Claudia Kutter

Scopus Publications

RAPseq enables large-scale identification of RBP–RNA interactions and reveals essentials of post-transcriptional gene regulation
Riccardo Mosca, Carlos J Gallardo-Dodd, Qun Li, Christian Sommerauer, Justas Šidiškis, Jonas Nørskov Søndergaard, Claudia Kutter
Nucleic Acids Research, 2026
Over the past decade, thousands of putative human RNA-binding proteins (RBPs) have been identified, increasing the need for methods that define their RNA-binding capacities across diverse biological settings. Existing methods rely either on antibody-based in vivo capture (e.g. CLIP-seq), which depends on cross-linking efficiency and antibody availability, or on synthetic oligonucleotide-based assays (e.g. RNAcompete), which use artificial RNA substrates and cannot assess binding across the native transcriptome. To bridge this gap, we developed RNA affinity purification followed by sequencing (RAPseq), an in vitro method that profiles RBP-binding to native cellular RNA, enabling large-scale transcriptome-wide characterization of RNA–protein interactions without antibodies or synthetic probes. Using RAPseq, we characterized the RNA interactomes of 11 canonical RBPs and 26 non-canonical RBPs, and uncovered novel and specialized moonlighting RNA-binding activities. Applying RAPseq to vertebrate HUR proteins revealed recognition of a conserved RNA-binding motif but showed species-specific binding preferences. Profiling of five pathological IGF2BP family variants exhibited distinct gain- and loss-of-function binding patterns, with implications for cancer biology. Our combinatorial RBP-binding assay (co-RAPseq) uncovered cooperative RNA-binding by HUR and PTBP1, including de novo estimation of the optimal binding distance. Lastly, we introduce a modification-sensitive assay (mod-RAPseq) to distinguish between modification-dependent and -independent RNA-binding sites of YTHDF1 and YBX1. Overall, our simple, scalable, and versatile method enables exploration of complex RNA–protein interactions and the regulatory layers that shape post-transcriptional gene regulation.
Author Correction: Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis (Molecular Systems Biology, (2024), 20, 4, (374-402), 10.1038/s44320-024-00024-x)
Christian Sommerauer, Carlos J Gallardo-Dodd, Christina Savva, Linnea Hases, Madeleine Birgersson, Rajitha Indukuri, Joanne X Shen, Pablo Carravilla, Keyi Geng, Jonas Nørskov Søndergaard, Clàudia Ferrer-Aumatell, Grégoire Mercier, Erdinc Sezgin, Marion Korach-André, Carl Petersson, Hannes Hagström, Volker M Lauschke, Amena Archer, Cecilia Williams, Claudia Kutter
Molecular Systems Biology, 2025
Intestinal estrogen receptor beta modulates the murine colon tumor immune microenvironment
Madeleine Birgersson, Matilda Holm, Carlos J. Gallardo-Dodd, Baizhen Chen, Lina Stepanauskaitė, Linnea Hases, Claudia Kutter, Amena Archer, Cecilia Williams
Cancer Letters, 2025
Chronic inflammation contributes to the development of colorectal cancer, partly through its regulation of the microenvironment and antitumor immunity. Interestingly, women have a lower incidence of colorectal cancer, and estrogen treatment has been shown to reduce the occurrence of colorectal tumors. While intestinal estrogen receptor beta (ERβ, Esr2) can protect against colitis and colitis-induced cancer in mice, its role in shaping the tumor microenvironment remains unknown. In this study, we performed RNA sequencing to analyze the transcriptome of colonic epithelia and tumors from azoxymethane/dextran sulfate sodium-treated wild-type and intestinal ERβ knockout (ERβKO Vil ) mice and vehicle-treated controls. This revealed significant differences in gene expression and enriched biological processes influenced by sex and genotype, with immune-related responses being overrepresented. Deconvolution supported differential immune cell abundance and immunostaining showed that tumors from ERβKO Vil mice displayed significantly increased macrophage infiltration, decreased T cell infiltration, and impaired natural killer cell infiltration. Further, ERβ mRNA levels in clinical colorectal tumors correlated with immune signaling profiles and better survival. Our findings indicate that intestinal ERβ promotes an antitumor microenvironment and could potentially affect the effectiveness of immunotherapy. These insights highlight the importance of ERβ in modulating antitumor immunity and underscore its therapeutic potential in colorectal cancer. • RNA sequencing of mouse colon tumors and intestinal epithelia with and without ERβ reveals its impact on sex differences. • Deconvolution and immunostaining demonstrates that intestinal ERβ impacts the proportion of tumor-infiltrating immune cells. • Absence of ERβ leads to increased macrophage and decreased T and natural killer cell infiltration into tumors. • ERβ mRNA in colorectal tumors correlates with survival and immune signaling pathways indicative of antitumor responses.
