: <a href="https: //www.wcb.ed.ac.uk/research/allshire" target="_blank">Wellcome Centre for Ce ll Biology</a><br /> Institute: Institute of Cell Biology, School of B iological Sciences, University of Edinburgh</p>' (655 chars)
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<p>Fungal survival in harsh environments involv es stress-sensing pathways that reprogram their proteomes. New conditions, i ncluding climate change, can push opportunistic fungi to colonise novel nich es, potentially becoming harmful pathogens. Effective antifungal/fungicide t reatments are limited in number precisely because fungi are adept at resisti ng challenges. Antifungal resistance is increasingly prevalent, raising fung al-borne disease frequencies in humans and crops1. Conventional wisdom that resistance results solely from genetic mutations was overturned by our disco very that external insults selects for cells with a distinct epigenetic land scape - repressive heterochromatin over various genes whose reduced expressi on confers resistance (e.g. mitochondrial proteins)2,3. Such heterochromatin -dependent ‘epimutations’ are unstable, slowly losing resistance upon ex ternal insult removal. We hypothesize that extracellular stresses, including fungicides widely used in agriculture, reprogramme fungal epigenomes so tha t they transiently acquire heterochromatin at locations which confer heritab le, but unstable, resistance. By employing single cell analysis of lineages seeded by just one cell we aim to provide insight into the mechanisms utiliz ed by cells to mediate epimutant-mediated resistance. This project will comb ine the power of classic Luria-Delbruck fluctuation tests with low cell numb er/single cell (ATAC-seq, Cut&Tag and RNA-seq) sequencing workflows to d issect the events that result in the emergence of transiently antifungal/fun gicide resistant lineages due to epimutation formation.</p>' (1655 chars)
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_versionedUid => protected22 (integer)modifiedpid => protected56624 (integer)00000000000011970000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=23, pid=56624)bodytext => protected'<p>Relevant Literature:</p>
<ul> <li>Fisher MC, Hawkins NJ, Sanglard D. &a mp; Gurr SJ. (2018) Worldwide emergence of resistance to antifungal drugs ch allenges human health and food security. Science 360, 739–742</li> <li>To rres-Garcia S, Yaseen I, Shukla M, Audergon PNCB, White SA, Pidoux AL, Allsh ire RC. (2020). Epigenetic gene silencing by heterochromatin primes fungal r esistance. Nature 585, 453–458</li> <li>Yaseen I, White SA, Torres-Garcia S, Spanos C, Lafos M, Gaberdiel E, Yeboah R, El Karoui M, Rappsilber J, Pid oux AL, Allshire RC. (2022) Proteasome-dependent truncation of the negative heterochromatin regulator Epe1 mediates antifungal resistance. Nature Struct ure & Molecular Biology (in press); BioRXiv: <a href="https://doi.o rg/10.1101/2021.12.20.473483" target="_blank">doi.org/10.1101/2021.12.20.473 483</a></li> <li>A. Danese, M.L. Richter, D.S. Fischer, F.J. Theis and M. C olomé-Tatché. EpiScanpy: integrated single-cell epigenomic analysis. Nat. Commun. 12, 5228 (2021).</li> <li>A. vd Graaf, R. Wardenaar, D.A. Neumann, A. Taudt, R.G. Shaw, R.C. Jansen, R.J. Schmitz*, M. Colomé-Tatché*, F. Joh annes*. Rate, spectrum and evolutionary dynamics of spontaneous epimutations . Proc. Natl. Acad. Sci. USA 112:6676-81 (2015). (* cocorresponding authors) </li> </ul>' (1303 chars)
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title => protected'The Evolution of Nuclear Sub-Compartmentalization and its Impact on Genome F unction' (83 chars)
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<p>Collaborating Supervisor: Dr. Joseph Marsh<br /> Group:<a href="https://www.wcb.ed.ac.uk/research/all shire" target="_blank"> </a><a href="https://www.ed.ac.uk/mrc-human-gen etics-unit/research/marsh-group" target="_blank">Marsh Lab</a><br /> Institu te: <a href="https://www.ed.ac.uk/mrc-human-genetics-unit" target="_bla nk">MRC Human Genetics Unit</a>, Institute of Genetics and Cancer, Universit y of Edinburgh</p>' (1082 chars)
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_versionedUid => protected24 (integer)modifiedpid => protected56624 (integer)000000000000119b0000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=25, pid=56624)bodytext => protected'<p>Project Description:</p>
