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Results for “Enhancer Elements, Genetic”

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PubMed2006

The effects of multiple features of alternatively spliced exons on the K(A)/K(S) ratio test.

BACKGROUND: The evolution of alternatively spliced exons (ASEs) is of primary interest because these exons are suggested to be a major source of functional diversity of proteins. Many exon features have been suggested to affect the evolution of ASEs. However, previous studies have relied on the KA/KS ratio test without taking into consideration information sufficiency (i.e., exon length > 75 bp, cross-species divergence > 5%) of the studied exons, leading to potentially biased interpretations. Furthermore, which exon feature dominates the results of the KA/KS ratio test and whether multiple exon features have additive effects have remained unexplored. RESULTS: In this study, we collect two different datasets for analysis - the ASE dataset (which includes lineage-specific ASEs and conserved ASEs) and the ACE dataset (which includes only conserved ASEs). We first show that information sufficiency can significantly affect the interpretation of relationship between exons features and the KA/KS ratio test results. After discarding exons with insufficient information, we use a Boolean method to analyze the relationship between test results and four exon features (namely length, protein domain overlapping, inclusion level, and exonic splicing enhancer (ESE) frequency) for the ASE dataset. We demonstrate that length and protein domain overlapping are dominant factors, and they have similar impacts on test results of ASEs. In addition, despite the weak impacts of inclusion level and ESE motif frequency when considered individually, combination of these two factors still have minor additive effects on test results. However, the ACE dataset shows a slightly different result in that inclusion level has a marginally significant effect on test results. Lineage-specific ASEs may have contributed to the difference. Overall, in both ASEs and ACEs, protein domain overlapping is the most dominant exon feature while ESE frequency is the weakest one in affecting test results. CONCLUSION: The proposed method can easily find additive effects of individual or multiple factors on the KA/KS ratio test results of exons. Therefore, the system can analyze complex conditions in evolution where multiple features are involved. More factors can also be added into the system to extend the scope of evolutionary analysis of exons. In addition, our method may be useful when orthologous exons can not be found for the KA/KS ratio test.

Alternative Splicing↗

PubMed2002

Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering.

BACKGROUND: Organisms simplify the orchestration of gene expression by coregulating genes whose products function together in the cell. Many proteins serve different roles depending on the demands of the organism, and therefore the corresponding genes are often coexpressed with different groups of genes under different situations. This poses a challenge in analyzing whole-genome expression data, because many genes will be similarly expressed to multiple, distinct groups of genes. Because most commonly used analytical methods cannot appropriately represent these relationships, the connections between conditionally coregulated genes are often missed. RESULTS: We used a heuristically modified version of fuzzy k-means clustering to identify overlapping clusters of yeast genes based on published gene-expression data following the response of yeast cells to environmental changes. We have validated the method by identifying groups of functionally related and coregulated genes, and in the process we have uncovered new correlations between yeast genes and between the experimental conditions based on similarities in gene-expression patterns. To investigate the regulation of gene expression, we correlated the clusters with known transcription factor binding sites present in the genes' promoters. These results give insights into the mechanism of the regulation of gene expression in yeast cells responding to environmental changes. CONCLUSIONS: Fuzzy k-means clustering is a useful analytical tool for extracting biological insights from gene-expression data. Our analysis presented here suggests that a prevalent theme in the regulation of yeast gene expression is the condition-specific coregulation of overlapping sets of genes.

Binding Sites↗

PubMed2004

Single nucleotide polymorphism-based validation of exonic splicing enhancers.

Because deleterious alleles arising from mutation are filtered by natural selection, mutations that create such alleles will be underrepresented in the set of common genetic variation existing in a population at any given time. Here, we describe an approach based on this idea called VERIFY (variant elimination reinforces functionality), which can be used to assess the extent of natural selection acting on an oligonucleotide motif or set of motifs predicted to have biological activity. As an application of this approach, we analyzed a set of 238 hexanucleotides previously predicted to have exonic splicing enhancer (ESE) activity in human exons using the relative enhancer and silencer classification by unanimous enrichment (RESCUE)-ESE method. Aligning the single nucleotide polymorphisms (SNPs) from the public human SNP database to the chimpanzee genome allowed inference of the direction of the mutations that created present-day SNPs. Analyzing the set of SNPs that overlap RESCUE-ESE hexamers, we conclude that nearly one-fifth of the mutations that disrupt predicted ESEs have been eliminated by natural selection (odds ratio = 0.82 +/- 0.05). This selection is strongest for the predicted ESEs that are located near splice sites. Our results demonstrate a novel approach for quantifying the extent of natural selection acting on candidate functional motifs and also suggest certain features of mutations/SNPs, such as proximity to the splice site and disruption or alteration of predicted ESEs, that should be useful in identifying variants that might cause a biological phenotype.

