Deciphering the Role of various cis-acting regulatory elements in controlling SamDC gene expression in Rice

About 8% of the human genome is covered with candidate cis-regulatory elements (cCREs). Disruptions of CREs, described as “cis-ruptions” have been identified as being involved in various genetic diseases. Thanks to the development of chromatin conformation study techniques, several long-range cystic fibrosis transmembrane conductance regulator (CFTR) regulatory elements were identified, but the regulatory mechanisms of the CFTR gene have yet to be fully elucidated. The aim of this work is to improve our knowledge of the CFTR gene regulation, and to identity factors that could impact the CFTR gene expression, and potentially account for the variability of the clinical presentation of cystic fibrosis as well as CFTR-related disorders. Here, we apply the robust GWAS3D score to determine which of the CFTR introns could be involved in gene regulation. This approach highlights four particular CFTR introns of interest. Using reporter gene constructs in intestinal cells, we show that two new introns display strong cooperative effects in intestinal cells. Chromatin immunoprecipitation analyses further demonstrate fixation of transcription factors network. These results provide new insights into our understanding of the CFTR gene regulation and allow us to suggest a 3D CFTR locus structure in intestinal cells. A better understand of regulation mechanisms of the CFTR gene could elucidate cases of patients where the phenotype is not yet explained by the genotype. This would thus help in better diagnosis and therefore better management. These cis-acting regions may be a therapeutic challenge that could lead to the development of specific molecules capable of modulating gene expression in the future.

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Identification of cis -Acting Regulatory Elements Controlling Interleukin-4 Gene Expression in T Cells: Roles for NF-Y and NF-AT c

Molecular and Cellular Biology ◽

10.1128/mcb.13.9.5928-5928b.1993 ◽

1993 ◽

Vol 13 (9) ◽

pp. 5928-5928

Keyword(s):

Gene Expression ◽

T Cells ◽

Regulatory Elements ◽

Interleukin 4 ◽

Cis Acting

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Control of yeast gene expression by transposable elements: maximum expression requires a functional Ty activator sequence and a defective Ty promoter.

Molecular and Cellular Biology ◽

10.1128/mcb.8.10.4009 ◽

1988 ◽

Vol 8 (10) ◽

pp. 4009-4017 ◽

Cited By ~ 9

Author(s):

L R Coney ◽

G S Roeder

Keyword(s):

Gene Expression ◽

Adjacent Gene ◽

Multiple Sequence ◽

Sequence Element ◽

Cis Acting ◽

Ty Elements ◽

The Relationship ◽

Maximum Expression ◽

Modest Effect

Integration of a transposable element adjacent to a gene frequently results in an alteration in expression of the nearby gene. The purpose of our experiments was to identify cis-acting sequences within a yeast transposon (Ty) that are important for expression of the adjacent gene. The role of these sequences in Ty transcription was also analyzed in order to examine the relationship between Ty and adjacent gene expression. Three naturally occurring Ty elements located at the HIS4 locus were examined. These Ty elements differed by multiple sequence changes and had different effects on HIS4 expression. To determine which sequences were important to Ty and HIS4 expression, Ty::lacZ and Ty::HIS4::lacZ fusion genes were constructed and analyzed. Results of these experiments indicated that a sequence element is present in the Ty epsilon region that is necessary for HIS4 expression but which has only a modest effect on Ty transcription. Additionally, a mutation in the Ty promoter region decreased Ty transcription and increased HIS4 expression. The opposite effects of this mutation on Ty and adjacent gene expression were probably caused by promoter competition.

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Genome-Wide Identification of WRKY Genes in Artemisia annua: Characterization of a Putative Ortholog of AtWRKY40

Plants ◽

10.3390/plants9121669 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1669

Author(s):

Angelo De Paolis ◽

Sofia Caretto ◽

Angela Quarta ◽

Gian-Pietro Di Sansebastiano ◽

Irene Sbrocca ◽

...

