Search

Your search keyword '"van Heesch, Sebastiaan"' showing total 217 results
Start Over Author "van Heesch, Sebastiaan"
217 results on '"van Heesch, Sebastiaan"'

1. Evolution of translational control and the emergence of genes and open reading frames in human and non-human primate hearts

Author

Ruiz-Orera, Jorge, Miller, Duncan C., Greiner, Johannes, Genehr, Carolin, Grammatikaki, Aliki, Blachut, Susanne, Mbebi, Jeanne, Patone, Giannino, Myronova, Anna, Adami, Eleonora, Dewani, Nikita, Liang, Ning, Hummel, Oliver, Muecke, Michael B., Hildebrandt, Thomas B., Fritsch, Guido, Schrade, Lisa, Zimmermann, Wolfram H., Kondova, Ivanela, Diecke, Sebastian, van Heesch, Sebastiaan, and Hübner, Norbert

Published
2024
Full Text
View/download PDF

3. Standardized annotation of translated open reading frames

Author

Mudge, Jonathan M, Ruiz-Orera, Jorge, Prensner, John R, Brunet, Marie A, Calvet, Ferriol, Jungreis, Irwin, Gonzalez, Jose Manuel, Magrane, Michele, Martinez, Thomas F, Schulz, Jana Felicitas, Yang, Yucheng T, Albà, M Mar, Aspden, Julie L, Baranov, Pavel V, Bazzini, Ariel A, Bruford, Elspeth, Martin, Maria Jesus, Calviello, Lorenzo, Carvunis, Anne-Ruxandra, Chen, Jin, Couso, Juan Pablo, Deutsch, Eric W, Flicek, Paul, Frankish, Adam, Gerstein, Mark, Hubner, Norbert, Ingolia, Nicholas T, Kellis, Manolis, Menschaert, Gerben, Moritz, Robert L, Ohler, Uwe, Roucou, Xavier, Saghatelian, Alan, Weissman, Jonathan S, and van Heesch, Sebastiaan

Subjects
Molecular Sequence Annotation, Open Reading Frames, Protein Biosynthesis, Ribosomes
Published
2022

4. Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma

Author

Hofman, Damon A., Ruiz-Orera, Jorge, Yannuzzi, Ian, Murugesan, Rakesh, Brown, Adam, Clauser, Karl R., Condurat, Alexandra L., van Dinter, Jip T., Engels, Sem A.G., Goodale, Amy, van der Lugt, Jasper, Abid, Tanaz, Wang, Li, Zhou, Kevin N., Vogelzang, Jayne, Ligon, Keith L., Phoenix, Timothy N., Roth, Jennifer A., Root, David E., Hubner, Norbert, Golub, Todd R., Bandopadhayay, Pratiti, van Heesch, Sebastiaan, and Prensner, John R.

Published
2024
Full Text
View/download PDF

6. Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames

Author

Sandmann, Clara-L., Schulz, Jana F., Ruiz-Orera, Jorge, Kirchner, Marieluise, Ziehm, Matthias, Adami, Eleonora, Marczenke, Maike, Christ, Annabel, Liebe, Nina, Greiner, Johannes, Schoenenberger, Aaron, Muecke, Michael B., Liang, Ning, Moritz, Robert L., Sun, Zhi, Deutsch, Eric W., Gotthardt, Michael, Mudge, Jonathan M., Prensner, John R., Willnow, Thomas E., Mertins, Philipp, van Heesch, Sebastiaan, and Hubner, Norbert

Published
2023
Full Text
View/download PDF

7. A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation

Author

Gaertner, Bjoern, van Heesch, Sebastiaan, Schneider-Lunitz, Valentin, Schulz, Jana Felicitas, Witte, Franziska, Blachut, Susanne, Nguyen, Steven, Wong, Regina, Matta, Ileana, Hübner, Norbert, and Sander, Maike

Subjects
Biochemistry and Cell Biology, Biological Sciences, Stem Cell Research, Diabetes, Regenerative Medicine, Genetics, Stem Cell Research - Embryonic - Human, 1.1 Normal biological development and functioning, CRISPR-Cas Systems, Cell Differentiation, Cells, Cultured, Gene Deletion, Gene Expression Regulation, Developmental, Gene Knockout Techniques, HEK293 Cells, Human Embryonic Stem Cells, Humans, Islets of Langerhans, Male, Protein Biosynthesis, RNA, Long Noncoding, Transcription Factors, ORF detection, computational biology, developmental biology, endocrine development, endoderm, human, lncRNA, microproteins, pancreas, systems biology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Long noncoding RNAs (lncRNAs) are a heterogenous group of RNAs, which can encode small proteins. The extent to which developmentally regulated lncRNAs are translated and whether the produced microproteins are relevant for human development is unknown. Using a human embryonic stem cell (hESC)-based pancreatic differentiation system, we show that many lncRNAs in direct vicinity of lineage-determining transcription factors (TFs) are dynamically regulated, predominantly cytosolic, and highly translated. We genetically ablated ten such lncRNAs, most of them translated, and found that nine are dispensable for pancreatic endocrine cell development. However, deletion of LINC00261 diminishes insulin+ cells, in a manner independent of the nearby TF FOXA2. One-by-one disruption of each of LINC00261's open reading frames suggests that the RNA, rather than the produced microproteins, is required for endocrine development. Our work highlights extensive translation of lncRNAs during hESC pancreatic differentiation and provides a blueprint for dissection of their coding and noncoding roles.