<p>The project aims to address the evolutionary dynamics of the different sub-compartments of the nucleus of eukaryotic cel ls and reveal how they relate to genome function. The compartmentalization o f the nucleus into functional condensates, so-called membraneless organelles (MLOs), contributes to transcriptional regulation. Some MLOs form by liquid -liquid phase separation in the cytoplasm and nucleoplasm of eukaryotic cell s and have been tightly linked to different aspects of RNA biogenesis and me tabolism. Homeostatic changes in MLOs occur during differentiation, and are also associated with diseases, including cancers and viral infections. In th e nucleus, the most prominent MLOs are nucleoli, which are sites dedicated t o the transcription of ribosomal RNA. Other nuclear MLOs include: 1) Cajal b odies (CBs) that are small compartments forming on active loci of small nucl ear (sn)RNA transcription, typically observed in cells with high transcripti onal and splicing demands, 2) nuclear speckles (NSs), which interact with ac tive genes and represent hubs for pre-mRNA synthesis and metabolism, 3) para speckles, compartments involved in the regulation of gene expression, and 4) PML (promyelocytic leukemia) nuclear bodies (PML-NBs), which play a role in SUMOylation and interact with chromatin, transcriptional regulators, and pr oteins involved in DNA damage response and apoptosis. PML-NBs are also thoug ht to function as hubs for protein modification in the nucleus, and to contr ol the rate of cell cycle progression. Recent evidence suggests that differe nt MLOs share homeostatic regulators, however their functional and evolution ary links remain poorly understood. This project comprises of three parts: P 1) to reconstruct the shared evolutionary history of the core protein and no n-coding RNA components of the different nuclear MLOs, using phylogenetic, s tructural bioinformatics and molecular evolution tools (Marsh lab). P2) to r eveal how MLO evolution ...' (2812 chars)
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<ul> <li>Berchtold D, Battich N, Pelkmans L, 2 018, A systems-level study reveals regulators of membrane-less organelles in human cells, Molecular Cell, 72, 6, 1035-1049.e5</li> <li>Battich N, Beume r J, de Barbanson B, Krenning L, Chloé B, Tanenbaum M, Clevers H, van Ouden aarden A, 2020, Sequencing metabolically labeled transcripts in single cells reveals mRNA turnover strategies, Science, 367, 6482, 1151-1156</li> <li>I lik İA, Malszycki M, Lübke AK, Schade C, Meierhofer D, Aktaş T, 2020, ON and SRRM2 are essential for nuclear speckle formation, eLife, 9, e60579</li> <li>Hirose T, Ninomiya K, Nakagawa S, Yamazaki T, 2022, A guide to membran eless organelles and their various roles in gene regulation, Nat Rev Mol Cel l Biol, online ahead of print.</li> <li>Badonyi M, Marsh JA, 2022, Large pr otein complex interfaces have evolved to promote cotranslational assembly, e Life, 10, e79602</li> </ul>' (939 chars)
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title => protected'Incorporating DNA methylation of the sex chromosomes in population research' (75 chars)
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<p>Collaborating Supervisor: Dr. Kathryn Evans<br /> Group: <a href="https://www.ed.ac.u k/centre-genomic-medicine/research-groups/evans-group" target="_blank">Centr e for Genomic and Experimental Medicine</a>, Institute for Genetics and Canc er, the University of Edinburgh<br /> Institute: <a href="https://www.e d.ac.uk/centre-genomic-medicine" target="_blank">Centre for Genomic and Expe rimental Medicine</a>, <a href="https://www.ed.ac.uk/institute-genetics -cancer" target="_blank">Institute for Genetics and Cancer</a>, the Universi ty of Edinburgh</p>' (1007 chars)
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_versionedUid => protected28 (integer)modifiedpid => protected56624 (integer)00000000000011a70000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=29, pid=56624)bodytext => protected'<p>Relevant Literature:</p>
<ul> <li>Hawe JS, Wilson R, Schmid KT, Zhou L, Lakshmanan LN, Lehne BC, Kühnel B, Scott WR, Wielscher M, Yew YW, Baumbach C, Lee DP, Marouli E, Bernard M, Pfeiffer L, Matías-García PR, Autio MI, Bourgeois S, Herder C, Karhunen V, Meitinger T, Prokisch H, Rathmann W, Rode n M, Sebert S, Shin J, Strauch K, Zhang W, Tan WLW, Hauck SM, Merl-Pham J, G rallert H, Barbosa EGV; MuTHER Consortium; Illig T, Peters A, Paus T, Pausov a Z, Deloukas P, Foo RSY, Jarvelin MR, Kooner JS, Loh M, Heinig M, Gieger C, Waldenberger M, Chambers JC. 2022. Genetic variation influencing DNA methyl ation provides insights into molecular mechanisms regulating genomic functio n. Nat Genet: 54(1):18-29</li> <li>Lohoff FW, Clarke TK, Kaminsky ZA, Walke r RM, Bermingham ML, Jung J, Morris SW, Rosoff D, Campbell A, Barbu M, Charl et K, Adams M, Lee J, Howard DM, O'Connell EM, Whalley H, Porteous DJ, McInt osh AM, Evans KL. 2022. Epigenome-wide association study of alcohol consumpt ion in N = 8161 individuals and relevance to alcohol use disorder pathophysi ology: identification of the cystine/glutamate transporter SLC7A11 as a top target. Mol Psychiatry Mar;27(3):1754-1764</li> <li>Walker RM, Bermingham M L, Vaher K, Morris SW, Clarke TK, Bretherick AD, Zeng Y, Amador C, Rawlik K, Pandya K, Hayward C, Campbell A, Porteous DJ, McIntosh AM, Marioni RE, Evan s KL. 2020. Epigenome-wide analyses identify DNA methylation signatures of d ementia risk. Alzheimers Dement (Amst). Aug 10;12(1):e12078</li> <li>Gadd D A, Hillary RF, McCartney DL, Zaghlool SB, Stevenson AJ, Cheng Y, Fawns-Ritch ie C, Nangle C, Campbell A, Flaig R, Harris SE, Walker RM, Shi L, Tucker-Dro b EM, Gieger C, Peters A, Waldenberger M, Graumann J, McRae AF, Deary IJ, Po rteous DJ, Hayward C, Visscher PM, Cox SR, Evans KL, McIntosh AM, Suhre K, M arioni RE. 2022. Epigenetic scores for the circulating proteome as tools for disease prediction. Elife: 11:e71802</li> <li>Singmann P, Shem-Tov D, Wahl S, Grallert H, Fiorito ...' (2349 chars)
