Research Groups


Publications of Kathi Zarnack (Results: 49)


Functional RNA Dynamics Are Progressively Governed by RNA Destabilization during the Adaptation to Chronic Hypoxia.
International journal of molecular sciences
Bauer R, Meyer SP, Kloss KA, Guerrero Ruiz VM, Reuscher S, Zhou Y, Fuhrmann DC, Zarnack K, Schmid T, Brüne B PubMed
May 2022 Volume: 23 Issue: 10 Pages:

Disruption of Prostaglandin E2 Signaling in Cancer-Associated Fibroblasts Limits Mammary Carcinoma Growth but Promotes Metastasis.
Cancer research
Elwakeel E, Brüggemann M, Wagih J, Lityagina O, Elewa MAF, Han Y, Frömel T, Popp R, Nicolas AM, Schreiber Y, Gradhand E, Thomas D, Nüsing R, Steinmetz-Späh J, Savai R, Fokas E, Fleming I, Greten FR, Zarnack K, Brüne B, Weigert A PubMed
04 2022 Volume: 82 Issue: 7 Pages: 1380-1395

Bioinformatics in theory and application - highlights of the 36th German Conference on Bioinformatics.
Biological chemistry
Koch I, Andrade-Navarro M, Schulz MH, Zarnack K PubMed
06 2021 Volume: 402 Issue: 8 Pages: 869-870

Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts.
Genome biology
Schulz L, Torres-Diz M, Cortés-López M, Hayer KE, Asnani M, Tasian SK, Barash Y, Sotillo E, Zarnack K, König J, Thomas-Tikhonenko A PubMed
06 2021 Volume: 22 Issue: 1 Pages: 190

Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning.
Nucleic acids research
Körtel N, Rücklé C, Zhou Y, Busch A, Hoch-Kraft P, Sutandy FXR, Haase J, Pradhan M, Musheev M, Ostareck D, Ostareck-Lederer A, Dieterich C, Hüttelmaier S, Niehrs C, Rausch O, Dominissini D, König J, Zarnack K PubMed
09 2021 Volume: 49 Issue: 16 Pages: e92

SRSF3 and SRSF7 modulate 3'UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels.
Genome biology
Schwich OD, Blümel N, Keller M, Wegener M, Setty ST, Brunstein ME, Poser I, Mozos IRL, Suess B, Münch C, McNicoll F, Zarnack K, Müller-McNicoll M PubMed
03 2021 Volume: 22 Issue: 1 Pages: 82

The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cells.
Life science alliance
Alvelos MI, Brüggemann M, Sutandy FR, Juan-Mateu J, Colli ML, Busch A, Lopes M, Castela Â, Aartsma-Rus A, König J, Zarnack K, Eizirik DL PubMed
03 2021 Volume: 4 Issue: 3 Pages:

Dynamic mRNP Remodeling in Response to Internal and External Stimuli.
Zarnack K, Balasubramanian S, Gantier MP, Kunetsky V, Kracht M, Schmitz ML, Sträßer K PubMed
09 2020 Volume: 10 Issue: 9 Pages:

Exon Definition Facilitates Reliable Control of Alternative Splicing in the RON Proto-Oncogene.
Biophysical journal
Enculescu M, Braun S, Thonta Setty S, Busch A, Zarnack K, König J, Legewie S PubMed
04 2020 Volume: 118 Issue: 8 Pages: 2027-2041

High-throughput approaches in RNA biology.
Methods (San Diego, Calif.)
König J, Zarnack K PubMed
06 2020 Volume: 178 Issue: Pages: 1-2

An autoinhibitory intramolecular interaction proof-reads RNA recognition by the essential splicing factor U2AF2.
Proceedings of the National Academy of Sciences of the United States of America
Kang HS, Sánchez-Rico C, Ebersberger S, Sutandy FXR, Busch A, Welte T, Stehle R, Hipp C, Schulz L, Buchbender A, Zarnack K, König J, Sattler M PubMed
03 2020 Volume: 117 Issue: 13 Pages: 7140-7149

