[en] ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues, coordinating the acquisition of generic cell fates and of specific subtype identities. How these factors, recognizing highly similar DNA motifs, display specific activities, is not yet fully understood. To address this issue, we overexpressed different ARP/ASCL factors in zebrafish ascl1a-/- mutant embryos to determine which ones are able to rescue the intestinal secretory lineage. We found that Ascl1a/b, Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors. Indeed, Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells. Gain-of-function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19-aa ultra-conserved element (UCE), present in all Neurod members but absent in the other ARP/ASCL proteins. Importantly, inserting the UCE into the Ascl1a protein reverse the rescuing capacity of this Ascl1a chimeric protein that cannot rescue the goblet cells anymore but efficiently rescue the enteroendocrine cells. This novel domain acts indeed as a goblet cell fate repressor that inhibits gfi1aa expression, known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of the enteroendocrine cells, phenotype also observed in the neurod1 null mutant. This highlight the crucial function of the UCE domain for NeuroD1 activity in the intestine. As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed, we can envision a similar role of the UCE in other tissues, allowing Neurod1 to repress Gfi1 to influence the balance between cell fates.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Reuter, Anne-Sophie ; Université de Liège - ULiège > GIGA > GIGA Stem Cells - Zebrafish Development and Disease Model
Stern, David ; Université de Liège - ULiège > GIGA > GIGA Platform Genomics ; Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège - ULiège
Bernard, Alice ; Université de Liège - ULiège > Integrative Biological Sciences (InBioS) ; Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of
Goossens, Chiara ; Université de Liège - ULiège > Département des sciences de la vie ; Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège - ULiège
Lavergne, Arnaud ; Université de Liège - ULiège > Département de gestion vétérinaire des Ressources Animales (DRA) > Génomique animale ; Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège - ULiège
Flasse, Lydie ; Université de Liège - ULiège > GIGA > GIGA Stem Cells - Zebrafish Development and Disease Model ; Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of
Von Berg, Virginie ; Centre Hospitalier Universitaire de Liège - CHU > > Service de génétique ; Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of
Manfroid, Isabelle ; Université de Liège - ULiège > GIGA > GIGA Stem Cells - Zebrafish Development and Disease Model ; Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège - ULiège
Peers, Bernard ; Université de Liège - ULiège > GIGA > GIGA Stem Cells - Zebrafish Development and Disease Model ; Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège - ULiège
Voz, Marianne ; Université de Liège - ULiège > GIGA > GIGA Stem Cells - Zebrafish Development and Disease Model ; Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège - ULiège
Language :
English
Title :
Identification of an evolutionarily conserved domain in Neurod1 favouring enteroendocrine versus goblet cell fate.
Bertrand N, Castro DS, Guillemot F. Proneural genes and the specification of neural cell types. Nat Rev Neurosci. 2002; 3: 517–530. https://doi.org/10.1038/nrn874 PMID: 12094208