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title => protected'Investigating how chromatin and proteome composition is remodelled across va rying growth conditions' (99 chars)
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<p>Collaborating Supervisor: Dr. Matthew Swaff er<br /> Group: <a href="https://www.wcb.ed.ac.uk/" target="_blank">Wel lcome Trust Centre for Cell Biology, Swaffer Group</a><br /> Institute:  ;<a href="https://www.wcb.ed.ac.uk/" target="_blank">Wellcome Trust Centre f or Cell Biology</a>, University of Edinburgh</p>' (656 chars)
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_versionedUid => protected30 (integer)modifiedpid => protected56624 (integer)00000000000013430000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=31, pid=56624)bodytext => protected'<p>Project Description:</p>
<p>Cells must constantly balance and adjust the precise composition of their proteome in response to external and internal cues. For many proteins, this requires matching their synthesis rates with t he size and growth rate of the cell. For example, ribosomes and other biosyn thetic machinery are tightly correlated with growth across a range of condit ions. However, specific subsets of proteins need to be regulated differently – one of the best examples of this is chromatin. Chromatinassociated prot eins, including core histone proteins, are directly coupled to DNA amount, a nd therefore cell cycle, but are independent of cell size or growth rate. Th is ensures that histones are kept at a 1-to-1 ratio with the genome, such th at the structure, composition, and function of chromatin can always be maint ained.</p>
<p><br /> Due to this variable requirement for different protein sectors, the proteome is constantly remodelled whenever cell size, cellular growth rate or cell cycle change. Ensuring correct proteome composition is therefore particularly challenging when moving between different environment al conditions, because, depending on the nutrients, all three of these param eters will change.</p>
<p><br /> Our preliminary results show that in buddi ng yeast, maintaining constant amounts of histones across different environm ental conditions requires both transcriptional and post-transcriptional regu latory controls. In this project, we will use a combination of single-cell i maging, quantitative functional genomics and high-throughput proteomics to d etermine how the production of other key chromatin components is regulated a s cells move between different nutritional states. In addition, we will also examine more generally how other proteome sectors are regulated in response to altered environmental conditions. After characterizing the proteome comp osition and revealing whether the responsible regulation is transcriptional or post-transcriptional ...' (2458 chars)
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_versionedUid => protected31 (integer)modifiedpid => protected56624 (integer)00000000000013460000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=32, pid=56624)bodytext => protected'<p>Relevant Literature:</p>
<ul> <li>Swaffer MP, Marinov GK, Zheng H, Jone s AW, Greenwood J, Kundaje A, Snijders AP, Greenleaf WJ, Reyes-Lamothe R, Sk otheim JM, 2022, RNA polymerase II dynamics and mRNA stability feedback dete rmine mRNA scaling with cell size, bioRxiv, <a href="https://doi.org/10 .1101/2021.09.20.461005" target="_blank">https://doi.org/10.1101/2021.09.20. 461005</a></li> <li>Seel A, Padovani F, Finster A, Mayer M, Bureik D, Osman C, Klecker T, Schmoller KM, 2021, Regulation with cell size ensures mitocho ndrial DNA homeostasis during cell growth, bioRxiv, <a href="http://doi .org/10.1101/2021.12.03.471050" target="_blank">doi.org/10.1101/2021.12.03.4 71050</a></li> <li>Swaffer MP, Kim J, Chandler-Brown D, Langhinrichs M, Mar inov GK, Greenleaf WJ, Kundaje A, Schmoller KM, Skotheim JM, 2021, Transcrip tional chromatin-based partitioning mechanisms uncouple protein scaling from cell cell size, Molecular Cell, 81, 1-15</li> <li>Claude K-L, Bureik D, Ch atzitheodoridou D, Adarska P, Singh A, Schmoller KM, 2020, Transcription coo rdinates histone amounts and genome content, Nature Communications, 12, 4202 </li> <li>Kukhtevich IV, Lohrberg N, Padovani F, Schneider R, Schmoller KM, 2020, Cell size sets the diameter of the budding yeast contractile ring, Na ture Communications, 22, 2952</li> </ul>' (1332 chars)
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uid => protected32 (integer)
_localizedUid => protected32 (integer)modified_languageUid => protectedNULL
_versionedUid => protected32 (integer)modifiedpid => protected56624 (integer)00000000000013370000000000000000 => FelixNagel\GenericGallery\Domain\Model\GalleryItemprototypepersistent entity (uid=33, pid=56624)ttContentUid => protected273331 (integer)