Published
2020

10. Targeting pediatric cancers via T-cell recognition of the monomorphic MHC class I-related protein MR1

Author

CTI Nierkens, Cancer, Infection & Immunity, MDL onderzoek 2, CDL Nanomedicine, CTI Kuball, MS Hematologie, Regenerative Medicine and Stem Cells, CTI Research, Cornel, Annelisa M, van der Sman, Loutje, van Dinter, Jip T, Arrabito, Marta, Dunnebach, Ester, van Hoesel, Marliek, Kluiver, Thomas A, Lopes, Ana P, Dautzenberg, Noël M M, Dekker, Linde, van Rijn, Jorik M, van den Beemt, Denise A M H, Buhl, Juliane L, du Chatinier, Aimee, Barneh, Farnaz, Lu, Yuyan, Lo Nigro, Luca, Krippner-Heidenreich, Anja, Sebestyén, Zsolt, Kuball, Jurgen, Hulleman, Esther, Drost, Jarno, van Heesch, Sebastiaan, Heidenreich, Olaf T, Peng, Weng Chuan, Nierkens, Stefan, CTI Nierkens, Cancer, Infection & Immunity, MDL onderzoek 2, CDL Nanomedicine, CTI Kuball, MS Hematologie, Regenerative Medicine and Stem Cells, CTI Research, Cornel, Annelisa M, van der Sman, Loutje, van Dinter, Jip T, Arrabito, Marta, Dunnebach, Ester, van Hoesel, Marliek, Kluiver, Thomas A, Lopes, Ana P, Dautzenberg, Noël M M, Dekker, Linde, van Rijn, Jorik M, van den Beemt, Denise A M H, Buhl, Juliane L, du Chatinier, Aimee, Barneh, Farnaz, Lu, Yuyan, Lo Nigro, Luca, Krippner-Heidenreich, Anja, Sebestyén, Zsolt, Kuball, Jurgen, Hulleman, Esther, Drost, Jarno, van Heesch, Sebastiaan, Heidenreich, Olaf T, Peng, Weng Chuan, and Nierkens, Stefan

Published
2024

11. A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion

Author

Witte, Franziska, Ruiz-Orera, Jorge, Mattioli, Camilla Ciolli, Blachut, Susanne, Adami, Eleonora, Schulz, Jana Felicitas, Schneider-Lunitz, Valentin, Hummel, Oliver, Patone, Giannino, Mücke, Michael Benedikt, Šilhavý, Jan, Heinig, Matthias, Bottolo, Leonardo, Sanchis, Daniel, Vingron, Martin, Chekulaeva, Marina, Pravenec, Michal, Hubner, Norbert, and van Heesch, Sebastiaan

Published
2021
Full Text
View/download PDF

12. The Translational Landscape of the Human Heart

Author

van Heesch, Sebastiaan, Witte, Franziska, Schneider-Lunitz, Valentin, Schulz, Jana F., Adami, Eleonora, Faber, Allison B., Kirchner, Marieluise, Maatz, Henrike, Blachut, Susanne, Sandmann, Clara-Louisa, Kanda, Masatoshi, Worth, Catherine L., Schafer, Sebastian, Calviello, Lorenzo, Merriott, Rhys, Patone, Giannino, Hummel, Oliver, Wyler, Emanuel, Obermayer, Benedikt, Mücke, Michael B., Lindberg, Eric L., Trnka, Franziska, Memczak, Sebastian, Schilling, Marcel, Felkin, Leanne E., Barton, Paul J.R., Quaife, Nicholas M., Vanezis, Konstantinos, Diecke, Sebastian, Mukai, Masaya, Mah, Nancy, Oh, Su-Jun, Kurtz, Andreas, Schramm, Christoph, Schwinge, Dorothee, Sebode, Marcial, Harakalova, Magdalena, Asselbergs, Folkert W., Vink, Aryan, de Weger, Roel A., Viswanathan, Sivakumar, Widjaja, Anissa A., Gärtner-Rommel, Anna, Milting, Hendrik, dos Remedios, Cris, Knosalla, Christoph, Mertins, Philipp, Landthaler, Markus, Vingron, Martin, Linke, Wolfgang A., Seidman, Jonathan G., Seidman, Christine E., Rajewsky, Nikolaus, Ohler, Uwe, Cook, Stuart A., and Hubner, Norbert

Published
2019
Full Text
View/download PDF

13. The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots

Author

Santuari, Luca, Sanchez-Perez, Gabino F., Luijten, Marijn, Rutjens, Bas, Terpstra, Inez, Berke, Lidija, Gorte, Maartje, Prasad, Kalika, Bao, Dongping, Timmermans-Hereijgers, Johanna L.P.M., Maeo, Kenichiro, Nakamura, Kenzo, Shimotohno, Akie, Pencik, Ales, Novak, Ondrej, Ljung, Karin, van Heesch, Sebastiaan, de Bruijn, Ewart, Cuppen, Edwin, Willemsen, Viola, Mähönen, Ari Pekka, Lukowitz, Wolfgang, Snel, Berend, de Ridder, Dick, Scheres, Ben, and Heidstra, Renze