Muscleblind-like 2 controls the hypoxia response of cancer cells.
RNA (New York, N.Y.)
Fischer S, Di Liddo A, Taylor K, Gerhardus JS, Sobczak K, Zarnack K, Weigand JE PubMed
05 2020 Volume: 26 Issue: 5 Pages: 648-663

Polypyrimidine tract-binding proteins are essential for B cell development.
Monzón-Casanova E, Matheson LS, Tabbada K, Zarnack K, Smith CW, Turner M PubMed
02 2020 Volume: 9 Issue: Pages:

Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation.
PLoS genetics
Dold A, Han H, Liu N, Hildebrandt A, Brüggemann M, Rücklé C, Hänel H, Busch A, Beli P, Zarnack K, König J, Roignant JY, Lasko P PubMed
01 2020 Volume: 16 Issue: 1 Pages: e1008581

iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites.
Methods (San Diego, Calif.)
Busch A, Brüggemann M, Ebersberger S, Zarnack K PubMed
06 2020 Volume: 178 Issue: Pages: 49-62

The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation.
Genome biology
Hildebrandt A, Brüggemann M, Rücklé C, Boerner S, Heidelberger JB, Busch A, Hänel H, Voigt A, Möckel MM, Ebersberger S, Scholz A, Dold A, Schmid T, Ebersberger I, Roignant JY, Zarnack K, König J, Beli P PubMed
10 2019 Volume: 20 Issue: 1 Pages: 216

A combined computational pipeline to detect circular RNAs in human cancer cells under hypoxic stress.
Journal of molecular cell biology
Di Liddo A, de Oliveira Freitas Machado C, Fischer S, Ebersberger S, Heumüller AW, Weigand JE, Müller-McNicoll M, Zarnack K PubMed
10 2019 Volume: 11 Issue: 10 Pages: 829-844

uORF-Tools-Workflow for the determination of translation-regulatory upstream open reading frames.
PloS one
Scholz A, Eggenhofer F, Gelhausen R, Grüning B, Zarnack K, Brüne B, Backofen R, Schmid T PubMed
2019 Volume: 14 Issue: 9 Pages: e0222459

Phenotypic Plasticity of Fibroblasts during Mammary Carcinoma Development.
International journal of molecular sciences
Elwakeel E, Brüggemann M, Fink AF, Schulz MH, Schmid T, Savai R, Brüne B, Zarnack K, Weigert A PubMed
Sep 2019 Volume: 20 Issue: 18 Pages:

The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs.
EMBO reports
Olgeiser L, Haag C, Boerner S, Ule J, Busch A, Koepke J, König J, Feldbrügge M, Zarnack K PubMed
01 2019 Volume: 20 Issue: 1 Pages:

Membrane-Associated RNA-Binding Proteins Orchestrate Organelle-Coupled Translation.
Trends in cell biology
Béthune J, Jansen RP, Feldbrügge M, Zarnack K PubMed
02 2019 Volume: 29 Issue: 2 Pages: 178-188

Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis.
Nature communications
Braun S, Enculescu M, Setty ST, Cortés-López M, de Almeida BP, Sutandy FXR, Schulz L, Busch A, Seiler M, Ebersberger S, Barbosa-Morais NL, Legewie S, König J, Zarnack K PubMed
08 2018 Volume: 9 Issue: 1 Pages: 3315

High-Throughput Screens for cis-Acting RNA Sequence Elements That Promote Nuclear Retention.
Zarnack K, Müller-McNicoll M PubMed
07 2018 Volume: 57 Issue: 26 Pages: 3542-3543

In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors.
Genome research
Sutandy FXR, Ebersberger S, Huang L, Busch A, Bach M, Kang HS, Fallmann J, Maticzka D, Backofen R, Stadler PF, Zarnack K, Sattler M, Legewie S, König J PubMed
05 2018 Volume: 28 Issue: 5 Pages: 699-713