title => protected'Single cell to lineage analysis of epimutation establishment and heritabilit y in response to external insults such as antifungal agents' (135 chars)
link => protected't3://page?uid=56626' (19 chars)
imageReference => protectedTYPO3\CMS\Extbase\Domain\Model\FileReferenceprototypepersistent entity (uid=157130, pid=56624)uidLocal => protected345693 (integer)
originalResource => protectedNULL
uid => protected157130 (integer)
_localizedUid => protected157130 (integer)modified_languageUid => protected0 (integer)modified_versionedUid => protected157130 (integer)modifiedpid => protected56624 (integer)image => protectedNULL
textItems => protectedTYPO3\CMS\Extbase\Persistence\ObjectStorageprototypeobject (3 items)000000000000133f0000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=33, pid=56624)bodytext => protected'<p>Direct Supervisor: Dr. Maria Colomé Tatché<br /> Group: <a href="h ttps://backup.helmholtz-munich.de/icb/research/groups/computational-epigenom ics/overview/index.html" target="_blank">Computational Epigenomics</a><br /> Institute: <a href="https://www.helmholtz-muenchen.de/icb/index.html" target="_blank">Institute for Computational Biology </a>, Helmholtz Cen ter Munich</p>
<p>Collaborating Supervisor: Dr. Robin Allshire<br /> Group: <a href="https://www.wcb.ed.ac.uk/research/allshire" target="_blank"> A llshire Lab</a><br /> Institute: <a href="https://www.wcb.ed.ac.uk/" ta rget="_blank">Wellcome Centre for Cell Biology</a>, Institute of Cell Biolog y, School of Biological Sciences, University of Edinburgh</p>' (745 chars)
position => protected'0,0' (3 chars)
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uid => protected33 (integer)
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_versionedUid => protected33 (integer)modifiedpid => protected56624 (integer)00000000000013510000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=34, pid=56624)bodytext => protected'<p>Project Description:</p>
<p>Fungal survival in harsh environments involv es stress-sensing pathways that reprogram their proteomes. New conditions, i ncluding climate change, can push opportunistic fungi to colonise novel nich es, potentially becoming harmful pathogens. Effective antifungal/fungicide t reatment are limited in number precisely because fungi are adept at re sisting challenges. Antifungal resistance is increasingly prevalent, raising fungal borne disease frequencies in humans and crops1. Conventional wisdom that resistance results solely from genetic mutations was overturned by our discovery that external insults selects for cells with a distinct epigenetic landscape - repressive heterochromatin over various genes whose reduced exp ression confers resistance (e.g. mitochondrial proteins)2,3. Such heterochro matin-dependent ‘epimutations’ are unstable, slowly losing resistance up on external insult removal. We hypothesize that extracellular stresses, incl uding fungicides widely used in agriculture, reprogramme fungal epigenomes s o that they transiently acquire heterochromatin at locations which confer he ritable, but unstable, resistance. By employing single cell analysis of line ages seeded by just one cell we aim to provide insight into the mechanisms u tilized by cells to mediate epimutant-mediated resistance. This project will combine the power of classic Luria-Delbruck fluctuation tests with low cell number/single cell (ATAC-seq, Cut&Tag and RNA-seq) sequencing workflows to dissect the events that result in the emergence of transiently antifunga l/fungicide resistant lineages due to epimutation formation.</p>' (1660 chars)
position => protected'0,0' (3 chars)
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uid => protected34 (integer)
_localizedUid => protected34 (integer)modified_languageUid => protectedNULL
_versionedUid => protected34 (integer)modifiedpid => protected56624 (integer)00000000000013680000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=35, pid=56624)bodytext => protected'<p>Relevant Literature:</p>
<ul> <li>Fisher MC, Hawkins NJ, Sanglard D. & Gurr SJ. (2018) Worldwide emergence of resistance to antifungal drugs challenges human health and food security. Science 360, 739–742</li> <li> Torres-Garcia S, Yaseen I, Shukla M, Audergon PNCB, White SA, Pidoux AL, All shire RC. (2020). Epigenetic gene silencing by heterochromatin primes fungal resistance. Nature 585, 453–458</li> <li>Yaseen I, White SA, Torres-Garc ia S, Spanos C, Lafos M, Gaberdiel E, Yeboah R, El Karoui M, Rappsilber J, P idoux AL, Allshire RC. (2022) Proteasome-dependent truncation of the negativ e heterochromatin regulator Epe1 mediates antifungal resistance. Nature Stru cture & Molecular Biology (in press); BioRXiv: <a href="https://doi .org/10.1101/2021.12.20.473483" target="_blank">https://doi.org/10.1101/2021 .12.20.473483</a></li> <li>A. Danese, M.L. Richter, D.S. Fischer, F.J. Thei s and M. Colomé-Tatché. EpiScanpy: integrated single-cell epigenomic analy sis. Nat. Commun. 12, 5228 (2021).</li> <li>A. vd Graaf, R. Wardenaar, D.A.