PHYSIOLOGICAL RESPONSE OF THE AQUATIC FERN Salvinia minima UNDER EXPOSURE TO METALS SUCH Pb, Ni, Cu, Zn AND Li
Gabriela Fuentes, Daniel Leal-Alvarado, Ignacio Fuentes-Franco, Tony Hoffmann, Claudia Kutter, David Uh-Ramos, Katiana Trejo, Neyi Estrella, Gerardo Carrillo-Niquete, Eduardo Gómez-Hernández, Jorge M Santamaría
Tropical and Subtropical Agroecosystems, 2025
Background: Metals can be found in nature, but they are also generated by anthropogenic activities associated with technological waste, such as batteries and electronic components. These metals, when released to the environment may contaminate and cause significant health damage. Phytoremediation is a process to de-contaminate water bodies from metals using plants. Obviously, those plants should be able not only to uptake high amounts of metals, but also, they should be able to tolerate those high concentrations in their tissues. Salvinia minima is a fast-growing, floating aquatic fern and its ability to take up metals from the environment has been evaluated. Objective: To characterize the physiological and molecular response of Salvinia minima plants exposed to different metals. Methodology: A system was designed to expose Salvinia minima plants to different metals such as Pb, Ni, Cu, Zn and Li, for seven days at different concentrations levels and take samples every 24 h. Various parameters were evaluated including metal uptake, metal concentration in the medium, leaf appearance, PSII efficiency (Fv/Fm), photosynthesis, transpiration, stomatal conductance. Results: S. minima plants were capable to accumulate Pb (28 mg /g DW at 40 uM), Zn (10 mg/g at 80uM) Li (10 mg/g at 20mM), Cu (8 mg/g at 40 uM) and Ni (4 mg/g at 40 uM), at their roots. At short times (0-24 h) and at low concentrations (of certain metals) no significant physiological damage was observed, however, at high concentrations or longer exposure times (48-144 h), physiological damage can be observed in terms of decreased photosynthesis and PSII efficiency, transpiration and stomatal conductance. Implications: Salvinia minima plant are capable to take Pb, Ni, Cu, Zn and Li from the medium, which indicates that it is a good candidate to be used in the phytoremediation of water bodies contaminated with these metals. Conclusions: Salvinia minima plants take up and accumulate high concentrations of Pb, Ni, Cu, Zn and Li in their tissues, thus reducing the metal content of aqueous media. Even though at high concentrations those metals may affect its physiological performance, this occurs at much higher concentrations than those normally found in natural water bodies, therefore S. minima is certainly a good candidate to be used for the phytoremediation of water bodies contaminated with metals.
The regulatory landscape of interacting RNA and protein pools in cellular homeostasis and cancer
Carlos J. Gallardo-Dodd, Claudia Kutter
Human Genomics, 2024
Biological systems encompass intricate networks governed by RNA-protein interactions that play pivotal roles in cellular functions. RNA and proteins constituting 1.1% and 18% of the mammalian cell weight, respectively, orchestrate vital processes from genome organization to translation. To date, disentangling the functional fraction of the human genome has presented a major challenge, particularly for noncoding regions, yet recent discoveries have started to unveil a host of regulatory functions for noncoding RNAs (ncRNAs). While ncRNAs exist at different sizes, structures, degrees of evolutionary conservation and abundances within the cell, they partake in diverse roles either alone or in combination. However, certain ncRNA subtypes, including those that have been described or remain to be discovered, are poorly characterized given their heterogeneous nature. RNA activity is in most cases coordinated through interactions with RNA-binding proteins (RBPs). Extensive efforts are being made to accurately reconstruct RNA-RBP regulatory networks, which have provided unprecedented insight into cellular physiology and human disease. In this review, we provide a comprehensive view of RNAs and RBPs, focusing on how their interactions generate functional signals in living cells, particularly in the context of post-transcriptional regulatory processes and cancer.
