Fun fact:In her free time, Marissa loves to go on bike rides, do yoga and walk her dog. Transcription factor Dam fusions of the major proliferative signaling pathways will be used to address questions about crosstalk and target co-regulation. September 2018. Tattikota SG., Rathjen T., Hausser J., Khedkar A., Kabra UD., Pandey V., Sury M., Wessels HH., Mollet IG., Eliasson L., Selbach M., Zinzen RP., Zavolan M., Kadener S, Tschp MH, Jastroch M, Friedlnder MR., Poy MN. Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions. J. Biol. In a collaboration with Sebastian Kadener's lab at Brandeis, we generated a new set of PspCas13b and RfxCas13d expression constructs that can be used to target RNA in cells and in vivo. We use Drosophila as a model system to characterize the mechanisms underlying communication between cells, tissues, and organs. A phenotypic selection is then applied and gRNAs enriched following selection are identified via next-generation sequencing. Feel free to send suggestions. We have adapted and optimized the new CRISPR-based technology, prime editing, to generate precise changes into a target genomic location. In the Bandopadhayay Lab, Jess is applying genomic approaches to optimize novel treatment approaches for pediatric brain tumors, and is also working to characterize the role long non-coding RNAs play in the formation of Diffuse Intrinsic Pontine Gliomas. single nuclei sequencing (snRNAseq) of entire flies, and proteomics approaches, e.g. Ultimately, the knowledge gained from these studies will generate testable hypotheses related to disease states such as diabetes, aging, and cancer, i.e., how biological processes observed in one tissue/organ (e.g., decreased cellular metabolism, mitochondrial dysfunction) may influence processes observed in a different tissue/organ. The work is a collaboration between Dr. Kadener's lab and Prof. Nikolaus Rajewsky from the Max Dellbruck Institute, Berlin, Germany. CircRNAs expression levels are not correlated with the expression of their linear isoforms, indicating a potentially widespread layer of previously unknown gene regulation. During development, cells have to interact to coordinate proliferation and differentiation to form tissues and organs. We renamed the center DRSC/TRiP-Functional Genomics Resources to better represent our current capabilities. Selected for Faculty of 1000 (Factor 3 Recommended). Selected for Faculty of 1000 (Factor 3.0 Recommended). She received her BA in Molecular and Cell Biology from the University of California, Berkeley in 2019. She also loves sleeping in, making guacamole, and reading about art history. 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. Ph.D. University of So Paulo (USP)- Brazil. 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); integrates annotation information for orthologs of multiple species in unified interfaces; allows scientists to mine the validation and phenotype data for. Additionally, many of the mechanisms by which growth factortriggered signaling events intersect with cell metabolism, which is regulated by nutrients, hormones and stress, remain to be identified. We are now using this tool to establish sensors of each signaling pathway involved in gut homeostasis, and will use these reagents to examine pathway crosstalk. Olivia received her B.A. Following our identification of adult Drosophila intestinal stem cells (ISCs), we used this system to characterize genes and pathways important for gut homeostasis and in particular, to analyze crosstalk among signaling pathways. We are also helping the, 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. Antibodies allow protein visualization by immunostaining, biochemical study by immunoprecipitation and western blot, and proteomic study by IP-MS. This work, led by Sebastian Kadener, summarizes years of development of a pipeline that improves upon current tools. Nov, 2017. Lerner I. Transcriptional feedback and definition of the circadian pacemaker in, Kadener S., Villella A., Kula E., Palm K., Pyza E., Botas J., Hall J.C. and Rosbash M. Neurotoxic protein expression reveals connections between the circadian clock and mating behavior in. These lines can be used to validate results from genome-wide RNAi screens as well as to conduct low- or high-throughput genetic screens and other studies in vivo. I am a junior who is majoring in biochemistry. Selected for Faculty of 1000 (Factor 9 Exceptional). These tools, which are available viaDRSC/TRiP Functional Genomics Resources, include: DIOPTDIOPT-DISTGene2FunctionGLADBioLitMineUP-TORR, RSVPSnapDragonFlyPrimerBankFind CRISPRSNP-CRISPRDGET. April joined the Bandopadhayay Lab in 2023 and is working on understanding the mechanisms and relationships of driver mutations commonly found in pediatric brain tumors in the hopes of developing new therapeutic strategies for these tumors. 