Keyword(s):

Artemisia Annua ◽

Antimalarial Activity ◽

Regulatory Elements ◽

Promoter Regions ◽

Cis Acting ◽

Protein Motifs ◽

Genome Wide ◽

A Genome ◽

Rapid Amplification

Artemisia annua L. is well-known as the plant source of artemisinin, a sesquiterpene lactone with effective antimalarial activity. Here, a putative ortholog of the Arabidopsis thaliana WRKY40 transcription factor (TF) was isolated via reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends in A. annua and named AaWRKY40. A putative nuclear localization domain was identified in silico and experimentally confirmed by using protoplasts of A. annua transiently transformed with AaWRKY40-GFP. A genome-wide analysis identified 122 WRKY genes in A. annua, and a manually curated database was obtained. The deduced proteins were categorized into the major WRKY groups, with group IIa containing eight WRKY members including AaWRKY40. Protein motifs, gene structure, and promoter regions of group IIa WRKY TFs of A. annua were characterized. The promoter region of AaWRKY group IIa genes contained several abiotic stress cis-acting regulatory elements, among which a highly conserved W-box motif was identified. Expression analysis of AaWRKY40 compared to AaWRKY1 in A. annua cell cultures treated with methyl jasmonate known to enhance artemisinin production, suggested a possible involvement of AaWRKY40 in terpenoid metabolism. Further investigation is necessary to study the role of AaWRKY40 and possible interactions with other TFs in A. annua.

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The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance

Genome Biology ◽

10.1186/s13059-019-1808-y ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 5

Author(s):

Wei Song ◽

Roded Sharan ◽

Ivan Ovcharenko

Keyword(s):

Gene Expression ◽

Cell Lines ◽

Target Gene ◽

Regulatory Elements ◽

Distal Enhancer ◽

Human Genes ◽

Multiple Cell ◽

A Chain ◽

Target Promoter

Abstract Background Robustness and evolutionary stability of gene expression in the human genome are established by an array of redundant enhancers. Results Using Hi-C data in multiple cell lines, we report a comprehensive map of promoters and active enhancers connected by chromatin contacts, spanning 9000 enhancer chains in 4 human cell lines associated with 2600 human genes. We find that the first enhancer in a chain that directly contacts the target promoter is commonly located at a greater genomic distance from the promoter than the second enhancer in a chain, 96 kb vs. 45 kb, respectively. The first enhancer also features higher similarity to the promoter in terms of tissue specificity and higher enrichment of loop factors, suggestive of a stable primary contact with the promoter. In contrast, a chain of enhancers which connects to the target promoter through a neutral DNA segment instead of an enhancer is associated with a significant decrease in target gene expression, suggesting an important role of the first enhancer in initiating transcription using the target promoter and bridging the promoter with other regulatory elements in the locus. Conclusions The widespread chained structure of gene enhancers in humans reveals that the primary, critical enhancer is distal, commonly located further away than other enhancers. This first, distal enhancer establishes contacts with multiple regulatory elements and safeguards a complex regulatory program of its target gene.

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Factors Involved in the Regulation of Type I Collagen Gene Expression: Implication in Fibrosis

Experimental Biology and Medicine ◽

10.1177/153537020222700502 ◽

2002 ◽

Vol 227 (5) ◽

pp. 301-314 ◽

Cited By ~ 172

Author(s):

Asish K. Ghosh

Keyword(s):

Gene Expression ◽

Collagen Synthesis ◽

Molecular Mechanisms ◽

Type I Collagen ◽

Regulatory Elements ◽

Transcriptional Level ◽

Type I ◽

Collagen Gene ◽

Cis Acting ◽

Collagen Gene Expression

Type I collagen, the major component of extracellular matrix in skin and other tissues, is a heterotrimer of two α1 and one α2 collagen polypeptides. The synthesis of both chains is highly regulated by different cytokines at the transcriptional level. Excessive synthesis and deposition of collagen in the dermal region causes thick and hard skin, a clinical manifestation of scleroderma. To better understand the causes of scleroderma or other tissue fibrosis, it is very Important to investigate the molecular mechanisms that cause upregulation of the Type I collagen synthesis in these tissues. Several cis-acting regulatory elements and trans-acting protein factors, which are involved in basal as well as cytokine-modulated Type I collagen gene expression, have been identified and characterized. Hypertranscription of Type I collagen in scleroderma skin fibroblasts may be due to abnormal activities of different positive or negative transcription factors In response to different abnormally induced signaling pathways. In this review, I discuss the present day understanding about the involvement of different factors in the regulation of basal as well as cytokine-modulated Type I collagen gene expression and its implication in scleroderma research.

