scholarly journals H19 and Igf2 monoallelic expression is regulated in two distinct ways by a shared cis acting regulatory region upstream of H19

2000 ◽  
Vol 14 (10) ◽  
pp. 1186-1195 ◽  
Author(s):  
Madhulika Srivastava ◽  
Sandra Hsieh ◽  
Alexander Grinberg ◽  
Lisa Williams-Simons ◽  
Sing-Ping Huang ◽  
...  
Keyword(s):  
Promoter Region ◽  
Regulatory Region ◽  
Regulatory Elements ◽  
Upstream Region ◽  
Monoallelic Expression ◽  
Direct Role ◽  
Specific Expression ◽  
Cis Acting ◽  
Allele Specific ◽  
Mammalian System

H19 and Igf2 are expressed in a monoallelic fashion from the maternal and paternal chromosomes, respectively. A region upstream of H19 has been shown to regulate such imprinted expression of both genes in cis. We have taken advantage of aloxP/cre recombinase-based strategy to delete this region in mice in a conditional manner to determine the temporal requirement of the upstream region in initiating and maintaining the imprinted expression of H19 and Igf2. Analysis of allele-specific expression of H19 and Igf2 and DNA methylation at the H19 promoter demonstrates that this region controls the monoallelic expression of the two genes in different ways, suggesting that it harbors two functionally distinct regulatory elements. Continued presence of the region is required to silence maternal Igf2 in accordance with its proposed role as an insulator. However, it does not have a direct role in keeping the paternal H19 promoter silenced. Instead, on the paternal chromosome, the upstream element mediates epigenetic modifications of the H19 promoter region during development, leading to transcriptional silencing of H19. Thereafter, its presence is redundant for preventing transcription. Presently, this temporal requirement of the silencing element appears to be a unique cisactivity in the mammalian system. However, it is likely that othercis-acting elements, positive and negative, have the ability to effect stable changes in the chromatin structure and are not constantly required to give signals to the transcriptional machinery.

scholarly journals Separable cis-regulatory elements that contribute to tissue- and site-specific alpha 2(XI) collagen gene expression in the embryonic mouse cartilage.

1996 ◽  
Vol 134 (6) ◽  
pp. 1573-1582 ◽  
Author(s):  
N Tsumaki ◽  
T Kimura ◽  
Y Matsui ◽  
K Nakata ◽  
T Ochi
Keyword(s):  
Promoter Region ◽  
Regulatory Elements ◽  
Collagen Gene ◽  
Lacz Expression ◽  
Specific Expression ◽  
Site Specific ◽  
Cis Acting ◽  
First Intron ◽  
Vertebral Bodies ◽  
Type Xi Collagen

Type XI collagen is a structural component of the cartilage extracellular matrix and plays an important role in skeletal morphogenesis. As a step toward defining the molecular mechanisms responsible for the regulation of type XI collagen expression, we characterized the promoter region of the mouse alpha 2(XI) collagen gene (Coll1a2). We also generated transgenic mice harboring various fragments of the promoter and the first intron of Coll1a2 linked to the Escherichia coli beta-galactosidase gene to identify the cis-acting elements responsible for tissue- and site-specific expression during development. Cloning and sequence analysis of the 5' flanking region of Coll1a2 showed that the putative 3' end of the retinoid X receptor beta gene was located 742 bp upstream of the Coll1a2 start site. This suggested that the promoter region of Coll1a2 was localized within this 742-bp sequence, which contained multiple consensus regulatory elements. Examination of the transgenic mice revealed that the longest DNA construct (containing the entire promoter and first intron sequences) directed lacZ expression in the notochord as well as in the primordial cartilage throughout the body, with the pattern of expression mimicking that of endogenous Coll1a2 transcripts. On the other hand, deletion of the upstream approximately 290 bp resulted in the elimination of lacZ expression in the primordial cartilage of the carpals, tarsals, and vertebral bodies, whereas lacZ expression in the notochord and in the other primordial cartilage elsewhere was not affected. Deletion of the first intron sequence also resulted in the loss of lacZ expression in the primordial cartilage of the carpals, tarsals, and vertebral bodies, as well as in the notochord. These results demonstrate that the upstream 742-bp and first intron segments of the mouse Coll1a2 gene contain the necessary information to confer high level tissue-specific expression in mouse embryos. In addition, our observations suggest the presence of site-specific cis-acting elements that control Coll11a2 gene expression in different cartilaginous components of the skeleton.

