scholarly journals Noncoding sequence variants define a novel regulatory element in the first intron of the N ‐acetylglutamate synthase gene

2021 ◽  
Author(s):  
Johannes Häberle ◽  
Marvin B. Moore ◽  
Nantaporn Haskins ◽  
Véronique Rüfenacht ◽  
Dariusz Rokicki ◽  
...  
Author(s):  
Johannes Häberle ◽  
Barry Moore ◽  
Nantaporn Haskins ◽  
Véronique Rüfenacht ◽  
Dariusz Rokicki ◽  
...  

N-acetylglutamate synthase deficiency (NAGSD, MIM #237310) is an autosomal recessive urea cycle disorder caused either by decreased expression of the NAGS gene or defective NAGS enzyme resulting in decreased production of N-acetylglutamate (NAG), an allosteric activator of carbamylphosphate synthetase 1 (CPS1). NAGSD is the only urea cycle disorder that can be effectively treated with a single drug, N-carbamylglutamate (NCG), a stable NAG analog, which activates CPS1 to restore ureagenesis. We describe three patients with NAGSD due to four novel sequence variants in the NAGS regulatory regions. All three patients had hyperammonemia that resolved upon treatment with NCG. Sequence variants NM_153006.2:c.-3065A>C and NM_153006.2:c-3098C>T reside in the NAGS enhancer, within known HNF1 and predicted glucocorticoid receptor binding sites, respectively. Sequence variants NM_153006.2:c.426+326G>A and NM_153006.2:c.427-218A>C reside in the first intron of NAGS and define a novel NAGS regulatory element that binds retinoic X receptor α. Reporter gene assays in HepG2 and HuH-7 cells demonstrated that all four substitutions could result in reduced expression of NAGS. These findings show that analyzing non-coding regions of NAGS and other urea cycle genes can reveal molecular causes of disease and identify novel regulators of ureagenesis.


1992 ◽  
Vol 286 (1) ◽  
pp. 179-185 ◽  
Author(s):  
C P Simkevich ◽  
J P Thompson ◽  
H Poppleton ◽  
R Raghow

The transcriptional activity of plasmid pCOL-KT, in which human pro alpha 1 (I) collagen gene upstream sequences up to -804 and most of the first intron (+474 to +1440) drive expression of the chloramphenicol acetyltransferase (CAT) gene [Thompson, Simkevich, Holness, Kang & Raghow (1991) J. Biol. Chem. 266, 2549-2556], was tested in a number of mesenchymal and non-mesenchymal cells. We observed that pCOL-KT was readily expressed in fibroblasts of human (IMR-90 and HFL-1), murine (NIH 3T3) and avian (SL-29) origin and in a human rhabdomyosarcoma cell line (A204), but failed to be expressed in human erythroleukaemia (K562) and rat pheochromocytoma (PC12) cells, indicating that the regulatory elements required for appropriate tissue-specific expression of the human pro alpha 1 (I) collagen gene were present in pCOL-KT. To delineate the nature of cis-acting sequences which determine the tissue specificity of pro alpha 1 (I) collagen gene expression, functional consequences of deletions in the promoter and first intron of pCOL-KT were tested in various cell types by transient expression assays. Cis elements in the promoter-proximal and intronic sequences displayed either a positive or a negative influence depending on the cell type. Thus deletion of fragments using EcoRV (nt -625 to -442 deleted), XbaI (-804 to -331) or SstII (+670 to +1440) resulted in 2-10-fold decreased expression in A204 and HFL-1 cells. The negative influences of deletions in the promoter-proximal sequences was apparently considerably relieved by deleting sequences in the first intron, and the constructs containing the EcoRV/SstII or XbaI/SstII double deletions were expressed to a much greater extent than either of the single deletion constructs. In contrast, the XbaI* deletion (nt -804 to -609), either alone or in combination with the intronic deletion, resulted in very high expression in all cells regardless of their collagen phenotype; the XbaI*/(-SstII) construct, which contained the intronic SstII fragment (+670 to +1440) in the reverse orientation, was not expressed in either mesenchymal or nonmesenchymal cells. Based on these results, we conclude that orientation-dependent interactions between negatively acting 5′-upstream sequences and the first intron determine the mesenchymal cell specificity of human pro alpha 1 (I) collagen gene transcription.