Published
2016

14. Widespread Translational Control of Fibrosis in the Human Heart by RNA-Binding Proteins

Author

Chothani, Sonia, Schäfer, Sebastian, Adami, Eleonora, Viswanathan, Sivakumar, Widjaja, Anissa A., Langley, Sarah R., Tan, Jessie, Wang, Mao, Quaife, Nicholas M., Jian Pua, Chee, D’Agostino, Giuseppe, Guna Shekeran, Shamini, George, Benjamin L., Lim, Stella, Yiqun Cao, Elaine, van Heesch, Sebastiaan, Witte, Franziska, Felkin, Leanne E., Christodoulou, Eleni G., Dong, Jinrui, Blachut, Susanne, Patone, Giannino, Barton, Paul J.R., Hubner, Norbert, Cook, Stuart A., and Rackham, Owen J.L.

Published
2019
Full Text
View/download PDF

15. Evolution and implications of de novo genes in humans

Author

Broeils, Luuk A., Ruiz-Orera, Jorge, Snel, Berend, Hubner, Norbert, van Heesch, Sebastiaan, Broeils, Luuk A., Ruiz-Orera, Jorge, Snel, Berend, Hubner, Norbert, and van Heesch, Sebastiaan

Abstract

Genes and translated open reading frames (ORFs) that emerged de novo from previously non-coding sequences provide species with opportunities for adaptation. When aberrantly activated, some human-specific de novo genes and ORFs have disease-promoting properties—for instance, driving tumour growth. Thousands of putative de novo coding sequences have been described in humans, but we still do not know what fraction of those ORFs has readily acquired a function. Here, we discuss the challenges and controversies surrounding the detection, mechanisms of origin, annotation, validation and characterization of de novo genes and ORFs. Through manual curation of literature and databases, we provide a thorough table with most de novo genes reported for humans to date. We re-evaluate each locus by tracing the enabling mutations and list proposed disease associations, protein characteristics and supporting evidence for translation and protein detection. This work will support future explorations of de novo genes and ORFs in humans.

Published
2023

16. Evolution and implications of de novo genes in humans

Author

Sub Bioinformatics, Theoretical Biology and Bioinformatics, Broeils, Luuk A., Ruiz-Orera, Jorge, Snel, Berend, Hubner, Norbert, van Heesch, Sebastiaan, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Broeils, Luuk A., Ruiz-Orera, Jorge, Snel, Berend, Hubner, Norbert, and van Heesch, Sebastiaan

Published
2023

18. Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma

Author

Hofman, Damon A, primary, Ruiz-Orera, Jorge, additional, Yannuzzi, Ian, additional, Murugesan, Rakesh, additional, Brown, Adam, additional, Clauser, Karl R, additional, Condurat, Alexandra L, additional, van Dinter, Jip T, additional, Engels, Sem A.G., additional, Goodale, Amy, additional, van der Lugt, Jasper, additional, Abid, Tanaz, additional, Wang, Li, additional, Zhou, Kevin N, additional, Vogelzang, Jayne, additional, Ligon, Keith L, additional, Phoenix, Timothy N, additional, Roth, Jennifer A, additional, Root, David E, additional, Hubner, Norbert, additional, Golub, Todd R, additional, Bandopadhayay, Pratiti, additional, van Heesch, Sebastiaan, additional, and Prensner, John R, additional

Published
2023
Full Text
View/download PDF

20. Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart

Author

Milenkovic, Ivan, primary, Santos Vieira, Helaine Graziele, additional, Lucas, Morghan C, additional, Ruiz-Orera, Jorge, additional, Patone, Giannino, additional, Kesteven, Scott, additional, Wu, Jianxin, additional, Feneley, Michael, additional, Espadas, Guadalupe, additional, Sabidó, Eduard, additional, Hübner, Norbert, additional, van Heesch, Sebastiaan, additional, Völkers, Mirko, additional, and Novoa, Eva Maria, additional

Published
2023
Full Text
View/download PDF

21. IL-11 is a crucial determinant of cardiovascular fibrosis

Author

Schafer, Sebastian, Viswanathan, Sivakumar, Widjaja, Anissa A., Lim, Wei-Wen, Moreno-Moral, Aida, DeLaughter, Daniel M., Ng, Benjamin, Patone, Giannino, Chow, Kingsley, Khin, Ester, Tan, Jessie, Chothani, Sonia P., Ye, Lei, Rackham, Owen J. L., Ko, Nicole S. J., Sahib, Norliza E., Pua, Chee Jian, Zhen, Nicole T. G., Xie, Chen, Wang, Mao, Maatz, Henrike, Lim, Shiqi, Saar, Kathrin, Blachut, Susanne, Petretto, Enrico, Schmidt, Sabine, Putoczki, Tracy, Guimares-Camboa, Nuno, Wakimoto, Hiroko, van Heesch, Sebastiaan, Sigmundsson, Kristmundur, Lim, See L., Soon, Jia L., Chao, Victor T. T., Chua, Yeow L., Tan, Teing E., Evans, Sylvia M., Loh, Yee J., Jamal, Muhammad H., Ong, Kim K., Chua, Kim C., Ong, Boon-Hean, Chakaramakkil, Mathew J., Seidman, Jonathan G., Seidman, Christine E., Hubner, Norbert, Sin, Kenny Y. K., and Cook, Stuart A.

