Genomics Core Facility

2023

Chan YC*, Kienle E*, Oti M*, Di Liddo A, Mendez-Lago M, Aschauer DF, Peter M, Pagani M, Arnold C, Vonderheit A, Schön C, Kreuz S, Stark A and Rumpel S (2023) An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo. Sci Rep, 13:6745 (*indicates joint contribution) Link

2022

Mkrtchian S, Ebberyd A, Veerman RE, Mendez-Lago M, Gabrielsson S, Eriksson LI and Gómez-Galán M (2022) Surgical trauma in mice modifies the content of circulating extracellular vesicles. Front Immunol, 12:824696 Link

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

2021

Redl S*, de Jesus Domingues AM*, Caspani E, Möckel S, Salvenmoser W, Mendez-Lago M and Ketting RF (2021) 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

2020

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

2024

Arnold B, Riegger RJ, Okuda EK, Slišković I, Keller M, Bakisoglu C, McNicoll F, Zarnack K and Müller-McNicoll M (2024) hGRAD: A versatile "one-fits-all" system to acutely deplete RNA binding proteins from condensates. J Cell Biol, 223:e202304030

Longo GMC*, Sayols S*, Kotini AG, Heinen S, Möckel MM, Beli P and Roukos V (2024) Linking CRISPR-Cas9 double-strand break profiles to gene editing precision with BreakTag. Nat Biotechnol, doi: 10.1038/s41587-024-02238-8 Link  

Schmidt A, Allmann S, Schwarzenbach C, Snyder P, Chen JX, Nagel G, Schöneis A, Rasenberger B, Beli P, Loewer A, Hofmann TG, Tomicic MT and Christmann M (2024) The p21CIP1-CDK4-DREAM axis is a master regulator of genotoxic stress-induced cellular senescence. Nucleic Acids Res, 23:gkae426 

2023

Braun H, Xu Z, Chang F, Viceconte N, Rane G, Levin M, Lototska L, Roth F, Hillairet A, Fradera-Sola A, Khanchandani V, Sin ZW, Yong WK, Dreesen O, Yang Y, Shi Y, Li F, Butter F and Kappei D (2023) ZNF524 directly interacts with telomeric DNA and supports telomere integrity. Nat Commun, 14:8252  

Bronkhorst AW, Lee CY, Möckel MM, Ruegenberg S, de Jesus Dominques AM, Sadouki S, Piccinno R, Sumiyoshi T, Siomi MC, Stelzl L, Luck K and Ketting RF (2023) An extended Tudor domain within Vreteno interconnects Gtsf1L and Ago3 for piRNA biogenesis in Bombyx mori. EMBO J, 42:e114072 

Ebersberger S*, Hipp C*, Mulorz MM*, Buchbender A, Hubrich D, Kang HS, Martínez-Lumbreras S, Kristofori P, Sutandy FXR, Llacsahuanga Allcca L, Schönfeld J, Bakisoglu C, Busch A, Hänel H, Tretow K, Welzel M, Di Liddo A, Möckel MM, Zarnack K, Ebersberger I, Legewie S, Luck K^#, Sattler M^# and König J^# (2023) FUBP1 is a general splicing factor facilitating 3’ splice site recognition and splicing of long introns. Mol Cell, 83:2653–2672.e15 (*indicates joint contribution, ^#indicates joint correspondence)

Fan W, Jurado-Arjona J, Alanis-Lobato G, Péron S, Berger C, Andrade-Navarro MA, Falk S and Berninger B (2023) The transcriptional co-activator Yap1 promotes adult hippocampal neural stem cell activation. EMBO J, 21:e110384

Kalita AI, Marois E*, Kozielska M, Weissing FJ, Jaouen E, Möckel MM, Rühle F, Butter F, Basilicata MF* and Keller Valsecchi CI* (2023) The sex-specific factor SOA controls dosage compensation in Anopheles mosquitos. Nature, 623:175-182 (*indicates joint contribution)

Kong KYE, Shankar S, Rühle F, Khmelinskii A (2022) Orphan quality control by an SCF ubiquitin ligase directed to pervasive C-degrons. Nat Commun, 14:8363 

Podvalnaya N*, Bronkhorst AW*, Lichtenberger R, Hellmann S, Nischwitz E, Falk T, Karaulanov E, Butter F, Falk S^# and Ketting RF^# (2023) piRNA processing by a trimeric Schlafen-domain nuclease. Nature, 622:402-409 (*indicates joint contribution, ^#indicates joint correspondence)

Rücklé C*, Körtel N*, Basilicata MF, Busch A, Zhou Y, Hoch-Kraft P, Tretow K, Kielisch F, Bertin M, Pradhan M, Musheev M, Schweiger S, Niehrs C, Rausch O, Zarnack K, Keller Valsecchi CI and König J (2023) RNA stability controlled by m6A methylation contributes to X-to-autosome dosage compensation in mammals. Nat Struct Mol Biol, 30:1207–1215 (*indicates joint contribution)

Seistrup AS, Choppin M, Govind S, Feldmeyer B, Kever M, Karaulanov E, Séguret A, Karunanithi S, Almeida M V, Ketting RF^# and Foitzik S^# (2023) Age- and caste-independent piRNAs in the germline and miRNA profiles linked to caste and fecundity in the ant Temnothorax rugatulus. Mol Ecol, 32:6027-6043 (^#indicates joint correspondence)

