{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T10:03:56Z","timestamp":1791453836781,"version":"4.3.3"},"reference-count":127,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2017,8,29]],"date-time":"2017-08-29T00:00:00Z","timestamp":1503964800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosbiology.org"],"crossmark-restriction":false},"short-container-title":["PLoS Biol"],"DOI":"10.1371\/journal.pbio.2002054","type":"journal-article","created":{"date-parts":[[2017,8,29]],"date-time":"2017-08-29T13:33:39Z","timestamp":1504013619000},"page":"e2002054","update-policy":"https:\/\/doi.org\/10.1371\/journal.pbio.corrections_policy","source":"Crossref","is-referenced-by-count":123,"title":["Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7312-6291","authenticated-orcid":true,"given":"Colin R.","family":"Lickwar","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. Gray","family":"Camp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Weiser","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jordan L.","family":"Cocchiaro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David M.","family":"Kingsley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Terrence S.","family":"Furey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shehzad Z.","family":"Sheikh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John F.","family":"Rawls","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2017,8,29]]},"reference":[{"issue":"3","key":"ref1","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1038\/nri3608","article-title":"Intestinal epithelial cells: regulators of barrier function and immune homeostasis","volume":"14","author":"LW Peterson","year":"2014","journal-title":"Nat Rev Immunol"},{"issue":"1","key":"ref2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/bjc.2015.214","article-title":"Stem vs non-stem cell origin of colorectal cancer","volume":"113","author":"DJ Huels","year":"2015","journal-title":"Br J Cancer"},{"issue":"9","key":"ref3","doi-asserted-by":"crossref","first-page":"R389","DOI":"10.1016\/j.cub.2013.02.043","article-title":"Mucosal immunology of food allergy","volume":"23","author":"MC Berin","year":"2013","journal-title":"Curr Biol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"5648","DOI":"10.1038\/ncomms6648","article-title":"Intestinal epithelial MyD88 is a sensor switching host metabolism towards obesity according to nutritional status","volume":"5","author":"A Everard","year":"2014","journal-title":"Nat Commun"},{"issue":"3","key":"ref5","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1016\/j.chom.2012.08.003","article-title":"Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish","volume":"12","author":"I Semova","year":"2012","journal-title":"Cell Host Microbe"},{"issue":"9","key":"ref6","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1111\/j.1753-4887.2008.00082.x","article-title":"Malnutrition as an enteric infectious disease with long-term effects on child development","volume":"66","author":"RL Guerrant","year":"2008","journal-title":"Nutr Rev"},{"issue":"2","key":"ref7","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1038\/nrmicro2053","article-title":"Enteric infection meets intestinal function: how bacterial pathogens cause diarrhoea","volume":"7","author":"VK Viswanathan","year":"2009","journal-title":"Nat Rev Microbiol"},{"issue":"1","key":"ref8","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1093\/molbev\/msl150","article-title":"Paleontological evidence to date the tree of life","volume":"24","author":"MJ Benton","year":"2007","journal-title":"Mol Biol Evol"},{"key":"ref9","first-page":"400","article-title":"Comparative physiology of the vertebrate digestive system","volume":"xvi","author":"CE Stevens","year":"2004"},{"issue":"1\u20132","key":"ref10","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1007\/s00427-012-0422-8","article-title":"Stem cells and lineages of the intestine: a developmental and evolutionary perspective","volume":"223","author":"S Takashima","year":"2013","journal-title":"Dev Genes Evol"},{"issue":"19","key":"ref11","doi-asserted-by":"crossref","first-page":"3470","DOI":"10.1242\/dev.134098","article-title":"Identification, visualization and clonal analysis of intestinal stem cells in fish","volume":"143","author":"N Aghaallaei","year":"2016","journal-title":"Development"},{"issue":"5","key":"ref12","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1242\/dev.01644","article-title":"Delta-Notch signalling controls commitment to a secretory fate in the zebrafish intestine","volume":"132","author":"C Crosnier","year":"2005","journal-title":"Development"},{"issue":"1","key":"ref13","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1016\/j.ydbio.2005.07.013","article-title":"Formation