Publications co-authored by the Genomics Core Facility
2022
Zinina VV, Ruehle F, Winkler P, Rebmann L, Lukas H, Möckel S, Diefenbach A, Mendez-Lago M and Soshnikova N (2022) ID2 controls differentiation of enteroendocrine cells in mouse small intestine. Acta Physiol, 234:e13773 Link
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 elegans. EMBO 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 damage. Nat 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 mutagenesis. Nat 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 function. EMBO 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 development. Cell 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 specification. Dev 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 aging. Genes 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 cofactors. Genome 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 landscapes. Cell 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 cells. Dev 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 cells. Nucleic 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 zebrafish. RNA 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 transition. Oncotarget, 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 development. EMBO 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. Elegans. Genes 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 program. EMBO J, 35: 24-45
Schick S, Becker K, Thakurala S, Fournier D, Hampel MH, Legewie S* and Tiwari VK* (2016) Identifying novel circadian transcriptional regulators. Mol 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 elegans. Dev 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 fate. EMBO 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 damage. J 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 neuroplasticity. Genome 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 elegans. Genes 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 transcript. Genes 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 H3K4me3. Genes 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 expression. Dev Cell, 23: 1032-1042