Castro DS, Guillemot F. Old and new functions of proneural factors revealed by the genome-wide characterization of their transcriptional targets. Cell Cycle. 2011; 10: 4026–4031. https://doi.org/10.4161/cc.10.23.18578 PMID: 22101262
Roach G, Heath Wallace R, Cameron A, Emrah Ozel R, Hongay CF, Baral R, et al. Loss of ascl1a prevents secretory cell differentiation within the zebrafish intestinal epithelium resulting in a loss of distal intestinal motility. Dev Biol. 2013; 376: 171–86. https://doi.org/10.1016/j.ydbio.2013.01.013 PMID: 23353550
Flasse LC, Stern DG, Pirson JL, Manfroid I, Peers B, Voz ML. The bHLH transcription factor Ascl1a is essential for the specification of the intestinal secretory cells and mediates Notch signaling in the zebrafish intestine. Dev Biol. 2013; 376: 187–197. https://doi.org/10.1016/j.ydbio.2013.01.011 PMID: 23352790
Yang Q, Bermingham NA, Finegold MJ, Zoghbi HY. Requirement of Math1 for secretory cell lineage commitment in the mouse intestine. Science (80-). 2001/12/12. 2001; 294: 2155–2158. https://doi.org/10.1126/science.1065718 294/5549/2155 [pii] PMID: 11739954
Gradwohl G, Dierich A, LeMeur M, Guillemot F. neurogenin3 is required for the development of the four endocrine cell lineages of the pancreas. Proc Natl Acad Sci U S A. 2000; 97: 1607–1611. https://doi.org/10.1073/pnas.97.4.1607 PMID: 10677506
Flasse LC, Pirson JL, Stern DG, Von Berg V, Manfroid I, Peers B, et al. Ascl1b and Neurod1, instead of Neurog3, control pancreatic endocrine cell fate in zebrafish. BMC Biol. 2013; 11: 1–18. https://doi.org/10.1186/1741-7007-11-1 PMID: 23294804
Kokubu H, Ohtsuka T, Kageyama R. Mash1 is required for neuroendocrine cell development in the glandular stomach. Genes Cells. 2008/01/05. 2008; 13: 41–51. GTC1146 [pii] https://doi.org/10.1111/j.1365-2443.2007.01146.x PMID: 18173746
Jensen J, Pedersen EE, Galante P, Hald J, Heller RS, Ishibashi M, et al. Control of endodermal endocrine development by Hes-1. Nat Genet. 2000; 24: 36–44. https://doi.org/10.1038/71657 PMID: 10615124
Jenny M, Uhl C, Roche C, Duluc I, Guillermin V, Guillemot F, et al. Neurogenin3 is differentially required for endocrine cell fate specification in the intestinal and gastric epithelium. Embo J. 2002; 21: 6338–6347. https://doi.org/10.1093/emboj/cdf649 PMID: 12456641
Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW, Bulyk ML. Compact, universal DNA micro-arrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol. 2006. https://doi.org/10.1038/nbt1246 PMID: 16998473
Grove CA, De Masi F, Barrasa MI, Newburger DE, Alkema MJ, Bulyk ML, et al. A multiparamater network reveals extensive divergence between C. elegans bHLH transcription factors. Cell. 2009; 138: 314–327. https://doi.org/10.1016/j.cell.2009.04.058 PMID: 19632181
Yu X, Lau D, Ng CP, Roy S. Cilia-driven fluid flow as an epigenetic cue for otolith biomineralization on sensory hair cells of the inner ear. Development. 2011/01/06. 2011; 138: 487–494. 138/3/487 [pii] https://doi.org/10.1242/dev.057752 PMID: 21205793
Millimaki BB, Sweet EM, Riley BB. Sox2 is required for maintenance and regeneration, but not initial development, of hair cells in the zebrafish inner ear. Dev Biol. 2009/12/23. 2010; 338: 262–269. S0012-1606(09)01400-6 [pii] https://doi.org/10.1016/j.ydbio.2009.12.011 PMID: 20025865
Lavergne A, Tarifeño-Saldivia E, Pirson J, Reuter AS, Flasse L, Manfroid I, et al. Pancreatic and intestinal endocrine cells in zebrafish share common transcriptomic signatures and regulatory programmes. BMC Biol. 2020. https://doi.org/10.1186/s12915-020-00840-1 PMID: 32867764