of the digestive system in zebrafish: III. Intestinal epithelium morphogenesis","volume":"286","author":"AN Ng","year":"2005","journal-title":"Dev Biol"},{"issue":"2","key":"ref14","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/j.mod.2004.10.009","article-title":"Intestinal growth and differentiation in zebrafish","volume":"122","author":"KN Wallace","year":"2005","journal-title":"Mech Dev"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1186\/1471-2164-11-392","article-title":"Morphological and molecular evidence for functional organization along the rostrocaudal axis of the adult zebrafish intestine","volume":"11","author":"Z Wang","year":"2010","journal-title":"BMC Genomics"},{"issue":"9","key":"ref16","doi-asserted-by":"crossref","first-page":"1504","DOI":"10.1101\/gr.165845.113","article-title":"Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape","volume":"24","author":"JG Camp","year":"2014","journal-title":"Genome Res"},{"issue":"7489","key":"ref17","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nature12903","article-title":"Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity","volume":"506","author":"TH Kim","year":"2014","journal-title":"Nature"},{"issue":"5","key":"ref18","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1016\/j.stemcr.2015.09.006","article-title":"Distinct Processes and Transcriptional Targets Underlie CDX2 Requirements in Intestinal Stem Cells and Differentiated Villus Cells","volume":"5","author":"AK San Roman","year":"2015","journal-title":"Stem Cell Reports"},{"issue":"9","key":"ref19","doi-asserted-by":"crossref","first-page":"a008284","DOI":"10.1101\/cshperspect.a008284","article-title":"Transcriptional networks in liver and intestinal development","volume":"4","author":"KL Sheaffer","year":"2012","journal-title":"Cold Spring Harb Perspect Biol"},{"issue":"4","key":"ref20","doi-asserted-by":"crossref","first-page":"588","DOI":"10.1016\/j.devcel.2009.02.010","article-title":"Establishment of intestinal identity and epithelial-mesenchymal signaling by Cdx2","volume":"16","author":"N Gao","year":"2009","journal-title":"Dev Cell"},{"issue":"2","key":"ref21","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1089\/zeb.2012.0784","article-title":"Transgenic overexpression of cdx1b induces metaplastic changes of gene expression in zebrafish esophageal squamous epithelium","volume":"10","author":"B Hu","year":"2013","journal-title":"Zebrafish"},{"issue":"11","key":"ref22","doi-asserted-by":"crossref","first-page":"1273","DOI":"10.1016\/j.bbagrm.2014.05.018","article-title":"GATA4 represses an ileal program of gene expression in the proximal small intestine by inhibiting the acetylation of histone H3, lysine 27","volume":"1839","author":"BE Aronson","year":"2014","journal-title":"Biochim Biophys Acta"},{"issue":"23","key":"ref23","doi-asserted-by":"crossref","first-page":"9060","DOI":"10.1128\/MCB.00124-06","article-title":"Gata4 is essential for the maintenance of jejunal-ileal identities in the adult mouse small intestine","volume":"26","author":"T Bosse","year":"2006","journal-title":"Mol Cell Biol"},{"issue":"2","key":"ref24","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1128\/MCB.01185-12","article-title":"Intestinal master transcription factor CDX2 controls chromatin access for partner transcription factor binding","volume":"33","author":"MP Verzi","year":"2013","journal-title":"Mol Cell Biol"},{"issue":"3","key":"ref25","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1016\/j.cellsig.2013.11.032","article-title":"Wnt signaling in adult intestinal stem cells and cancer","volume":"26","author":"M Krausova","year":"2014","journal-title":"Cell Signal"},{"key":"ref26","article-title":"Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha","author":"JM Davison","year":"2017","journal-title":"Genome Res"},{"issue":"7478","key":"ref27","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1038\/nature12687","article-title":"Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis","volume":"504","author":"T Alenghat","year":"2013","journal-title":"Nature"},{"issue":"3","key":"ref28","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1016\/j.cell.2015.01.006","article-title":"Enhancer evolution across 20 mammalian species","volume":"160","author":"D Villar","year":"2015","journal-title":"Cell"},{"issue":"7409","key":"ref29","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/nature11243","article-title":"A map of the cis-regulatory sequences in the mouse genome","volume":"488","author":"Y Shen","year":"2012","journal-title":"Nature"},{"issue":"6","key":"ref30","doi-asserted-by":"crossref","first-page":"2458","DOI":"10.1016\/S0021-9258(18)61526-1","article-title":"The cellular