Selected for Faculty of 1000 (Factor 3 Recommended). Sebastian Kadener Activities Collapse all Works (11) sort Sort The chromatin factor ROW cooperates with BEAF 32 in regulating longrange inducible genes EMBO reports 2022-12-06 | Journal article DOI: 10.15252/embr.202254720 Contributors : Neta Herman; Sebastian Kadener; Sagiv Shifman Show more detail Source : Crossref SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs. *, Afik S., Menet J., Wolfson V., Weissbein U., Haimovich D., Gafni C., Friedman N., Rosbash M. and Kadener S. . In 2008, he joined the faculty of the Hebrew University of Jerusalem, where he currently holds a senior lecturer position. Laboratory Profile Principal Investigator: Sebastian Kadener A systemic view of circadian clocks: from gene expression to neuronal networks and behavior. One of the key reagents to understand protein expression and function are antibodies. Fun in the Lab. Biol., The University of Buenos Aires, Buenos Aires, Argentina, Ph.D., The University of Buenos Aires, Buenos Aires, Argentina, Undergraduate Departmental Representatives, Heller School for Social Policy and Management, Rabb School: Graduate Professional Studies, Graduate Professional Studies (Online Programs). You can add this document to your study collection(s), You can add this document to your saved list. Kadener, Sebastian / Brandeis University Publications. Nov, 2017. Riley is currently working to understand genetic and epigenetic mechanisms of resistance in brain tumors, focusing on resistance to BET-bromodomain inhibitors and vulnerabilities induced by loss of mismatch repair proteins. We showed that their translation is mediated by IRES-like sequences, is enhanced in response to starvation and happens in association with membranes and in synapses. Coupling of transcription with alternative splicing: RNA pol II promoters modulate SF2/ASF and 9G8 effects on an exonic splicing enhancer. Informative set of videos on insect physiology and endocrinology: New paper: Simchovitz A, Hanan M, Niederhoffer N, Madrer N, Yayon N, Bennett ER, Greenberg DS, Kadener S, Soreq H. Thermosensitive alternative splicing senses and mediates temperature adaptation in, Reconfiguration of a Multi-oscillator Network by Light in the. Hanan M, Simchovitz A, Yayon N, Vaknine S, Cohen-Fultheim R, Karmon M, Madrer N, Rohrlich TM, Maman M, Bennett ER, Greenberg DS, Meshorer E, Levanon EY, Soreq H, Kadener S. Past, present, and future of circRNAs. as achieved by mapping signal pathway activities in various cell types), and the physiological roles of various cells. and Torres H.N. Gene Expression Omnibus (GEO) is a database repository of high throughput gene expression data and hybridization arrays, chips, microarrays. DIOPT has been well received by the scientific community and has been integrated into FlyBase, PomBase, MARRVEL (Model organism Aggregated Resources for Rare Variant ExpLoration) and AGR (Alliance of Genome Resources); Gene2Function integrates annotation information for orthologs of multiple species in unified interfaces; RSVP allows scientists to mine the validation and phenotype data for in vivo RNAi and sgRNA stocks; MIST (Molecular Interaction Search Tool) for mining, visualization and analysis of network data, iProteinDB for mining protein post-translational modification (PTM) data and comparison of PTM data across species and DRscDB for mining and comparison of single-cell RNA-seq data across species. Circadian clocks are remarkably robust: they are able to keep time without timing cues and are resilient to large variations in environmental conditions. What are the neural and molecular basis of temperature adaptation and compensation? Zaffagni M, Kadener S. NEAT1 is overexpressed in Parkinson's disease substantia nigra and confers drug-inducible neuroprotection from oxidative stress. and Torres H.N. leptin), neural development, and behavior are conserved. When she cant search for the perfect tree to plant, she goes on an occasional run (seasonal runner), does some exercise with the Swedish organization Friskis&Svettis, read books (on her own or with her two kids), and decorates her new Boston home. Site developed by Health Communication Core, April received her BS in Cellular and Molecular Biology from Beloit College in 2017, where she worked in the lab of Dr. Amy Briggs studying the role of. in Physics. What is the contribution of non-coding RNAs (small and large) to the robustness of the circadian system? How do circRNAs work at the molecular level? Nucleic Acids Research47(11): e95; 1-16 (2017). Among the next significant questions to address are how complex phenotypes arise in the context of the whole organism and how the programs regulating these phenotypes are influenced by genetic background and environment. In the Bandopadhayay Lab, Michelle is interested in using computational efforts to better characterize pediatric brain tumors. Third, we found that the stretch activated calcium channel