Lizio M, Ishizu Y, Itoh M, Lassmann T, Hasegawa A, Kubosaki A, et al. Mapping mammalian cell-type-specific transcriptional regulatory networks using KD-CAGE and ChIP-seq data in the TC-YIK cell line. Front Genet. 2015. https://doi.org/10.3389/fgene.2015.00331 PMID: 26635867
Gehart H, van Es JH, Hamer K, Beumer J, Kretzschmar K, Dekkers JF, et al. Identification of Enteroendocrine Regulators by Real-Time Single-Cell Differentiation Mapping. Cell. 2019; 176: 1158–1173.e16. https://doi.org/10.1016/j.cell.2018.12.029 PMID: 30712869
Bjerknes M, Cheng H. Cell Lineage metastability in Gfi1-deficient mouse intestinal epithelium. Dev Biol. 2010. https://doi.org/10.1016/j.ydbio.2010.06.021 PMID: 20599897
Thambyrajah R, Ucanok D, Jalali M, Hough Y, Wilkinson RN, McMahon K, et al. A gene trap transposon eliminates haematopoietic expression of zebrafish Gfi1aa, but does not interfere with haematopoiesis. Dev Biol. 2016; 417: 25–39. https://doi.org/10.1016/j.ydbio.2016.07.010 PMID: 27432513
Wallace KN, Akhter S, Smith EM, Lorent K, Pack M. Intestinal growth and differentiation in zebrafish. Mech Dev. 2005/01/18. 2005; 122: 157–173. S0925-4773(04)00250-3 [pii] https://doi.org/10.1016/j.mod.2004.10.009 PMID: 15652704
Delporte FM, Pasque V, Devos N, Manfroid I, Voz ML, Motte P, et al. Expression of zebrafish pax6b in pancreas is regulated by two enhancers containing highly conserved cis-elements bound by PDX1, PBX and PREP factors. BMC Dev Biol. 2008. https://doi.org/10.1186/1471-213X-8-53 PMID: 18485195
Mapes J, Li Q, Kannan A, Anandan L, Laws M, Lydon JP, et al. CUZD1 is a critical mediator of the JAK/ STAT5 signaling pathway that controls mammary gland development during pregnancy. PLoS Genet. 2017; 13: 1–22. https://doi.org/10.1371/journal.pgen.1006654 PMID: 28278176
Surbek M, Tse W, Moriggl R, Han X. A centric view of JAK/STAT5 in intestinal homeostasis, infection, and inflammation. Cytokine. 2021. https://doi.org/10.1016/j.cyto.2020.155392 PMID: 33482575
Kanda M, Shimizu D, Tanaka H, Shibata M, Iwata N, Hayashi M, et al. Metastatic pathway-specific transcriptome analysis identifies MFSD4 as a putative tumor suppressor and biomarker for hepatic metastasis in patients with gastric cancer. Oncotarget. 2016. https://doi.org/10.18632/oncotarget.7269 PMID: 26872374
Brophy PD, Rasmussen M, Parida M, Bonde G, Darbro BW, Hong X, et al. A gene implicated in activation of retinoic acid receptor targets is a novel renal agenesis gene in humans. Genetics. 2017. https://doi.org/10.1534/genetics.117.1125 PMID: 28739660
Lorberbaum DS, Kishore S, Rosselot C, Sarbaugh D, Brooks EP, Aragon E, et al. Retinoic acid signaling within pancreatic endocrine progenitors regulates mouse and human β cell specification. Dev. 2020. https://doi.org/10.1242/dev.189977 PMID: 32467243
Öström M, Loffler KA, Edfalk S, Selander L, Dahl U, Ricordi C, et al. Retinoic acid promotes the generation of pancreatic endocrine progenitor cells and their further differentiation into β-cells. PLoS One. 2008. https://doi.org/10.1371/journal.pone.0002841 PMID: 18665267
Crosnier C, Vargesson N, Gschmeissner S, Ariza-McNaughton L, Morrison A, Lewis J. Delta-Notch signalling controls commitment to a secretory fate in the zebrafish intestine. Development. 2005; 132: 1093–104. https://doi.org/10.1242/dev.01644 PMID: 15689380
Quan XJ, Denayer T, Yan J, Jafar-Nejad H, Philippi A, Lichtarge O, et al. Evolution of neural precursor selection: functional divergence of proneural proteins. Development. 2004/04/16. 2004; 131: 1679–1689. https://doi.org/10.1242/dev.01055 [pii] PMID: 15084454
