Publications

Publications 2022

Papers including work performed in the frame of iGE3

Alphabetical order of first authors’ names

PubMed

  • Abdul F, Diman A, Baechler B, Ramakrishnan D, Kornyeyev D, Beran RK, Fletcher SP, Strubin M. Smc5/6 silences episomal transcription by a three-step function. Nat Struct Mol Biol. 2022 Sep;29(9):922-931. ► Pubmed
  • Ademi H, Djari C, Mayère C, Neirijnck Y, Sararols P, Rands CM, Stévant I, Conne B, Nef S. Deciphering the origins and fates of steroidogenic lineages in the mouse testis. Cell Rep. 2022 Jun 14;39(11):110935. ► Pubmed
  • Antonarakis SE. Short arms of human acrocentric chromosomes and the completion of the human genome sequence. Genome Res. 2022 Apr;32(4):599-607. ► Pubmed
  • Barbieri S, Nurni Ravi A, Griffin EE, Gotta M. Modeling protein dynamics in Caenorhabditis elegans embryos reveals that the PLK-1 gradient relies on weakly coupled reaction-diffusion mechanisms. Proc Natl Acad Sci U S A. 2022 Mar 15;119(11):e2114205119. ► Pubmed
  • Bolt CC, Lopez-Delisle L, Hintermann A, Mascrez B, Rauseo A, Andrey G, Duboule D. Context-dependent enhancer function revealed by targeted inter-TAD relocation. Nat Commun. 2022 Jun 17;13(1):3488. ► Pubmed
  • Broccard N, Silva NM, Currat M. Simulated patterns of mitochondrial diversity are consistent with partial population turnover in Bronze Age Central Europe. Am J Biol Anthropol. 2022 Jan;177(1):134-146. ► Pubmed
  • Buzgariu W, Aubry-Lachainaye JP, Galliot B. Studying stem cell biology in intact and whole-body regenerating Hydra by flow cytometry. Methods Mol Biol. 2022;2450:373-398. ► Pubmed
  • Cenerenti M, Saillard M, Romero P, Jandus C. The era of cytotoxic CD4 T cells. Front Immunol. 2022 Apr 27;13:867189. ► Pubmed
  • Conod A, Silvano M, Ruiz I Altaba A. On the origin of metastases: Induction of pro-metastatic states after impending cell death via ER stress, reprogramming, and a cytokine storm. Cell Rep. 2022 Mar 8;38(10):110490. ► Pubmed
  • Darbellay F, Rouco R, Andrey G. MAZ regulates chromatin domain insulation and genome architecture. Nat Genet. 2022 Feb;54(2):96-97. ► Pubmed
  • Di D, Simon Thomas J, Currat M, Nunes JM, Sanchez-Mazas A. Challenging ancient DNA results about putative HLA protection or susceptibility to Yersinia pestis. Mol Biol Evol. 2022 Apr 10;39(4):msac073. ► Pubmed
  • Fang F, Lin L, Zhang Q, Lu M, Skvortsova MY, Podolec R, Zhang Q, Pi J, Zhang C, Ulm R, Yin R. Mechanisms of UV-B light-induced photoreceptor UVR8 nuclear localization dynamics. New Phytol. 2022 Dec;236(5):1824-1837. ► Pubmed
  • Gloor Y, Matthey A, Sobo K, Mouterde M, Kosek E, Pickering G, Poloni ES, Cedraschi C, Ehret G, Desmeules JA. Uncovering a genetic polymorphism located in Huntingtin associated protein 1 in modulation of central pain sensitization signaling pathways. Front Neurosci. 2022 Jun 28;16:807773. ► Pubmed
  • Graf M, Interlandi M, Moreno N, Holdhof D, Göbel C, Melcher V, Mertins J, Albert TK, Kastrati D, Alfert A, Holsten T, de Faria F, Meisterernst M, Rossig C, Warmuth-Metz M, Nowak J, Meyer Zu Hörste G, Mayère C, Nef S, Johann P, Frühwald MC, Dugas M, Schüller U, Kerl K. Single-cell transcriptomics identifies potential cells of origin of MYC rhabdoid tumors. Nat Commun. 2022 Mar 22;13(1):1544. ► Pubmed