The human Na+/H+ exchangerNHE2 gene: genomic organization and promoter characterization

2001 ◽  
Vol 280 (4) ◽  
pp. G763-G773 ◽  
Author(s):  
Jaleh Malakooti ◽  
Refka Y. Dahdal ◽  
Pradeep K. Dudeja ◽  
Thomas J. Layden ◽  
Krishnamurthy Ramaswamy
Keyword(s):  
Transcription Initiation ◽  
Promoter Region ◽  
Zinc Finger Protein ◽  
Regulatory Region ◽  
Cell Volume Regulation ◽  
Nuclear Factor Κb ◽  
Regulatory Elements ◽  
Upstream Region ◽  
Activity Levels ◽  
Donor And Acceptor

The Na+/H+ exchanger (NHE) 2 belongs to a family of plasma membrane transporters involved in intracellular pH and cell volume regulation. We recently reported cloning of human NHE2 ( hNHE2) from a colonic cDNA library. Northern blot analysis has identified NHE2 mRNA only in small intestine, prostate, kidney, colon, and skeletal muscle. In this study, we describe the structure and 5′-regulatory region of the hNHE2 gene. The hNHE2 gene spans >90 kb and is organized in 12 exons intervened by 11 introns. All introns contain the conserved GT and AG dinucleotides at the donor and acceptor sites, respectively. The hNHE2 gene was mapped to chromosome 2q11.2. Primer extension analysis revealed a single transcription initiation site in human colonic adenocarcinoma cell lines. Analysis of the DNA nucleotide sequences of a 1.4-kb fragment of the 5′-flanking region shows no canonical TATA or CAAT boxes. However, the promoter region contains several potential cis-regulatory elements such as Sp1, early growth response-1, activator protein-2, MyoD, p300, nuclear factor-κB, myeloid zinc finger protein-1, caudal-related homeobox (Cdx) gene A, and Cdx protein-2 binding sites. In transient transfection studies, a reporter construct containing the 1.4-kb promoter region exhibited low luciferase activity levels. However, after deletion upstream of −664, its activity increased approximately threefold. Thus our data suggest that an inhibitory element may exist in the NHE2 promoter 5′-upstream region.

scholarly journals The transcriptional tissue specificity of the human proα1(I) collagen gene is determined by a negative cis-regulatory element in the promoter

1992 ◽  
Vol 286 (1) ◽  
pp. 179-185 ◽  
Author(s):  
C P Simkevich ◽  
J P Thompson ◽  
H Poppleton ◽  
R Raghow
Keyword(s):  
Tissue Specificity ◽  
Regulatory Element ◽  
Mesenchymal Cell ◽  
Cell Types ◽  
Regulatory Elements ◽  
Negative Influence ◽  
Collagen Gene ◽  
Specific Expression ◽  
Cis Acting ◽  
First Intron

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.

scholarly journals Genome-Wide Regulatory Interactions in the Early Stages of Drosophila Speciation

2020 ◽  
Author(s):  
◽  
Alwyn Clark Go
Keyword(s):  
Reproductive Isolation ◽  
Expression Analysis ◽  
Regulatory Elements ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Regulatory Interactions ◽  
Early Stages ◽  
Genome Wide ◽  
Allele Specific ◽  
Incomplete Reproductive Isolation

