Publications co-authored by the Genomics Core Facility

2020

Redl S*, de Jesus Domingues AM*, Caspani E, Möckel S, Salvenmoser W, Mendez-Lago M and Ketting RF (2020) Extensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafish. Development, doi: 10.1242/dev.193060 (*indicates joint contribution) Link

Sayols S, Klassek J, Werner C, Möckel S, Ritz S, Mendez-Lago M and Soshnikova N (2020) Signalling codes for the maintenance and lineage commitment of embryonic gastric epithelial progenitors. Development, 147:dev188839 Link

Sriramachandran AM, Petrosino G, Méndez-Lago M, Schäfer AJ, Batista-Nascimento LS, Zilio N# and Ulrich HD# (2020) Genome-wide nucleotide-resolution mapping of DNA replication patterns, single-strand breaks, and lesions by GLOE-Seq. Mol Cell, 78:975-985.e7 (#indicates joint correspondence) Link

2019

Almeida MV, de Jesus Domingues AM, Lukas H, Mendez-Lago M and Ketting RF (2019) RppH can faithfully replace TAP to allow cloning of 5′-triphosphate carrying small RNAs. MethodsX, 6:265–272 Link

Francesconi M, Di Stefano B, Berenguer C, de Andrés-Aguayo L, Plana-Carmona M, Mendez-Lago M, Guillaumet-Adkins A, Rodriguez-Esteban G, Gut M, Gut IG, Heyn H, Lehner B and Graf T (2019) Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming. eLife, 8:e41627 Link

2018

Roovers EF, Kaaij LJT, Redl S, Bronkhorst AW, Wiebrands K, de Jesus Domingues AM, Huang HY, Han CT, Riemer S, Dosch R, Salvenmoser W, Grün D, Butter F, van Oudenaarden A and Ketting RF (2018) Tdrd6a regulates the aggregation of Buc into functional subcellular compartments that drive germ cell specification. Dev Cell, 46:285–301.e9 Link

2017

De Azua IR, Mancini G, Srivastava RK, Rey AA, Cardinal P, Tedesco L, Zingaretti CM, Sassmann A, Quarta C, Schwitter C, Conrad A, Wettschureck N, Vemuri VK, Makriyannis A, Hartwig J, Mendez-Lago M, Bindila L, Monory K, Giordano A, Cinti S, Marsicano G, Offermanns S, Nisoli E, Pagotto U, Cota D and Lutz B. (2017). Adipocyte cannabinoid receptor CB1 regulates energy homeostasis and alternatively activated macrophages. J Clin Invest, 127: 4148–4162 Link

Jahn A*, Rane G*, Paszkowski‐Rogacz M, Sayols S, Bluhm A, Han CT, Draškovič I, Londoño‐Vallejo JA, Kumar AP, Buchholz F#, Butter F# and Kappei D# (2017) ZBTB48 is both a vertebrate telomere‐binding protein and a transcriptional activator. EMBO Rep, 18:929–946 (*indicates joint contribution, #indicates joint correspondence) Link

2016

Volckmar AL*, Han CT*, Pütter C, Haas S, Vogel CIG, Knoll N, Struve C, Göbel M, Haas K, Herrfurth N, Jarick I, Grallert H, Schürmann A, Al-Hasani H, Hebebrand J, Sauer S and Hinney A (2016) Analysis of genes involved in body weight regulation by targeted re-sequencing. PLOS One, 11:e0147904 (*indicates joint contribution) Link

2015

Roovers EF, Rosenkranz D, Mahdipour M, Han CT, He N, Chuva de Sousa Lopes SM, van der Westerlaken LAJ, Zischler H, Butter F, Roelen BAJ and Ketting RF (2015) Piwi proteins and piRNAs in mammalian oocytes and early embryos. Cell Rep, 10:2069–2082 Link

Rosenkranz D, Han CT, Roovers EF, Zischler H and Ketting RF (2015) Piwi proteins and piRNAs in mammalian oocytes and early embryos: From sample to sequence. Genomics Data, 5:309–313 Link