Piezzo regulates ISC proliferation and differentiation. Jazmin is currently investigating how circRNA levels change at synapses and whether they are modulated by neuronal activity. Our laboratory is interested for understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. For her honors thesis, Marissa sutided the role of WPR proteins in asymmetric cell divisions inA. thalianaroots. From a number of screens (receptome-wide RNAi screen, miRNA screens, etc. Pvf1 produced by yki-gut tumors activates MEK/ERK signaling and enhances catabolism in multiple tissues. Second, we identified 53 transcription factors, specifically expressed or enriched in the ISCs, and are characterizing how they cooperate to integrate signal inputs. Community support Reprint. Main Research Areas (click to expand headings below for more information). We are particularly interested on the role of circular RNAs (circRNAs) at the molecular and neural levels as well as the mechanisms underlying circadian clocks. 1 / 3 Looking for Postdoctoral researchers Lic. Circadian clocks are also exceptionallyplasticas they can quickly and specifically adjust to specific environmental cues. Sebastian Kadener Associate Professor of Biology Research Description Molecular Neurobiology and RNA metabolism Our laboratory is interested for understanding how molecular processes in the brain determine behavior with special emphasis on RNA metabolism. The work is a collaboration between Dr. Kadener's lab and Prof. Nikolaus Rajewsky from the Max Dellbruck Institute, Berlin, Germany. News. Alexander M. van der Linden, Matthew Beverly, Sebastian Kadener, Joseph Rodriguez, Sara Wasserman, Michael Rosbash, Piali Sengupta. 369. In this context, the most important question looking forward are: Afik S. 1, Bartok O. ), we have identified and validated novel mechanisms of how stem cells adjust their rate of proliferation/differentiation to meet the demand for tissue regeneration. bioRxiv 2023.02.20.529262; doi: Copyright 2023 The President and Fellows of Harvard College. I am a PhD student in the lab since 2018 after graduating from The College of Wooster. Determine the nature of circadian rhythms within organisms. . Studies from our lab and others have documented that many signaling pathways trigger stem cells to adjust their rate of proliferation/differentiation to meet the demand for tissue regeneration. Cohen-Hadad Y., Altarescu G., Eldar-Geva T., Levi-Lahad E., Zhang M., Rogaeva, E. Gotkine M., Bartok O., Ashwal-Fluss R., Kadener S., Epsztejn-Litman S., Eiges R. Marked differences in C9orf72 methylation status and isoform expression between C9/ALS human embryonic and induced pluripotent stem cells. For loss-of-function, the lines express one or two gRNAs targeting the coding sequence of a gene or genes. Cold Spring Harbor Laboratory Online. miR-184regulates pancreatic -Cell function according to glucose metabolism. Pandey V., Turm H., Bekenstein U., Shifman S. and Kadener S. A new. 502. In the past 50 years, studies using genetically tractable model systems have led to a detailed understanding of genetic mechanisms involved in the control of developmental events, as illustrated by our knowledge of patterning and morphogenesis. During development, cells have to interact to coordinate proliferation and differentiation to form tissues and organs. For example, little is understood about how the simultaneous growth and differentiation of different tissues and organs are coordinated and how the development of different cell types and tissues is integrated within an organ. Control of alternative pre-mRNA splicing by RNA Pol II elongation: faster is not always better. As an underlying mechanism, the balance or critical reaction hypothesis have been proposed. UAS-gypsy structure and functional test. He received his BS in Biochemistry and Molecular Biology in 2022 from Dickinson College in Carlisle Pennsylvania. Patop IL, Wst S, Kadener S. Craving for Introns. Antibodies allow protein visualization by immunostaining, biochemical study by immunoprecipitation and western blot, and proteomic study by IP-MS. PubMed ID: 31702556 During development, cells have to interact to coordinate proliferation and differentiation to form tissues and organs. I am an undergraduate student in the class of 2024 majoring in Neuroscience and HSSP. NanoTags, VHH05- and 127D01-tagsthat are 14 and 10 amino acids in length, and their corresponding nanobodies (NbVHH05 and Nb127D01) are excellent reagents for both, We have developed a series of bioinformatics tools that provide the research community with well-designed, user-friendly resources that impact research at all stages, from project design to data analysis and integration. Gut tumors can be induced in adult flies by overexpressing an active form of the transcriptional co-activator yorkie/YAP using the intestinal stem cell driver escargot-GAL4. 