Speciation occurs when reproductive barriers prevent the exchange of genetic information between individuals. A common form of reproductive barrier between species capable of interbreeding is hybrid sterility. Genomic incompatibilities between the divergent genomes of different species contribute to a reduction in hybrid fitness. These incompatibilities continue to accumulate after speciation, therefore, young divergent taxa with incomplete reproductive isolation are important in understating the genetics leading to speciation. Here, I use two Drosophila subspecies pairs. The first is D. willistoni consisting of D. w. willistoni and D. w. winge. The second subspecies pair is D. pseudoobscura, which is composed of D. p. pseudoobscura and D. p. bogotana. Both subspecies pairs are at the early stages of speciation and show incomplete reproductive isolation through unidirectional hybrid male sterility. In this thesis, I performed an exploratory survey of genome-wide expression analysis using RNA-sequencing on D. willistoni and determined the extent of regulatory divergence between the subspecies using allele-specific expression analysis. I found that misexpressed genes showed a degree of tissue specificity and that the sterile male hybrids had a higher proportion of misexpressed genes in the testes relative to the fertile hybrids. The analysis of regulatory divergence between this subspecies pair found a large (66-70%) proportion of genes with conserved regulatory elements. Of the genes showing evidence or regulatory divergence between subspecies, cis-regulatory divergence was more common than other types. In the D. pseudoobscura subspecies pair, I compared sequence and expression divergence and found no support for directional selection driving gene misexpression in their hybrids. Allele-specific expression analysis revealed that compensatory cis-trans mutations partly explained gene misexpression in the hybrids. The remaining hybrid misexpression occurs due to interacting gene networks or possible co-option of cis-regulatory elements by divergent transacting factors. Overall, the results of this thesis highlight the role of regulatory interactions in a hybrid genome and how these interactions could lead to hybrid breakdown by disrupting gene interaction networks.

scholarly journals Genetic influences on cell type specific gene expression and splicing during neurogenesis elucidate regulatory mechanisms of brain traits

2020 ◽  
Author(s):  
Nil Aygün ◽  
Angela L. Elwell ◽  
Dan Liang ◽  
Michael J. Lafferty ◽  
Kerry E. Cheek ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulatory Elements ◽  
Regulatory Mechanisms ◽  
Specific Gene ◽  
Cell Type ◽  
Specific Expression ◽  
Risk Variants ◽  
Allele Specific ◽  
Cell Type Specific ◽  
Regulatory Effects

SummaryInterpretation of the function of non-coding risk loci for neuropsychiatric disorders and brain-relevant traits via gene expression and alternative splicing is mainly performed in bulk post-mortem adult tissue. However, genetic risk loci are enriched in regulatory elements of cells present during neocortical differentiation, and regulatory effects of risk variants may be masked by heterogeneity in bulk tissue. Here, we map e/sQTLs and allele specific expression in primary human neural progenitors (n=85) and their sorted neuronal progeny (n=74). Using colocalization and TWAS, we uncover cell-type specific regulatory mechanisms underlying risk for these traits.

scholarly journals Regulatory elements in the upstream region of metallothionein gene in tilapia species

2021 ◽  
Vol 30 (1) ◽  
pp. 95-103
Author(s):  
Mohammad Shamimul Alam ◽  
Israt Jahan ◽  
Sadniman Rahman ◽  
Hawa Jahan ◽  
Kaniz Fatema
Keyword(s):  
Tissue Specificity ◽  
Regulatory Region ◽  
Regulatory Elements ◽  
Metal Resistance ◽  
Genomic Region ◽  
Upstream Region ◽  
Upstream Sequence ◽  
Oreochromis Aureus ◽  
Metallothionein Gene ◽  
Genomic Regions