imutations. Proc. Natl. Acad. Sci. USA 112:6676-81 (2015). (* cocorrespondin g authors)</li> </ul>' (1313 chars)
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uid => protected33 (integer)
_localizedUid => protected33 (integer)modified_languageUid => protectedNULL
_versionedUid => protected33 (integer)modifiedpid => protected56624 (integer)00000000000013480000000000000000 => FelixNagel\GenericGallery\Domain\Model\GalleryItemprototypepersistent entity (uid=34, pid=56624)ttContentUid => protected273331 (integer)
title => protected'Targeting translocation-specific downstream signaling to treat MLL-AF4 rearr anged leukaemia' (91 chars)
link => protected't3://page?uid=56627' (19 chars)
imageReference => protectedTYPO3\CMS\Extbase\Domain\Model\FileReferenceprototypepersistent entity (uid=157131, pid=56624)uidLocal => protected345692 (integer)
originalResource => protectedNULL
uid => protected157131 (integer)
_localizedUid => protected157131 (integer)modified_languageUid => protected0 (integer)modified_versionedUid => protected157131 (integer)modifiedpid => protected56624 (integer)image => protectedNULL
textItems => protectedTYPO3\CMS\Extbase\Persistence\ObjectStorageprototypeobject (3 items)00000000000013530000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=36, pid=56624)bodytext => protected'<p>Direct Supervisor: Prof. Dr. Irmela Jeremias<br /> Group: <a href="h ttps://backup.helmholtz-munich.de/en/ahs/index.html" target="_blank">Researc h Unit Apoptosis in Hematopoietic Stem Cells</a><br /> institute:<a href="ht tps://www.helmholtz-munich.de/en/stem-cells" target="_blank"> Institute of Stem Cell Research</a>, Helmholtz Center Munich</p>
<p>Collaborating Su pervisor: Dr. Katrin Ottersbach<br /> Group: <a href="https://www.ed.ac .uk/regenerative-medicine/research/katrin-ottersbach" target="_blank">Otters bach Group</a><br /> Institute: <a href="https://www.ed.ac.uk/regenerat ive-medicine" target="_blank">Centre for Regenerative Medicine</a>, Universi ty of Edinburgh</p>' (703 chars)
position => protected'0,0' (3 chars)
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uid => protected36 (integer)
_localizedUid => protected36 (integer)modified_languageUid => protectedNULL
_versionedUid => protected36 (integer)modifiedpid => protected56624 (integer)000000000000136c0000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=37, pid=56624)bodytext => protected'<p>Project Description:</p>
<p>Translocation t(4;11) drives highly aggressi ve MLL-AF4 (KMT2A-AFF1) positive acute leukemias, associated with poor progn osis. Due to the aberrant fusion of the two epigenetic regulators, MLL and A F4, and recruitment of their associated complexes, MLL-AF4 positive leukaemi a is characterized by multiple epigenetic changes which drive the malignant disease. MLL is a positive regulator of gene expression by mediating e.g. H3 K4 methylation. AF4 is the central scaffold protein of the super elongation complex (SEC), which increases the catalytic rate of RNA polymerase II trans cription. The transcriptional changes caused by the MLL-AF4 driver mutation that result in various leukemic outcomes are largely unknown. A better under standing of the mechanisms responsible for disease progression is a prerequi site to developing innovative, targeted and efficient treatment to improve t he prognosis of patients.</p>
<p><br /> Previously, the two PIs in Edinburg h and Munich have studied MLL-AF4 positive leukaemia using complementary in vivo models. In syngeneic mice, we recently showed that distinct microRNAs a nd their dysregulated targets are important downstream mediators of MLL-AF4- driven leukemic growth and lineage choice (Malouf et al, Blood 2021). Using patient-derived xenograft models, we recently demonstrated that MLL-AF4 posi tive leukaemia remains dependent on the MLL-AF4 translocation, also when est ablished patient-derived xenograft (PDX) leukaemia grows in mice (Carlet et al., Nature Comm. 2021).</p>
<p><br /> We now plan to join forces in a sear ch for downstream signaling molecules which are upregulated by MLL-AF4 and r elevant for leukaemia survival and growth. To study the functional relevance of published and own candidate genes, we will use CRISPR/Cas9 knockout scre ens in existing MLL-AF4 positive PDX leukaemia models in vivo, followed by s ingle gene validation. Epigenetic changes induced by the genetic interventio n will be monitored usin...' (2588 chars)
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uid => protected37 (integer)
_localizedUid => protected37 (integer)modified_languageUid => protectedNULL
_versionedUid => protected37 (integer)modifiedpid => protected56624 (integer)00000000000013700000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=38, pid=56624)bodytext => protected'<p>Relevant Literature:</p>