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis
Christian Sommerauer, Carlos J Gallardo-Dodd, Christina Savva, Linnea Hases, Madeleine Birgersson, Rajitha Indukuri, Joanne X Shen, Pablo Carravilla, Keyi Geng, Jonas Nørskov Søndergaard, Clàudia Ferrer-Aumatell, Grégoire Mercier, Erdinc Sezgin, Marion Korach-André, Carl Petersson, Hannes Hagström, Volker M Lauschke, Amena Archer, Cecilia Williams, Claudia Kutter
Molecular Systems Biology, 2024
Sex-based differences in obesity-related hepatic malignancies suggest the protective roles of estrogen. Using a preclinical model, we dissected estrogen receptor (ER) isoform-driven molecular responses in high-fat diet (HFD)-induced liver diseases of male and female mice treated with or without an estrogen agonist by integrating liver multi-omics data. We found that selective ER activation recovers HFD-induced molecular and physiological liver phenotypes. HFD and systemic ER activation altered core liver pathways, beyond lipid metabolism, that are consistent between mice and primates. By including patient cohort data, we uncovered that ER-regulated enhancers govern central regulatory and metabolic genes with clinical significance in metabolic dysfunction-associated steatotic liver disease (MASLD) patients, including the transcription factor TEAD1. TEAD1 expression increased in MASLD patients, and its downregulation by short interfering RNA reduced intracellular lipid content. Subsequent TEAD small molecule inhibition improved steatosis in primary human hepatocyte spheroids by suppressing lipogenic pathways. Thus, TEAD1 emerged as a new therapeutic candidate whose inhibition ameliorates hepatic steatosis.
Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9–mediated genome engineering in HAP1 cells mimicking cancer profiles
Keyi Geng, Lara G Merino, Raül G Veiga, Christian Sommerauer, Janine Epperlein, Eva K Brinkman, Claudia Kutter
Life Science Alliance, 2024
The CRISPR-Cas9 system is a powerful tool for studying gene functions and holds potential for disease treatment. However, precise genome editing requires thorough assessments to minimize unintended on- and off-target effects. Here, we report an unexpected 283-kb deletion on Chromosome 10 (10q23.31) in chronic myelogenous leukemia-derived HAP1 cells, which are frequently used in CRISPR screens. The deleted region encodes regulatory genes, includingPAPSS2,ATAD1,KLLN, andPTEN. We found that this deletion was not a direct consequence of CRISPR-Cas9 off-targeting but rather occurred frequently during the generation of CRISPR-Cas9–modified cells. The deletion was associated with global changes in histone acetylation and gene expression, affecting fundamental cellular processes such as cell cycle and DNA replication. We detected this deletion in cancer patient genomes. As in HAP1 cells, the deletion contributed to similar gene expression patterns among cancer patients despite interindividual differences. Our findings suggest that the unintended deletion of 10q23.31 can confound CRISPR-Cas9 studies and underscore the importance to assess unintended genomic changes in CRISPR-Cas9–modified cells, which could impact cancer research.
Coinhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills pancreatic cancer via readthrough transcription
Donald P. Cameron, Jan Grosser, Swetlana Ladigan, Vladislav Kuzin, Evanthia Iliopoulou, Anika Wiegard, Hajar Benredjem, Kathryn Jackson, Sven T. Liffers, Smiths Lueong, Phyllis F. Cheung, Deepak Vangala, Michael Pohl, Richard Viebahn, Christian Teschendorf, Heiner Wolters, Selami Usta, Keyi Geng, Claudia Kutter, Marie Arsenian-Henriksson, Jens T. Siveke, Andrea Tannapfel, Wolff Schmiegel, Stephan A. Hahn, Laura Baranello
Science Advances, 2023
Pancreatic carcinoma lacks effective therapeutic strategies resulting in poor prognosis. Transcriptional dysregulation due to alterations in KRAS and MYC affects initiation, development, and survival of this tumor type. Using patient-derived xenografts of KRAS- and MYC-driven pancreatic carcinoma, we show that coinhibition of topoisomerase 1 (TOP1) and bromodomain-containing protein 4 (BRD4) synergistically induces tumor regression by targeting promoter pause release. Comparing the nascent transcriptome with the recruitment of elongation and termination factors, we found that coinhibition of TOP1 and BRD4 disrupts recruitment of transcription termination factors. Thus, RNA polymerases transcribe downstream of genes for hundreds of kilobases leading to readthrough transcription. This occurs during replication, perturbing replisome progression and inducing DNA damage. The synergistic effect of TOP1 + BRD4 inhibition is specific to cancer cells leaving normal cells unaffected, highlighting the tumor’s vulnerability to transcriptional defects. This preclinical study provides a mechanistic understanding of the benefit of combining TOP1 and BRD4 inhibitors to treat pancreatic carcinomas addicted to oncogenic drivers of transcription and replication.
Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells
Carlos J. Gallardo-Dodd, Christian Oertlin, Julien Record, Rômulo G. Galvani, Christian Sommerauer, Nikolai V. Kuznetsov, Evangelos Doukoumopoulos, Liaqat Ali, Mariana M. S. Oliveira, Christina Seitz, Mathias Percipalle, Tijana Nikić, Anastasia A. Sadova, Sofia M. Shulgina, Vjacheslav A. Shmarov, Olga V. Kutko, Daria D. Vlasova, Kseniya D. Orlova, Marina P. Rykova, John Andersson, Piergiorgio Percipalle, Claudia Kutter, Sergey A. Ponomarev, Lisa S. Westerberg
Science Advances, 2023
The next steps of deep space exploration are manned missions to Moon and Mars. For safe space missions for crew members, it is important to understand the impact of space flight on the immune system. We studied the effects of 21 days dry immersion (DI) exposure on the transcriptomes of T cells isolated from blood samples of eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14, and 21 during DI, and 7 days after DI. RNA sequencing of CD3 + T cells revealed transcriptional alterations across all time points, with most changes occurring 14 days after DI exposure. At day 21, T cells showed evidence of adaptation with a transcriptional profile resembling that of 7 days before DI. At 7 days after DI, T cells again changed their transcriptional profile. These data suggest that T cells adapt by rewiring their transcriptomes in response to simulated weightlessness and that remodeling cues persist when reexposed to normal gravity.
Molecular programming modulates hepatic lipid metabolism and adult metabolic risk in the offspring of obese mothers in a sex-specific manner
Christina Savva, Luisa A. Helguero, Marcela González-Granillo, Tânia Melo, Daniela Couto, Bo Angelin, Maria Rosário Domingues, Xidan Li, Claudia Kutter, Marion Korach-André
Communications Biology, 2022
Male and female offspring of obese mothers are known to differ extensively in their metabolic adaptation and later development of complications. We investigate the sex-dependent responses in obese offspring mice with maternal obesity, focusing on changes in liver glucose and lipid metabolism. Here we show that maternal obesity prior to and during gestation leads to hepatic steatosis and inflammation in male offspring, while female offspring are protected. Females from obese mothers display important changes in hepatic transcriptional activity and triglycerides profile which may prevent the damaging effects of maternal obesity compared to males. These differences are sustained later in life, resulting in a better metabolic balance in female offspring. In conclusion, sex and maternal obesity drive differently transcriptional and posttranscriptional regulation of major metabolic processes in offspring liver, explaining the sexual dimorphism in obesity-associated metabolic risk.