retinol binding protein II gene. Sequence analysis of the rat gene, chromosomal localization in mice and humans, and documentation of its close linkage to the cellular retinol binding protein gene","volume":"262","author":"LA Demmer","year":"1987","journal-title":"J Biol Chem"},{"issue":"12","key":"ref31","doi-asserted-by":"crossref","first-page":"e50810","DOI":"10.1371\/journal.pone.0050810","article-title":"The ileal lipid binding protein is required for efficient absorption and transport of bile acids in the distal portion of the murine small intestine","volume":"7","author":"D Praslickova","year":"2012","journal-title":"PLoS ONE"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1146\/annurev-physiol-021113-170404","article-title":"The role of gut hormone peptide YY in energy and glucose homeostasis: twelve years on","volume":"76","author":"S Manning","year":"2014","journal-title":"Annu Rev Physiol"},{"issue":"7568","key":"ref33","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1038\/nature14966","article-title":"Single-cell messenger RNA sequencing reveals rare intestinal cell types","volume":"525","author":"D Grun","year":"2015","journal-title":"Nature"},{"issue":"5","key":"ref34","doi-asserted-by":"crossref","first-page":"1455","DOI":"10.1053\/gast.2002.32990","article-title":"Inactivation of the transcription factor Elf3 in mice results in dysmorphogenesis and altered differentiation of intestinal epithelium","volume":"122","author":"AY Ng","year":"2002","journal-title":"Gastroenterology"},{"issue":"8","key":"ref35","doi-asserted-by":"crossref","first-page":"2744","DOI":"10.2337\/db14-0993","article-title":"Glucose Tolerance Is Improved in Mice Invalidated for the Nuclear Receptor HNF-4gamma: A Critical Role for Enteroendocrine Cell Lineage","volume":"64","author":"F Baraille","year":"2015","journal-title":"Diabetes"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"2384","DOI":"10.1038\/ncomms3384","article-title":"Microbiome remodelling leads to inhibition of intestinal farnesoid X receptor signalling and decreased obesity","volume":"4","author":"F Li","year":"2013","journal-title":"Nat Commun"},{"issue":"1\u20132","key":"ref37","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1007\/s10735-004-2908-9","article-title":"Epithelial lineages of the small intestine have unique patterns of GATA expression","volume":"36","author":"MR Dusing","year":"2005","journal-title":"J Mol Histol"},{"issue":"7\u201310","key":"ref38","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1016\/j.mod.2011.07.005","article-title":"Wnt signaling specifies and patterns intestinal endoderm","volume":"128","author":"RI Sherwood","year":"2011","journal-title":"Mech Dev"},{"issue":"40","key":"ref39","doi-asserted-by":"crossref","first-page":"5664","DOI":"10.3748\/wjg.v18.i40.5664","article-title":"Role of Smad7 in inflammatory bowel diseases","volume":"18","author":"G Monteleone","year":"2012","journal-title":"World J Gastroenterol"},{"issue":"7422","key":"ref40","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/nature11582","article-title":"Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease","volume":"491","author":"L Jostins","year":"2012","journal-title":"Nature"},{"issue":"2","key":"ref41","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1007\/s12026-015-8651-3","article-title":"Epithelial-specific ETS-1 (ESE1\/ELF3) regulates apoptosis of intestinal epithelial cells in ulcerative colitis via accelerating NF-kappaB activation","volume":"62","author":"L Li","year":"2015","journal-title":"Immunol Res"},{"issue":"3","key":"ref42","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1097\/MIB.0b013e31828028ad","article-title":"Deletion of intestinal epithelial cell STAT3 promotes T-lymphocyte STAT3 activation and chronic colitis following acute dextran sodium sulfate injury in mice","volume":"19","author":"TA Willson","year":"2013","journal-title":"Inflamm Bowel Dis"},{"issue":"7475","key":"ref43","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/nature12599","article-title":"Paneth cells as a site of origin for intestinal inflammation","volume":"503","author":"TE Adolph","year":"2013","journal-title":"Nature"},{"issue":"12","key":"ref44","doi-asserted-by":"crossref","first-page":"1330","DOI":"10.1038\/ng.483","article-title":"Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region","volume":"41","author":"UIG Consortium","year":"2009","journal-title":"Nat Genet"},{"issue":"11","key":"ref45","doi-asserted-by":"crossref","first-page":"1950","DOI":"10.1097\/MIB.0000000000000192","article-title":"Opposite effects of interferon regulatory factor 1 and osteopontin on the apoptosis of epithelial cells induced by TNF-alpha in inflammatory bowel disease","volume":"20","author":"R