scholarly journals Cis- and trans-acting elements required for constitutive and cytokine-regulated expression of the mouse complement C3 gene

1992 ◽  
Vol 283 (3) ◽  
pp. 705-712 ◽  
Author(s):  
N Kawamura ◽  
L Singer ◽  
R A Wetsel ◽  
H R Colten
Keyword(s):  
Gene Expression ◽  
Hepg2 Cells ◽  
Interleukin 1 ◽  
Constitutive Expression ◽  
Regulatory Elements ◽  
Initiation Site ◽  
Complement C3 ◽  
Enhancer Activity ◽  
Transcriptional Initiation ◽  
C3 Gene

The third component of complement (C3) is an important mediator of inflammation. Murine and human genomic cosmid clones were isolated, characterized and sequenced 5′ to the complement C3 gene transcriptional initiation sites to determine cis elements that participate in constitutive and regulated C3 gene expression. The murine and human 5′ flanking regions are 51% identical overall, with positions -36 to -1 and -146 to -68 showing 80% identity. Four TATA boxes were identified upstream of the murine transcriptional initiation site, but deletion and transfection analysis using reporter gene constructs in HepG2 cells indicated that only the TATA element at position -30, together with sequences -395 to -111, are essential for constitutive expression of murine C3 in hepatocytes. Deletion analysis also suggested that sequences between -1457 and -800 contain regulatory elements that are involved in suppressing basal expression. Sequences between -90 to -41 confer both enhancer activity and interleukin-1/-6 (IL-1/IL-6)-responsiveness. Mutation analyses showed that both sequences between -88 and -83 and -77 to -72 are essential for enhancer activity and responsiveness to IL-1, but only sequences between -88 and -83 are necessary for IL-6-responsiveness. A gel-retardation assay showed that several nucleoproteins, perhaps of the C/EBP family, from HepG2 cells bound to sequences between -88 to -83. Collectively, these results localize cis-acting elements involved in constitutive and IL-1/IL-6-regulated murine C3 gene expression and provide evidence for specific transacting factors.

Multiple functional motifs in the chicken U1 RNA gene enhancer

1987 ◽  
Vol 7 (12) ◽  
pp. 4185-4193
Author(s):  
K A Roebuck ◽  
R J Walker ◽  
W E Stumph
Keyword(s):  
Gene Expression ◽  
Dna Sequences ◽  
Initiation Site ◽  
Sequence Motifs ◽  
Small Nuclear Rna ◽  
Multiple Sequence ◽  
Transcriptional Initiation ◽  
Transcription System ◽  
Cell Extracts ◽  
Gene Enhancer

The DNA sequence requirements of chicken U1 RNA gene expression have been examined in an oocyte transcription system. An enhancer region, which was required for efficient U1 RNA gene expression, is contained within a region of conserved DNA sequences spanning nucleotide positions -230 to -183, upstream of the transcriptional initiation site. These DNA sequences can be divided into at least two distinct subregions or domains that acted synergistically to provide a greater than 20-fold stimulation of U1 RNA synthesis. The first domain contains the octamer sequence ATGCAAAT and was recognized by a DNA-binding factor present in HeLa cell extracts. The second domain (the SPH domain) consists of conserved sequences immediately downstream of the octamer and is an essential component of the enhancer. In the oocyte, the DNA sequences of the SPH domain were able to enhance gene expression at least 10-fold in the absence of the octamer domain. In contrast, the octamer domain, although required for full U1 RNA gene activity, was unable to stimulate expression in the absence of the adjacent downstream DNA sequences. These findings imply that sequences 3' of the octamer play a major role in the function of the chicken U1 RNA gene enhancer. This concept was supported by transcriptional competition studies in which a cloned chicken U4B RNA gene was used to compete for limiting transcription factors in oocytes. Multiple sequence motifs that can function in a variety of cis-linked configurations may be a general feature of vertebrate small nuclear RNA gene enhancers.

Chronic complement C3 gene expression in the CNS of transgenic mice with astrocyte-targeted interleukin-6 expression

Glia ◽  
1996 ◽  
Vol 18 (2) ◽  
pp. 107-117 ◽  
Author(s):  
Scott R. Barnum ◽  
Jennifer L. Jones ◽  
Ulf Müller-Ladner ◽  
Ana Samimi ◽  
Ian L. Campbell
Keyword(s):  
Gene Expression ◽  
Transgenic Mice ◽  
Interleukin 6 ◽  
Complement C3 ◽  
C3 Gene

scholarly journals Characterization of two atypical promoters and alternate mRNA processing in the mouse Thy-1.2 glycoprotein gene.