1994 ◽  
Vol 300 (1) ◽  
pp. 147-152 ◽  
Author(s):  
A Manohar ◽  
R A Anwar

A cell-specific negative regulatory element has been identified in the first intron of the gene for elastin in a region between 442 and 464 bp from the translational start site. This regulatory element functions both when it is located 5′ of the promoter and 3′ of the chloramphenicol acetyltransferase (CAT) gene. The inhibition is observed both with the homologous elastin promoter and the heterologous SV1 promoter in transient expression experiments using rat aortic smooth-muscle cells. No inhibition was observed with NIH 3T3, Hep G2 and little, if any, with HeLa cells. Cell specificity was further confirmed by DNA mobility shift assays and the position of the negative regulatory element was localized with the use of synthetic duplex oligomers. It is proposed that this negative element plays a significant role in the modulation of the expression of the gene for elastin in the smooth-muscle cells of the aorta during development.


2014 ◽  
Vol 11 (3) ◽  
pp. 294-296 ◽  
Author(s):  
Graham R S Ritchie ◽  
Ian Dunham ◽  
Eleftheria Zeggini ◽  
Paul Flicek

2007 ◽  
Vol 3 (4) ◽  
pp. 377-387 ◽  
Author(s):  
Erin A. Jones ◽  
Sung-Wook Jang ◽  
Gennifer M. Mager ◽  
Li-Wei Chang ◽  
Rajini Srinivasan ◽  
...  

AbstractMyelination in the PNS is accompanied by a large induction of the myelin protein zero (Mpz) gene to produce the most abundant component in peripheral myelin. Analyses of knockout mice have shown that the EGR2/Krox20 and SOX10 transcription factors are required for Mpz expression. Our recent work has shown that the dominant EGR2 mutations associated with human peripheral neuropathies cause disruption of EGR2/SOX10 synergy at specific sites, including a conserved enhancer element in the first intron of the Mpz gene. Further investigation of Egr2/Sox10 interactions reveals that activation of the Mpz intron element by Egr2 requires both Sox10-binding sites. In addition, both Egr1 and Egr3 cooperate with Sox10 to activate this element, which indicates that this capacity is conserved among Egr family members. Finally, a conserved composite structure of Egr2/Sox10-binding sites in the genes encoding Mpz, myelin-associated glycoprotein and myelin basic protein genes was used to screen for similar modules in other myelin genes, revealing a potential regulatory element in the periaxin gene. Overall, these results elucidate a working model for developmental regulation of Mpz expression, several facets of which extend to regulation of other peripheral myelin genes.


Neurogenetics ◽  
2017 ◽  
Vol 19 (1) ◽  
pp. 17-26 ◽  
Author(s):  
Anthony J. Griswold ◽  
Derek Van Booven ◽  
Michael L. Cuccaro ◽  
Jonathan L. Haines ◽  
John R. Gilbert ◽  
...  

1998 ◽  
Vol 17 (8) ◽  
pp. 689-697 ◽  
Author(s):  
FRANKLIN D. SHULER ◽  
WILLIAM W. CHU ◽  
SHIYI WANG ◽  
MARILYN I. EVANS

2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
T. D. Matos ◽  
H. Simões-Teixeira ◽  
H. Caria ◽  
R. Cascão ◽  
H. Rosa ◽  
...  

Involvement of GJB2 noncoding regions in hearing loss (HL) has not been extensively investigated. However, three noncoding mutations, c.-259C>T, c.-23G>T, and c.-23+1G>A, were reported. Also, c.-684_-675del, of uncertain pathogenicity, was found upstream of the basal promoter. We performed a detailed analysis of GJB2 noncoding regions in Portuguese HL patients (previously screened for GJB2 coding mutations and the common GJB6 deletions) and in control subjects, by sequencing the basal promoter and flanking upstream region, exon 1, and 3'UTR. All individuals were genotyped for c.-684_-675del and 14 SNPs. Novel variants (c.-731C>T, c.-26G>T, c.*45G>A, and c.*985A>T) were found in controls. A hearing individual homozygous for c.-684_-675del was for the first time identified, supporting the nonpathogenicity of this deletion. Our data indicate linkage disequilibrium (LD) between SNPs rs55704559 (c.*168A>G) and rs5030700 (c.*931C>T) and suggest the association of c.[*168G;*931T] allele with HL. The c.*168A>G change, predicted to alter mRNA folding, might be involved in HL.


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