Tang","year":"2014","journal-title":"Inflamm Bowel Dis"},{"issue":"9","key":"ref46","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1038\/ng.3359","article-title":"Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations","volume":"47","author":"JZ Liu","year":"2015","journal-title":"Nat Genet"},{"issue":"8","key":"ref47","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.1136\/gutjnl-2011-301104","article-title":"Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88","volume":"61","author":"E Larsson","year":"2012","journal-title":"Gut"},{"issue":"7","key":"ref48","doi-asserted-by":"crossref","first-page":"913","DOI":"10.1016\/j.chembiol.2012.05.018","article-title":"Visualization of lipid metabolism in the zebrafish intestine reveals a relationship between NPC1L1-mediated cholesterol uptake and dietary fatty acid","volume":"19","author":"JW Walters","year":"2012","journal-title":"Chem Biol"},{"issue":"5","key":"ref49","doi-asserted-by":"crossref","first-page":"G1080","DOI":"10.1152\/ajpgi.2000.279.5.G1080","article-title":"A duodenum-specific enhancer regulates expression along three axes in the small intestine","volume":"279","author":"MR Dusing","year":"2000","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"issue":"6","key":"ref50","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1194\/jlr.R054114","article-title":"Intestinal transport and metabolism of bile acids","volume":"56","author":"PA Dawson","year":"2015","journal-title":"J Lipid Res"},{"issue":"1","key":"ref51","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1111\/j.1365-2249.2006.03188.x","article-title":"Cathepsins B, L and D in inflammatory bowel disease macrophages and potential therapeutic effects of cathepsin inhibition in vivo","volume":"146","author":"K Menzel","year":"2006","journal-title":"Clin Exp Immunol"},{"issue":"7414","key":"ref52","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"EP Consortium","year":"2012","journal-title":"Nature"},{"issue":"7539","key":"ref53","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1038\/nature14248","article-title":"Integrative analysis of 111 reference human epigenomes","volume":"518","author":"A Kundaje","year":"2015","journal-title":"Nature"},{"issue":"7527","key":"ref54","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/nature13992","article-title":"A comparative encyclopedia of DNA elements in the mouse genome","volume":"515","author":"F Yue","year":"2014","journal-title":"Nature"},{"issue":"15","key":"ref55","doi-asserted-by":"crossref","first-page":"e151","DOI":"10.1093\/nar\/gkt557","article-title":"Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish","volume":"41","author":"M Hiller","year":"2013","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"ref56","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1101\/gr.6929408","article-title":"Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b","volume":"18","author":"DM McGaughey","year":"2008","journal-title":"Genome Res"},{"issue":"3","key":"ref57","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/jbiol130","article-title":"Conservation of core gene expression in vertebrate tissues","volume":"8","author":"ET Chan","year":"2009","journal-title":"J Biol"},{"issue":"3","key":"ref58","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1038\/nprot.2006.230","article-title":"Evaluating the biological relevance of putative enhancers using Tol2 transposon-mediated transgenesis in zebrafish","volume":"1","author":"S Fisher","year":"2006","journal-title":"Nat Protoc"},{"issue":"4","key":"ref59","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"S Heinz","year":"2010","journal-title":"Mol Cell"},{"issue":"11","key":"ref60","first-page":"1417","article-title":"Ets transcription factors in intestinal morphogenesis, homeostasis and disease","volume":"23","author":"P Jedlicka","year":"2008","journal-title":"Histol Histopathol"},{"issue":"6","key":"ref61","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1002\/bies.20581","article-title":"The diverse functions of Kruppel-like factors 4 and 5 in epithelial biology and pathobiology","volume":"29","author":"BB McConnell","year":"2007","journal-title":"Bioessays"},{"issue":"19","key":"ref62","doi-asserted-by":"crossref","first-page":"2702","DOI":"10.1016\/j.yexcr.2011.09.006","article-title":"Intestinal development and differentiation","volume":"317","author":"TK Noah","year":"2011","journal-title":"Exp Cell Res"},{"issue":"3","key":"ref63","doi-asserted-by":"crossref","first-page":"G277","DOI":"10.1152\/ajpgi.00362.2011","article-title":"Current and emerging approaches to define intestinal epithelium-specific transcriptional networks","volume":"302","author":"AK