1986 ◽  
Vol 6 (8) ◽  
pp. 2923-2931 ◽  
Author(s):  
H A Ingraham ◽  
G A Evans
Keyword(s):  
Genomic Sequence ◽  
Regulatory Elements ◽  
Initiation Site ◽  
Lymphoid Cells ◽  
Gene Encoding ◽  
Specific Expression ◽  
Transcriptional Initiation ◽  
Glycoprotein Gene ◽  
Cell Type Specific Expression ◽  
Flanking Region

The promoter and 5' flanking region of the mouse Thy-1.2 glycoprotein gene were characterized by DNA sequencing, primer extension analysis, and deletion analysis. Transcriptional initiation sites were identified which corresponded to two separate exons upstream of the portion of the gene encoding the Thy-1.2 glycoprotein. We demonstrated that the mouse Thy-1.2 gene was transcribed from two atypical promoters separated by 260 base pairs in the genomic sequence. These promoters contained neither TATAAG nor GGPyCCAATCT homologous sequences but defined a conserved nonamer CTCCCTGCT at -48 from each initiation site. Two Thy-1.2 mRNA species of 1,835 and 1,939 nucleotides, differing in the 5' untranslated region of the mRNA, were thus transcribed from the single Thy-1.2 gene by mRNA splicing to the same downstream exon. Recombinant genomes in which the bacterial chloramphenicol acetyltransferase gene was expressed from either of the two Thy-1.2 promoters demonstrated that each promoter functioned independently and did not direct cell-specific expression in lymphoid cells. The 5' flanking region of the Thy-1.2 gene upstream of -68 could be eliminated without altering cell-type-specific expression. This suggests that regulatory elements responsible for tissue and developmental stage-specific expression of the Thy-1.2 gene are not present in the 5' flanking DNA but may reside downstream of the promoters.

256 LINES OF PIGS SELECTED FOR COMPONENT TRAITS OF LITTER SIZE EXHIBIT DIFFERENTIAL GENE REGULATION AT THE ONSET OF EMBRYO (TROPHECTODERM) ELONGATION

2006 ◽  
Vol 18 (2) ◽  
pp. 235 ◽  
Author(s):  
J. R. Miles ◽  
L. A. Blomberg ◽  
B. A. Freking ◽  
K. A. Zuelke
Keyword(s):  
Gene Expression ◽  
Immune Modulation ◽  
Interleukin 1 ◽  
Regulatory Protein ◽  
Constitutive Expression ◽  
Cell Interaction ◽  
Ovulation Rate ◽  
Control Line ◽  
Embryo Survival ◽  
Cytochrome P450scc

Significant embryonic (<18%) loss occurs in the pig as the pre-implantation embryo undergoes a dramatic morphological change from ovoid (8-10 mm) at gestational Day 11 to a long, thin filament (<150 mm) by Day 12. Lines of pigs selected for increased uterine capacity have improved embryonic survival, whereas pigs selected for increased ovulation rate have decreased embryo survival. Alterations in the expression of genes that play key roles in embryo elongation and maternal recognition of pregnancy may reflect differences in embryo survival observed in these lines of pigs. The objective of the current study was to evaluate the expression level of transcripts involved in developmentally important processes, such as steroidogenesis, cellular differentiation, cell-cell interaction, and immune modulation, at the onset of porcine embryo elongation (gestational Day 11) in control animals and lines selected for increased ovulation rate or uterine capacity. Total RNA was isolated from Day 11 ovoid embryos, and gene expression was measured via real-time PCR. Data were analyzed for analysis of variance using GLM procedures. Expression of steroidogenic acute regulatory protein mRNA was decreased (P = 0.02) in embryos from the ovulation rate and uterine capacity lines compared with controls. Similarly, expression of cytochrome P450scc and aromatase mRNA were decreased (P < 0.003) in embryos from the ovulation rate and uterine capacity lines, compared with the control line. Interestingly, 17�-hydroxylase mRNA expression was decreased (P = 0.0004) only in embryos from the ovulation rate line compared with the control and uterine capacity lines. In contrast, expression of cytokeratin-8 and -18 mRNA were increased (P < 0.02) in embryos from the uterine capacity and ovulation rate lines, compared with controls. Expression of galectin 1 mRNA was increased (P = 0.02) in embryos from the uterine capacity line, compared with the ovulation rate line. Expression of interleukin-1 receptor type 1 mRNA was increased (P = 0.03) in embryos from the uterine capacity line, compared with both the control and the uterine capacity lines. Constitutive expression of 17�-hydroxysteroid dehydrogenase, stratifin, and interleukin-1� mRNA were observed in embryos from all lines. These results demonstrate altered gene expression in embryos from pigs selected for increased uterine capacity and ovulation rate compared with controls, and may contribute to differences observed in embryo survival between these lines of pigs.

scholarly journals Interleukin-1? repressesMRP2 gene expression through inactivation of interferon regulatory factor 3 in HepG2 cells