312. Mosquito cell lines exist that are able to become infected with viruses and are susceptible to mosquitocidal toxins, parasites, and drugs, but tools to allow deeper understanding of pathogen interactions with mosquito cells are lacking. Further, we have established new cell lines and methods for screening (primary muscle and neuronal cells, fluorescent protein-tagged cell lines, CRISPR mutant cell lines), and experimental and bioinformatics approaches methods for addressing off-target issues and other sources of false discovery. Lacadie S.A., Tardiff D.F., Kadener S. and Rosbash M. In vivo commitment to yeast cotranscriptional splicing is sensitive to transcription elongation mutants. Adam is currently studying approaches to therapeutically target cancers that harbor mutations in the Mismatch Repair pathway. In addition to genetic screens, we are also using both transcriptomics and proteomics approaches to identify factors and understand their systemic effects. CRISPR-generated mutant cell lines, in combination with RNAi, provide a robust platform for combinatorial screening. Cohen-Hadad Y., Altarescu G., Eldar-Geva T., Levi-Lahad E., Zhang M., Rogaeva, E. Gotkine M., Bartok O., Ashwal-Fluss R., Kadener S., Epsztejn-Litman S., Eiges R. Marked differences in C9orf72 methylation status and isoform expression between C9/ALS human embryonic and induced pluripotent stem cells. Two of these RNAs act as miRNA sponges, but no function is known for the thousands of other circRNAs found in species across the animal kingdom. SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs. Selected for Faculty of 1000 (Factor 9 Exceptional). Mezan S., Ashwal-Fluss R., Shenhav R., Garber M. and Kadener S. Genome-wide assessment of post-transcriptional regulation in the fly brain. One point of focus for DRSC-BTRR efforts is establishment of CRISPR pooled screening in cell lines from mosquito vectors of infectious diseases. For his honors thesis, Sher characterized the role of the MAPK/ERK signaling modulator SPRY2 in regulating the transcriptome of the HL-60 Acute Myeloid Leukemia cell line. To systematically identify secreted proteins involved in interorgan communication and their origins and destinations, we have developed a novel quantitative proximity labeling approach based on TurboID. NanoTags: One of the key reagents to understand protein expression and function are antibodies. Fededa J.P., Petrillo E., Gelfand M.S., Neverov A.D., Kadener S., Nogues G., Pelisch F., Baralle F.E., Muro A.F. Are circRNAs involved in neurodevelopmental and neurodegenerative diseases? Send us removal request. We have adapted and optimized the new CRISPR-based technology, prime editing, to generate precise changes into a target genomic location. Dana joined the Bandopadhayay Lab in 2021 where is she working to apply single-cell methods to evaluate the heterogeneity of pediatric gliomas, and to understand spatial associations. Software. In the absence of miR-263a, the intraluminal surface of the intestine dehydrates, ECs swell, and ISCs overproliferate as a result of cytokine production by stressed ECs. First, we developed a new method to visualize the dynamic activation of pathway activities. We have taken a number of approaches to address the spatial and temporal regulation of signaling pathway activities in the gut epithelium. During his time at Dickinson, Sher worked in Dr. Michael Roberts lab, investigating gene targets for potential Acute Myeloid Leukemia therapies. Stelzer Y., Bar S., Bartok O., Afik S., Ronen D., Kadener S.* and Benvenisty N.* Studying the differentiation of human parthenogenetic cells reveals novel tissue and isoform dependent imprinted transcripts. Hanan M., Soreq H. and Kadener S. CircRNAs in the brain. Lacadie S.A., Tardiff D.F., Kadener S. and Rosbash M. In vivo commitment to yeast cotranscriptional splicing is sensitive to transcription elongation mutants. Advantages of CRISPRi as compared with RNAi are that the level of knockdown can be more tightly controlled and the system appears to have reduced off-target effects. Elife 8. 10.1261/rna.068692.118 References. The tagged endogenous proteins can then be isolated for further analysis by MS. To analyze protein-protein interactions or identify components that localize to discrete subcellular compartments, we developed tools based on. Anna developed a fascination for cancer biology while working towards her bachelors degree at Lund University, Sweden. . Eric studied how the interaction of cell surface proteins expressed by different cell types can regulate blood vessel formation in normal cells and tumors. This plasticity is the result of the existence of very efficient input pathways that convey the external signals into the core oscillator machinery. Jens is co-mentored by Dr. David Jones at the DKFZ. at USC we have extended this approach to the mouse. Fun fact: Leslie played basketball through college and is now an avid cyclist. Bartok O., Kyriacou C., Levine J., Sehgal A. and Kadener S. Adaptation of molecular circadian clockwork to