Olsen","year":"2012","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"issue":"12","key":"ref64","doi-asserted-by":"crossref","first-page":"2399","DOI":"10.1101\/gr.138776.112","article-title":"CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters","volume":"22","author":"R Fenouil","year":"2012","journal-title":"Genome Res"},{"issue":"7492","key":"ref65","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nature12974","article-title":"Two independent transcription initiation codes overlap on vertebrate core promoters","volume":"507","author":"V Haberle","year":"2014","journal-title":"Nature"},{"issue":"2","key":"ref66","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1046\/j.1432-1033.2003.03932.x","article-title":"Spatio-temporal distribution of cellular retinol-binding protein gene transcripts (CRBPI and CRBPII) in the developing and adult zebrafish (Danio rerio)","volume":"271","author":"RZ Liu","year":"2004","journal-title":"Eur J Biochem"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1016\/S0091-679X(04)77027-2","article-title":"Spatial and temporal expression of the zebrafish genome by large-scale in situ hybridization screening","volume":"77","author":"B Thisse","year":"2004","journal-title":"Methods Cell Biol"},{"issue":"3","key":"ref68","doi-asserted-by":"crossref","first-page":"e1002585","DOI":"10.1371\/journal.pgen.1002585","article-title":"Intronic cis-regulatory modules mediate tissue-specific and microbial control of angptl4\/fiaf transcription","volume":"8","author":"JG Camp","year":"2012","journal-title":"PLoS Genet"},{"issue":"3","key":"ref69","doi-asserted-by":"crossref","first-page":"1850","DOI":"10.1074\/jbc.M114.620211","article-title":"Transcription factors GATA4 and HNF4A control distinct aspects of intestinal homeostasis in conjunction with transcription factor CDX2","volume":"290","author":"AK San Roman","year":"2015","journal-title":"J Biol Chem"},{"issue":"13","key":"ref70","doi-asserted-by":"crossref","first-page":"3325","DOI":"10.1111\/j.1742-4658.2008.06480.x","article-title":"Spatio-temporal distribution of fatty acid-binding protein 6 (fabp6) gene transcripts in the developing and adult zebrafish (Danio rerio)","volume":"275","author":"FA Alves-Costa","year":"2008","journal-title":"FEBS J"},{"issue":"3","key":"ref71","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1038\/ncb3106","article-title":"Developmental regulation of apical endocytosis controls epithelial patterning in vertebrate tubular organs","volume":"17","author":"AE Rodriguez-Fraticelli","year":"2015","journal-title":"Nat Cell Biol"},{"issue":"1","key":"ref72","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1002\/gene.10248","article-title":"Zebrafish intestinal fatty acid binding protein (I-FABP) gene promoter drives gut-specific expression in stable transgenic fish","volume":"38","author":"GM Her","year":"2004","journal-title":"Genesis"},{"issue":"1","key":"ref73","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1053\/j.gastro.2011.03.042","article-title":"Microbial colonization induces dynamic temporal and spatial patterns of NF-kappaB activation in the zebrafish digestive tract","volume":"141","author":"M Kanther","year":"2011","journal-title":"Gastroenterology"},{"issue":"2","key":"ref74","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/j.taap.2007.04.018","article-title":"Up-regulation of early growth response gene 1 (EGR-1) via ERK1\/2 signals attenuates sulindac sulfide-mediated cytotoxicity in the human intestinal epithelial cells","volume":"223","author":"Y Moon","year":"2007","journal-title":"Toxicol Appl Pharmacol"},{"issue":"4","key":"ref75","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1016\/j.cell.2013.04.020","article-title":"Homeostasis in intestinal epithelium is orchestrated by the circadian clock and microbiota cues transduced by TLRs","volume":"153","author":"A Mukherji","year":"2013","journal-title":"Cell"},{"issue":"1","key":"ref76","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1093\/intimm\/11.1.47","article-title":"Serum response elements activate and cAMP responsive elements inhibit expression of transcription factor Egr-1 in synovial fibroblasts of rheumatoid arthritis patients","volume":"11","author":"WK Aicher","year":"1999","journal-title":"Int Immunol"},{"issue":"5\u20136","key":"ref77","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1007\/s002960050086","article-title":"Analysis of functional elements in the human Egr-1 gene promoter","volume":"18","author":"WK Aicher","year":"1999","journal-title":"Rheumatol Int"},{"issue":"13","key":"ref78","doi-asserted-by":"crossref","first-page":"4454","DOI":"10.1182\/blood-2002-02-0415","article-title":"The proximal serum response element in the Egr-1 promoter mediates response to thrombin in