Alleles↗

PubMed2001

META-controlled env-initiated transcripts encoding superantigens of murine Mtv29 and Mtv7 and their possible role in B cell lymphomagenesis.

Spontaneous germinal center (GC)-derived B cell lymphomas of SJL mice (RCS) transcribe a 1.8-kb Mtv-29 mRNA under control of the META-env promoter. The encoded vSAg29 stimulates syngeneic Vbeta16(+) CD4(+) T cells, thereby acquiring T cell help necessary for RCS growth. Other strains of B cell lymphoma-prone mice include Mtv29(+) C57L and MA/MyJ, and the Mtv29(-) Mtv7(+)-recombinant inbred strain, SW x J-1. The lymphomas of these mice produce similar mouse mtv-vSAg-encoding mRNA, as characterized by Northern blotting, PCR, and RNase protection. A 1.8-kb mRNA in C57L/J and MA/MyJ lymphomas hybridized with an Mtv29-specific oligonucleotide, whereas SW x J-1 lymphomas produced 1.8-kb transcripts hybridizing with an Mtv7-specific oligonucleotide. Similar META-env-initiated transcripts were absent from LPS-activated B cells from any strain examined but were detected in Peyer's patch RNA from SJL mice. Like typical SJL-derived RCS, all these lymphomas stimulated syngeneic CD4(+) T cells and Vbeta16(+) T hybridoma cells. Immunohistochemical staining of primary tumors showed the presence of peanut agglutinin binding (PNA(+)) highly mitotic lymphoblasts, suggesting their GC derivation. The findings indicate that this novel mRNA for Mtv29 is present in B cell lymphomas from several Mtv29(+) mouse strains. Additionally, this is the first description of the ability of Mtv7 to produce transcripts that are controlled and spliced identically to those of Mtv29 and that are expressed in SW x J-1, I-A(s+), lymphomas that also stimulate Vbeta16(+) T cells. Our results suggest an important role for mouse mtv-vSAgs and Vbeta16 T cell stimulation in the development of GC-derived murine B cell lymphomas.

Animals↗

PubMed1985

[Enhancement of expression of Escherichia coli uridine phosphorylase gene as a result of duplication].

The thymine-requiring (thy) Escherichia coli strains normally convert thymine to thymidine through the action of thymidine phosphorylase, an enzyme, whose synthesis is directed by tpp gene of the deo operon. Selection for efficient thymine utilization in the thy mutants carrying a deletion in the tpp gene allows to obtain clones with constitutive synthesis of an alternative enzyme, uridine phosphorylase coded by the udp gene. Such clones are usually formed, due to "promoter-up" constitutive udpP mutants. Further selection for increased expression of the udp gene was performed on the background of udpP1 and udpP18 "promoter-up" constitutive mutants isolated previously. Several lines of evidence obtained by using transposon insertions suggest that the increased synthesis of uridine phosphorylase in some newly isolated mutants is due to duplications of the udp gene. In two mutants the adjacent metE gene is involved in duplications simultaneously with the udp gene.

Cloning, Molecular↗

PubMed1998

Enhancer requirement for murine cytomegalovirus growth and genetic complementation by the human cytomegalovirus enhancer.

The cytomegalovirus (CMV) enhancer is a highly complex regulatory region containing multiple elements that interact with a variety of host-encoded transcription factors. Many of these sequence elements are conserved among the different species strains of CMV, although the arrangement of the various elements and overall sequence composition of the CMV enhancers differ remarkably. To delineate the importance of this region to a productive infection and to explore the possibility of generating a murine CMV (MCMV) under the control of human CMV (HCMV) genetic elements, the MCMV enhancer was resected and replaced either with nonregulatory sequences or with paralogous sequences from HCMV. The effects of these various deletions and substitutions on viral growth in transfected or infected tissue-culture cells were evaluated. We found that mutations in MCMV that eliminate or substitute for the enhancer with nonregulatory sequences showed a severe deficiency in virus synthesis. This growth defect is effectively complemented by the homologous MCMV enhancer as well as the HCMV enhancer. In the latter case, the chimeric viruses (hybrid MCMV strains) containing the molecularly shuffled human enhancer exhibit infectious kinetics similar to that of parental wild-type and wild-type revertant MCMV. These results also show that open reading frames m124, m124.1, and m125 located within the enhancer region are nonessential for growth of MCMV in cells. Most importantly, we conclude that the enhancer of MCMV is required for optimal infection and that its diverged human counterpart can advantageously replace its role in promoting viral infectivity.