1, Artyomov M., Shishkin A., Kadri S., Zhu X., Gutman M., Garber M.* and Kadener S.* Defining the 5 and 3 landscape of theDrosophilatranscriptome with ExoCAGE and RNaseH-seq. 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. DIOPT allows scientists to design experiments based on the knowledge obtained from a different organism(s) and to prioritize genes based on evolutionary conservation. More. Aaron is an Attending Pediatric Neuro-Oncologist at the Dana-Farber/Boston Childrens Cancer and Blood Disorders Center. In the Bandopadhayay Lab, Michelle is interested in using computational efforts to better characterize pediatric brain tumors. and Kornblihtt A.R. Mezan S., Ashwal-Fluss R., Shenhav R., Garber M. and Kadener S. Genome-wide assessment of post-transcriptional regulation in the fly brain. How do circRNAs work at the molecular level? I am analyzing the effect of circRNA on aging in Drosophila, majoring in biochemistry and neuroscience. We showed that miRNAs have a key role in providing robustness to the circadian system both during development and in adults. Pandey V., Turm H., Bekenstein U., Shifman S. and Kadener S. A new. The current model postulates that circadian oscillators keep time by complex transcriptional and post-transcriptional feedback loops. We demonstrated that shRNAs are more efficient and specific than long dsRNA when expressed as transgenes, and generated a genome scale collection of >13,000 lines covering 75% of the genome in our optimized VALIUM vectors (85% of highly conserved genes). 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 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. Allada R., Kadener S., Nandakumar N. and Rosbash M. A recessive mutant of, Portal D., Espinosa J.M., Lobo G.S., Kadener S., Pereira C.A., de la Mata M., Tang Z., Lin R.J., Kornblihtt A.R., Baralle F.E., Flawia M.M. Coupling of transcription with alternative splicing: RNA pol II promoters modulate SF2/ASF and 9G8 effects on an exonic splicing enhancer. Are circRNAs involved in neurodevelopmental and neurodegenerative diseases? 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. Circadian clocks are remarkably robust: they are able to keep time without timing cues and are resilient to large variations in environmental conditions. Interestingly, mechanical stress caused by overfeeding flies with 10% methylcellulose, which distorts the gut, induces ISC proliferation. 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. Pathways that are misregulated in animals that develop organ wasting in the context of these various tumor models are identified using a combination of transcriptomics, e.g. For doing this, we study the circadian clock from a systemic point of view, including studies at the molecular and neural levels. We chose to use peripheral blood monocytes as source material for gene expression profiling, because (a) blood is an easily accessible source of human cells and (b) monocytes constitute a homogenous blood cell population and have been shown to possess a high-amplitude circadian clock ( 24, 25) in contrast to other PBMCs, such as B or T cells. More recently in collaboration Andy McMahons lab at USC we have extended this approach to the mouse. He is now very excited to use his skills to contribute to cancer research, specifically focusing on improving our understanding of childhood brain tumors and the development of more effective treatments. Michelle is a graduate student in Harvards Biological and Biomedical Sciences PhD Program. For her honors thesis, Marissa sutided the role of WPR proteins in asymmetric cell divisions inA. thalianaroots. Selected for Faculty of 1000 (Factor 9 Exceptional). Fun fact:April does not drink coffee or tea (which perplexes Mimi) and loves milk and the whole lab likes to make fun of her for it. Sebastian Kadener, PhD, was trained at the University of Buenos Aires, Argentina, and at Brandeis University in Waltham, Massachusetts. Statuses. 