Subjects
Physiological aspects, Health aspects, Interleukins -- Health aspects, Cardiovascular diseases -- Physiological aspects, Fibrosis -- Physiological aspects
Abstract

Author(s): Sebastian Schafer [1, 2]; Sivakumar Viswanathan [2]; Anissa A. Widjaja [2]; Wei-Wen Lim [1]; Aida Moreno-Moral [2]; Daniel M. DeLaughter [3]; Benjamin Ng [1]; Giannino Patone [4]; Kingsley Chow [...]

Published
2017
Full Text
View/download PDF

22. Epigenetic modulation of neuroblastoma enhances T cell and NK cell immunogenicity by inducing a tumor-cell lineage switch

Author

Cornel, Annelisa M, primary, Dunnebach, Ester, additional, Hofman, Damon A, additional, Das, Sanjukta, additional, Sengupta, Satyaki, additional, van den Ham, Femke, additional, Wienke, Judith, additional, Strijker, Josephine G M, additional, van den Beemt, Denise A M H, additional, Essing, Anke H W, additional, Koopmans, Bianca, additional, Engels, Sem A G, additional, Lo Presti, Vania, additional, Szanto, Celina S, additional, George, Rani E, additional, Molenaar, Jan J, additional, van Heesch, Sebastiaan, additional, Dierselhuis, Miranda P, additional, and Nierkens, S, additional

Published
2022
Full Text
View/download PDF

24. Large-Scale Genetic Perturbations Reveal Regulatory Networks and an Abundance of Gene-Specific Repressors

Author

Kemmeren, Patrick, Sameith, Katrin, van de Pasch, Loes A.L., Benschop, Joris J., Lenstra, Tineke L., Margaritis, Thanasis, O’Duibhir, Eoghan, Apweiler, Eva, van Wageningen, Sake, Ko, Cheuk W., van Heesch, Sebastiaan, Kashani, Mehdi M., Ampatziadis-Michailidis, Giannis, Brok, Mariel O., Brabers, Nathalie A.C.H., Miles, Anthony J., Bouwmeester, Diane, van Hooff, Sander R., van Bakel, Harm, Sluiters, Erik, Bakker, Linda V., Snel, Berend, Lijnzaad, Philip, van Leenen, Dik, Groot Koerkamp, Marian J.A., and Holstege, Frank C.P.

Published
2014
Full Text
View/download PDF

25. Aging-regulated TUG1 is dispensable for endothelial cell function

Author

Gimbel, Anna Theresa, Koziarek, Susanne, Theodorou, Kosta, Schulz, Jana Felicitas, Stanicek, Laura, Kremer, Veerle, Ali, Tamer, Günther, Stefan, Kumar, Sandeep, Jo, Hanjoong, Hübner, Norbert, Maegdefessel, Lars, Dimmeler, Stefanie, van Heesch, Sebastiaan, Boon, Reinier A., ACS - Microcirculation, Physiology, ACS - Heart failure & arrhythmias, and ACS - Atherosclerosis & ischemic syndromes

Subjects
Cardiovascular and Metabolic Diseases
Abstract

The evolutionary conserved Taurine Upregulated Gene 1 (TUG1) is a ubiquitously expressed gene that is one of the highest expressed genes in human and rodent endothelial cells (ECs). We here show that TUG1 expression decreases significantly in aging mouse carotid artery ECs and human ECs in vitro, indicating a potential role in the aging endothelial vasculature system. We therefore investigated if, and how, TUG1 might function in aging ECs, but despite extensive phenotyping found no alterations in basal EC proliferation, apoptosis, barrier function, migration, mitochondrial function, or monocyte adhesion upon TUG1 silencing in vitro. TUG1 knockdown did slightly and significantly decrease cumulative sprout length upon vascular endothelial growth factor A stimulation in human umbilical vein endothelial cells (HUVECs), though TUG1-silenced HUVECs displayed no transcriptome-wide mRNA expression changes explaining this effect. Further, ectopic expression of the highly conserved and recently discovered 153 amino acid protein translated from certain TUG1 transcript isoforms did not alter angiogenic sprouting in vitro. Our data show that, despite a high expression and strong evolutionary conservation of both the TUG1 locus and the protein sequence it encodes, TUG1 does not seem to play a major role in basic endothelial cell function.

Published
2022
Full Text
View/download PDF

27. Epigenetics and Control of RNAs

Author

Maatz, Henrike, primary, van Heesch, Sebastiaan, additional, Kreuchwig, Franziska, additional, Faber, Allison, additional, Adami, Eleonora, additional, Hubner, Norbert, additional, and Heinig, Matthias, additional

Published
2016
Full Text
View/download PDF

28. Epigenetic modulation of neuroblastoma enhances T cell and NK cell immunogenicity by inducing a tumor-cell lineage switch