Tilapia is a hardy fish which can survive in water bodies polluted with heavy metals. Metal resistance is conferred by higher expression of metallothionein gene (mt) in many organisms. Level, time and tissue-specificity of gene expression is regulated through transcription factor binding sites (TFBS) which may be present in the upstream, downstream, or even in the introns of a gene. So, as a candidate regulatory region, the 5’upstream sequence of mt gene in three tilapia species, Oreochromis aureus, O. niloticus and O. mossambicus was studied. The targeted region was PCR-amplified and then sequenced using a pair of custom-designed primer. A total of only 2.7% variation was found in the sequenced genomic region among the three species. Metal-related TFBS were predicted from these sequences. A total of twenty eight TFBS were found in O. aureus and twenty nine in O. mossambicus and O. niloticus. The number of metalrelated TFBS predicted in the targeted sequence was significantly higher compared to that found in randomly selected other genomic regions of same size from O. niloticus genome. Thus, the results suggest the presence of putative regulatory elements in the targeted upstream region which might have important role in the regulation of mt gene function. Dhaka Univ. J. Biol. Sci. 30(1): 95-103, 2021 (January)

Targeted modification of promoters

2021 ◽  
pp. 247-278
Author(s):  
Andika Gunadi ◽  
◽  
Ning Zhang ◽  
John J. Finer ◽  
◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Editing ◽  
Promoter Region ◽  
Regulatory Region ◽  
Regulatory Elements ◽  
Upstream Regulatory Region ◽  
Precise Control ◽  
Coding Regions ◽  
Gene Coding ◽  
Altered Regulation

Although most genome editing efforts focus on modifications to gene coding regions, this chapter emphasizes genome editing of the upstream regulatory regions. Thoughtful editing of the promoter region will ultimately lead to improved plants, modified for more precise control of the intensity and specificity of native gene expression. In this chapter, we present an overview of the promoter or upstream regulatory region of a gene, and describe how this sequence is defined and studied. We then describe how the composition and arrangements of cis-regulatory elements within the promoter and the leading intron associated with the promoter region have been studied using classical transgenic approaches to reveal what regulatory components might be suitable for genome editing approaches. Finally, we offer some suggestions for pursuit of promoter editing and gene expression modulation, which will eventually lead to modified plants with an altered regulation of native gene expression.

scholarly journals Genome-Wide Analysis of Allele-Specific Expression Patterns in Seventeen Tissues of Korean Cattle (Hanwoo)

Animals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 727
Author(s):  
Kyu-Sang Lim ◽  
Sun-Sik Chang ◽  
Bong-Hwan Choi ◽  
Seung-Hwan Lee ◽  
Kyung-Tai Lee ◽  
...  
Keyword(s):  
Phenotypic Variation ◽  
Expression Patterns ◽  
Monoallelic Expression ◽  
Specific Expression ◽  
Adult Cattle ◽  
Korean Cattle ◽  
Family Trio ◽  
Epigenetic Effects ◽  
Genome Wide ◽  
Allele Specific

The functional hemizygosity could be caused by the MAE of a given gene and it can be one of the sources to affect the phenotypic variation in cattle. We aimed to identify MAE genes across the transcriptome in Korean cattle (Hanwoo). For three Hanwoo family trios, the transcriptome data of 17 tissues were generated in three offspring. Sixty-two MAE genes had a monoallelic expression in at least one tissue. Comparing genotypes among each family trio, the preferred alleles of 18 genes were identified (maternal expression, n = 9; paternal expression, n = 9). The MAE genes are involved in gene regulation, metabolic processes, and immune responses, and in particular, six genes encode transcription factors (FOXD2, FOXM1, HTATSF1, SCRT1, NKX6-2, and UBN1) with tissue-specific expression. In this study, we report genome-wide MAE genes in seventeen tissues of adult cattle. These results could help to elucidate epigenetic effects on phenotypic variation in Hanwoo.

124 Functional analysis of porcine OCT4 transcriptional regulatory region-based reporter system

2019 ◽  
Vol 31 (1) ◽  
pp. 187
Author(s):  
S.-H. Kim ◽  
K.-H. Choi ◽  
D.-K. Lee ◽  
M. Lee ◽  
M.-H. Cho ◽  
...  
Keyword(s):  
Stem Cells ◽  
Functional Analysis ◽  
Embryonic Stem Cells ◽  
Promoter Region ◽  
Fluorescent Protein ◽  
Regulatory Region ◽  
Embryonic Stem ◽  
Upstream Region ◽  
Reporter Assay ◽  
Reporter System