environmental changes: a role for alternative splicing and miRNAs. I am researching the role of circular RNAs (circRNAs) in aging processes in Drosophila melanogaster. Zaffagni M, Kadener S. NEAT1 is overexpressed in Parkinson's disease substantia nigra and confers drug-inducible neuroprotection from oxidative stress. A Biblioteca Virtual em Sade uma colecao de fontes de informacao cientfica e tcnica em sade organizada e armazenada em formato eletrnico nos pases da Regio Latino-Americana e do Caribe, acessveis de forma universal na Internet de modo compatvel com as bases internacionais. Understanding how circadian rhythms are generated, maintained, and adapted to changing conditions is key, as several diseases such as cancer and depression are associated with misalignment of the circadian clock with the environment. Jess earned her PhD in Neuroscience working in the laboratory of Dr. Thomas Clandinin, utilizing the Drosophila visual system and forward genetics to study synapse development and axon degeneration. Mezan S., Ashwal-Fluss R., Shenhav R., Garber M. and Kadener S. Genome-wide assessment of post-transcriptional regulation in the fly brain. Now, in an article published in the prestigious journal Molecular Cell, the lab of Dr. Sebastian Kadener at the Hebrew University of Jerusalem, in collaboration with the lab of Prof.. Chem. * Corresponding authors. Regulation of alternative splicing by a transcriptional enhancer through RNA pol II elongation. From 2002 to 2008, Sebastian Kadener was a postdoc working in the Michael Rosbash laboratory. Belacortu Y., Weiss R., Kadener S. and Paricio N. Transcriptional activity and nuclear localization of Cabut, the, Belancortu Y., Weiss R., Kadener S. and Paricio N. Expression of, Van der Linden A.M., Beverly M., Kadener S., Rodriguez J., Wasserman S., Rosbash M. and Sengupta P. Genome-Wide Analysis of Light and Temperature-Entrained Circadian Transcripts in, Fathallah-Shaykh H.M., Bona J.L. Proximity labeling-based methods coupled with mass spectrometry (MS) offer a high-throughput approach for systematic analysis of spatially-restricted proteomes. Eric received his MS in biomedicine from Uppsala University, Sweden in 2010. Thermosensitive alternative splicing senses and mediates temperature adaptation in Drosophila. Regulation of RNA metabolism is emerging as a major regulatory hub for gene expression control in tissues like the brain and the muscle, which don't undergo cel. Simchovitz A, Hanan M, Yayon N, Lee S, Bennett ER, Greenberg DS, Kadener S, Soreq H. A Parkinson's disease CircRNAs Resource reveals a link between circSLC8A1 and oxidative stress. Fun fact: Adams passions expand beyond the lab and include weightlifting, hot yoga, singing acappella, heading to the ballpark for a game, and visiting craft breweries. I am in the Class of 2024 studying neuroscience and biology. She is the Co-Director of Research for a non-profit, the STEM Advocacy Institute, which is focused on building a future where there is equitable access and exposure to science for all people. He is returning to Brandeis as an Associate Professor of Biology. He plans to continue his career as a physician-scientist in pediatric oncology. Studying the function of circRNAs in the brain. Mezan S., Feuz JD, Deplancke B. and Kadener S. PDF signaling is an integral part of the. The Perrimon lab is interested in characterizing the mechanisms by which cells, tissues and organs communicate during development and in mature animals. What are the neural and molecular basis of temperature adaptation and compensation? Fun fact: Michelle is a huge Stephen King fan. Is the category for this document correct. Proximity Labeling: Characterizing the proteome composition of organelles and subcellular regions of living cells can facilitate the understanding of cellular organization as well as protein interactome networks. Among the next significant questions to address are how complex phenotypes arise in the context of the whole organism and how the programs regulating these phenotypes are influenced by genetic background and environment. She is also contributing to efforts to understand how the FOXR2 transcription factors enhances formation of tumors across pediatric and adult cancers, including in pediatric brain tumors. Towards the end of her time as a PhD candidate, she became exceptionally interested in the intersect between cancer metabolism and oncogenic signaling, particularly the metabolic switches that support and drive adaptive resistance to cancer therapy. Lerner I. The challenge is now to understand how these pathways intersect and cooperate, as it is not clear if some pathways regulate the activity of others, or if they act concomitantly. Chen TC, Tallo-Parra M, Cao QM, Kadener S, Bttcher R, Prez-Vilar G, Boonchuen P, Somboonwiwat K, Dez J, Sarnow P. A lncRNA survey finds increases in neuroprotective LINC-PINT in Parkinson's disease substantia nigra. Weiss R., Bartok O., Mezan S., Malka Y and