Interaction profiling of RNA-binding ubiquitin ligases reveals a link between posttranscriptional regulation and the ubiquitin system.
Scientific reports
Hildebrandt A, Alanis-Lobato G, Voigt A, Zarnack K, Andrade-Navarro MA, Beli P, König J PubMed
11 2017 Volume: 7 Issue: 1 Pages: 16582

Erratum to: Insights into the design and interpretation of iCLIP experiments.
Genome biology
Haberman N, Huppertz I, Attig J, König J, Wang Z, Hauer C, Hentze MW, Kulozik AE, Le Hir H, Curk T, Sibley CR, Zarnack K, Ule J PubMed
08 2017 Volume: 18 Issue: 1 Pages: 154

Cellular differentiation state modulates the mRNA export activity of SR proteins.
The Journal of cell biology
Botti V, McNicoll F, Steiner MC, Richter FM, Solovyeva A, Wegener M, Schwich OD, Poser I, Zarnack K, Wittig I, Neugebauer KM, Müller-McNicoll M PubMed
07 2017 Volume: 216 Issue: 7 Pages: 1993-2009

Differential Binding of Mitochondrial Transcripts by MRB8170 and MRB4160 Regulates Distinct Editing Fates of Mitochondrial mRNA in Trypanosomes.
Dixit S, Müller-McNicoll M, David V, Zarnack K, Ule J, Hashimi H, Lukeš J PubMed
01 2017 Volume: 8 Issue: 1 Pages:

Insights into the design and interpretation of iCLIP experiments.
Genome biology
Haberman N, Huppertz I, Attig J, König J, Wang Z, Hauer C, Hentze MW, Kulozik AE, Le Hir H, Curk T, Sibley CR, Zarnack K, Ule J PubMed
01 2017 Volume: 18 Issue: 1 Pages: 7

Splicing repression allows the gradual emergence of new Alu-exons in primate evolution.
Attig J, Ruiz de Los Mozos I, Haberman N, Wang Z, Emmett W, Zarnack K, König J, Ule J PubMed
11 2016 Volume: 5 Issue: Pages:

SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export.
Genes & development
Müller-McNicoll M, Botti V, de Jesus Domingues AM, Brandl H, Schwich OD, Steiner MC, Curk T, Poser I, Zarnack K, Neugebauer KM PubMed
Mar 2016 Volume: 30 Issue: 5 Pages: 553-66

Recognition of distinct RNA motifs by the clustered CCCH zinc fingers of neuronal protein Unkempt.
Nature structural & molecular biology
Murn J, Teplova M, Zarnack K, Shi Y, Patel DJ PubMed
Jan 2016 Volume: 23 Issue: 1 Pages: 16-23

Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends.
Nucleic acids research
Tajnik M, Vigilante A, Braun S, Hänel H, Luscombe NM, Ule J, Zarnack K, König J PubMed
Dec 2015 Volume: 43 Issue: 21 Pages: 10492-505

Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt.
Genes & development
Murn J, Zarnack K, Yang YJ, Durak O, Murphy EA, Cheloufi S, Gonzalez DM, Teplova M, Curk T, Zuber J, Patel DJ, Ule J, Luscombe NM, Tsai LH, Walsh CA, Shi Y PubMed
Mar 2015 Volume: 29 Issue: 5 Pages: 501-12

The RNA-binding protein HuR is essential for the B cell antibody response.
Nature immunology
Diaz-Muñoz MD, Bell SE, Fairfax K, Monzon-Casanova E, Cunningham AF, Gonzalez-Porta M, Andrews SR, Bunik VI, Zarnack K, Curk T, Heggermont WA, Heymans S, Gibson GE, Kontoyiannis DL, Ule J, Turner M PubMed
Apr 2015 Volume: 16 Issue: 4 Pages: 415-25

Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements.
Zarnack K, König J, Tajnik M, Martincorena I, Eustermann S, Stévant I, Reyes A, Anders S, Luscombe NM, Ule J PubMed
Jan 2013 Volume: 152 Issue: 3 Pages: 453-66

Protein-RNA interactions: new genomic technologies and perspectives.
Nature reviews. Genetics
König J, Zarnack K, Luscombe NM, Ule J PubMed
Jan 2012 Volume: 13 Issue: 2 Pages: 77-83

Analysis of alternative splicing associated with aging and neurodegeneration in the human brain.
Genome research
Tollervey JR, Wang Z, Hortobágyi T, Witten JT, Zarnack K, Kayikci M, Clark TA, Schweitzer AC, Rot G, Curk T, Zupan B, Rogelj B, Shaw CE, Ule J PubMed
Oct 2011 Volume: 21 Issue: 10 Pages: 1572-82

The RNA-binding protein Rrm4 is essential for efficient secretion of endochitinase Cts1.
Molecular & cellular proteomics : MCP
Koepke J, Kaffarnik F, Haag C, Zarnack K, Luscombe NM, König J, Ule J, Kellner R, Begerow D, Feldbrügge M PubMed
Dec 2011 Volume: 10 Issue: 12 Pages: M111.011213

iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution.
Journal of visualized experiments : JoVE
Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J PubMed
Apr 2011 Volume: Issue: 50 Pages:

iCLIP predicts the dual splicing effects of TIA-RNA interactions.
PLoS biology
Wang Z, Kayikci M, Briese M, Zarnack K, Luscombe NM, Rot G, Zupan B, Curk T, Ule J PubMed
Oct 2010 Volume: 8 Issue: 10 Pages: e1000530

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution.
Nature structural & molecular biology
König J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J PubMed
Jul 2010 Volume: 17 Issue: 7 Pages: 909-15

Microtubule-dependent mRNA transport in fungi.
Eukaryotic cell
Zarnack K, Feldbrügge M PubMed
Jul 2010 Volume: 9 Issue: 7 Pages: 982-90

Tandem KH domains of Khd4 recognize AUACCC and are essential for regulation of morphology as well as pathogenicity in Ustilago maydis.
RNA (New York, N.Y.)
Vollmeister E, Haag C, Zarnack K, Baumann S, König J, Mannhaupt G, Feldbrügge M PubMed
Dec 2009 Volume: 15 Issue: 12 Pages: 2206-18

The fungal RNA-binding protein Rrm4 mediates long-distance transport of ubi1 and rho3 mRNAs.
The EMBO journal
König J, Baumann S, Koepke J, Pohlmann T, Zarnack K, Feldbrügge M PubMed
Jul 2009 Volume: 28 Issue: 13 Pages: 1855-66

Pheromone-regulated target genes respond differentially to MAPK phosphorylation of transcription factor Prf1.
Molecular microbiology
Zarnack K, Eichhorn H, Kahmann R, Feldbrügge M PubMed
Aug 2008 Volume: 69 Issue: 4 Pages: 1041-53

The posttranscriptional machinery of Ustilago maydis.
Fungal genetics and biology : FG & B
Feldbrügge M, Zarnack K, Vollmeister E, Baumann S, Koepke J, König J, Münsterkötter M, Mannhaupt G PubMed
Aug 2008 Volume: 45 Suppl 1 Issue: Pages: S40-6

mRNA trafficking in fungi.
Molecular genetics and genomics : MGG
Zarnack K, Feldbrügge M PubMed
Oct 2007 Volume: 278 Issue: 4 Pages: 347-59

Tetracycline-regulated gene expression in the pathogen Ustilago maydis.
Fungal genetics and biology : FG & B
Zarnack K, Maurer S, Kaffarnik F, Ladendorf O, Brachmann A, Kämper J, Feldbrügge M PubMed
Nov 2006 Volume: 43 Issue: 11 Pages: 727-38