Gene OCT4 plays pivotal roles in maintaining pluripotency of early mammalian embryonic development and embryonic stem cells. It is essential to establish a reporter system based on the OCT4 promoter region for the study of pluripotency. However, there is still a lack of sufficient information about the porcine OCT4 upstream reporter system. To improve our understanding of the porcine OCT4 regulatory region, first, we conducted an investigation to find conserved regions in the porcine OCT4 promoter upstream region by sequence-based comparative analysis using various mammalian genome sequences. A similarity of nucleotide sequences of the 5′ upstream region was low among mammalian species. However, the OCT4 promoter and 4 regulatory regions including distal and proximal enhancer elements have a high similarity. Next, a functional analysis of the porcine OCT4 promoter region was conducted. Luciferase reporter assay indicated that the porcine OCT4 distal enhancer and proximal enhancer are highly activated in mouse embryonic stem cells and embryonic carcinoma cells, respectively (n=3). Comparison analysis of naïve (Tbx3, Nr0b1, Rex1, Esrrb, Nanog, Klf2) or primed (Gata6, Mixl1, Fgf5, Otx2) state marker gene expression in a dual-reporter assay using pOCT4-DE-eGFP and pOCT4-PE-DsRed2 showed that expression of naïve and primed markers were up-regulated in cells with high green fluorescent protein and red fluorescent protein expression, respectively (n=3). Porcine OCT4-upstream region-based reporter constructs showed exclusive expression patterns depending on the state of pluripotency. This work could provide basic information for the porcine OCT4 upstream region and the various porcine OCT4-fluorescence reporter constructs, which can be applied to study species-specific pluripotency in early embryo development and for the establishment of embryonic stem cells in pigs. This work was supported by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries (IPET) through the Development of High Value-Added Food Technology Program, funded by the Ministry of Agriculture, Food and Rural Affairs (MAFRA, 118042-03-1-HD020).

scholarly journals Allele-specific expression identified rs2509956 as a novel long-distance cis-regulatory SNP for SCGB1A1, an important gene for multiple pulmonary diseases

2019 ◽  
Vol 317 (4) ◽  
pp. L456-L463
Author(s):  
Xiu-Xiong Li ◽  
Tao Peng ◽  
Jing Gao ◽  
Jia-Gang Feng ◽  
Dan-Dan Wu ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Pulmonary Diseases ◽  
Chronic Obstructive ◽  
Long Distance ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Chromosome Conformation ◽  
Functional Region ◽  
Gene Assay ◽  
Allele Specific

SCGB1A1 (secretoglobin family 1A member 1) is an important protein for multiple pulmonary diseases, especially asthma, chronic obstructive pulmonary disease, and lung cancer. One single-nucleotide polymorphism (SNP) at 5′-untranslated region of SCGB1A1, rs3741240, has been suggested to be associated with reduced protein expression and further asthma susceptibility. However, it was still unclear whether there were other cis-regulatory elements for SCGB1A1 that might further contribute to pulmonary diseases. Allele-specific expression (ASE) is a novel approach to identify the functional region in human genome. In the present study, we measured ASE on rs3741240 in lung tissues and observed a consistent excess of G allele over A ( P < 10−6), which indicated that this SNP or the one(s) in linkage disequilibrium (LD) could regulate SCGB1A1 expression. By analyzing 1000 Genomes Project data for Chinese, one SNP locating ~10.2 kb away and downstream of SCGB1A1, rs2509956, was identified to be in strong LD with rs3741240. Reporter gene assay confirmed that both SNPs could regulate gene expression in the lung cell. By chromosome conformation capture, it was verified that the region surrounding rs2509956 could interact with SCGB1A1 promoter region and act as an enhancer. Through chromatin immunoprecipitation and overexpression assay, the related transcription factor RELA (RELA proto-oncogene, NF-kB subunit) was recognized to bind the region spanning rs2509956. Our work identified a novel long-distance cis-regulatory SNP for SCGB1A1, which might contribute to multiple pulmonary diseases.

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