HNF4 factors control chromatin accessibility and are redundantly required for maturation of the fetal intestine

Abstract

18As an embryo matures into a fetus, cells undergo remarkable transitions, accompanied by shifts 19 in transcription factor regulatory networks and chromatin landscapes. The mechanisms of these 20 developmental transitions are not completely understood. The embryonic intestine transitions 21 from a rapidly proliferating tube with pseudostratified epithelium prior to embryonic day (E) 22 14.5, to an exquisitely folded columnar epithelium in the fetus. We sought to define factors that 23 drive fetal maturation of the intestine. ATAC-seq profiling revealed a dramatic restructuring of 24intestinal chromatin during the embryonic-to-fetal transition, with CDX2 transcription factor 25 motifs abundant at chromatin-accessible regions of the embryo, and hepatocyte nuclear factor 26 4 (HNF4) transcription factor motifs the most abundant in the fetal stages. Genetic inactivation 27of Hnf4and its paralog, Hnf4, revealed that HNF4 factors are redundantly and vitally required 28 for fetal maturation. In the embryo, CDX2 binds to and activates Hnf4 gene loci to drive HNF4 29 expression at fetal stages. HNF4 and CDX2 transcription factors then occupy shared genomic 30 regulatory sites and are required for chromatin accessibility at genes expressed in the maturing 31 fetal intestine. Thus, intestinal transcription factor regulatory networks shift to accompany 32 changing chromatin landscapes and gene expression profiles that occur during the transition of 33 an embryonic tissue to its mature state. 34 35 KEY WORDS 36 HNF4 transcription factors, Developing intestine, Maturation, Chromatin 37 38 39

Control of Cell Identity by the Nuclear Receptor HNF4 in Organ Pathophysiology

“…Many studies, including several using cell-specific HNF4 deletion in mice, have supported the critical role of HNF4 in the functions of the aforementioned organs (reviewed in [ 54 ]). This is notably underlined by the role of HNF4 in the acquisition and maintenance of cell differentiation including hepatocytes [ 56 ], enterocytes [ 57 , 58 , 59 ], and renal proximal tubular cells [ 60 ]. HNF4 is not required for engagement into these lineages but rather exerts essential roles during later specification stages giving rise to fully differentiated cells [ 60 , 61 ].…”

“…Contrary to the liver, deletion of the Hnf4a gene alone only triggers a moderate intestinal phenotype [ 75 ]. This was recently shown to be due to redundant functions exerted by HNF4A and HNF4G [ 57 ]. In this context, deletion of both Hnf4a and Hnf4g is required to severely impact the intestine through impaired fetal maturation [ 57 , 58 ].…”

“…In addition to its key role in TF networks controlling hepatocellular identity, HNF4A is also a central node of transcriptional regulatory networks promoting and stabilizing cell identity in other endodermal organs including the pancreas [ 94 ] and the intestine [ 95 ] where it acts redundantly with its paralog HNF4G to regulate enterocyte identity [ 57 ]. Reminiscent of the observations in liver, HNF4 displays extensive autoregulation and cross regulation with other enterocyte TFs, as exemplified by the reciprocal activation of HNF4 and SMAD Family Member 4 (SMAD4) in murine intestinal villi [ 58 ].…”

“…Numerous studies have demonstrated that HNF4 controls the expression of genes involved in tissue-specific functions of adult endodermal organs including the liver, the pancreas, and the intestine [ 57 , 94 , 100 ], through widespread binding to their cis-regulatory modules (CRMs). While enhancers traditionally display strong cell-specific activities as compared with promoters [ 101 , 102 ], HNF4A was found to bind not only to liver-specific enhancers and also substantially to gene promoters in adult liver [ 103 ].…”

“…Interaction with the TATA-Box Binding Protein Associated Factor 4 (TAF4) subunit of the general transcription factor IID (TFIID), a member of the transcription preinitiation complex, stabilizes HNF4A occupancy of promoters [ 104 ] where it facilitates recruitment of RNA Polymerase II (POLR2) [ 73 ]. A fraction of HNF4 promoter-bound genes are involved in housekeeping functions, probably more related to the requirement for cell-specific control of cellular homeostasis including HNF4-mediated regulation of cell proliferation in hepatocytes or intestinal cells [ 57 , 59 , 64 , 65 , 105 ]. At liver identity genes, HNF4A recruitment to enhancers, organized into super-enhancers, add up to promoter binding [ 7 ].…”