  • Hadadi N, Spiljar M, Steinbach K, Çolakoǧlu M, Chevalier C, Salinas G, Merkler D, Trajkovski M. Comparative multi-tissue profiling reveals extensive tissue-specificity in transcriptome reprogramming during thermal adaptation. Elife. 2022 May 17;11:e78556. ► Pubmed
  • Horgue LF, Assens A, Fodoulian L, Marconi L, Tuberosa J, Haider A, Boillat M, Carleton A, Rodriguez I. Transcriptional adaptation of olfactory sensory neurons to GPCR identity and activity. Nat Commun. 2022 May 25;13(1):2929. ► Pubmed
  • Ifrid E, Ouertatani-Sakouhi H, Jauslin T, Kicka S, Chiriano G, Harrison CF, Hilbi H, Scapozza L, Soldati T, Cosson P. 5-ethyl-2'-deoxyuridine fragilizes Klebsiella pneumoniae outer wall and facilitates intracellular killing by phagocytic cells. PLoS One. 2022 Oct 31;17(10):e0269093. ► Pubmed
  • Iwasaki M, Penfield S, Lopez-Molina L. Parental and environmental control of seed dormancy in Arabidopsis thaliana. Annu Rev Plant Biol. 2022 May 20;73:355-378. ► Pubmed
  • Kieser S, Zdobnov EM, Trajkovski M. Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart. PLoS Comput Biol. 2022 Mar 8;18(3):e1009947. ► Pubmed
  • Larasati YA, Savitsky M, Koval A, Solis GP, Valnohova J, Katanaev VL. Restoration of the GTPase activity and cellular interactions of Gαo mutants by Zn2+ in GNAO1 encephalopathy models. Sci Adv. 2022 Oct 7;8(40):eabn9350. ► Pubmed
  • Lemopoulos A, Montoya-Burgos JI. Whole genome assembly of the armored loricariid catfish Ancistrus triradiatus highlights herbivory signatures. Mol Genet Genomics. 2022 Nov;297(6):1627-1642. ► Pubmed
  • Li L, Krasnykov K, Homolka D, Gos P, Mendel M, Fish RJ, Pandey RR, Pillai RS. The XRN1-regulated RNA helicase activity of YTHDC2 ensures mouse fertility independently of m6A recognition. Mol Cell. 2022 May 5;82(9):1678-1690.e12. ► Pubmed
  • Lunghi M, Kloehn J, Krishnan A, Varesio E, Vadas O, Soldati-Favre D. Pantothenate biosynthesis is critical for chronic infection by the neurotropic parasite Toxoplasma gondii. Nat Commun. 2022 Jan 17;13(1):345. ► Pubmed
  • Mayère C, Regard V, Perea-Gomez A, Bunce C, Neirijnck Y, Djari C, Bellido-Carreras N, Sararols P, Reeves R, Greenaway S, Simon M, Siggers P, Condrea D, Kühne F, Gantar I, Tang F, Stévant I, Batti L, Ghyselinck NB, Wilhelm D, Greenfield A, Capel B, Chaboissier MC, Nef S. Origin, specification and differentiation of a rare supporting-like lineage in the developing mouse gonad. Sci Adv. 2022 May 27;8(21):eabm0972. ► Pubmed
  • Mercey O, Kostic C, Bertiaux E, Giroud A, Sadian Y, Gaboriau DCA, Morrison CG, Chang N, Arsenijevic Y, Guichard P, Hamel V. The connecting cilium inner scaffold provides a structural foundation that protects against retinal degeneration. PLoS Biol. 2022 Jun 16;20(6):e3001649. ► Pubmed
  • Miozzo F, Valencia-Alarcón EP, Stickley L, Majcin Dorcikova M, Petrelli F, Tas D, Loncle N, Nikonenko I, Bou Dib P, Nagoshi E. Maintenance of mitochondrial integrity in midbrain dopaminergic neurons governed by a conserved developmental transcription factor. Nat Commun. 2022 Mar 17;13(1):1426. ► Pubmed