<ul> <li>Malouf C, Antunes ETB, O'Dwyer M, Jak obczyk H, Sahm F, Landua SL, Anderson RA, Soufi A, Halsey C and K. Ottersbac h (2021) “miR-130b and miR-128a are essential lineage-specific codrivers o f t(4;11) MLL-AF4 acute leukemia.” Blood. 2021 Nov 25;138(21):2066-2092</l i> <li>Symeonidou V, Jakobczyk H, Bashanfer S, Malouf C, Fotopoulou F, Kote cha RS, Anderson RA, Finch AJ and K. Ottersbach (2021) “Defining the fetal origin of MLL-AF4 infant leukemia highlights specific fatty acid requiremen ts.” Cell Rep. 37(4):109900</li> <li>Carlet M, Völse K, Vergalli J, Beck er M, Herold T, Arner A, Senft D, Jurinovic V, Liu WH, Gao Y, Dill V, Fehse B, Baldus CD, Bastian L, Lenk L, Schewe DM, Bagnoli JW, Vick B, Schmid JP, W ilhelm A, Marschalek R, Jost PJ, Miething C, Riecken K, Schmidt-Supprian M, Binder V and Jeremias I. (2021) „In vivo inducible reverse genetics in pat ients' tumors to identify individual therapeutic targets.” Nat Commun. 202 1 Sep 27;12(1):5655</li> <li>Ebinger, S., E. Z. Ozdemir, C. Ziegenhain, S. Tiedt, C. Castro Alves, M. Grunert, M. Dworzak, C. Lutz, V. A. Turati, T. En ver, H. P. Horny, K. Sotlar, S. Parekh, K. Spiekermann, W. Hiddemann, A. Sch epers, B. Polzer, S. Kirsch, M. Hoffmann, B. Knapp, J. Hasenauer, H. Pfeifer , R. Panzer-Grumayer, W. Enard, O. Gires and I. Jeremias (2016). "Characteri zation of Rare, Dormant, and Therapy-Resistant Cells in Acute Lymphoblastic Leukemia." Cancer Cell 30(6): 849-862</li> </ul>' (1492 chars)
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width => protected'0' (1 chars)
uid => protected38 (integer)
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_versionedUid => protected38 (integer)modifiedpid => protected56624 (integer)imageProperties => protectedNULL
uid => protected34 (integer)
_localizedUid => protected34 (integer)modified_languageUid => protectedNULL
_versionedUid => protected34 (integer)modifiedpid => protected56624 (integer)00000000000013500000000000000000 => FelixNagel\GenericGallery\Domain\Model\GalleryItemprototypepersistent entity (uid=35, pid=56624)ttContentUid => protected273331 (integer)
title => protected'RNA modification in development and disease' (43 chars)
link => protected't3://page?uid=56628' (19 chars)
imageReference => protectedTYPO3\CMS\Extbase\Domain\Model\FileReferenceprototypepersistent entity (uid=157132, pid=56624)uidLocal => protected345691 (integer)
originalResource => protectedNULL
uid => protected157132 (integer)
_localizedUid => protected157132 (integer)modified_languageUid => protected0 (integer)modified_versionedUid => protected157132 (integer)modifiedpid => protected56624 (integer)image => protectedNULL
textItems => protectedTYPO3\CMS\Extbase\Persistence\ObjectStorageprototypeobject (3 items)000000000000134c0000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=39, pid=56624)bodytext => protected'<p>Direct Supervisor: Prof. Dr. Robert Schneider<br /> Group: <a href=" https://www.helmholtz-munich.de/en/ife/research-groups/schneider-lab" target ="_blank">Chromatin Dynamics and Epigenetics</a><br /> Institute: <a hr ef="https://www.helmholtz-munich.de/en/ife" target="_blank">Institute of Fun ctional Epigenetics</a>, Helmholtz Center Munich</p>
<p>Collaborating Super visor: Prof. Dónal O’Carroll <br /> Group: <a href="https://www .ed.ac.uk/regenerative-medicine/research/donal-o-carroll" target="_blank">RN A Function in Germ and Stem Cell Biology</a><br /> Institute: <a href=" https://www.ed.ac.uk/regenerative-medicine" target="_blank"><strong>Center f or Regeneration and Repair </strong>Centre for Regenerative Medicine</a >, University of Edinburgh</p>' (790 chars)
position => protected'0,0' (3 chars)
width => protected'0' (1 chars)
uid => protected39 (integer)
_localizedUid => protected39 (integer)modified_languageUid => protectedNULL
_versionedUid => protected39 (integer)modifiedpid => protected56624 (integer)00000000000013740000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=40, pid=56624)bodytext => protected'<p>The emerging research field of ‘Epitranscriptomics’ tackles one of th e next challenges for molecular biology: the understanding of how modificati ons of RNAs affect the function of RNAs and of their vital role in cellular homeostasis. Such modifications of RNAs occur on all types of cellular RNAs and are involved in the regulation of diverse biological processes. Misregul ated RNA methyltransferases have been found in multiple cancer types and are promising targets for a new generation of anti-cancer drugs.</p>