Author

CTI Nierkens, Cancer, Infection & Immunity, CMM Groep Klumperman, Arts-assistenten Kinderen, CTI Research, Cornel, Annelisa M., Dunnebach, Ester, Hofman, Damon A., Das, Sanjukta, Sengupta, Satyaki, Van Den Ham, Femke, Wienke, Judith, Strijker, Josephine G.M., Van Den Beemt, Denise A.M.H., Essing, Anke H.W., Koopmans, Bianca, Engels, Sem A.G., Lo Presti, Vania, Szanto, Celina S., George, Rani E., Molenaar, Jan J., Van Heesch, Sebastiaan, Dierselhuis, Miranda P., Nierkens, S., CTI Nierkens, Cancer, Infection & Immunity, CMM Groep Klumperman, Arts-assistenten Kinderen, CTI Research, Cornel, Annelisa M., Dunnebach, Ester, Hofman, Damon A., Das, Sanjukta, Sengupta, Satyaki, Van Den Ham, Femke, Wienke, Judith, Strijker, Josephine G.M., Van Den Beemt, Denise A.M.H., Essing, Anke H.W., Koopmans, Bianca, Engels, Sem A.G., Lo Presti, Vania, Szanto, Celina S., George, Rani E., Molenaar, Jan J., Van Heesch, Sebastiaan, Dierselhuis, Miranda P., and Nierkens, S.

Published
2022

29. The Specificity and Topology of Chromatin Interaction Pathways in Yeast

Author

Lenstra, Tineke L., Benschop, Joris J., Kim, TaeSoo, Schulze, Julia M., Brabers, Nathalie A.C.H., Margaritis, Thanasis, van de Pasch, Loes A.L., van Heesch, Sebastiaan A.A.C., Brok, Mariel O., Groot Koerkamp, Marian J.A., Ko, Cheuk W., van Leenen, Dik, Sameith, Katrin, van Hooff, Sander R., Lijnzaad, Philip, Kemmeren, Patrick, Hentrich, Thomas, Kobor, Michael S., Buratowski, Stephen, and Holstege, Frank C.P.

Published
2011
Full Text
View/download PDF

30. Multifunctional RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes

Author

Schneider-Lunitz, Valentin, Ruiz-Orera, Jorge, Hubner, Norbert, and van Heesch, Sebastiaan

Subjects
RNA splicing, QH301-705.5, Gene Expression, RNA-binding proteins, Biochemistry, Untranslated Regions, Genetics, Medicine and Health Sciences, Humans, Gene Regulation, RNA, Messenger, Biology (General), Biology and life sciences, Messenger RNA, Myocardium, Proteins, Computational Biology, Heart, Nucleic acids, 5' Utr, RNA processing, Gene Expression Regulation, Cardiovascular and Metabolic Diseases, Protein Biosynthesis, Cardiovascular Anatomy, RNA, Protein Translation, Anatomy, Research Article
Abstract

RNA-binding proteins (RBPs) can regulate more than a single aspect of RNA metabolism. We searched for such previously undiscovered multifunctionality within a set of 143 RBPs, by defining the predictive value of RBP abundance for the transcription and translation levels of known RBP target genes across 80 human hearts. This led us to newly associate 27 RBPs with cardiac translational regulation in vivo. Of these, 21 impacted both RNA expression and translation, albeit for virtually independent sets of target genes. We highlight a subset of these, including G3BP1, PUM1, UCHL5, and DDX3X, where dual regulation is achieved through differential affinity for target length, by which separate biological processes are controlled. Like the RNA helicase DDX3X, the known splicing factors EFTUD2 and PRPF8—all identified as multifunctional RBPs by our analysis—selectively influence target translation rates depending on 5’ UTR structure. Our analyses identify dozens of RBPs as being multifunctional and pinpoint potential novel regulators of translation, postulating unanticipated complexity of protein-RNA interactions at consecutive stages of gene expression., Author summary The lifecycle of an RNA molecule is controlled by hundreds of proteins that can bind RNA, also known as RNA-binding proteins (RBPs). These proteins recognize landing sites within the RNA and guide the RNA’s transcription from DNA, its processing into a mature messenger RNA, its translation into protein, or its degradation once the RNA is no longer needed. Although we now mechanistically understand how certain RBPs regulate these processes, for many RBP-target interactions the consequences imposed by RNA binding are not well understood. For 143 RBPs with known RNA binding positions, the authors of the current study investigated how RNA molecules responded to fluctuations in the expression levels of these RBPs, across each of 80 human hearts. Using statistical approaches, they could show that many RBPs influenced stages of the RNA lifecycle that they were not known to be involved in. Some RBPs turned out to be true "all-rounders" of RNA metabolism: they controlled the RNA transcript levels of some genes, whereas they influenced the translation rates of others. This unexpected multifunctionality unveiled previously hidden aspects of the everyday RNA-binding protein working life.

Published
2021

31. Aging-regulated TUG1 is dispensable for endothelial cell function

Author

Gimbel, Anna Theresa, primary, Koziarek, Susanne, additional, Theodorou, Kosta, additional, Schulz, Jana Felicitas, additional, Stanicek, Laura, additional, Ali, Tamer, additional, Günther, Stefan, additional, Kumar, Sandeep, additional, Jo, Hanjoong, additional, Hübner, Norbert, additional, Maegdefessel, Lars, additional, Dimmeler, Stefanie, additional, van Heesch, Sebastiaan, additional, and Boon, Reinier A., additional

Published
2022
Full Text
View/download PDF

33. Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart

Author

Milenkovic, Ivan, primary, Santos Vieira, Helaine Graziele, additional, Lucas, Morghan C, additional, Ruiz-Orera, Jorge, additional, Patone, Giannino, additional, Kesteven, Scott, additional, Wu, Jianxin, additional, Feneley, Michael, additional, Espadas, Guadalupe, additional, Sabidó, Eduard, additional, Hubner, Norbert, additional, van Heesch, Sebastiaan, additional, Voelkers, Mirko, additional, and Novoa, Eva Maria, additional