2013

Ammerpohl O, Bens S, Appari M, Werner R, Korn B, Drop SLS, Verheijen F, van der Zwan Y, Bunch T, Hughes I, Cools M, Riepe FG, Hiort O, Siebert R and Holterhus P-M (2013) Androgen receptor function links human sexual dimorphism to DNA methylation. PLOS One, 8:e73288 Link

2012

Wiench B, Eichhorn T, Korn B, Paulsen M and Efferth T (2012) Utilizing inherent fluorescence of therapeutics to analyze real-time uptake and multi-parametric effector kinetics.Methods, 57:376–382 Link

2011

Bartholomae CC, Arens A, Balaggan KS, Yáñez-Muñoz RJ, Montini E, Howe SJ, Paruzynski A, Korn B, Appelt JU, Macneil A, Cesana D, Abel U, Glimm H, Naldini L, Ali RR, Thrasher AJ, von Kalle C and Schmidt M (2011) Lentiviral vector integration profiles differ in rodent postmitotic tissues.Mol Ther, 19:703–710 Link

Breitling LP, Yang R, Korn B, Burwinkel B and Brenner H (2011) Tobacco-smoking-related differential DNA methylation: 27K discovery and replication.Am J Hum Genet, 88:450–457 Link


Publications acknowledging the Genomics Core Facility

2021

Bawankar P*, Lence T*, Paolantoni C*, Haussmann IU, Kazlauskiene M, Jacob D, Heidelberger JB, Richter FM, Nallasivan MP, Morin V, Kreim N, Beli P, Helm M, Jinek M, Soller M# and Roignant JY# (2021) Hakai is required for stabilization of core components of the m6A mRNA methylation machinery. Nat Commun, 12:3778 (*indicates joint contribution, #indicates joint correspondence)

Chongtham MC, Butto T, Mungikar K, Gerber S and Winter J (2021) INTACT vs. FANS for cell-type-specific nuclei sorting: a comprehensive qualitative and quantitative comparison. Int J Mol Sci, 22:5335

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# and Zarnack K# (2021) Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning. Nucleic Acids Res, doi: 10.1093/nar/gkab485 (*indicates joint contribution, #indicates joint correspondence)

Perez-Borrajero C, Podvalnaya N*, Holleis K*, Lichtenberger R, Karaulanov E, Simon B, Basquin J, Hennig J#, Ketting RF# and Falk S# (2021) Structural basis of PETISCO complex assembly during piRNA biogenesis in C. elegans. Genes Dev, 35:1304-1323 (*indicates joint contribution, #indicates joint correspondence)

Placentino M, Jesus Domingues AM, Schreier J, Dietz S, Hellmann S, Albuquerque BF, Butter F and Ketting RF (2021) Intrinsically disordered protein PID‐2 modulates Z granules and is required for heritable piRNA‐induced silencing in the Caenorhabditis elegans embryo. EMBO J, 40:e105280

Worpenberg L, Paolantoni C, Longhi S, Mulorz MM, Lence T, Wessels HH, Dassi E, Aiello G, Sutandy FXR, Scheibe M, Edupuganti RR, Busch A, Möckel MM, Vermeulen M, Butter F, König J, Notarangelo M, Ohler U, Dieterich C, Quattrone A#, Soldano A# and Roignant JY# (2021) Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila.EMBO J, 40:e104975 (#indicates joint correspondence)

2020

Buchbender A, Mutter H, Sutandy FXR, Körtel N, Hänel H, Busch A, Ebersberger S and König J (2020) Improved library preparation with the new iCLIP2 protocol. Methods, 178:33–48

Dold A*, Han H*, Liu N*, Hildebrandt A, Brüggemann M, Rücklé C, Hänel H, Busch A, Beli P, Zarnack K, König J, Roignant JY# and Lasko P# (2020) Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation. PLOS Genet, 16:e1008581 (*indicates joint contribution, #indicates joint correspondence)