Bjerknes M, Cheng H. Cell Lineage metastability in Gfi1-deficient mouse intestinal epithelium. Dev Biol. 2010; 345: 49–63. https://doi.org/10.1016/j.ydbio.2010.06.021 PMID: 20599897
Jafar-Nejad H, Acar M, Nolo R, Lacin H, Pan H, Parkhurst SM, et al. Senseless acts as a binary switch during sensory organ precursor selection. Genes Dev. 2003. https://doi.org/10.1101/gad.1122403 PMID: 14665671
Xie B, Charlton-Perkins M, McDonald E, Gebelein B, Cook T. Senseless functions as a molecular switch for color photoreceptor differentiation in Drosophila. Development. 2007. https://doi.org/10.1242/dev.012781 PMID: 17978002
Thambyrajah R, Mazan M, Patel R, Moignard V, Stefanska M, Marinopoulou E, et al. GFI1 proteins orchestrate the emergence of haematopoietic stem cells through recruitment of LSD1. Nat Cell Biol. 2016. https://doi.org/10.1038/ncb3276 PMID: 26619147
Matern MS, Milon B, Lipford EL, McMurray M, Ogawa Y, Tkaczuk A, et al. GFI1 functions to repress neuronal gene expression in the developing inner ear hair cells. Development. 2020. https://doi.org/10.1242/dev.186015 PMID: 32917668
Qu X, Nyeng P, Xiao F, Dorantes J, Jensen J. Growth Factor Independence-1 (Gfi1) Is Required for Pancreatic Acinar Unit Formation and Centroacinar Cell Differentiation. CMGH. 2015. https://doi.org/10.1016/j.jcmgh.2014.12.004 PMID: 28247862
Gasa R, Mrejen C, Lynn FC, Skewes-Cox P, Sanchez L, Yang KY, et al. Induction of pancreatic islet cell differentiation by the neurogenin-neuroD cascade. Differentiation. 2008; 76: 381–391. https://doi.org/10.1111/j.1432-0436.2007.00228.x PMID: 17924961
Cara L, Baitemirova M, Follis J, Larios-Sanz M, Ribes-Zamora A. The ATM- and ATR-related SCD domain is over-represented in proteins involved in nervous system development. Sci Rep. 2016. https://doi.org/10.1038/srep19050 PMID: 26743489
Yang DQ, Kastan MB. Participation of ATM in insulin signalling through phosphorylation of elF-4E-binding protein 1. Nat Cell Biol. 2000. https://doi.org/10.1038/35046542 PMID: 11146653
Moore KB, Schneider ML, Vetter ML, Hall R. Posttranslational Mechanisms Control the Timing of bHLH Function and Regulate Retinal Cell Fate. 2002; 34: 183–195.
Kimmel CB, Ballard WW, Kimmel SR, Ullmann B, Schilling TF. Stages of embryonic development of the zebrafish. Dev Dyn. 1995; 203: 253–310. https://doi.org/10.1002/aja.1002030302 PMID: 8589427
Pogoda HM, von der Hardt S, Herzog W, Kramer C, Schwarz H, Hammerschmidt M. The proneural gene ascl1a is required for endocrine differentiation and cell survival in the zebrafish adenohypophysis. Development. 2006/02/17. 2006; 133: 1079–1089. dev.02296 [pii] https://doi.org/10.1242/dev.02296 PMID: 16481349
Field HA, Ober EA, Roeser T, Stainier DY. Formation of the digestive system in zebrafish. I. Liver morphogenesis. Dev Biol. 2003; 253: 279–290. https://doi.org/10.1016/s0012-1606(02)00017-9 PMID: 12645931
Provost E, Rhee J, Leach SD. Viral 2A peptides allow expression of multiple proteins from a single ORF in transgenic zebrafish embryos. Genesis. 2007/10/18. 2007; 45: 625–629. https://doi.org/10.1002/dvg. 20338 PMID: 17941043
Horton RM, Hunt HD, Ho SN, Pullen JK, Pease LR. Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene. 1989. https://doi.org/10.1016/0378-1119(89) 90359-4 PMID: 2744488
Kwan KM, Fujimoto E, Grabher C, Mangum BD, Hardy ME, Campbell DS, et al. The Tol2kit: A multisite gateway-based construction Kit for Tol2 transposon transgenesis constructs. Dev Dyn. 2007. https://doi.org/10.1002/dvdy.21343 PMID: 17937395
Picelli S, Faridani OR, Björklund AK, Winberg G, Sagasser S, Sandberg R. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc. 2014; 9: 171–81. https://doi.org/10.1038/nprot.2014.006 PMID: 24385147