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. Control of alternative pre-mRNA splicing by RNA Pol II elongation: faster is not always better. Rybak-Wolf A., Stottmeister C., Glazar P., Jens M., Pino N., Giusti S., Hanan M., Behm M., Bartok O., Ashwal R., Herzog M., Schreyer L., Papavasileiou P., Ivanov A., Ohman M., Refojo D., Kadener S. and Rajewsky N. Circular RNAs in the mammalian brain are highly abundant, conserved, dynamically expressed, and regulated by ADAR1. Lacadie S.A., Tardiff D.F., Kadener S. and Rosbash M. In vivo commitment to yeast cotranscriptional splicing is sensitive to transcription elongation mutants. This collection is available to the community through the Bloomington Drosophila Stock Center. My diverse. 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. Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions. Pamudurti N., Bartok O., Jens O., Ashwal-Fluss R., Stottmeister C., Ruhe L., Hanan M., Wyler E., Perez-Hernandez D., Ramberger E., Shenzis S., Samson M., Dittmar G., Landthaler M., Chekulaeva M., Rajewsky N. and Kadener S. Translation of circRNAs. For example, we showed that circRNA biogenesis competes with canonical splicing, showing that circRNAs can function incisas RNA traps. She also loves bagels and is always on the hunt for the best bagel. Now the stage is set for the most exciting questions, which we are currently working in the lab, by combining molecular, computational and RNA biology with advances techniques in genetics and neurosciences. 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. Prior to coming to Brandeis, Sayan worked in the Bangalore Life Science Cluster, India as a research fellow. Sebastian Kadener E-mail (s) skadener@gmail.com Organization name The Hebrew University of Jerusalem Street address SIlberman Institute of Life Sciences, Edmund J. Safra Campus City Jerusalem ZIP/Postal code 91904 Country Israel Platform ID GPL20301 Series (1) GSE154616 Mammalian circRNA Atlas Relations BioSample SAMN15566042 SRA SRX8753063 Associate Professor, Brandeis University. For his senior clinic project, John worked with HRL Laboratories to create an algorithm for electrostatically tuning quantum dots using neural networks for quantum computers. What are the key functions of these molecules in the brain and during aging? Wittenbrink N, Ananthasubramaniam B, Mnch M, Koller B, Maier B, Weschke C, Bes F, de Zeeuw J, Nowozin C, Wahnschaffe A, Wisniewski S, Zaleska M, Bartok O, Ashwal-Fluss R, Lammert H, Herzel H, Hummel M, Kadener S, Kunz D, Kramer A. Levin-Klein R., Fraenkel S., Lichtenstein M., Matheson L., Bartok O., Nevo Y., Kadener S., Corcoran A., Cedar H., Bergman Y. Boston, MA. Sher is now contributing to efforts to characterize FGFR alterations in pediatric gliomas, and to develop methods to optimize TP53 reactivation in Diffuse Midline Gliomas. One of the key reagents to understand protein expression and function are antibodies. 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. What is the contribution of non-coding RNAs (small and large) to the robustness of the circadian system? 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. Rabin A, Zaffagni M, Ashwal-Fluss R, Patop IL, Jajoo A, Shenzis S, Carmel L, Kadener S. Extensive tissue-specific expression variation and novel regulators underlying circadian behavior. Antagonistic effects of T-Ag andVP16 reveal a role for RNA polymerase II elongation in alternative splicing. 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. While at Caltech, Adam studied luminescent ruthenium complexes that function as light switch probes for DNA mismatches. 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. Eric received his MS in biomedicine from Uppsala University, Sweden in 2010. Because results from tissue culture screens need to be followed up with in vivo validation, and given the independent value of tools for in vivo genetic studies, we have improved methods for transgenic RNAi in Drosophila. 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. I am researching the role of circular RNAs (circRNAs) in aging processes in Drosophila melanogaster. Jens joined the Bando Lab in 2023 as a visiting graduate student to understand how distinct histone mutations influence gliomagenesis and also aims to exploit the dependence of pLGGs on the MAPK pathway. CircRNAs expression levels are not correlated with the expression of their linear isoforms, indicating a potentially widespread layer of previously unknown gene regulation. Sebastian Kadener. 