Enculescu M#, Braun S, Thonta Setty S, Busch A, Zarnack K, König J# and Legewie S# (2020) Exon definition facilitates reliable control of alternative splicing in the RON proto-oncogene. Biophys J, 118:2027–2041 (#indicates joint correspondence)

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# and Sattler M# (2020) An autoinhibitory intramolecular interaction proof-reads RNA recognition by the essential splicing factor U2AF2. Proc Natl Acad Sci, 117:7140–7149 (*indicates joint contribution, #indicates joint correspondence)

Petrosino G*, Zilio N*, Sriramachandran AM and Ulrich HD (2020) Preparation and analysis of GLOE-Seq libraries for genome-wide mapping of DNA replication patterns, single-strand breaks, and lesions. STAR Protoc, 1:100076 (*indicates joint contribution)

Vydzhak O*, Bender K*, Klermund J, Busch A, Reimann S and Luke B (2020) Checkpoint adaptation in recombination-deficient cells drives aneuploidy and resistance to genotoxic agents. DNA Repair, 95:102939 (*indicates joint contribution)

2019

Akhtar J, Kreim N, Marini F, Mohana G, Brüne D, Binder H and Roignant JY (2019) Promoter-proximal pausing mediated by the exon junction complex regulates splicing. Nat Commun, 10:521

Aparisi Rey A, Karaulanov E, Sharopov S, Arab K, Schäfer A, Gierl M, Guggenhuber S, Brandes C, Pennella L, Gruhn WH, Jelinek R, Maul C, Conrad A, Kilb W, Luhmann HJ, Niehrs C# and Lutz B# (2019) Gadd45α modulates aversive learning through post‐transcriptional regulation of memory‐related mRNAs. EMBO Rep, 20:e46022 (#indicates joint correspondence)

Arab K, Karaulanov E, Musheev M, Trnka P, Schäfer A, Grummt I# and Niehrs C# (2019) GADD45A binds R-loops and recruits TET1 to CpG island promoters. Nat Genet, 51:217–223 (#indicates joint correspondence)

Auber M, Fröhlich D, Drechsel O, Karaulanov E and Krämer-Albers EM (2019) Serum-free media supplements carry miRNAs that co-purify with extracellular vesicles. J Extracell Vesicles, 8:1656042

Bluhm A, Viceconte N, Li F, Rane G, Ritz S, Wang S, Levin M, Shi Y, Kappei D and Butter F (2019) ZBTB10 binds the telomeric variant repeat TTGGGG and interacts with TRF2. Nucleic Acids Res, 47:1896–1907

Gothe HJ, Bouwman BAM*, Gusmao EG*, Piccinno R, Petrosino G, Sayols S, Drechsel O, Minneker V, Josipovic N, Mizi A, Nielsen CF, Wagner EM, Takeda S, Sasanuma H, Hudson DF, Kindler T, Baranello L, Papantonis A*, Crosetto N* and Roukos V (2019) Spatial chromosome folding and active transcription drive DNA fragility and formation of oncogenic MLL translocations. Mol Cell, 75:267-283.e12 (*indicates joint contribution)

Han D*, Schomacher L*, Schüle KM*, Mallick M, Musheev MU, Karaulanov E, Krebs L, von Seggern A and Niehrs C (2019) NEIL1 and NEIL2 DNA glycosylases protect neural crest development against mitochondrial oxidative stress. eLife, e49044 (*indicates joint contribution)

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# and Beli P# (2019) The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. Genome Biol, 20:216 (#indicates joint correspondence) 

Olgeiser L, Haag C, Boerner S, Ule J, Busch A, Koepke J, König J, Feldbrügge M and Zarnack K (2019) The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs. EMBO Rep, 20:e46588

Schüle KM*, Leichsenring M*, Andreani T, Vastolo V, Mallick M, Musheev MU, Karaulanov E and Niehrs C (2019) GADD45 promotes locus-specific DNA demethylation and 2C cycling in embryonic stem cells. Genes Dev, 33:782–798 (*indicates joint contribution)