Noncoding RNAs and RNA-binding proteins: emerging governors of liver physiology and metabolic diseases
Christian Sommerauer, Claudia Kutter
American Journal of Physiology Cell Physiology, 2022
Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells
Keyi Geng, Lara G. Merino, Linda Wedemann, Aniek Martens, Małgorzata Sobota, Yerma P. Sanchez, Jonas Nørskov Søndergaard, Robert J. White, Claudia Kutter
Genome Research, 2022
Myeloid cell-specific topoisomerase 1 inhibition using DNA origami mitigates neuroinflammation
Keying Zhu, Yang Wang, Heela Sarlus, Keyi Geng, Erik Nutma, Jingxian Sun, Shin‐Yu Kung, Cindy Bay, Jinming Han, Jin‐Hong Min, Irene Benito‐Cuesta, Harald Lund, Sandra Amor, Jun Wang, Xing‐Mei Zhang, Claudia Kutter, André Ortlieb Guerreiro‐Cacais, Björn Högberg, Robert A Harris
EMBO Reports, 2022
FOXO1 and FOXO3 Cooperatively Regulate Innate Lymphoid Cell Development
Thuy T. Luu, Jonas Nørskov Søndergaard, Lucía Peña-Pérez, Shabnam Kharazi, Aleksandra Krstic, Stephan Meinke, Laurent Schmied, Nicolai Frengen, Yaser Heshmati, Marcin Kierczak, Thibault Bouderlique, Arnika Kathleen Wagner, Charlotte Gustafsson, Benedict J. Chambers, Adnane Achour, Claudia Kutter, Petter Höglund, Robert Månsson, Nadir Kadri
Frontiers in Immunology, 2022
Inhibition of Respiratory Syncytial Virus Infection by Small Non-Coding RNA Fragments
Sandra Axberg Pålsson, Vaishnovi Sekar, Claudia Kutter, Marc R. Friedländer, Anna-Lena Spetz
International Journal of Molecular Sciences, 2022
ZFP207 sustains pluripotency by coordinating OCT4 stability, alternative splicing and RNA export
Sandhya Malla, Devi Prasad Bhattarai, Paula Groza, Dario Melguizo‐Sanchis, Ionut Atanasoai, Carlos Martinez‐Gamero, Ángel‐Carlos Román, Dandan Zhu, Dung‐Fang Lee, Claudia Kutter, Francesca Aguilo
EMBO Reports, 2022
Cell type-specific analysis by single-cell profiling identifies a stable mammalian tRNA-mRNA interface and increased translation efficiency in neurons
William Gao, Carlos J. Gallardo-Dodd, Claudia Kutter
Genome Research, 2022
Expression Profiles of Estrogen-Regulated MicroRNAs in Cancer Cells
Amena Archer, Claudia Kutter, Cecilia Williams
Methods in Molecular Biology, 2022
CCT3-LINC00326 axis regulates hepatocarcinogenic lipid metabolism
Jonas Nørskov Søndergaard, Christian Sommerauer, Ionut Atanasoai, Laura C Hinte, Keyi Geng, Giulia Guiducci, Lars Bräutigam, Myriam Aouadi, Lovorka Stojic, Isabel Barragan, Claudia Kutter
Gut, 2022
Obese mother offspring have hepatic lipidic modulation that contributes to sex-dependent metabolic adaptation later in life
Christina Savva, Luisa A. Helguero, Marcela González-Granillo, Daniela Couto, Tânia Melo, Xidan Li, Bo Angelin, Maria Rosário Domingues, Claudia Kutter, Marion Korach-André
Communications Biology, 2021
Genome Size Reduction and Transposon Activity Impact tRNA Gene Diversity While Ensuring Translational Stability in Birds
Jente Ottenburghs, Keyi Geng, Alexander Suh, Claudia Kutter
Genome Biology and Evolution, 2021
Chenodeoxycholic Acid Modulates Bile Acid Synthesis Independent of Fibroblast Growth Factor 19 in Primary Human Hepatocytes
Helene Johansson, Jonas Nørskov Søndergaard, Carl Jorns, Claudia Kutter, Ewa C. S. Ellis
Frontiers in Endocrinology, 2021
Author Correction: Liver macrophages regulate systemic metabolism through non-inflammatory factors (Nature Metabolism, (2019), 1, 4, (445-459), 10.1038/s42255-019-0044-9)