3T3 Cells↗

PubMed2001

The sea urchin sns insulator blocks CMV enhancer following integration in human cells.

Insulators are a new class of genetic elements that attenuate enhancer function directionally. Previously, we characterized in sea urchin a 265-bp-long insulator, termed sns. To test insulator activity following stable integration in human cells, we placed sns between the CMV enhancer and a tk promoter upstream of a GFP transgene of plasmid or retroviral vectors. In contrast to controls, cells transfected or transduced with insulated constructs displayed a barely detectable fluorescence. Southern blot and PCR ruled out vector rearrangement following integration into host DNA; RNase protection confirmed the enhancer blocking activity. Finally, we demonstrate that two cis-acting sequences, previously characterized in sea urchin, are also specific binding sites for human proteins. We conclude that sns interferes with enhancer promoter interaction also in a human chromatin context. The relatively small size, evolutionary conservation and apparent lack of enhancer specificity might result useful in gene transfer experiments in human cells.

Animals↗

PubMed1987

Discrete elements within the SV40 enhancer region display different cell-specific enhancer activities.

The SV40 enhancer contains three genetically defined elements, called A, B and C, that can functionally compensate for one another. By using short, synthetic DNA oligonucleotides, we show that each of these elements can act autonomously as an enhancer when present as multiple tandem copies. Analysis of a progressive series of B element oligomers shows a single element is ineffective as an enhancer and that the activity of two or more elements increases with copy number. Assay in five different cell lines of two separate enhancers containing six tandem copies of either the B or C element shows that these elements possess different cell-specific activities. Parallel oligomer enhancer constructs containing closely spaced double point mutations display no enhancer activity in any of the cell lines tested, indicating that these elements represent single units of enhancer function. These elements contain either a 'core' or 'octamer' consensus sequence but these consensus sequences alone are not sufficient for enhancer activity. The different cell-specific activities of the B and C elements are consistent with functional interactions with different trans-acting factors. We discuss how tandem duplication of such dissimilar elements, as in the wild-type SV40 72-bp repeats, can serve to expand the conditions under which an enhancer can function.

Animals↗

PubMed1996

[Analysis of motifs of functional MDG2 sites in assuring its possible molecular functions].

We analyzed the location and possible interaction of motifs of functional sites in a DNA sequence of MDG2 (Dm412) revealed by means of computer context analysis. It was shown that motifs of functional sites in the appropriate location can ensure the basic molecular functions of MDG2: expression of its ORF, transcription, induction of transposition, modification of adjacent genes and polygenes, etc. MDG2 ILTR does not contain the NTCAGTYN motif required for initiation of transcription by RNA polymerase II in the absence of the TATA box and located close to the transcription start site in most gypsy-like retrotransposons of Drosophila. Therefore, MDG2 ILTR appears to contain the classic promoter region for RNA polymerase II, contrary to other retrotransposons of the gypsy group. Enhancers of mobile genetic elements are assumed to determine modification of adjacent genes and polygenes. Excisions and transpositions of mobile elements seem to be induced by external stress factors or physiological factors through a heat-shock system.

Enhancer Elements, Genetic↗

PubMed1998

Role of c-fos in hypoxia-induced AP-1 cis-element activity and tyrosine hydroxylase gene expression.