2018

Almeida MV, Dietz S, Redl S, Karaulanov E, Hildebrandt A, Renz C, Ulrich HD, König J, Butter F and Ketting RF (2018) GTSF‐1 is required for formation of a functional RNA‐dependent RNA Polymerase complex in Caenorhabditis elegansEMBO J, 37: e99325

Borisova ME, Voigt A, Tollenaere MAX, Sahu SK, Juretschke T, Kreim N, Mailand N, Choudhary C, Bekker-Jensen S, Akutsu M, Wagner SA and Beli P (2018) p38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damageNat Commun, 9: 1017

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 and Zarnack K (2018) Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesisNat Commun, 9: 3315 

Heidelberger JB, Voigt A, Borisova ME, Petrosino G, Ruf S, Wagner SA and Beli P (2018) Proteomic profiling of VCP substrates links VCP to K6‐linked ubiquitylation and c‐Myc functionEMBO Rep, pii: e44754

Kaaij LJT, van der Weide RH, Ketting RF and de Wit E (2018) Systemic loss and gain of chromatin architecture throughout zebrafish developmentCell Rep, 24: 1–10.e4

Knuckles P, Lence T, Haussmann IU, Jacob D, Kreim N, Carl SH, Masiello I, Hares T, Villaseñor R, Hess D, Andrade-Navarro MA, Biggiogera M, Helm M, Soller M, Bühler M and Roignant JY (2018) Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m6A machinery component Wtap/Fl(2)d. Genes Dev, 32:415–429 

Roovers EF, Kaaij LJT, Redl S, Bronkhorst AW, Wiebrands K, de Jesus Domingues AM, Huang HY, Han CT, Riemer S, Dosch R, Salvenmoser W, Grün D, Butter F, van Oudenaarden A and Ketting RF (2018) Tdrd6a regulates the aggregation of buc into functional subcellular compartments that drive germ cell specificationDev Cell, 46: 285–301.e9

Schäfer A, Mekker B, Mallick M, Vastolo V, Karaulanov E, Sebastian D, von der Lippen C, Epe B, Downes DJ, Scholz C and Niehrs C (2018) Impaired DNA demethylation of C/EBP sites causes premature agingGenes Dev, 32: 742–762

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 and König J (2018) In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactorsGenome Res, 28: 699–713 

Tiwari N, Pataskar A, Péron S, Thakurela S, Sahu SK, Figueres-Oñate M, Marichal N, López-Mascaraque L, Tiwari VK and Berninger B (2018) Stage-Specific transcription factors drive astrogliogenesis by remodeling gene regulatory landscapesCell Stem Cell, 23: 557–571.e8

2017

Dinges N, Morin V, Kreim N, Southall TD and Roignant JY (2017) Comprehensive characterization of the complex lola locus reveals a novel role in the octopaminergic pathway via tyramine beta-hydroxylase regulation. Cell Rep, 21:2911–2925

Dzama MM, Nigmatullina L, Sayols S, Kreim N and Soshnikova N (2017) Distinct populations of embryonic epithelial progenitors generate Lgr5+ intestinal stem cellsDev Biol, 432: 258–264

Kazakevych J, Sayols S, Messner B, Krienke C and Soshnikova N (2017) Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cellsNucleic Acids Res, 45: 5770–5784

Lebedeva S, de Jesus Domingues AM, Butter F and Ketting RF (2017) Characterization of genetic loss-of-function of Fus in zebrafishRNA Biol, 14: 29–35

Navandar M, Garding A, Kumar Sahu S, Pataskar A, Schick S and Tiwari VK (2017) ERK signalling modulates epigenome to drive epithelial to mesenchymal transitionOncotarget, 8: 29269–29281

Nigmatullina L, Norkin M, Dzama MM, Messner B, Sayols S and Soshnikova N (2017) Id2 controls specification of Lgr5(+) intestinal stem cell progenitors during gut developmentEMBO J, 36: 869–885