<p><br /> Recent breakthroughs have transformed our understanding of the epitranscrip tome and allow us now to interrogate RNA modifications at an unprecedented s cale. The epitranscriptome constitutes a new layer of (epi)genetic informati on and will thus change the way how we look at RNA and also open new avenues to identify novel druggable pathways. We recently identified two novel RNA methyltransferases and revealed their function in vitro and in animals creat ing new models for human diseases (Ignatova et al., 2020a; Ignatova et al., 2020b).</p>
<p><br /> The aim of the project, joint with the O’Carroll la b will be i) to identify potential methyltransferases, and their targets and to (ii) unravel the role of the respective modification(s) by applying a co mbination of in vitro and in vivo assays. We will build on the expertise in our laboratory in the identification of novel modifying enzymes and in genom e-wide mapping of modifications as well as on the expertise of the O’Carro ll lab in cellular manipulations and mouse and cancer models.</p>
<p><br /> This project includes the possibility to be part of a dynamic and internati onal team and to learn state of the art technologies both in Munich and Edin burgh (such as novel NGS based approaches to map RNA modifications and their bioinformatic analysis in low to single cells, as wells as ES cell and mous e models, Crispr/Cas9/Cas13 mediated manipulations, advanced imaging techniq ues, biochemical approac...' (2629 chars)
position => protected'0,0' (3 chars)
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uid => protected40 (integer)
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_versionedUid => protected40 (integer)modifiedpid => protected56624 (integer)00000000000013780000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=41, pid=56624)bodytext => protected'<p>Relevant Literature:</p>
<ul> <li>Ignatova, V.V., Kaiser, S., Sook Yuin , S., Bing, X., Stolz, P., Tan, Y.X., Xim Tan, Y., Leng Lee, C., Hoon Gay, F .P., Rico Lastres, P.,Gerlini, R., Rathkolb, B., Aguilar-Pimentel., A. Sanz- Moreno, A., Klein-Rodewald, T., Calzada-Wack, J., Ibragimov, E., Valenta, M ., Lukauskas, S., Marscha, S., Leuchtenberger, S., Fuchs, H., Gaius-Durner, V., Hrabe de Angelis, M., Bultmann, S., Rando, O.J., Guccione, E., Kellner, S.M. and Schneider, R. (2020) METTL6 is a tRNA m3C methyltransferase that re gulates pluripotency and tumor cell growth. Science Advances, 6, eaaz4551</l i> <li>Zoch, A., Auchynnikava, T., Berrens, R. V., Kabayama, Y., Schöpp, T ., Heep, M., Vasiliauskaitė, L., Pérez-Rico, Y. A., Cook, A. G., Shkumatav a, A., Rappsilber, J., Allshire, R. C. and O'Carroll, D. (2020) SPOCD1 is an essential executor of piRNA-directed 1 de novo DNA methylation. Nature 584, 635-639</li> <li>Ignatova, V.V., Stolz, P., Kaiser, S., Gustafsson, T.H., Rico Lastres, P., Sanz-Moreno, A., Cho, Y.L., Amarie, O.V., Aguilar-Pimentel , A., Klein-Rodewald, T., Calzada-Wack, J., Becker, L., Marschall, S., Kraig er, M., Garrett, L., Seisenberger, C., Hölter, S.M., Borland, K., Van De Lo gt, E., Jansen, P., Baltissen, M.P., Vermeulen, M., Wurst, W., Gailus-Durner , V., Fuchs, H., Hrabe de Angelis, M., Rando, O.J., Kellner, S.M., Bultmann, S. and Schneider. R. (2020) The rRNA m6A methyltransferase METTL5 regulates pluripotency and developmental programmes. Genes and Development , 34, 715- 729</li> <li>Morgan, M., Much, C., DiGiacomo, M., Azzi, C., Ivanova, I., Vi tsios, D. M., Pistolic, J., Collier, P., Ventura De Oliveira Moreira, P., Be nes, V., Enright, A. J. and O'Carroll, D. (2017) mRNA 3ʹ uridylation and po ly(A) tail length sculpt the mammalian maternal transcriptome Nature 548, 34 7-351</li> </ul>' (1840 chars)
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width => protected'0' (1 chars)
uid => protected41 (integer)
_localizedUid => protected41 (integer)modified_languageUid => protectedNULL
_versionedUid => protected41 (integer)modifiedpid => protected56624 (integer)imageProperties => protectedNULL
uid => protected35 (integer)
_localizedUid => protected35 (integer)modified_languageUid => protectedNULL
_versionedUid => protected35 (integer)modifiedpid => protected56624 (integer)000000000000136d0000000000000000 => FelixNagel\GenericGallery\Domain\Model\GalleryItemprototypepersistent entity (uid=36, pid=56624)ttContentUid => protected273331 (integer)
title => protected'Mechanisms of context-specific glucocorticoid gene regulation inferred from transcriptional bursting kinetics' (109 chars)
link => protected't3://page?uid=56629' (19 chars)
imageReference => protectedTYPO3\CMS\Extbase\Domain\Model\FileReferenceprototypepersistent entity (uid=157133, pid=56624)uidLocal => protected345690 (integer)
originalResource => protectedNULL
uid => protected157133 (integer)
_localizedUid => protected157133 (integer)modified_languageUid => protected0 (integer)modified_versionedUid => protected157133 (integer)modifiedpid => protected56624 (integer)image => protectedNULL