Cecilia Morgantini, Jennifer Jager, Xidan Li, Laura Levi, Valerio Azzimato, André Sulen, Emelie Barreby, Connie Xu, Michaela Tencerova, Erik Näslund, Chanchal Kumar, Francisco Verdeguer, Sara Straniero, Kjell Hultenby, Niklas K. Björkström, Ewa Ellis, Mikael Rydén, Claudia Kutter, Tracey Hurrell, Volker M. Lauschke, Jeremie Boucher, Aleš Tomčala, Gabriela Krejčová, Adam Bajgar, Myriam Aouadi
Nature Metabolism, 2021
5´XP sRNA-seq: efficient identification of transcripts with and without 5´ phosphorylation reveals evolutionary conserved small RNA
Unn Kugelberg, Daniel Nätt, Signe Skog, Claudia Kutter, Anita Öst
RNA Biology, 2021
High expression of linc01268 is positively associated with hepatocellular carcinoma progression via regulating map3k7
Xiuli Jin, Weixin Fu, Dan Li, Ningning Wang, Jiayu Chen, Zilu Zeng, Jiaqi Guo, Hao Liu, Xinping Zhong, Hu Peng, Xin Yu, Jing Sun, Xinhe Zhang, Xue Wang, Beibei Xu, Yingbo Lin, Jianping Liu, Claudia Kutter, Yiling Li
Oncotargets and Therapy, 2021
JAK inhibition reduces SARS-CoV-2 liver infectivity and modulates inflammatory responses to reduce morbidity and mortality
Justin Stebbing, Ginés Sánchez Nievas, Marco Falcone, Sonia Youhanna, Peter Richardson, Silvia Ottaviani, Joanne X. Shen, Christian Sommerauer, Giusy Tiseo, Lorenzo Ghiadoni, Agostino Virdis, Fabio Monzani, Luis Romero Rizos, Francesco Forfori, Almudena Avendaño Céspedes, Salvatore De Marco, Laura Carrozzi, Fabio Lena, Pedro Manuel Sánchez-Jurado, Leonardo Gianluca Lacerenza, Nencioni Cesira, David Caldevilla Bernardo, Antonio Perrella, Laura Niccoli, Lourdes Sáez Méndez, Daniela Matarrese, Delia Goletti, Yee-Joo Tan, Vanessa Monteil, George Dranitsaris, Fabrizio Cantini, Alessio Farcomeni, Shuchismita Dutta, Stephen K. Burley, Haibo Zhang, Mauro Pistello, William Li, Marta Mas Romero, Fernando Andrés Pretel, Rafaela Sánchez Simón-Talero, Rafael García-Molina, Claudia Kutter, James H. Felce, Zehra F. Nizami, Andras G. Miklosi, Josef M. Penninger, Francesco Menichetti, Ali Mirazimi, Pedro Abizanda, Volker M. Lauschke
Science Advances, 2021
Successful delivery of large-size CRISPR/Cas9 vectors in hard-to-transfect human cells using small plasmids
Jonas Nørskov Søndergaard, Keyi Geng, Christian Sommerauer, Ionut Atanasoai, Xiushan Yin, Claudia Kutter
Communications Biology, 2020
A comprehensive analysis of coding and non-coding transcriptomic changes in cutaneous squamous cell carcinoma
Kunal Das Mahapatra, Lorenzo Pasquali, Jonas Nørskov Søndergaard, Jan Lapins, István Balazs Nemeth, Eszter Baltás, Lajos Kemény, Bernhard Homey, Liviu-Ionut Moldovan, Jørgen Kjems, Claudia Kutter, Enikö Sonkoly, Lasse Sommer Kristensen, Andor Pivarcsi
Scientific Reports, 2020
Liver macrophages regulate systemic metabolism through non-inflammatory factors
Cecilia Morgantini, Jennifer Jager, Xidan Li, Laura Levi, Valerio Azzimato, André Sulen, Emelie Barreby, Connie Xu, Michaela Tencerova, Erik Näslund, Chanchal Kumar, Francisco Verdeguer, Sara Straniero, Kjell Hultenby, Niklas K. Björkström, Ewa Ellis, Mikael Rydén, Claudia Kutter, Tracey Hurrell, Volker M. Lauschke, Jeremie Boucher, Aleš Tomčala, Gabriela Krejčová, Adam Bajgar, Myriam Aouadi
Nature Metabolism, 2019
Author Correction: Liver macrophages regulate systemic metabolism through non-inflammatory factors (Nature Metabolism, (2019), 1, 4, (445-459), 10.1038/s42255-019-0044-9)