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Immunoglobulin molecular genetics: the prospects for mutational analysis of the chromosomal immunoglobulin genes

Genome ◽

10.1139/g89-030 ◽

1989 ◽

Vol 31 (1) ◽

pp. 175-181 ◽

Cited By ~ 1

Author(s):

Marc J. Shulman ◽

Lucine Bosnoyan ◽

Catherine Collins ◽

Nancy Pennell ◽

Mark D. Baker

Keyword(s):

Gene Expression ◽

Homologous Recombination ◽

Mutational Analysis ◽

Regulatory Elements ◽

Hybridoma Cells ◽

Immunoglobulin Genes ◽

Chromosomal Dna ◽

Cis Acting ◽

Chromosomal Genes ◽

Recombination Gene

Homologous recombination between transferred and chromosomal DNA can be used to effect precise, predetermined modifications of the chromosomal genes. Ultimately this phenomenon should allow the assessment of genetic regulatory elements as they function in the normal chromosomal environment. We have previously described a system for isolating mutant hybridoma cells that are defective in immunoglobulin (Ig) production, with a view toward using these mutants to define cis-acting elements that influence Ig gene expression. Here we describe results that indicate that homologous recombination between transferred and chromosomal Ig genes can be used to map Ig mutations by marker rescue.Key words: homologous recombination, gene expression.

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Stress affects the epigenetic marks added by natural transposable element insertions in Drosophila melanogaster

10.1101/037598 ◽

2016 ◽

Author(s):

Lain Guio ◽

Cristina Vieira ◽

Josefa González

Keyword(s):

Oxidative Stress ◽

Gene Expression ◽

Transposable Element ◽

Stress Conditions ◽

Regulatory Sequences ◽

Epigenetic Marks ◽

Cis Acting ◽

Comprehensive Picture ◽

Epigenetic Gene Regulation

ABSTRACTTransposable elements are emerging as an important source of cis-acting regulatory sequences and epigenetic marks that could influence gene expression. However, few studies have dissected the role of specific transposable element insertions on epigenetic gene regulation. Bari-Jheh is a natural transposon that mediates resistance to oxidative stress by adding cis-regulatory sequences that affect expression of nearby genes. In this work, we integrated publicly available data with chromatin immunoprecipitation experiments to get a more comprehensive picture of Bari-Jheh molecular effects. We showed that Bari-Jheh was enriched for H3K9me3 in nonstress conditions, and for H3K9me3, H3K4me3 and H3K27me3 in oxidative stress conditions, which is consistent with expression changes in adjacent genes. We further showed that under oxidative stress conditions, H3K4me3 and H3K9me3 spread to the promoter region of Jheh1 gene. Finally, another insertion of the Bari1 family was associated with increased H3K27me3 in oxidative stress conditions suggesting that Bari1 histone marks are copy-specific. We concluded that besides adding cis-regulatory sequences, Bari-Jheh influences gene expression by affecting the local chromatin state.

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Analysis of (δβ)0 Thalassemia and HPFH Deletions Suggest a Hierarchy of Cis-Acting Elements Regulating Fetal Hemoglobin Gene Expression.

Blood ◽

10.1182/blood.v124.21.54.54 ◽

2014 ◽

Vol 124 (21) ◽

pp. 54-54 ◽

Cited By ~ 1

Author(s):

Heather L Edward ◽

Tasha Morrison ◽

Jacqueline N Milton ◽

Hong-yuan Luo ◽

Lance Davis ◽

...

Keyword(s):