Sahu SK, Tiwari N, Pataskar A, Zhuang Y, Borisova M, Diken M, Strand S, Beli P and Tiwari VK (2017) FBXO32 promotes microenvironment underlying epithelial-mesenchymal transition via CtBP1 during tumour metastasis and brain development. Nat Commun, 8: 1523

Wilhelm T, Byrne J, Medina R, Kolundžić E, Geisinger J, Hajduskova M, Tursun B and Richly H (2017) Neuronal inhibition of the autophagy cucleation complex extends life span in post-reproductive C. ElegansGenes Dev, 31: 1561–1572

2016

Kaaij LJT, Mokry M, Zhou M, Musheev M, Geeven G, Melquiond ASJ, de Jesus Domingues AM, de Laat W, Niehrs C, Smith AD and Ketting RF (2016) Enhancers reside in a unique epigenetic environment during early zebrafish development. Genome Biol, 17:146

Lence T, Akhtar J, Bayer M, Schmid K, Spindler L, Ho CH, Kreim N, Andrade-Navarro MA, Poeck B, Helm M and Roignant JY (2016) m6A modulates neuronal functions and sex determination in Drosophila. Nature, 540:242–247

Papadopoulou T, Kaymak A, Sayols S and Richly H (2016) Dual role of Med12 in PRC1-dependent gene repression and ncRNA-mediated transcriptional activation. Cell Cycle, 15: 1479–1493

Pataskar A, Jung J, Smialowski P, Noack F, Calegari F, Straub T and Tiwari VK (2016) NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal programEMBO J, 35: 24-45

Schick S, Becker K, Thakurala S, Fournier D, Hampel MH, Legewie S* and Tiwari VK* (2016) Identifying novel circadian transcriptional regulatorsMol Cell Biol, 36: 545-58. (*indicates joint contribution)

Thakurela S*, Garding A*, Jung RB, Müller C, Goebbels S, White R, Werner HB# and Tiwari VK# (2016) The transcriptome of mouse central nervous system myelin. Sci Rep, 6: 25828 (*indicates joint contribution, #indicates joint correspondence)

2015

de Albuquerque BF, Placentino M and Ketting RF (2015) Maternal piRNAs are essential for germline development following de-novo establishment of endo-siRNAs in Caenorhabditis elegansDev Cell, 34: 448-56

Sahu SK, Garding A, Tiwari N, Thakurela S, Toedling J, Gebhard S, Ortega F, Schmarowski N, Berninger B, Nitsch R, Schmidt M and Tiwari VK (2015) JNK-dependent gene regulatory circuitry governs mesenchymal fateEMBO J, 34: 2162-2181

Schick S, Fournier D, Thakurela S, Sahu SK, Garding A and Tiwari VK (2015) Dynamics of chromatin accessibility and epigenetic state in response to UV damageJ Cell Sci, 128: 4380-4394

Thakurela S, Sahu SK, Garding A and Tiwari VT (2015) Dynamics and function of distal regulatory elements during neurogenesis and neuroplasticityGenome Res, 25: 1309-1324

2014

de Albuquerque BF, Luteijn MJ, Cordeiro Rodrigues RJ, van Bergeijk P, Waaijers S, Kaaij LJ, Klein H, Boxem M and Ketting RF (2014) PID-1 is a novel factor that operates during 21U-RNA biogenesis in Caenorhabditis elegansGenes Dev, 28: 683-688

Malone CD, Mestdagh C, Akhtar J, Kreim N, Deinhard P, Sachidanandam R, Treisman J and Roignant JY (2014) The exon junction complex controls transposable element activity by ensuring faithful splicing of the piwi transcriptGenes Dev, 28: 1786-1799

2013

Schäfer A, Karaulanov E, Stapf U, Döderlein G and Niehrs C (2013) Ing1 functions in DNA demethylation by directing Gadd45a to H3K4me3Genes Dev, 27: 261-273

2012

Gierl MS, Gruhn WH, von Seggern A, Maltry N, and Niehrs C (2012) GADD45G functions in male sex de-termination by promoting p38 signaling and Sry expressionDev Cell, 23: 1032-1042