Hepatology ◽  
2004 ◽  
Vol 39 (6) ◽  
pp. 1574-1582 ◽  
Author(s):  
Keiji Hisaeda ◽  
Akihiko Inokuchi ◽  
Takanori Nakamura ◽  
Yukihide Iwamoto ◽  
Kimitoshi Kohno ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepg2 Cells ◽  
Interleukin 1 ◽  
Interferon Regulatory Factor ◽  
Regulatory Factor ◽  
Interferon Regulatory Factor 3

scholarly journals Imprinted gene expression at the Dlk1-Dio3 cluster is controlled by both maternal and paternal IG-DMRs in a tissue-specific fashion

2019 ◽  
Author(s):  
Katherine A. Alexander ◽  
María J. García-García
Keyword(s):  
Gene Expression ◽  
Regulatory Elements ◽  
Enhancer Activity ◽  
Enhancer Element ◽  
Tissue Specific ◽  
Imprinted Gene ◽  
Imprinting Control Region ◽  
Regulatory Landscape ◽  
Insight Into ◽  
Different Tissues

ABSTRACTImprinting at the Dlk1-Dio3 cluster is controlled by the IG-DMR, an imprinting control region differentially methylated between maternal and paternal chromosomes. The maternal IG-DMR is essential for imprinting control, functioning as a cis enhancer element. Meanwhile, DNA methylation at the paternal IG-DMR is thought to prevent enhancer activity. To explore whether suppression of enhancer activity at the methylated IG-DMR requires the transcriptional repressor TRIM28, we analyzed Trim28chatwo embryos and performed epistatic experiments with IG-DMR deletion mutants. We found that while TRIM28 regulates the enhancer properties of the paternal IG-DMR, it also controls imprinting through other mechanisms. Additionally, we found that the paternal IG-DMR, previously deemed dispensable for imprinting, is required in certain tissues, demonstrating that imprinting is regulated in a tissue-specific manner. Using PRO-seq to analyze nascent transcription, we identified 30 novel transcribed regulatory elements, including 23 that are tissue-specific. These results demonstrate that different tissues have a distinctive regulatory landscape at the Dlk1-Dio3 cluster and provide insight into potential mechanisms of tissue-specific imprinting control. Together, our findings challenge the premise that Dlk1-Dio3 imprinting is regulated through a single mechanism and demonstrate that different tissues use distinct strategies to accomplish imprinted gene expression.

scholarly journals A non-coding genetic variant maximally associated with serum urate levels is functionally linked to HNF4A-dependent PDZK1 expression

2018 ◽  
Author(s):  
Sarada Ketharnathan ◽  
Megan Leask ◽  
James Boocock ◽  
Amanda J. Phipps-Green ◽  
Jisha Antony ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepg2 Cells ◽  
Molecular Mechanisms ◽  
Genetic Variant ◽  
Fluorescent Protein ◽  
Serum Urate ◽  
Specific Gene ◽  
Specific Expression ◽  
Enhancer Activity ◽  
Tissue Specific

ABSTRACTSeveral dozen genetic variants associate with serum urate levels, but the precise molecular mechanisms by which they affect serum urate are unknown. Here we tested for functional linkage of the maximally-associated genetic variant rs1967017 at the PDZK1 locus to elevated PDZK1 expression.We performed expression quantitative trait locus (eQTL) and likelihood analyses followed by gene expression assays. Zebrafish were used to determine the ability of rs1967017 to direct tissue-specific gene expression. Luciferase assays in HEK293 and HepG2 cells measured the effect of rs1967017 on transcription amplitude.PAINTOR analysis revealed rs1967017 as most likely to be causal and rs1967017 was an eQTL for PDZK1 in the intestine. The region harboring rs1967017 was capable of directly driving green fluorescent protein expression in the kidney, liver and intestine of zebrafish embryos, consistent with a conserved ability to confer tissue-specific expression. The urate-increasing T-allele of rs1967017 strengthens a binding site for the transcription factor HNF4A. siRNA depletion of HNF4A reduced endogenous PDZK1 expression in HepG2 cells. Luciferase assays showed that the T-allele of rs1967017 gains enhancer activity relative to the urate-decreasing C-allele, with T-allele enhancer activity abrogated by HNF4A depletion. HNF4A physically binds the rs1967017 region, suggesting direct transcriptional regulation of PDZK1 by HNF4A.With other reports our data predict that the urate-raising T-allele of rs1967017 enhances HNF4A binding to the PDZK1 promoter, thereby increasing PDZK1 expression. As PDZK1 is a scaffold protein for many ion channel transporters, increased expression can be predicted to increase activity of urate transporters and alter excretion of urate.