textItems => protectedTYPO3\CMS\Extbase\Persistence\ObjectStorageprototypeobject (3 items)000000000000136f0000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=42, pid=56624)bodytext => protected'<p>Main Supervisor: Prof. Dr. Nina Henriette Uhlenhaut<br /> Group: Division Molecular Endocrinology<br /> Institute:<a href="https://www.helmholtz-muni ch.de/en/hdc" target="_blank"> Institute for Diabetes and Endocrinology </a></p>
<p>Collaborating Supervisor: Prof. Dr. Ramon Grima<br /> Group:&nb sp;<a href="https://grimagroup.bio.ed.ac.uk/" target="_blank">Grima Group</a >, Institute of Quantitative Biology, Biochemistry and Biotechnology<br /> I nstitute:<a href="https://www.ed.ac.uk/biology/quantitative-biology-biochemi stry-biotechnology" target="_blank"> Institute of Quantitative Biology, Biochemistry and Biotechnology</a>, School of Biological Sciences, Universi ty of Edinburgh</p>' (703 chars)
position => protected'0,0' (3 chars)
width => protected'0' (1 chars)
uid => protected42 (integer)
_localizedUid => protected42 (integer)modified_languageUid => protectedNULL
_versionedUid => protected42 (integer)modifiedpid => protected56624 (integer)000000000000137c0000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=43, pid=56624)bodytext => protected'<p>Project Description:</p>
<p>Glucocorticoids are widely prescribed anti-i nflammatory drugs in the treatment of COVID-19, asthma, sepsis and others. H owever, chronic and systemic treatment comes with severe adverse effects lik e diabetes type 2, obesity, osteoporosis, muscle atrophy etc. Molecularly, g lucocorticoids diffuse across the cellular membrane and engage with the gluc ocorticoid receptor (GR), which translocates into the nucleus. In the nucleu s, the GR binds glucocorticoid response elements and represses as well as ac tivates target gene expression. Interestingly, gene activation is a hallmark of glucocorticoid-mediated side effects in metabolic tissues, whereas gene repression is associated with its anti-inflammatory function. Therefore, the Uhlenhaut Lab is exploring the molecular circuits employed by the GR to und erstand gene repression versus activation; a biological conundrum not only r estricted to nuclear hormone receptors. Our aim is to identify new therapeut ically targets to improve glucocorticoid therapy and reduce adverse effects. </p>
<p><br /> In recent years, we have studied the molecular mechanisms of gene activation versus repression in macrophages using next-generation sequ encing technologies and were able to describe factors required for gene acti vation in a gene-specific manner. We also discovered that the chromatin stat es at glucocorticoid binding sites associated with gene repression are highl y diverse, pointing towards gene-specific repression mechanisms employed by the glucocorticoid receptor. Those observations are in line with the diverse mechanisms described in the literature.</p>
<p><br /> In this project, we will explore the molecular mechanisms employed by GR in the regulation of in flammatory gene expression. We will use the bacteriophage-derived RNA stem-l oops as transcriptional reporters co-expressed with fluorescently labelled c oat proteins (MS2/MCP and PP7/PCP) in combination with CRISPR/Cas9-mediated gene targeting to monito...' (2692 chars)
position => protected'0,0' (3 chars)
width => protected'0' (1 chars)
uid => protected43 (integer)
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_versionedUid => protected43 (integer)modifiedpid => protected56624 (integer)00000000000013800000000000000000 => FelixNagel\GenericGallery\Domain\Model\TextItemprototypepersistent entity (uid=44, pid=56624)bodytext => protected'<p>Relevant Literature:</p>
<ul> <li>Greulich F, Bielefeld KA, Scheundel R , Mechtidou A, Strickland B, Uhlenhaut NH, 2021, Research article, Enhancer RNA Expression in Response to Glucocorticoid Treatment in Murine Macrophages ., Cells;11(1):28</li> <li>Greulich F, Wierer M, Mechtidou A, Gonzalez-Garc ia O, Uhlenhaut NH, 2021, Research article, The glucocorticoid receptor recr uits the COMPASS complex to regulate inflammatory transcription at macrophag e enhancers., Cell Rep.;34(6):108742</li> <li>Strickland BA, Ansari SA, Dan toft W, Uhlenhaut NH., 2022, Review, How to tame your genes: mechanisms of i nflammatory gene repression by glucocorticoids. FEBS Lett. Epub ahead of pri nt</li> <li>Cao Z, Grima R., 2020, Analytical distributions for detailed mo dels of stochastic gene expression in eukaryotic cells. Proceedings of the N ational Academy of Sciences 117.9: 4682-4692</li> <li>Jiang Q, Fu X, Yan S, Li R, Du W, Cao Z, Qian F and Grima R, 2021. Neural network aided approxima tion and parameter inference of non-Markovian models of gene expression. Nat ure communications, 12(1), pp.1-12</li> </ul>' (1109 chars)
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