primary human endothelial cells","volume":"100","author":"SQ Wu","year":"2002","journal-title":"Blood"},{"issue":"24","key":"ref79","doi-asserted-by":"crossref","first-page":"13763","DOI":"10.1073\/pnas.231499798","article-title":"Degeneracy and complexity in biological systems","volume":"98","author":"GM Edelman","year":"2001","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"12","key":"ref80","doi-asserted-by":"crossref","first-page":"1277","DOI":"10.1038\/ni.2760","article-title":"T cell development requires constraint of the myeloid regulator C\/EBP-alpha by the Notch target and transcriptional repressor Hes1","volume":"14","author":"ME De Obaldia","year":"2013","journal-title":"Nat Immunol"},{"issue":"1","key":"ref81","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1007\/s00441-014-1888-7","article-title":"Dynamic expression and roles of Hes factors in neural development","volume":"359","author":"R Kageyama","year":"2015","journal-title":"Cell Tissue Res"},{"issue":"20","key":"ref82","doi-asserted-by":"crossref","first-page":"17672","DOI":"10.1074\/jbc.M111.236612","article-title":"DDR1 receptor tyrosine kinase promotes prosurvival pathway through Notch1 activation","volume":"286","author":"HG Kim","year":"2011","journal-title":"J Biol Chem"},{"issue":"1","key":"ref83","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1038\/71657","article-title":"Control of endodermal endocrine development by Hes-1","volume":"24","author":"J Jensen","year":"2000","journal-title":"Nat Genet"},{"issue":"2","key":"ref84","doi-asserted-by":"crossref","first-page":"e1000363","DOI":"10.1371\/journal.pgen.1000363","article-title":"hnRNP I inhibits Notch signaling and regulates intestinal epithelial homeostasis in the zebrafish","volume":"5","author":"J Yang","year":"2009","journal-title":"PLoS Genet"},{"issue":"2","key":"ref85","doi-asserted-by":"crossref","first-page":"e55620","DOI":"10.1371\/journal.pone.0055620","article-title":"Bacteria regulate intestinal epithelial cell differentiation factors both in vitro and in vivo","volume":"8","author":"S Becker","year":"2013","journal-title":"PLoS ONE"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"3963","DOI":"10.1038\/srep03963","article-title":"Hes1 is involved in the self-renewal and tumourigenicity of stem-like cancer cells in colon cancer","volume":"4","author":"F Gao","year":"2014","journal-title":"Sci Rep"},{"issue":"6","key":"ref87","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1242\/dev.072439","article-title":"The metalloproteinase inhibitor Reck is essential for zebrafish DRG development","volume":"139","author":"A Prendergast","year":"2012","journal-title":"Development"},{"issue":"6547","key":"ref88","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/377355a0","article-title":"Signalling downstream of activated mammalian Notch","volume":"377","author":"S Jarriault","year":"1995","journal-title":"Nature"},{"issue":"10","key":"ref89","doi-asserted-by":"crossref","first-page":"898","DOI":"10.1016\/j.mod.2009.07.002","article-title":"Notch-responsive cells initiate the secondary transition in larval zebrafish pancreas","volume":"126","author":"MJ Parsons","year":"2009","journal-title":"Mech Dev"},{"issue":"3","key":"ref90","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1136\/gutjnl-2015-310283","article-title":"Microbiota-induced obesity requires farnesoid X receptor","volume":"66","author":"A Parseus","year":"2017","journal-title":"Gut"},{"issue":"6","key":"ref91","doi-asserted-by":"crossref","first-page":"1071","DOI":"10.1242\/dev.069070","article-title":"The role of Hes genes in intestinal development, homeostasis and tumor formation","volume":"139","author":"T Ueo","year":"2012","journal-title":"Development"},{"issue":"5","key":"ref92","doi-asserted-by":"crossref","first-page":"1329","DOI":"10.1084\/jem.20060268","article-title":"E proteins and Notch signaling cooperate to promote T cell lineage specification and commitment","volume":"203","author":"T Ikawa","year":"2006","journal-title":"J Exp Med"},{"issue":"8","key":"ref93","doi-asserted-by":"crossref","first-page":"5687","DOI":"10.1074\/jbc.M111.286484","article-title":"Novel cis-regulatory modules control expression of the Hairy and Enhancer of Split-1 (HES1) transcription factor in myoblasts","volume":"287","author":"DM Jeziorska","year":"2012","journal-title":"J Biol Chem"},{"issue":"10","key":"ref94","doi-asserted-by":"crossref","first-page":"e25785","DOI":"10.1371\/journal.pone.0025785","article-title":"Notch lineages and activity in intestinal stem cells determined by a new set of knock-in mice","volume":"6","author":"S Fre","year":"2011","journal-title":"PLoS ONE"},{"issue":"1\u20133","key":"ref95","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/S0014-5793(02)03896-6","article-title":"Candidate