scholarly journals FoxA Proteins Regulate H19 Endoderm Enhancer E1 and Exhibit Developmental Changes in Enhancer Binding In Vivo

2004 ◽  
Vol 24 (21) ◽  
pp. 9601-9609 ◽  
Author(s):  
Lingyun Long ◽  
Brett T. Spear
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Fetal Liver ◽  
Carcinoma Cells ◽  
Specific Factor ◽  
Specific Expression ◽  
Tissue Specific ◽  
Parietal Endoderm ◽  
F9 Embryonal Carcinoma Cells

ABSTRACT Multiple enhancers govern developmental and tissue-specific expression of the H19-Igf2 locus, but factors that bind these elements have not been identified. Using chromatin immunoprecipitation, we have found two FoxA binding sites in the H19 E1 enhancer. Mutating these sites diminishes E1 activity in hepatoma cells. Additional chromatin immunoprecipitations show that FoxA binds to E1 in fetal liver, where H19 is abundantly expressed, but that binding decreases in adult liver, where H19 is no longer transcribed, even though FoxA proteins are present at both times. FoxA proteins are induced when F9 embryonal carcinoma cells differentiate into visceral endoderm (VE) and parietal endoderm (PE). We show that FoxA binds E1 in VE cells, where H19 is expressed, but not in PE cells, where H19 is silent. This correlation between FoxA binding and H19 expression indicates a role for FoxA in regulating H19, including developmental activation in the yolk sac and liver and postnatal repression in the liver. This is the first demonstration of a tissue-specific factor involved in developmental control of H19 expression. These data also indicate that the presence of FoxA proteins is not sufficient for binding but that additional mechanisms must govern the accessibility of FoxA proteins to their cognate binding sites within the H19 E1 enhancer.

scholarly journals Uncovering tissue-specific binding features from differential deep learning

2019 ◽  
Author(s):  
Mike Phuycharoen ◽  
Peyman Zarrineh ◽  
Laure Bridoux ◽  
Shilu Amin ◽  
Marta Losa ◽  
...  
Keyword(s):  
Deep Learning ◽  
Binding Sites ◽  
Specific Binding ◽  
Specific Expression ◽  
Tissue Specific ◽  
Dimensional Classification ◽  
Branchial Arches ◽  
Gradient Based ◽  
Differential Binding

ABSTRACTMotivationTranscription factors (TFs) can bind DNA in a cooperative manner, enabling a mutual increase in occupancy. Through this type of interaction, alternative binding sites can be preferentially bound in different tissues to regulate tissue-specific expression programmes. Recently, deep learning models have become state-of-the-art in various pattern analysis tasks, including applications in the field of genomics. We therefore investigate the application of convolutional neural network (CNN) models to the discovery of sequence features determining cooperative and differential TF binding across tissues.ResultsWe analyse ChIP-seq data from MEIS, TFs which are broadly expressed across mouse branchial arches, and HOXA2, which is expressed in the second and more posterior branchial arches. By developing models predictive of MEIS differential binding in all three tissues we are able to accurately predict HOXA2 co-binding sites. We evaluate transfer-like and multitask approaches to regularising the high-dimensional classification task with a larger regression dataset, allowing for creation of deeper and more accurate models. We test the performance of perturbation and gradient-based attribution methods in identifying the HOXA2 sites from differential MEIS data. Our results show that deep regularised models significantly outperform shallow CNNs as well as k-mer methods in the discovery of tissue-specific sites bound in vivo.AvailabilityFor implementation and models please visit https://doi.org/10.5281/zenodo.2635463.

scholarly journals Uncovering tissue-specific binding features from differential deep learning

2020 ◽  
Vol 48 (5) ◽  
pp. e27-e27 ◽  
Author(s):  
Mike Phuycharoen ◽  
Peyman Zarrineh ◽  
Laure Bridoux ◽  
Shilu Amin ◽  
Marta Losa ◽  
...  
Keyword(s):  
Deep Learning ◽  
Binding Sites ◽  
Specific Binding ◽  
Specific Expression ◽  
Tissue Specific ◽  
Dimensional Classification ◽  
Branchial Arches ◽  
Gradient Based ◽  
Differential Binding