  • Mohammadi Ghahhari N, Sznurkowska MK, Hulo N, Bernasconi L, Aceto N, Picard D. Cooperative interaction between ERα and the EMT-inducer ZEB1 reprograms breast cancer cells for bone metastasis. Nat Commun. 2022 Apr 19;13(1):2104. ► Pubmed
  • Molinard-Chenu A, Godel M, Rey A, Musardo S, Bodogan T, Vutskits L, Bellone C, Dayer A. Downregulation of the schizophrenia risk-gene Dgcr2 alters early microcircuit development in the mouse medial prefrontal cortex. Int J Dev Neurosci. 2022 May;82(3):277-285. ► Pubmed
  • Mouterde M, Daali Y, Rollason V, Čížková M, Mulugeta A, Al Balushi KA, Fakis G, Constantinidis TC, Al-Thihli K, Černá M, Makonnen E, Boukouvala S, Al-Yahyaee S, Yimer G, Černý V, Desmeules J, Poloni ES. Joint analysis of phenotypic and genomic diversity sheds light on the evolution of xenobiotic metabolism in humans. Genome Biol Evol. 2022 Dec 8;14(12):evac167. ► Pubmed
  • Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PGS, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sović I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O'Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM. The complete sequence of a human genome. Science. 2022 Apr;376(6588):44-53. ► Pubmed
  • Perez-Frances M, Abate MV, Baronnier D, Scherer PE, Fujitani Y, Thorel F, Herrera PL. Adult pancreatic islet endocrine cells emerge as fetal hormone-expressing cells. Cell Rep. 2022 Feb 15;38(7):110377. ► Pubmed
  • Petrenko V, Sinturel F, Loizides-Mangold U, Montoya JP, Chera S, Riezman H, Dibner C. Type 2 diabetes disrupts circadian orchestration of lipid metabolism and membrane fluidity in human pancreatic islets. PLoS Biol. 2022 Aug 3;20(8):e3001725. ► Pubmed
  • Podolec R, Wagnon TB, Leonardelli M, Johansson H, Ulm R. Arabidopsis B-box transcription factors BBX20-22 promote UVR8 photoreceptor-mediated UV-B responses. Plant J. 2022 Jul;111(2):422-439. ► Pubmed
  • Romanova-Michaelides M, Hadjivasiliou Z, Aguilar-Hidalgo D, Basagiannis D, Seum C, Dubois M, Jülicher F, Gonzalez-Gaitan M. Morphogen gradient scaling by recycling of intracellular Dpp. Nature. 2022 Feb;602(7896):287-293. ► Pubmed
  • Shore D, Albert B. Ribosome biogenesis and the cellular energy economy. Curr Biol. 2022 Jun 20;32(12):R611-R617. ► Pubmed
  • Silva NM, Kreutzer S, Souleles A, Triantaphyllou S, Kotsakis K, Urem-Kotsou D, Halstead P, Efstratiou N, Kotsos S, Karamitrou-Mentessidi G, Adaktylou F, Chondroyianni-Metoki A, Pappa M, Ziota C, Sampson A, Papathanasiou A, Vitelli K, Cullen T, Kyparissi-Apostolika N, Lanz AZ, Peters J, Rio J, Wegmann D, Burger J, Currat M, Papageorgopoulou C. Ancient mitochondrial diversity reveals population homogeneity in Neolithic Greece and identifies population dynamics along the Danubian expansion axis. Sci Rep. 2022 Aug 5;12(1):13474. ► Pubmed
  • Simmler LD, Li Y, Hadjas LC, Hiver A, van Zessen R, Lüscher C. Dual action of ketamine confines addiction liability. Nature. 2022 Aug;608(7922):368-373. ► Pubmed