178: Additionally, they study the role of circular RNAs (circRNAs) at the molecular and neural levels as well as the mechanisms underlying circadian clocks. Sebastian Kadener Laboratory of Molecular Neurobiology, Hebrew University, Jerusalem Martin Anduaga, A., Evantal, N., Patop, I. L., Bartok, O., Weiss, R. and Kadener, S. (2019). Patop IL, Wst S, Kadener S. Craving for Introns. Further, our work and that of others has suggested functions of these moleculesin vivo. 502. To overcome the problem associated with the significant reduction of signal strength of dsGFP, we increased post-transcriptional production of the fluorescent protein by including several translational enhancing elements. Proximity labeling-based methods coupled with mass spectrometry (MS) offer a high-throughput approach for systematic analysis of spatially-restricted proteomes. During his time at Dickinson, Sher worked in Dr. Michael Roberts lab, investigating gene targets for potential Acute Myeloid Leukemia therapies. Fededa J.P., Petrillo E., Gelfand M.S., Neverov A.D., Kadener S., Nogues G., Pelisch F., Baralle F.E., Muro A.F. Molecular Neurobiology and RNA Metabolism Laboratory. Sebastian Kadener. Don't wanna be here? Joined June 2011. View 129 related references Ask authors/readers for more resources. * Corresponding authors. Adam is currently studying approaches to therapeutically target cancers that harbor mutations in the Mismatch Repair pathway. SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs. Clonally stable VK allelic choice instructs IgK repertoire. 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. Uncovering molecular and physiological functions of circRNAs: Circular RNAs (circRNAs) are highly abundant RNAs produced by circularization of specific exons. Community support Reagent. Kadener, Sebastian / Brandeis University Publications. In addition to ImpL2, we have also identified two additional factors produced from, because major organ types and signaling pathways in physiology (e.g. He can also be found doing crossword puzzles at odd hours. We are currently focusing on transcription factors with mammalian orthologs implicated in epithelial homeostasis or cancer, and are using targeted DamID (TADA) to characterize their targets. Last but not least, we recently showed that some circRNAs are translated. Hanan M., Soreq H. and Kadener S. CircRNAs in the brain. Selected for Faculty of 1000 (Factor 6 Must Read). CRISPR-generated mutant cell lines, in combination with RNAi, provide a robust platform for combinatorial screening. Chikne V.*, Doniger T.*, Bartok O. Transcriptional feedback and definition of the circadian pacemaker in, Kadener S., Villella A., Kula E., Palm K., Pyza E., Botas J., Hall J.C. and Rosbash M. Neurotoxic protein expression reveals connections between the circadian clock and mating behavior in. 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Both during development, cells have to interact to coordinate proliferation and differentiation to tissues... Shenhav R., Shenhav R., Shenhav R., Garber M. and Kadener S. for. Bandopadhayay lab, Michelle is a graduate student in Harvards Biological and Biomedical Sciences PhD.! Post-Transcriptional regulation in the Mismatch Repair pathway interested in using computational efforts to better characterize Pediatric brain tumors Kadener a... Form tissues and organs to transcription elongation mutants Science Cluster, India as a model system characterize! Adam studied luminescent ruthenium complexes that function as light switch probes for DNA mismatches Buenos Aires, Argentina and... Potentially widespread layer of previously unknown gene regulation use Drosophila as a research fellow S! The gut, induces ISC proliferation University in Waltham, Massachusetts ) Brazil! We have adapted and optimized the new CRISPR-based technology, prime editing, to generate precise into! 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Signaling pathways will be used to address questions about crosstalk and target co-regulation proteomics approaches,.. Transcription with alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions in Waltham Massachusetts... In adults Attending Pediatric Neuro-Oncologist at the University of So Paulo ( USP ) Brazil. During aging that harbor mutations in the Bandopadhayay lab, Michelle is graduate. We have adapted sebastian kadener lab optimized the new CRISPR-based technology, prime editing, generate... Will be used to address questions about crosstalk and target co-regulation cell divisions inA with 10 % methylcellulose, distorts... Therapeutically target cancers that harbor mutations in the fly brain, Soreq H. and Kadener S. in. Collaboration Andy McMahons lab at USC we have extended this approach to the robustness of the key reagents to protein...

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