Abstract Transcription factors (TFs) can bind DNA in a cooperative manner, enabling a mutual increase in occupancy. Through this type of interaction, alternative binding sites can be preferentially bound in different tissues to regulate tissue-specific expression programmes. Recently, deep learning models have become state-of-the-art in various pattern analysis tasks, including applications in the field of genomics. We therefore investigate the application of convolutional neural network (CNN) models to the discovery of sequence features determining cooperative and differential TF binding across tissues. We analyse ChIP-seq data from MEIS, TFs which are broadly expressed across mouse branchial arches, and HOXA2, which is expressed in the second and more posterior branchial arches. By developing models predictive of MEIS differential binding in all three tissues, we are able to accurately predict HOXA2 co-binding sites. We evaluate transfer-like and multitask approaches to regularizing the high-dimensional classification task with a larger regression dataset, allowing for the creation of deeper and more accurate models. We test the performance of perturbation and gradient-based attribution methods in identifying the HOXA2 sites from differential MEIS data. Our results show that deep regularized models significantly outperform shallow CNNs as well as k-mer methods in the discovery of tissue-specific sites bound in vivo.

scholarly journals Two-Step Regulation of Ad4BP/SF-1 Gene Transcription during Fetal Adrenal Development: Initiation by a Hox-Pbx1-Prep1 Complex and Maintenance via Autoregulation by Ad4BP/SF-1

2006 ◽  
Vol 26 (11) ◽  
pp. 4111-4121 ◽  
Author(s):  
Mohamad Zubair ◽  
Satoru Ishihara ◽  
Sanae Oka ◽  
Katsuzumi Okumura ◽  
Ken-ichirou Morohashi
Keyword(s):  
Adrenal Cortex ◽  
Binding Sites ◽  
Orphan Nuclear Receptor ◽  
Specific Expression ◽  
Steroidogenic Factor 1 ◽  
Tissue Specific ◽  
Adrenal Cells ◽  
Tissue Specific Expression ◽  
And Function ◽  
Intron 4

ABSTRACT The orphan nuclear receptor Ad4BP/SF-1 (adrenal 4 binding protein/steroidogenic factor 1) is essential for the proper development and function of reproductive and steroidogenic tissues. Although the expression of Ad4BP/SF-1 is specific for those tissues, the mechanisms underlying this tissue-specific expression remain unknown. In this study, we used transgenic mouse assays to examine the regulation of the tissue-specific expression of Ad4BP/SF-1. An investigation of the entire Ad4BP/SF-1 gene locus revealed a fetal adrenal enhancer (FAdE) in intron 4 containing highly conserved binding sites for Pbx-Prep, Pbx-Hox, and Ad4BP/SF-1. Transgenic assays revealed that the Ad4 sites, together with Ad4BP/SF-1, develop an autoregulatory loop and thereby maintain transcription, while the Pbx/Prep and Pbx/Hox sites initiate transcription prior to the establishment of the autoregulatory loop. Indeed, a limited number of Hox family members were found to be expressed in the adrenal primordia. Whether a true fetal-type adrenal cortex is present in mice remained controversial, and this argument was complicated by the postnatal development of the so-called X zone. Using transgenic mice with lacZ driven by the FAdE, we clearly identified a fetal adrenal cortex in mice, and the X zone is the fetal adrenal cells accumulated at the juxtamedullary region after birth.

In vitro and in vivo analysis of murine lipoprotein lipase gene promoter: tissue-specific expression

1995 ◽  
Vol 268 (2) ◽  
pp. E213-E218 ◽  
Author(s):  
J. M. Gimble ◽  
X. Hua ◽  
F. Wanker ◽  
C. Morgan ◽  
C. Robinson ◽  
...  
Keyword(s):  
Transgenic Mice ◽  
Lipoprotein Lipase ◽  
Reporter Gene ◽  
Luciferase Reporter ◽  
Luciferase Reporter Gene ◽  
Specific Expression ◽  
Tissue Specific ◽  
Brown Adipose ◽  
Octamer Motif

Lipoprotein lipase, an enzyme of central importance to lipid metabolism, is most abundant in adipose tissues, cardiac and skeletal muscle, and portions of the brain. The current work examined the murine lipoprotein lipase promoter using transient transfection, gel-retention analyses, and transgenic mice. Maximum expression of the luciferase reporter gene in transfected cells was observed with -101 bp of the promoter. Nuclear extracts from tissues expressing lipoprotein lipase contained DNA binding proteins that recognize the CCAAT box (-64 bp) and an octamer motif (-46 bp); this combination of factors was absent in nonexpressing tissues. Transgenic mice from three of five founders prepared with -1,824-bp promoter constructs expressed the luciferase reporter gene at highest levels in brown adipose tissue and brain. These findings suggest that the -1,824-bp promoter region contains sequence elements responsible for the tissue-specific transcription of lipoprotein lipase in vivo.