Published
2021
Full Text
View/download PDF

34. Additional file 1 of A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion

Author

Witte, Franziska, Ruiz-Orera, Jorge, Mattioli, Camilla Ciolli, Blachut, Susanne, Adami, Eleonora, Schulz, Jana Felicitas, Schneider-Lunitz, Valentin, Hummel, Oliver, Patone, Giannino, Mücke, Michael Benedikt, Šilhavý, Jan, Heinig, Matthias, Bottolo, Leonardo, Sanchis, Daniel, Vingron, Martin, Chekulaeva, Marina, Pravenec, Michal, Hubner, Norbert, and van Heesch, Sebastiaan

Abstract

Additional file 1: Figure S1-S6, related to Figs. 1, 2, 3, 4 - Document with supplemental Figures 1, 2, 3, 4, 5, 6, including figure captions.

Published
2021
Full Text
View/download PDF

35. Additional file 7 of A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion

Author

Witte, Franziska, Ruiz-Orera, Jorge, Mattioli, Camilla Ciolli, Blachut, Susanne, Adami, Eleonora, Schulz, Jana Felicitas, Schneider-Lunitz, Valentin, Hummel, Oliver, Patone, Giannino, Mücke, Michael Benedikt, Šilhavý, Jan, Heinig, Matthias, Bottolo, Leonardo, Sanchis, Daniel, Vingron, Martin, Chekulaeva, Marina, Pravenec, Michal, Hubner, Norbert, and van Heesch, Sebastiaan

Abstract

Additional file 7. Review history.

Published
2021
Full Text
View/download PDF

37. A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq

Author

Mudge, Jonathan M., primary, Ruiz-Orera, Jorge, additional, Prensner, John R., additional, Brunet, Marie A., additional, Gonzalez, Jose Manuel, additional, Magrane, Michele, additional, Martinez, Thomas, additional, Schulz, Jana Felicitas, additional, Yang, Yucheng T., additional, Albà, M. Mar, additional, Baranov, Pavel V., additional, Bazzini, Ariel, additional, Bruford, Elspeth, additional, Martin, Maria Jesus, additional, Carvunis, Anne-Ruxandra, additional, Chen, Jin, additional, Couso, Juan Pablo, additional, Flicek, Paul, additional, Frankish, Adam, additional, Gerstein, Mark, additional, Hubner, Norbert, additional, Ingolia, Nicholas T., additional, Menschaert, Gerben, additional, Ohler, Uwe, additional, Roucou, Xavier, additional, Saghatelian, Alan, additional, Weissman, Jonathan, additional, and van Heesch, Sebastiaan, additional

Published
2021
Full Text
View/download PDF

38. A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion

Author

Witte, Franziska, Ruiz-Orera, Jorge, Mattioli, Camilla Ciolli, Blachut, Susanne, Adami, Eleonora, Schulz, Jana Felicitas, Schneider-Lunitz, Valentin, Hummel, Oliver, Patone, Giannino, Mücke, Michael Benedikt, Šilhavý, Jan, Heinig, Matthias, Bottolo, Leonardo, Sanchis, Daniel, Vingron, Martin, Chekulaeva, Marina, Pravenec, Michal, Hubner, Norbert, and van Heesch, Sebastiaan

Subjects
Research, Genetic variation, Translational efficiency, Ribosome profiling, Cardiac hypertrophy, Ribosome biogenesis, Ribosomopathy, Complex disease, Spontaneously hypertensive rats (SHR), HXB/BXH rat recombinant inbred panel, ddc
Published
2020

40. A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation

Author

Gaertner, Bjoern, primary, van Heesch, Sebastiaan, additional, Schneider-Lunitz, Valentin, additional, Schulz, Jana Felicitas, additional, Witte, Franziska, additional, Blachut, Susanne, additional, Nguyen, Steven, additional, Wong, Regina, additional, Matta, Ileana, additional, Hübner, Norbert, additional, and Sander, Maike, additional

Published
2020
Full Text
View/download PDF

41. Author response: A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation

Author

Gaertner, Bjoern, primary, van Heesch, Sebastiaan, additional, Schneider-Lunitz, Valentin, additional, Schulz, Jana Felicitas, additional, Witte, Franziska, additional, Blachut, Susanne, additional, Nguyen, Steven, additional, Wong, Regina, additional, Matta, Ileana, additional, Hübner, Norbert, additional, and Sander, Maike, additional

Published
2020
Full Text
View/download PDF

42. Transcontrol of cardiac mRNA translation in a protein length-dependent fashion

Author

Witte, Franziska, primary, Ruiz-Orera, Jorge, additional, Ciolli Mattioli, Camilla, additional, Blachut, Susanne, additional, Adami, Eleonora, additional, Schulz, Jana Felicitas, additional, Schneider-Lunitz, Valentin, additional, Hummel, Oliver, additional, Patone, Giannino, additional, Mücke, Michael Benedikt, additional, Šilhavý, Jan, additional, Heinig, Matthias, additional, Bottolo, Leonardo, additional, Sanchis, Daniel, additional, Vingron, Martin, additional, Chekulaeva, Marina, additional, Pravenec, Michal, additional, Hubner, Norbert, additional, and van Heesch, Sebastiaan, additional