scholarly journals A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures

2021 ◽  
Author(s):  
Arushi Varshney ◽  
Yasuhiro Kyono ◽  
Venkateswaran Ramamoorthi Elangovan ◽  
Collin Wang ◽  
Michael R. Erdos ◽  
...  
Keyword(s):  
Pancreatic Islets ◽  
Transcription Initiation ◽  
Genome Wide Association Study ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Transcriptional Enhancer ◽  
Transcription Start ◽  
Enhancer Activity ◽  
Transcriptional Initiation ◽  
Human Pancreatic Islets

Identifying the tissue-specific molecular signatures of active regulatory elements is critical to understand gene regulatory mechanisms. Here, we identify transcription start sites (TSS) using cap analysis of gene expression (CAGE) across 57 human pancreatic islet samples. We identify 9,954 reproducible CAGE tag clusters (TCs), ~20% of which are islet-specific and occur mostly distal to known gene TSSs. We integrated islet CAGE data with histone modification and chromatin accessibility profiles to identify epigenomic signatures of transcription initiation. Using a massively parallel reporter assay, we validated the transcriptional enhancer activity for 2,279 of 3,378 (~68%) tested islet CAGE elements (5% FDR). TCs within accessible enhancers show higher enrichment to overlap type 2 diabetes genome-wide association study (GWAS) signals than existing islet annotations, which emphasizes the utility of mapping CAGE profiles in disease-relevant tissue. This work provides a high-resolution map of transcriptional initiation in human pancreatic islets with utility for dissecting active enhancers at GWAS loci.

scholarly journals A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures

2021 ◽  
Author(s):  
Arushi Varshney ◽  
Yasuhiro Kyono ◽  
Venkateswaran Ramamoorthi Elangovan ◽  
Collin Wang ◽  
Michael R. Erdos ◽  
...  
Keyword(s):  
Pancreatic Islets ◽  
Transcription Initiation ◽  
Genome Wide Association Study ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Transcriptional Enhancer ◽  
Transcription Start ◽  
Enhancer Activity ◽  
Transcriptional Initiation ◽  
Human Pancreatic Islets

Identifying the tissue-specific molecular signatures of active regulatory elements is critical to understand gene regulatory mechanisms. Here, we identify transcription start sites (TSS) using cap analysis of gene expression (CAGE) across 57 human pancreatic islet samples. We identify 9,954 reproducible CAGE tag clusters (TCs), ~20% of which are islet-specific and occur mostly distal to known gene TSSs. We integrated islet CAGE data with histone modification and chromatin accessibility profiles to identify epigenomic signatures of transcription initiation. Using a massively parallel reporter assay, we validated the transcriptional enhancer activity for 2,279 of 3,378 (~68%) tested islet CAGE elements (5% FDR). TCs within accessible enhancers show higher enrichment to overlap type 2 diabetes genome-wide association study (GWAS) signals than existing islet annotations, which emphasizes the utility of mapping CAGE profiles in disease-relevant tissue. This work provides a high-resolution map of transcriptional initiation in human pancreatic islets with utility for dissecting active enhancers at GWAS loci.

scholarly journals Influence of genetic polymorphism on transcriptional enhancer activity in the malaria vector Anopheles coluzzii

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Luisa Nardini ◽  
Inge Holm ◽  
Adrien Pain ◽  
Emmanuel Bischoff ◽  
Daryl M. Gohl ◽  
...  
Keyword(s):  
Gene Expression ◽  
Malaria Vector ◽  
Functional Activity ◽  
Regulatory Elements ◽  
Transmission Efficiency ◽  
Luciferase Reporter ◽  
Anopheles Coluzzii ◽  
Transcriptional Enhancer ◽  
Enhancer Activity ◽  
Enhancer Sequences

Abstract Enhancers are cis-regulatory elements that control most of the developmental and spatial gene expression in eukaryotes. Genetic variation of enhancer sequences is known to influence phenotypes, but the effect of enhancer variation upon enhancer functional activity and downstream phenotypes has barely been examined in any species. In the African malaria vector, Anopheles coluzzii, we identified candidate enhancers in the proximity of genes relevant for immunity, insecticide resistance, and development. The candidate enhancers were functionally validated using luciferase reporter assays, and their activity was found to be essentially independent of their physical orientation, a typical property of enhancers. All of the enhancers segregated genetically polymorphic alleles, which displayed significantly different levels of functional activity. Deletion mutagenesis and functional testing revealed a fine structure of positive and negative regulatory elements that modulate activity of the enhancer core. Enhancer polymorphisms segregate in wild A. coluzzii populations in West Africa. Thus, enhancer variants that modify target gene expression leading to likely phenotypic consequences are frequent in nature. These results demonstrate the existence of naturally polymorphic A. coluzzii enhancers, which may help explain important differences between individuals or populations for malaria transmission efficiency and vector adaptation to the environment.

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