Suryo Rahmanto A, Blum CJ, Scalera C, Heidelberger JB, Mesitov M, Horn-Ghetko D, Gräf JF, Mikicic I, Hobrecht R, Orekhova A, Ostermaier M, Ebersberger S, Möckel MM, Krapoth N, Da Silva Fernandes N, Mizi A, Zhu Y, Chen JX, Choudhary C, Papantonis A, Ulrich HD, Schulman BA, König J and Beli P (2023) K6-linked ubiquitylation marks formaldehyde-induced RNA-protein crosslinks for resolution. Mol Cell, 83:4272-4289.e10 

Zinina VV, Sauer M, Nigmatullina L, Kreim N and Soshnikova N (2023) TCF7L1 controls the differentiation of tuft cells in mouse small intestine. Cells, 12:1452

2022

Cortés-López M, Schulz L, Enculescu M, Paret C, Spiekermann B, Quesnel-Vallières M, Torres-Diz M, Unic S, Busch A, Orekhova A, Kuban M, Mesitov M, Mulorz MM, Shraim R, Kielisch F, Faber J, Barash Y, Thomas-Tikhonenko A, Zarnack K, Legewie S and König J (2022) High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance. Nat Commun, 13:5570

Gehrke N, Hofmann LJ, Straub BK, Rühle F, Waisman A, Galle PR and Schattenberg JM (2022) Hepatic interleukin-1 receptor type 1 signalling regulates insulin sensitivity in the early phases of nonalcoholic fatty liver disease. Clin Transl Med, 12:e1048

Marnik EA*, Almeida MV*, Cipriani PG*, Chung G, Caspani E, Karaulanov E, Gan HH, Zinno J, Isolehto IJ, Kielisch F, Butter F, Sharp CS, Flanagan RM, Bonnet FX, Piano F, Ketting RF^#, Gunsalus KC^# and Updike DL^# (2022) The Caenorhabditis elegans TDRD5/7-like protein, LOTR-1, interacts with the helicase ZNFX-1 to balance epigenetic signals in the germline. PLOS Genet, 18:e1010245 (*indicates joint contribution, ^#indicates joint correspondence)

Öztürk M, Freiwald A, Cartano J, Schmitt R, Dejung M, Luck K, Al-Sady B, Braun S, Levin M and Butter F (2022) Proteome effects of genome-wide single gene perturbations. Nat Commun, 13:6153

Schreier J, Dietz S, Boermel M, Oorschot V, Seistrup AS, de Jesus Domingues AM, Bronkhorst AW, Nguyen DAH, Phillis S, Gleason EJ, L'Hernault SW, Phillips CM, Butter FK and Ketting RF (2022) Membrane-associated cytoplasmic granules carrying the Argonaute protein WAGO-3 enable paternal epigenetic inheritance in Caenorhabditis elegans. Nat Cell Biol, 24:217-229

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

Dietz S, Almeida MV, Nischwitz E, Schreier J, Viceconte N, Fradera-Sola A, Renz C, Ceron-Noriega A, Ulrich HD, Kappei D, Ketting RF and Butter F (2021) The double-stranded DNA-binding proteins TEBP-1 and TEBP-2 form a telomeric complex with POT-1. Nat Commun, 12:2668 

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)

Mosler T, Conte F, Longo GMC, Mikicic I, Kreim N, Möckel MM, Petrosino G, Flach J, Barau J, Luke B, Roukos V and Beli P (2021) R-loop proximity proteomics identifies a role of DDX41 in transcription-associated genomic instability. Nat Commun, 12:7314 

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

Spiecker L, Witte I, Mehlig J, Shah V, Meyerhöfer M, Haehnel PS, Petermann V, Schüler A, More P, Cabezas-Wallscheid N, Horke S, Pautz A, Daiber A, Sasca D, Kindler T and Kleinert H (2021) Deficiency of antioxidative paraoxonase 2 (Pon2) leads to increased number of phenotypic LT-HSCs and disturbed erythropoiesis. Oxid Med Cell Longev, 2021:3917028 

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)

Leismann J, Spagnuolo M, Pradhan M, Wacheul L, Vu MA, Musheev M, Mier P, Andrade-Navarro MA, Graille M, Niehrs C, Lafontaine DL and Roignant JY (2020) The 18S ribosomal RNA m6 A methyltransferase Mettl5 is required for normal walking behavior in Drosophila. EMBO Rep, 21:e49443  

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

Cordeiro Rodrigues RJ, de Jesus Domingues AM, Hellmann S, Dietz S, de Albuquerque BFM, Renz C, Ulrich HD, Sarkies P, Butter F and Ketting RF (2019) PETISCO is a novel protein complex required for 21U RNA biogenesis and embryonic viability. Genes Dev, 33:857-870

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

Becker K, Bluhm A, Casas-Vila N, Dinges N, Dejung M, Sayols S, Kreutz C, Roignant JY, Butter F and Legewie S (2018) Quantifying post-transcriptional regulation in the development of Drosophila melanogaster. Nat Commun, 9:4970  

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