Distinct functional contributions of 2 GABP–NRF-2 recognition sites within the context of the human TOMM70 promoter

2006 ◽  
Vol 84 (5) ◽  
pp. 813-822 ◽  
Author(s):  
José R. Blesa ◽  
José Hernández-Yago
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Site Directed Mutagenesis ◽  
Outer Mitochondrial Membrane ◽  
Mobility Shift ◽  
A Subunit ◽  
Expression Evidence ◽  
Electrophoretic Mobility Shift Assays

TOMM70 is a subunit of the outer mitochondrial membrane translocase that plays a major role as a receptor of hydrophobic preproteins targeted to mitochondria. We have previously reported 2 binding sites for the transcription factor GABP–NRF-2 in the promoter region of the human TOMM70 gene that are important in activating transcription. To assess the functionality and actual role of these sites, chromatin immunoprecipitation, site-directed mutagenesis, and electrophoretic mobility shift assays were carried out. We conclude that GABP–NRF-2 binds in vivo to the TOMM70 promoter, and that the 2 GABP–NRF-2 binding sites of the promoter have different functional contributions in promoting TOMM70 expression. Evidence is provided that they work in an additive manner as single sites.

scholarly journals Interaction of a tissue-specific factor with an essential rat growth hormone gene promoter element.

1987 ◽  
Vol 7 (3) ◽  
pp. 1193-1197 ◽  
Author(s):  
B L West ◽  
D F Catanzaro ◽  
S H Mellon ◽  
P A Cattini ◽  
J D Baxter ◽  
...  
Keyword(s):  
Growth Hormone ◽  
Dna Sequences ◽  
Site Directed Mutagenesis ◽  
Specific Factor ◽  
Growth Hormone Gene ◽  
Base Pairs ◽  
Hybrid Gene ◽  
Specific Expression ◽  
Tissue Specific ◽  
Rat Growth

Rat growth hormone (rGH) gene expression is normally restricted to the anterior pituitary. As a model of this tissue specificity, we compared the transient expression of an rGH-chloramphenicol acetyltransferase (CAT) hybrid gene in rGH-producing rat pituitary tumor (GC) cells and in non-rGH-producing rat fibroblast (rat-2) cells. Deletion analysis of the rGH portion of this hybrid gene demonstrated that DNA sequences within 140 base pairs 5' to the rGH gene were sufficient for correct cell type-specific expression. Deletion of an additional 35 base pairs of the rGH 5'-flanking DNA resulted in a loss of expression of the transfected hybrid gene and correlated with the interaction of a putative trans-acting factor with this region of the rGH promoter. This factor was detectable by DNase I footprinting in a crude nuclear extract from GC cells but not from rat-2 cells. Site-directed mutagenesis of the footprint region caused complete loss of expression of a hybrid gene containing 530 base pairs 5' to the rGH gene. Thus, the interaction of this factor, which we term GC2, is likely to be essential for the tissue-specific expression of the rGH gene.

Human glucagon gene promoter sequences regulating tissue-specific versus nutrient-regulated gene expression

2002 ◽  
Vol 282 (1) ◽  
pp. R173-R183 ◽  
Author(s):  
Min Nian ◽  
Jun Gu ◽  
David M. Irwin ◽  
Daniel J. Drucker
Keyword(s):  
Gene Expression ◽  
Gene Promoter ◽  
Regulatory Sequences ◽  
Dependent Manner ◽  
Specific Expression ◽  
Tissue Specific ◽  
High Fiber ◽  
Fiber Diet ◽  
Regulated Gene Expression

The glucagon-like peptides (GLPs) are synthesized and secreted in a nutrient-dependent manner in rodents; however, the factors regulating human GLP-1 and GLP-2 biosynthesis remain unclear. To understand how nutrients regulate human proglucagon gene expression, we studied the expression of a human proglucagon promoter-growth hormone (GH) transgene in 1.6 human glucagon-GH transgenic mice. Fasting-refeeding significantly decreased and increased the levels of circulating mouse insulin and transgene-derived hGH ( P < 0.05 fasting vs. refeeding) and decreased and upregulated, respectively, the levels of endogenous mouse proglucagon RNA in the ileum but not in the jejunum or colon. High-fiber feeding significantly increased the levels of glucose-stimulated circulating hGH and upregulated levels of mouse intestinal proglucagon gene expression in the jejunum, ileum, and colon ( P < 0.05, 0 vs. 30% fiber diet). In contrast, neither fasting-refeeding nor a high-fiber diet upregulated the expression of the human proglucagon promoter-hGH transgene. These findings demonstrate that human proglucagon gene regulatory sequences specifying tissue-specific expression in gut endocrine cells are not sufficient for recognition of energy-derived signals regulating murine glucagon gene expression in enteroendocrine cells in vivo.