Published
2020
Full Text
View/download PDF

43. A functional screen of translated pancreatic lncRNAs identifies a microprotein-independent role for LINC00261 in endocrine cell differentiation

Author

Gaertner, Bjoern, primary, van Heesch, Sebastiaan, additional, Schneider-Lunitz, Valentin, additional, Schulz, Jana Felicitas, additional, Witte, Franziska, additional, Blachut, Susanne, additional, Nguyen, Steven, additional, Wong, Regina, additional, Matta, Ileana, additional, Hubner, Norbert, additional, and Sander, Maike, additional

Published
2020
Full Text
View/download PDF

44. Abstract 860: Functional Characterization of a Novel Human Heart-specific Microprotein With a Potential Mitochondrial Localization and Role in Sarcomere Dynamics

Author

Muecke, Michael Benedikt B, primary, Schulz, Jana F, additional, Schneider, Valentin, additional, Sharma, Arun, additional, Toepfer, Christopher N, additional, van Heesch, Sebastiaan, additional, Seidman, Jonathan G, additional, Seidman, Christine E, additional, and Hübner, Norbert, additional

Published
2019
Full Text
View/download PDF

45. The Translational Landscape of the Human Heart

Author

Onderzoek Precision medicine, Team Medisch, Circulatory Health, Pathologie Pathologen staf, Pathologie Moleculair, Cancer, van Heesch, Sebastiaan, Witte, Franziska, Schneider-Lunitz, Valentin, Schulz, Jana F, Adami, Eleonora, Faber, Allison B, Kirchner, Marieluise, Maatz, Henrike, Blachut, Susanne, Sandmann, Clara-Louisa, Kanda, Masatoshi, Worth, Catherine L, Schafer, Sebastian, Calviello, Lorenzo, Merriott, Rhys, Patone, Giannino, Hummel, Oliver, Wyler, Emanuel, Obermayer, Benedikt, Mücke, Michael B, Lindberg, Eric L, Trnka, Franziska, Memczak, Sebastian, Schilling, Marcel, Felkin, Leanne E, Barton, Paul J R, Quaife, Nicholas M, Vanezis, Konstantinos, Diecke, Sebastian, Mukai, Masaya, Mah, Nancy, Oh, Su-Jun, Kurtz, Andreas, Schramm, Christoph, Schwinge, Dorothee, Sebode, Marcial, Harakalova, Magdalena, Asselbergs, Folkert W, Vink, Aryan, de Weger, Roel A, Viswanathan, Sivakumar, Widjaja, Anissa A, Gärtner-Rommel, Anna, Milting, Hendrik, Dos Remedios, Cris, Knosalla, Christoph, Mertins, Philipp, Landthaler, Markus, Vingron, Martin, Linke, Wolfgang A, Seidman, Jonathan G, Seidman, Christine E, Rajewsky, Nikolaus, Ohler, Uwe, Cook, Stuart A, Hubner, Norbert, Onderzoek Precision medicine, Team Medisch, Circulatory Health, Pathologie Pathologen staf, Pathologie Moleculair, Cancer, van Heesch, Sebastiaan, Witte, Franziska, Schneider-Lunitz, Valentin, Schulz, Jana F, Adami, Eleonora, Faber, Allison B, Kirchner, Marieluise, Maatz, Henrike, Blachut, Susanne, Sandmann, Clara-Louisa, Kanda, Masatoshi, Worth, Catherine L, Schafer, Sebastian, Calviello, Lorenzo, Merriott, Rhys, Patone, Giannino, Hummel, Oliver, Wyler, Emanuel, Obermayer, Benedikt, Mücke, Michael B, Lindberg, Eric L, Trnka, Franziska, Memczak, Sebastian, Schilling, Marcel, Felkin, Leanne E, Barton, Paul J R, Quaife, Nicholas M, Vanezis, Konstantinos, Diecke, Sebastian, Mukai, Masaya, Mah, Nancy, Oh, Su-Jun, Kurtz, Andreas, Schramm, Christoph, Schwinge, Dorothee, Sebode, Marcial, Harakalova, Magdalena, Asselbergs, Folkert W, Vink, Aryan, de Weger, Roel A, Viswanathan, Sivakumar, Widjaja, Anissa A, Gärtner-Rommel, Anna, Milting, Hendrik, Dos Remedios, Cris, Knosalla, Christoph, Mertins, Philipp, Landthaler, Markus, Vingron, Martin, Linke, Wolfgang A, Seidman, Jonathan G, Seidman, Christine E, Rajewsky, Nikolaus, Ohler, Uwe, Cook, Stuart A, and Hubner, Norbert

Published
2019

46. The Tug1 Locus is Essential for Male Fertility

Author

Lewandowski, Jordan P., primary, Dumbović, Gabrijela, additional, Watson, Audrey R., additional, Hwang, Taeyoung, additional, Jacobs-Palmer, Emily, additional, Chang, Nydia, additional, Much, Christian, additional, Turner, Kyle, additional, Kirby, Christopher, additional, Schulz, Jana Felicitas, additional, Müller, Clara-Louisa, additional, Rubinstein, Nimrod D., additional, Groff, Abigail F., additional, Liapis, Steve C., additional, Gerhardinger, Chiara, additional, Hubner, Norbert, additional, van Heesch, Sebastiaan, additional, Hoekstra, Hopi E., additional, Sauvageau, Martin, additional, and Rinn, John L., additional