Gene Expression ◽

Binding Site ◽

Conflicts Of Interest ◽

Globin Gene ◽

Regression Tree ◽

Fetal Hemoglobin ◽

Regulatory Elements ◽

Globin Genes ◽

Cis Acting ◽

Cart Analysis

Abstract Hereditary persistence of fetal hemoglobin (HPFH) and (δβ)0 thalassemia are caused by deletions within the β-globin gene (HBB) cluster that remove elements that affect the expression of the γ-globin genes (HBG2 and HBG1, or HBG). These deletions are of different lengths and have different 5’ and 3’ breakpoints. The phenotypes associated with heterozygous carriers of (δβ)0 thalassemia and HPFH deletions are differentiated by levels of 5-15% HbF distributed heterocellularly in the former and 15-30% HbF distributed pancellularly in the latter. We found a novel 588.6 kb deletion that removed both the 3.5 kb fragment 5’ to HBD that is deleted in Corfu β thalassemia and contains a BCL11A binding site, and the known cis-acting elements downstream of HBB. The proband with this deletion had a HbF of 5.4% (Morrison et al, Blood, 2014 abstract 3452). To study the relative importance of 5’ and 3’ regulatory elements in HBG expression we studied 209 cases culled from the literature and from our laboratory where the 3.5 kb element 5’ to HBD and enhancers 3’ to HBB were deleted and HBG remained intact. We used a backwards stepwise regression statistical analysis to determine which deleted elements had the greatest effect on HbF levels. The combination of the deletion of 3.5 kb intergenic region 5’ to HBD, the presence of the HPFH-1 “3D” enhancer juxtaposed to HBG, and the deletion of the 3’ HS1 region accounted for 66.7% of the HbF variation in heterozygotes for HPFH and (δβ)0-thalassemia deletions. The HPFH-1 “3D” enhancer juxtaposed to HBG— the main difference between HPFH-1 and 2 compared with Spanish (δβ)0-thalassemia—was associated with an increase in HbF of 20.78% (p<2e-16) after adjusting for the effects of the other 5’ and 3’ cis-acting elements. The next most significant factor was the deletion of the 3.5 kb fragment 5’ to HBD which resulted in an increase of 10.62% HbF after similar adjustments (p<2e-16); deletion of the 3’ HS1 region accounted for an increase in HbF of 5.25% (p<1.05e-5). The HPFH-3 and HPFH-6 enhancer regions each accounted for a less than 1% increase in HbF and were not significantly associated with HbF in this model. Among 194 individuals where both 5’ and some 3’ elements affecting γ-globin gene expression—excluding the “3D” enhancer—were deleted, HbF was 20±9.3%; in 13 cases where all 3’ enhancers—including the “3D” enhancer—were deleted, HbF was 6.8±3.7% (p=8.9e-07). To determine which combinations of cis-acting elements were associated with high and low HbF levels we performed a classification and regression tree (cART) analysis on HbF. The results of the regression tree (Figure) only included the deletion of the 5’ 3.5 kb fragment region, the presence of the HPFH-1 “3D” enhancer and the deletion of the 3’ HS1 region and were consistent with the results of the backwards selection model. The absence of the 5’ 3.5 kb fragment 5’ to HBD combined with the presence of the HPFH-1 “3D” enhancer was associated with the highest average HbF of 27.02%. The absence of the 3.5 kb fragment 5’ to HBD combined with the absence of the HPFH-1 “3D” enhancer was associated with the lowest average HbF of 6.82%.The 588.6 kb deletion is the largest deletion reported in the HBB cluster that leaves the γ-globin genes intact, and the second to remove both the BCL11A binding site and all known 3’ enhancer elements. By studying deletions in the HBBgene cluster we have further defined the hierarchy of cis-acting elements that modulate HbF levels in adults and suggest a paramount role of the distal “3D” enhancer. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

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Transcriptional Enhancers in Drosophila

Genetics ◽

10.1534/genetics.120.301370 ◽

2020 ◽

Vol 216 (1) ◽

pp. 1-26 ◽

Cited By ~ 1

Author(s):

Stephen Small ◽

David N. Arnosti

Keyword(s):

Gene Expression ◽

Critical Role ◽

Regulation Of Gene Expression ◽

Regulatory Elements ◽

Comprehensive Analysis ◽

Special Focus ◽

Transcriptional Enhancers ◽

Quantitative Understanding ◽

Developmental Role

Key discoveries in Drosophila have shaped our understanding of cellular “enhancers.” With a special focus on the fly, this chapter surveys properties of these adaptable cis-regulatory elements, whose actions are critical for the complex spatial/temporal transcriptional regulation of gene expression in metazoa. The powerful combination of genetics, molecular biology, and genomics available in Drosophila has provided an arena in which the developmental role of enhancers can be explored. Enhancers are characterized by diverse low- or high-throughput assays, which are challenging to interpret, as not all of these methods of identifying enhancers produce concordant results. As a model metazoan, the fly offers important advantages to comprehensive analysis of the central functions that enhancers play in gene expression, and their critical role in mediating the production of phenotypes from genotype and environmental inputs. A major challenge moving forward will be obtaining a quantitative understanding of how these cis-regulatory elements operate in development and disease.

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