Kadener S. Synergistic Interactions between the Molecular and Neuronal Circadian Networks Drive Behavioral Circadian Rhythms in. Fun fact:In her free time, Marissa loves to go on bike rides, do yoga and walk her dog. Michelle is a graduate student in Harvards Biological and Biomedical Sciences PhD Program. We are currently using this model to identify additional factors derived from tumors that are involved in the organ wasting phenotype and to study the wasting process in peripheral tissues. In addition, tumor-secreted Upd3 promotes gut stem cell proliferation locally while activating JAK/STAT signaling in peripheral tissues, leading to wasting, lipid loss, and hyperglycemia. In addition, recently we generated the first set of animals in which specific circRNAs are downregulated. Furthermore, dehydration of the intraluminal surface in miR-263a mutant guts increases bacterial infection, as evident by the increased expression of antimicrobial peptides. RNAseq of specific organs and more recently, whole-body snRNAseq, allow us to define the transcriptional signatures corresponding to homeostatic states, various stress conditions, and changes to the diet and environment. In addition to ImpL2, we have also identified two additional factors produced from yki-gut tumors that contribute to tissue wasting: the Pvr receptor tyrosine kinase ligand Pvf1 and the IL6-like cytokine Unpaired 3 (Upd3). In this context, the most important question looking forward are: Afik S. 1, Bartok O. We have developed a series of bioinformatics tools that provide the research community with well-designed, user-friendly resources that impact research at all stages, from project design to data analysis and integration. Transcription factor Dam fusions of the major proliferative signaling pathways will be used to address questions about crosstalk and target co-regulation. Litovchenko M, Meireles-Filho ACA, Frochaux MV, Bevers RPJ, Prunotto A, Anduaga AM, Hollis B, Gardeux V, Braman VS, Russeil JMC, Kadener S, Dal Peraro M, Deplancke B. Host-derived circular RNAs display proviral activities in Hepatitis C virus-infected cells. High-accuracy determination of internal circadian time from a single blood sample. Selected for Faculty of 1000 (Factor 6 Must Read). Our lab is interested in determining how molecular and neural circadian components regulate each other and generate a system that is both robust and plastic. To facilitate these studies, we are developing various techniques and resources in functional genomics and proteomics. In addition and most importantly, genome-wide libraries of transgenic RNAi lines are available that allow knockdown of any Drosophila gene in an organ or tissue-specific manner. Nogues G., Kadener S., Cramer P., Bentley D. and Kornblihtt A.R. The Kadener laboratory studies how molecular processes in the brain determines behavior with a special emphasis on RNA metabolism. Molecular Neurobiology and RNA metabolism. I am interested in studying circular RNA formation. Interestingly, JAK/STAT signaling in the muscle or fat body directly triggers the expression of ImpL2, which in turn impairs local insulin signaling and its associated energy balance. He also enjoys playing handball and online chess. Strikingly, these phenotypes are reminiscent of the pathophysiology of cystic fibrosis (CF), as in CF the non-functional CF transmembrane conductance regulator (CFTR) increases ENaC activity resulting in chronic dehydration of the intraluminal surface liquid in organs such as kidney, colon, lung and sweat glands. Coordination between transcription and pre-mRNA processing. Rosenstiel332781-736-4915skadener@brandeis.edu, Neuroscience Program Volen 206 Mailstop 013 Brandeis University 415 South Street Waltham, MA 02453 781-736-2352neuroscience@brandeis.edu. Metazoan MicroRNAs (2018) David P. Bartel CELL Non-canonical functions of microRNA pathway enzymes - Drosha, DGCR8, Dicer and Ago proteins While the former supposes a temperature-dependent balancing of reactions with opposite effects on circadian period, the . The tagged endogenous proteins can then be isolated for further analysis by MS. To analyze protein-protein interactions or identify components that localize to discrete subcellular compartments, we developed tools based on APEX, an engineered ascorbate peroxidase derived from plants, and BioID, a mutant form of the biotin ligase BirA from E coli and demonstrated their use for in vivo studies. In the Bandopadhayay Lab, Leslie has been able to combine her background in cancer cell metabolism with genomic, transcriptomic and gene editing approaches to understand the biology of pediatric brain tumors and elucidate mechanisms of resistance to targeted therapies such as BET-bromodomain inhibition. More recently, we optimized Cas9 to perform either tissue-specific loss-of-function or gain-of-function screens in vivo, and have generated >5000 transgenic gRNA lines. 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