Published
2019
Full Text
View/download PDF

47. Translational control of cardiac fibrosis

Author

Chothani, Sonia, primary, Schafer, Sebastian, additional, Adami, Eleonora, additional, Viswanathan, Sivakumar, additional, Widjaja, Anissa A, additional, Langley, Sarah R, additional, Tan, Jessie, additional, Pua, Chee Jian, additional, D’Agostino, Giuseppe, additional, van Heesch, Sebastiaan, additional, Witte, Franziska, additional, Felkin, Leanne E, additional, Christodoulou, Eleni G., additional, Dong, Jinrui, additional, Blachut, Susanne, additional, Patone, Giannino, additional, Barton, Paul JR, additional, Hubner, Norbert, additional, Cook, Stuart A, additional, and Rackham, Owen JL, additional

Published
2018
Full Text
View/download PDF

49. Translational regulation shapes the molecular landscape of complex disease phenotypes

Author

Schafer, Sebastian, Adami, Eleonora, Heinig, Matthias, Rodrigues, Katharina E. Costa, Kreuchwig, Franziska, Silhavy, Jan, van Heesch, Sebastiaan, Simaite, Deimante, Rajewsky, Nikolaus, Cuppen, Edwin, Pravenec, Michal, Vingron, Martin, Cook, Stuart A., Hubner, Norbert, Hubrecht Institute for Developmental Biology and Stem Cell Research, and Commission of the European Communities

Subjects
Male, Proteome, Chemistry(all), Sequence Analysis, RNA, Biochemistry, Genetics and Molecular Biology(all), Myocardium, Physics and Astronomy(all), Article, Phenotype, Gene Expression Regulation, Liver, Cardiovascular and Metabolic Diseases, Rats, Inbred BN, Rats, Inbred SHR, MD Multidisciplinary, Hypertension, Animals, Ribosomes
Abstract

The extent of translational control of gene expression in mammalian tissues remains largely unknown. Here we perform genome-wide RNA sequencing and ribosome profiling in heart and liver tissues to investigate strain-specific translational regulation in the spontaneously hypertensive rat (SHR/Ola). For the most part, transcriptional variation is equally apparent at the translational level and there is limited evidence of translational buffering. Remarkably, we observe hundreds of strain-specific differences in translation, almost doubling the number of differentially expressed genes. The integration of genetic, transcriptional and translational data sets reveals distinct signatures in 3′UTR variation, RNA-binding protein motifs and miRNA expression associated with translational regulation of gene expression. We show that a large number of genes associated with heart and liver traits in human genome-wide association studies are primarily translationally regulated. Capturing interindividual differences in the translated genome will lead to new insights into the genes and regulatory pathways underlying disease phenotypes., To what extent translational control can contribute to global gene expression patterns in the disease state is poorly defined. Here the authors conduct genome-wide RNA-seq and ribosome profiling in a rat model of hypertension and uncover altered translation patterns in disease associated genes.

Published
2015

50. Titin-truncating variants affect heart function in disease cohorts and the general population

Author

Schafer, Sebastian, De Marvao, Antonio, Adami, Eleonora, Fiedler, Lorna R., Ng, Benjamin, Khin, Ester, Rackham, Owen J L, Van Heesch, Sebastiaan, Pua, Chee J., Kui, Miao, Walsh, Roddy, Tayal, Upasana, Prasad, Sanjay K., Dawes, Timothy J W, Ko, Nicole S J, Sim, David, Chan, Laura L H, Chin, Calvin W L, Mazzarotto, Francesco, Barton, Paul J., Kreuchwig, Franziska, De Kleijn, Dominique P V, Totman, Teresa, Biffi, Carlo, Tee, Nicole, Rueckert, Daniel, Schneider, Valentin, Faber, Allison, Regitz-Zagrosek, Vera, Seidman, Jonathan G., Seidman, Christine E., Linke, Wolfgang A., Kovalik, Jean Paul, O'Regan, Declan, Ware, James S., Hubner, Norbert, Cook, Stuart A., Schafer, Sebastian, De Marvao, Antonio, Adami, Eleonora, Fiedler, Lorna R., Ng, Benjamin, Khin, Ester, Rackham, Owen J L, Van Heesch, Sebastiaan, Pua, Chee J., Kui, Miao, Walsh, Roddy, Tayal, Upasana, Prasad, Sanjay K., Dawes, Timothy J W, Ko, Nicole S J, Sim, David, Chan, Laura L H, Chin, Calvin W L, Mazzarotto, Francesco, Barton, Paul J., Kreuchwig, Franziska, De Kleijn, Dominique P V, Totman, Teresa, Biffi, Carlo, Tee, Nicole, Rueckert, Daniel, Schneider, Valentin, Faber, Allison, Regitz-Zagrosek, Vera, Seidman, Jonathan G., Seidman, Christine E., Linke, Wolfgang A., Kovalik, Jean Paul, O'Regan, Declan, Ware, James S., Hubner, Norbert, and Cook, Stuart A.

Published
2017

Catalog

Books, media, physical & digital resources
See catalog results