markers for stem and early progenitor cells, Musashi-1 and Hes1, are expressed in crypt base columnar cells of mouse small intestine","volume":"535","author":"T Kayahara","year":"2003","journal-title":"FEBS Lett"},{"issue":"2","key":"ref96","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/j.ydbio.2011.12.009","article-title":"Origin of the brush cell lineage in the mouse intestinal epithelium","volume":"362","author":"M Bjerknes","year":"2012","journal-title":"Dev Biol"},{"issue":"12","key":"ref97","doi-asserted-by":"crossref","first-page":"4248","DOI":"10.1128\/MCB.01894-06","article-title":"Cooperative interaction between hepatocyte nuclear factor 4 alpha and GATA transcription factors regulates ATP-binding cassette sterol transporters ABCG5 and ABCG8","volume":"27","author":"K Sumi","year":"2007","journal-title":"Mol Cell Biol"},{"issue":"2","key":"ref98","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/labinvest.2015.144","article-title":"The evolving roles of canonical WNT signaling in stem cells and tumorigenesis: implications in targeted cancer therapies","volume":"96","author":"K Yang","year":"2016","journal-title":"Lab Invest"},{"issue":"Suppl 1","key":"ref99","doi-asserted-by":"crossref","first-page":"4570","DOI":"10.1073\/pnas.1000072107","article-title":"Epithelial cell proliferation in the developing zebrafish intestine is regulated by the Wnt pathway and microbial signaling via Myd88","volume":"108","author":"SE Cheesman","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"4","key":"ref100","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1038\/sj.embor.7400638","article-title":"Adenomatous polyposis coli-deficient zebrafish are susceptible to digestive tract neoplasia","volume":"7","author":"AP Haramis","year":"2006","journal-title":"EMBO Rep"},{"issue":"3","key":"ref101","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1136\/gut.2006.093310","article-title":"The canonical Wnt signalling pathway and its APC partner in colon cancer development","volume":"56","author":"J Schneikert","year":"2007","journal-title":"Gut"},{"issue":"7446","key":"ref102","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1038\/nature12111","article-title":"The zebrafish reference genome sequence and its relationship to the human genome","volume":"496","author":"K Howe","year":"2013","journal-title":"Nature"},{"key":"ref103","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1186\/1471-2164-13-246","article-title":"Profiling of gene duplication patterns of sequenced teleost genomes: evidence for rapid lineage-specific genome expansion mediated by recent tandem duplications","volume":"13","author":"J Lu","year":"2012","journal-title":"BMC Genomics"},{"issue":"12","key":"ref104","doi-asserted-by":"crossref","first-page":"1890","DOI":"10.1101\/gr.164800","article-title":"Zebrafish comparative genomics and the origins of vertebrate chromosomes","volume":"10","author":"JH Postlethwait","year":"2000","journal-title":"Genome Res"},{"issue":"6","key":"ref105","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1007\/s00438-014-0889-2","article-title":"Whole-genome duplication in teleost fishes and its evolutionary consequences","volume":"289","author":"SM Glasauer","year":"2014","journal-title":"Mol Genet Genomics"},{"issue":"10","key":"ref106","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1016\/j.tig.2004.08.001","article-title":"Subfunction partitioning, the teleost radiation and the annotation of the human genome","volume":"20","author":"J Postlethwait","year":"2004","journal-title":"Trends Genet"},{"issue":"5771","key":"ref107","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1126\/science.1124070","article-title":"Conservation of RET regulatory function from human to zebrafish without sequence similarity","volume":"312","author":"S Fisher","year":"2006","journal-title":"Science"},{"issue":"7527","key":"ref108","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1038\/nature13985","article-title":"Principles of regulatory information conservation between mouse and human","volume":"515","author":"Y Cheng","year":"2014","journal-title":"Nature"},{"issue":"7","key":"ref109","doi-asserted-by":"crossref","first-page":"1385","DOI":"10.1242\/dev.084459","article-title":"Conserved non-coding elements and cis regulation: actions speak louder than words","volume":"140","author":"AC Nelson","year":"2013","journal-title":"Development"},{"issue":"3","key":"ref110","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1038\/nrg2522","article-title":"Nucleosome positioning and gene regulation: advances through genomics","volume":"10","author":"C Jiang","year":"2009","journal-title":"Nat Rev