Placental lactogen and GH receptors in sheep liver: striking differences in ontogeny and function

1986 ◽  
Vol 251 (3) ◽  
pp. E328-E333 ◽  
Author(s):  
M. Freemark ◽  
M. Comer ◽  
S. Handwerger
Keyword(s):  
Binding Sites ◽  
Specific Binding ◽  
Fetal Liver ◽  
Late Gestation ◽  
Placental Lactogen ◽  
Ontogenetic Changes ◽  
Pregnant Sheep ◽  
Hepatic Receptors ◽  
Ovine Fetal

To determine whether changes in the relative biological potencies of ovine placental lactogen (oPL) and ovine growth hormone (oGH) during development derive from ontogenetic changes in the binding of these hormones to hepatic receptors, we have compared the binding of 125I-oPL and 125I-oGH to hepatic membranes from fetal lambs and pregnant sheep at mid- and late gestation and from postnatal sheep at 1 day to 7 mo of age. Specific high-affinity 125I-oPL binding sites in ovine fetal liver were detected as early as day 70 of gestation (term = 145 days), and the number of fetal 125I-oPL binding sites increased progressively throughout the latter half of gestation, reaching a maximum (11.2 fmol/mg protein) at 3-7 days before parturition. The potency of oPL (Kd 0.27 nM) in competing for 125I-oPL binding sites was 90 and 1,300 times greater than that of oGH and ovine prolactin, respectively. Although the number of fetal 125I-oPL binding sites increased throughout pregnancy, there was little or no specific binding of 125I-oGH noted in the fetus. Treatment of fetal liver membranes with 4 M MgCl2 did not enhance the subsequent specific binding of 125I-oGH, suggesting that the low specific binding of oGH did not result from occupation of hepatic receptors by endogenous circulating oPL or oGH. In contrast, MgCL2 treatment markedly increased the apparent number of fetal 125I-oPL binding sites, suggesting that oPL receptors in fetal liver are partly saturated in vivo by oPL.(ABSTRACT TRUNCATED AT 250 WORDS)

Tissue-specific expression of the rat insulin 1 gene in vivo requires both the enhancer and promoter regions

1995 ◽  
Vol 58 (4) ◽  
pp. 291-295 ◽  
Author(s):  
Françoise Dandoy-Dron ◽  
Jean-Michel Itier ◽  
Eliane Monthioux ◽  
Danielle Bucchini ◽  
Jacques Jami
Keyword(s):  
Promoter Regions ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression

scholarly journals Chorionic enhancer is dispensable for regulated expression of the human renin gene

2008 ◽  
Vol 294 (2) ◽  
pp. R279-R287 ◽  
Author(s):  
Xiyou Zhou ◽  
Curt D. Sigmund
Keyword(s):  
Cellular Localization ◽  
Artificial Chromosome ◽  
Convincing Evidence ◽  
Specific Cell ◽  
Specific Expression ◽  
Tissue Specific ◽  
Human Renin ◽  
Regulated Expression ◽  
Renin Gene

We tested the hypothesis that a transcriptional chorionic enhancer (CE), previously identified to increase human renin expression in choriodecidual cells is required to mediate tissue-specific, cell-specific, and regulated expression of human renin in transgenic mice. Recombineering was used to delete the CE upstream of the renin gene alone or in combination with the kidney enhancer (KE) in a large artificial chromosome construct containing the entire human renin gene and extensive flanking sequences. Deletion of the CE had no qualitative or quantitative effect on the tissue-specific expression of human renin, nor on the cellular localization of human renin in the kidney or placenta. Combined deletion of both the CE and KE caused a decrease in the level of renal renin expression consistent with the established role of the KE. We also considered the possibility that the CE is a downstream enhancer of the KiSS1 gene, which lies directly upstream of renin and is also expressed in the placenta. Deletion of the CE alone, or the CE and KE together, had no effect on the level of KiSS1 expression in the placenta. These data provide convincing evidence that the CE is silent in vivo, at least in the mouse. The absence of a phenotype caused by deletion of the CE is consistent with the observation that the sequence is not evolutionarily conserved.

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