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNAseq aligner. Bioinformatics. 2013; 29: 15–21. https://doi.org/10.1093/bioinformatics/bts635 PMID: 23104886
Anders S, Pyl PT, Huber W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics. 2014; btu638. https://doi.org/10.1093/bioinformatics/btu638 PMID: 25260700
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15: 550. https://doi.org/10.1186/s13059-014-0550-8 PMID: 25516281
Mi H, Ebert D, Muruganujan A, Mills C, Albou LP, Mushayamaha T, et al. PANTHER version 16: A revised family classification, tree-based classification tool, enhancer regions and extensive API. Nucleic Acids Res. 2021. https://doi.org/10.1093/nar/gkaa1106 PMID: 33290554
Binot AC, Manfroid I, Flasse L, Winandy M, Motte P, Martial JA, et al. Nkx6.1 and nkx6.2 regulate alpha- and beta-cell formation in zebrafish by acting on pancreatic endocrine progenitor cells. Dev Biol. 2010; 340: 397–407. https://doi.org/10.1016/j.ydbio.2010.01.025 PMID: 20122912
Tarifeño-saldivia E, Lavergne A, Bernard A, Padamata K, Bergemann D, Voz ML, et al. Transcriptome analysis of pancreatic cells across distant species highlights novel important regulator genes. BMC Biol. 2017; 15: 1–19. https://doi.org/10.1186/s12915-016-0343-5 PMID: 28100223
Shih LJ, Lu YF, Chen YH, Lin CC, Chen JA, Hwang SPL. Characterization of the agr2 gene, a homologue of X. laevis anterior gradient 2, from the zebrafish, Danio rerio. Gene Expr Patterns. 2007; 7: 452–460.
Mavropoulos A, Devos N, Argenton F, Edlund H, Motte P, Martial JA, et al. sox4b is a key player of pancreatic a cell differentiation in zebrafish. 2005; 285: 211–223. https://doi.org/10.1016/j.ydbio.2005.06. 024 PMID: 16055112
Krauss S, Johansen T, Korzh V, Moens U, Ericson JU, Fjose A. Zebrafish pax[zf-a]: a paired box-containing gene expressed in the neural tube. EMBO J. 1991; 10: 3609–3619. https://doi.org/10.1002/j.1460-2075.1991.tb04927.x
Devos N, Deflorian G, Biemar F, Bortolussi M, Martial JA, Peers B, et al. Differential expression of two somatostatin genes during zebrafish embryonic development. Mech Dev. 2002; 115: 133–137. https://doi.org/10.1016/S0925-4773(02)00082-5
Argenton F, Zecchin E, Bortolussi M. Early appearance of pancreatic hormone-expressing cells in the zebrafish embryo. Mech Dev. 1999; 87: 217–221. https://doi.org/10.1016/S0925-4773(99)00151-3
Mutterer J, Zinck E. Quick-and-clean article figures with FigureJ. J Microsc. 2013. https://doi.org/10.1111/jmi.12069 PMID: 23906423
Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, et al. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol. 2013; 31: 227–229. https://doi.org/10.1038/nbt.2501 PMID: 23360964
Varshney GK, Pei W, Lafave MC, Idol J, Xu L, Gallardo V, et al. High-throughput gene targeting and phenotyping in zebrafish using CRISPR / Cas9. 2015; 1030–1042. https://doi.org/10.1101/gr.186379. 114 PMID: 26048245
Burger A, Lindsay H, Felker A, Hess C, Anders C, Chiavacci E, et al. Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes. Dev. 2016. https://doi.org/10.1242/dev.134809 PMID: 27130213
Ota S, Hisano Y, Muraki M, Hoshijima K, Dahlem TJ, Grunwald DJ, et al. Efficient identification of TALEN-mediated genome modifications using heteroduplex mobility assays. Genes Cells. 2013; 18: 450–458. https://doi.org/10.1111/gtc.12050 PMID: 23573916
Field HA, Dong PD, Beis D, Stainier DY. Formation of the digestive system in zebrafish. II. Pancreas morphogenesis. Dev Biol. 2003; 261: 197–208. https://doi.org/10.1016/s0012-1606(03)00308-7 PMID: 12941629