Genet"},{"issue":"7393","key":"ref111","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1038\/nature10985","article-title":"Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function","volume":"484","author":"CR Lickwar","year":"2012","journal-title":"Nature"},{"issue":"6123","key":"ref112","doi-asserted-by":"crossref","first-page":"1074","DOI":"10.1126\/science.1232542","article-title":"Genome-wide quantitative enhancer activity maps identified by STARR-seq","volume":"339","author":"CD Arnold","year":"2013","journal-title":"Science"},{"key":"ref113","article-title":"Molecular classification of Crohn&apos;s disease reveals two clinically relevant subtypes","author":"M Weiser","year":"2016","journal-title":"Gut"},{"issue":"2","key":"ref114","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1038\/nprot.2011.444","article-title":"Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA","volume":"7","author":"JM Simon","year":"2012","journal-title":"Nat Protoc"},{"issue":"9","key":"ref115","doi-asserted-by":"crossref","first-page":"2178","DOI":"10.1097\/MIB.0000000000000478","article-title":"MicroRNAs Classify Different Disease Behavior Phenotypes of Crohn&apos;s Disease and May Have Prognostic Utility","volume":"21","author":"BC Peck","year":"2015","journal-title":"Inflamm Bowel Dis"},{"issue":"7","key":"ref116","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1093\/bioinformatics\/btq057","article-title":"Fast and SNP-tolerant detection of complex variants and splicing in short reads","volume":"26","author":"TD Wu","year":"2010","journal-title":"Bioinformatics"},{"issue":"21","key":"ref117","doi-asserted-by":"crossref","first-page":"2839","DOI":"10.1093\/bioinformatics\/btp527","article-title":"TagDust\u2014a program to eliminate artifacts from next generation sequencing data","volume":"25","author":"T Lassmann","year":"2009","journal-title":"Bioinformatics"},{"key":"ref118","first-page":"265","article-title":"A functional biology of sticklebacks","author":"RJ Wootton","year":"1984"},{"issue":"3","key":"ref119","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nprot.2012.016","article-title":"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks","volume":"7","author":"C Trapnell","year":"2012","journal-title":"Nat Protoc"},{"key":"ref120","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.margen.2013.04.001","article-title":"Genomic organization and transcription of the medaka and zebrafish cellular retinol-binding protein (rbp) genes","volume":"11","author":"MB Parmar","year":"2013","journal-title":"Mar Genomics"},{"issue":"1","key":"ref121","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"W Huang da","year":"2009","journal-title":"Nat Protoc"},{"key":"ref122","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1186\/1471-2105-14-128","article-title":"Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool","volume":"14","author":"EY Chen","year":"2013","journal-title":"BMC Bioinformatics"},{"issue":"9","key":"ref123","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1093\/bioinformatics\/bth078","article-title":"Open source clustering software","volume":"20","author":"MJ de Hoon","year":"2004","journal-title":"Bioinformatics"},{"issue":"9","key":"ref124","doi-asserted-by":"crossref","first-page":"1728","DOI":"10.1038\/nprot.2012.101","article-title":"Identifying ChIP-seq enrichment using MACS","volume":"7","author":"J Feng","year":"2012","journal-title":"Nat Protoc"},{"issue":"11","key":"ref125","doi-asserted-by":"crossref","first-page":"3088","DOI":"10.1002\/dvdy.21343","article-title":"The Tol2kit: a multisite gateway-based construction kit for Tol2 transposon transgenesis constructs","volume":"236","author":"KM Kwan","year":"2007","journal-title":"Dev Dyn"},{"key":"ref126","article-title":"The Zebrafish Book: A Guide for the Laboratory Use of Zebrafish (Danio Rerio): Institute of Neuroscience","author":"M Westerfield","year":"2000"},{"key":"ref127","article-title":"A classification system for zebrafish adipose tissues","author":"JE Minchin","year":"2017","journal-title":"Dis Model Mech"}],"container-title":["PLOS Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pbio.2002054","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,8,1]],"date-time":"2022-08-01T18:32:11Z","timestamp":1659378731000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pbio.2002054"}},"subtitle":[],"editor":[{"given":"Mary","family":"Mullins","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,8,29]]},"references-count":127,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2017,8,29]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pbio.2002054","relation":{},"ISSN":["1545-7885"],"issn-type":[{"value":"1545-7885","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,8,29]]}}}