  • Simonin JL, Luscher A, Losa D, Badaoui M, van Delden C, Köhler T, Chanson M. Surface hydration protects cystic fibrosis airways from infection by restoring junctional networks. Cells. 2022 May 9;11(9):1587. ► Pubmed
  • Sinturel F, Spaleniak W, Dibner C. Circadian rhythm of lipid metabolism. Biochem Soc Trans. 2022 Jun 30;50(3):1191-1204. ► Pubmed
  • Solis GP, Kazemzadeh A, Abrami L, Valnohova J, Alvarez C, van der Goot FG, Katanaev VL. Local and substrate-specific S-palmitoylation determines subcellular localization of Gαo. Nat Commun. 2022 Apr 19;13(1):2072. ► Pubmed
  • Tafur L, Hinterndorfer K, Gabus C, Lamanna C, Bergmann A, Sadian Y, Hamdi F, Kyrilis FL, Kastritis PL, Loewith R. Cryo-EM structure of the SEA complex. Nature. 2022 Nov;611(7935):399-404. ► Pubmed
  • Tzanoulinou S, Musardo S, Contestabile A, Bariselli S, Casarotto G, Magrinelli E, Jiang YH, Jabaudon D, Bellone C. Inhibition of Trpv4 rescues circuit and social deficits unmasked by acute inflammatory response in a Shank3 mouse model of Autism. Mol Psychiatry. 2022 Apr;27(4):2080-2094. ► Pubmed
  • Vafeiadou V, Hany D, Picard D. Hyperactivation of MAPK induces tamoxifen resistance in SPRED2-deficient ERα-positive breast cancer. Cancers (Basel). 2022 Feb 14;14(4):954. ► Pubmed
  • van Gurp L, Fodoulian L, Oropeza D, Furuyama K, Bru-Tari E, Vu AN, Kaddis JS, Rodríguez I, Thorel F, Herrera PL. Generation of human islet cell type-specific identity genesets. Nat Commun. 2022 Apr 19;13(1):2020. ► Pubmed
  • Vogg MC, Ferenc J, Buzgariu WC, Perruchoud C, Sanchez PGL, Beccari L, Nuninger C, Le Cras Y, Delucinge-Vivier C, Papasaikas P, Vincent S, Galliot B, Tsiairis CD. The transcription factor Zic4 promotes tentacle formation and prevents epithelial transdifferentiation in Hydra. Sci Adv. 2022 Dec 23;8(51):eabo0694. ► Pubmed
  • Vogg MC, Galliot B. Combining RNAi-mediated β-catenin inhibition and reaggregation to study Hydra whole-body regeneration. Methods Mol Biol. 2022;2450:635-647. ► Pubmed
  • Wang C, Barnoud C, Cenerenti M, Sun M, Caffa I, Kizil B, Bill R, Liu Y, Pick R, Garnier L, Gkountidi OA, Ince LM, Holtkamp S, Fournier N, Michielin O, Speiser DE, Hugues S, Nencioni A, Pittet MJ, Jandus C, Scheiermann C. Dendritic cells direct circadian anti-tumor immune responses. Nature. 2022 Dec 5. Online ahead of print. ► Pubmed
  • Weiss B, Jaquier-Gubler P, Curran JA. Preinitiation complex loading onto mRNAs with long versus short 5' TLs. Int J Mol Sci. 2022 Nov 2;23(21):13369. ► Pubmed
  • Zakany S, Smirnov S, Milinkovitch MC. Lizard skin patterns and the Ising model. Phys Rev Lett. 2022 Jan 27;128(4):048102. ► Pubmed
  • Zencir S, Dilg D, Shore D, Albert B. Pitfalls in using phenanthroline to study the causal relationship between promoter nucleosome acetylation and transcription. Nat Commun. 2022 Jun 29;13(1):3726. ► Pubmed
  • Zomer A, Croci D, Kowal J, van Gurp L, Joyce JA. Multimodal imaging of the dynamic brain tumor microenvironment during glioblastoma progression and in response to treatment. iScience. 2022 Jun 9;25(7):104570. doi: 10.1016/j.isci.2022.104570. ► Pubmed

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