Cecilia Morgantini, Jennifer Jager, Xidan Li, Laura Levi, Valerio Azzimato, André Sulen, Emelie Barreby, Connie Xu, Michaela Tencerova, Erik Näslund, Chanchal Kumar, Francisco Verdeguer, Sara Straniero, Kjell Hultenby, Niklas K. Björkström, Ewa Ellis, Mikael Rydén, Claudia Kutter, Tracey Hurrell, Volker M. Lauschke, Jeremie Boucher, Aleš Tomčala, Gabriela Krejčová, Adam Bajgar, Myriam Aouadi
Nature Metabolism, 2019
Bridging gaps in transposable element research with single-molecule and single-cell technologies
Claudia Kutter, Patric Jern, Alexander Suh
Mobile DNA, 2018
The emergence of piRNAs against transposon invasion to preserve mammalian genome integrity
Christina Ernst, Duncan T. Odom, Claudia Kutter
Nature Communications, 2017
Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosis
Christina Ernst, Jeremy Pike, Sarah J Aitken, Hannah K Long, Nils Eling, Lovorka Stojic, Michelle C Ward, Frances Connor, Timothy F Rayner, Margus Lukk, Robert J Klose, Claudia Kutter, Duncan T Odom
Elife, 2016
Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States
Konrad L. M. Rudolph, Bianca M. Schmitt, Diego Villar, Robert J. White, John C. Marioni, Claudia Kutter, Duncan T. Odom
Plos Genetics, 2016
High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface
Bianca M. Schmitt, Konrad L.M. Rudolph, Panagiota Karagianni, Nuno A. Fonseca, Robert J. White, Iannis Talianidis, Duncan T. Odom, John C. Marioni, Claudia Kutter
Genome Research, 2014
Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways
Benoit Ballester, Alejandra Medina-Rivera, Dominic Schmidt, Mar Gonzàlez-Porta, Matthew Carlucci, Xiaoting Chen, Kyle Chessman, Andre J Faure, Alister PW Funnell, Angela Goncalves, Claudia Kutter, Margus Lukk, Suraj Menon, William M McLaren, Klara Stefflova, Stephen Watt, Matthew T Weirauch, Merlin Crossley, John C Marioni, Duncan T Odom, Paul Flicek, Michael D Wilson
Elife, 2014
Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders
Sandra Blanco, Sabine Dietmann, Joana V Flores, Shobbir Hussain, Claudia Kutter, Peter Humphreys, Margus Lukk, Patrick Lombard, Lucas Treps, Martyna Popis, Stefanie Kellner, Sabine M Hölter, Lillian Garrett, Wolfgang Wurst, Lore Becker, Thomas Klopstock, Helmut Fuchs, Valerie Gailus‐Durner, Martin Hrabĕ de Angelis, Ragnhildur T Káradóttir, Mark Helm, Jernej Ule, Joseph G Gleeson, Duncan T Odom, Michaela Frye
EMBO Journal, 2014
Global Gene Expression Profiling Reveals SPINK1 as a Potential Hepatocellular Carcinoma Marker
Aileen Marshall, Margus Lukk, Claudia Kutter, Susan Davies, Graeme Alexander, Duncan T. Odom
Plos One, 2013
Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates
Hannah K Long, David Sims, Andreas Heger, Neil P Blackledge, Claudia Kutter, Megan L Wright, Frank Grützner, Duncan T Odom, Roger Patient, Chris P Ponting, Robert J Klose
Elife, 2013
Latent Regulatory Potential of Human-Specific Repetitive Elements
Michelle C. Ward, Michael D. Wilson, Nuno L. Barbosa-Morais, Dominic Schmidt, Rory Stark, Qun Pan, Petra C. Schwalie, Suraj Menon, Margus Lukk, Stephen Watt, David Thybert, Claudia Kutter, Kristina Kirschner, Paul Flicek, Benjamin J. Blencowe, Duncan T. Odom
Molecular Cell, 2013
The evolutionary landscape of alternative splicing in vertebrate species
Nuno L. Barbosa-Morais, Manuel Irimia, Qun Pan, Hui Y. Xiong, Serge Gueroussov, Leo J. Lee, Valentina Slobodeniuc, Claudia Kutter, Stephen Watt, Recep Çolak, TaeHyung Kim, Christine M. Misquitta-Ali, Michael D. Wilson, Philip M. Kim, Duncan T. Odom, Brendan J. Frey, Benjamin J. Blencowe
Science, 2012
Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines
Matthew P. A. Davis, Cei Abreu-Goodger, Stijn van Dongen, Dong Lu, Peri H. Tate, Nenad Bartonicek, Claudia Kutter, Pentao Liu, William C. Skarnes, Anton J. Enright, Ian Dunham
Plos One, 2012
Rapid turnover of long noncoding RNAs and the evolution of gene expression
Claudia Kutter, Stephen Watt, Klara Stefflova, Michael D. Wilson, Angela Goncalves, Chris P. Ponting, Duncan T. Odom, Ana C. Marques
Plos Genetics, 2012
Erratum: Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages (Cell (2012) 148 (335-348))
Dominic Schmidt, Petra C. Schwalie, Michael D. Wilson, Benoit Ballester, Ângela Gonçalves, Claudia Kutter, Gordon D. Brown, Aileen Marshall, Paul Flicek, Duncan T. Odom
Cell, 2012
Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages
Dominic Schmidt, Petra C. Schwalie, Michael D. Wilson, Benoit Ballester, Ângela Gonçalves, Claudia Kutter, Gordon D. Brown, Aileen Marshall, Paul Flicek, Duncan T. Odom
Cell, 2012
Role of cis-12-Oxo-phytodienoic acid in tomato embryo development
Stephan Goetz, Anja Hellwege, Irene Stenzel, Claudia Kutter, Valeska Hauptmann, Susanne Forner, Bonnie McCaig, Gerd Hause, Otto Miersch, Claus Wasternack, Bettina Hause
Plant Physiology, 2012
Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes
Claudia Kutter, Gordon D Brown, Ângela Gonçalves, Michael D Wilson, Stephen Watt, Alvis Brazma, Robert J White, Duncan T Odom
Nature Genetics, 2011
miR393 and secondary siRNAs regulate expression of the TIR1/AFB2 auxin receptor clade and auxin-related development of Arabidopsis leaves
Azeddine Si-Ammour, David Windels, Estelle Arn-Bouldoires, Claudia Kutter, Jérôme Ailhas, Frederick Meins, Franck Vazquez
Plant Physiology, 2011
Five-vertebrate ChlP-seq reveals the evolutionary dynamics of transcription factor binding
Dominic Schmidt, Michael D. Wilson, Benoit Ballester, Petra C. Schwalie, Gordon D. Brown, Aileen Marshall, Claudia Kutter, Stephen Watt, Celia P. Martinez-Jimenez, Sarah Mackay, Iannis Talianidis, Paul Flicek, Duncan T. Odom
Science, 2010
Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression
Anna Git, Heidi Dvinge, Mali Salmon-Divon, Michelle Osborne, Claudia Kutter, James Hadfield, Paul Bertone, Carlos Caldas
RNA, 2010
miRNA, siRNA, piRNA: Knowns of the unknown
Claudia Kutter, Petr Svoboda
RNA Biology, 2008
MicroRNA-mediated regulation of stomatal development in Arabidopsis
Claudia Kutter, Hanspeter Schöb, Michael Stadler, Frederick Meins, Azeddine Si-Ammour
Plant Cell, 2007
MicroRNA-mediated regulation of stomatal development in Arabidopsis (Plant Cell (2007) 19, (2417-2429))
Plant Cell, 2007
The wound response in tomato - Role of jasmonic acid
Claus Wasternack, Irene Stenzel, Bettina Hause, Gerd Hause, Claudia Kutter, Helmut Maucher, Jana Neumerkel, Ivo Feussner, Otto Miersch
Journal of Plant Physiology, 2006
Molecular characterization of geminivirus-derived small RNAs in different plant species
R. Akbergenov
Nucleic Acids Research, 2006
Capacity of Salvinia minima baker to tolerate and accumulate As and Pb
T. Hoffmann, C. Kutter, J. Santamaría
Engineering in Life Sciences, 2004
Enzymes of jasmonate biosynthesis occur in tomato sieve elements
Bettina Hause, Gerd Hause, Claudia Kutter, Otto Miersch, Claus Wasternack
Plant and Cell Physiology, 2003

Claudia Kutter

EDUCATION

RESEARCH INTERESTS

Scopus Publications

RECENT SCHOLAR PUBLICATIONS

MOST CITED SCHOLAR PUBLICATIONS