Previous studies have demonstrated that hypoxia stimulates expression of the c-fos gene in intact animals and isolated cells. The purpose of the present study was to assess the functional significance of c-fos activation during hypoxia. Using antisense c-fos strategy, we tested the hypothesis that c-fos is essential for activation of activator protein-1 transcription factor complex (AP-1) and subsequent stimulation of down stream genes such as tyrosine hydroxylase (TH) gene during hypoxia. Experiments were performed on rat pheochromocytoma 12 (PC12) cells. AP-1 activity was determined by a reporter gene assay using a luciferase expression vector driven by two copies of an AP-1 cis-element (AP-1-Luc). Cells transfected with AP-1-Luc construct were exposed to normoxia (21% O2) or to varying intensities and/or durations of hypoxia. AP-1 activity increased in response to hypoxia. The magnitude of the response depended on the intensity and duration of the hypoxic stimulus. Increases in AP-1 activity could not be elicited in neuroblastoma cells, indicating that hypoxia-induced increase in AP-1 activity is a cell selective phenomenon. Antisense c-fos abolished hypoxia-induced AP-1 activation in PC12 cells. Hypoxia increased tyrosine hydroxylase-chloramphenicol acetyl transferase activity (TH-CAT), and antisense c-fos and mutations at AP-1 binding sites in TH promoter abolished this effect. These results provide direct evidence that c-fos is essential for functional activation of AP-1 and subsequent activation of delayed response genes such as TH in PC12 cells.

Animals↗

PubMed2026

The transcription factor BACH1 couples chromatin priming and repression to enable macrophage plasticity and adaptation.

Macrophage activation and tissue adaptation involve precise transcriptional control by lineage-determining transcription factors (LDTFs) and stimulus-dependent TFs. The heme-regulated transcriptional repressor BACH1 clusters with myeloid LDTFs in unstimulated macrophages, suggesting a role in shaping macrophage identity and function. We found that BACH1 bound to both inactive and active regulatory regions, including latent enhancers. BACH1 recruited the NuRD complex and had dual functions, establishing early chromatin accessibility while actively repressing transcription. Upon inflammatory stimulation, BACH1 rapidly redistributed in cis to nearby promoters, reshaping chromatin occupancy, motif specificity, and enhancer-promoter interactions. BACH1 constrained 3D chromatin architecture, limiting enhancer mobility and TF complex dynamics. In vivo, Bach1 deletion impaired macrophage polarization and tissue adaptation and limited resilience during systemic and regenerative inflammation. Thus, BACH1 acts as an early chromatin accessibility-priming factor while actively repressing transcription-a regulatory activity that can be defined as pioneer repression-thereby shaping the macrophage epigenome in response to inflammatory and tissue contexts.

Basic-Leucine Zipper Transcription Factors↗

PubMed1992

A constitutive enhancer in the bovine papillomavirus upstream regulatory region shares genetic elements with the viral P1 promoter.

The bovine papillomavirus upstream regulatory region represents a common element in the regulation of transcription from the five early viral promoters. We have determined the sequences required for transcription from the viral P1 promoter, which is located at the 5' end of the upstream regulatory region. In vitro transcription from P1 requires a 123-bp fragment (nucleotides 7153 to 7275; -33 to +90) consisting of an upstream TATA-like sequence as well as an unidentified protein which binds to sequences immediately downstream of the initiation site. In vivo, this promoter requires additional downstream sequences (to position +160; nucleotide 7345) for maximal activity but does not require any additional DNA sequence upstream of a putative TATA box. Four regions within the downstream sequence from +9 to +160 are protected from DNase I digestion by proteins present in a HeLa cell extract. The presence of these sites correlates with the level of P1 activity. A constitutive enhancer maps to this same region, and mutations in this enhancer have been shown to affect downstream promoters. Deletion analysis indicates that the same sequences are required by both the P1 promoter and the constitutive enhancer, suggesting that the same proteins function in both activities.

Animals↗

PubMed2002

Evolution of functionally conserved enhancers can be accelerated in large populations: a population-genetic model.

The evolution of cis-regulatory elements (or enhancers) appears to proceed at dramatically different rates in different taxa. Vertebrate enhancers are often very highly conserved in their sequences, and relative positions, across distantly related taxa. In contrast, functionally equivalent enhancers in closely related Drosophila species can differ greatly in their sequences and spatial organization. We present a population-genetic model to explain this difference. The model examines the dynamics of fixation of pairs of individually deleterious, but compensating, mutations. As expected, small populations are predicted to have a high rate of evolution, and the rate decreases with increasing population size. In contrast to previous models, however, this model predicts that the rate of evolution by pairs of compensatory mutations increases dramatically for population sizes above several thousand individuals, to the point of greatly exceeding the neutral rate. Application of this model predicts that species with moderate population sizes will have relatively conserved enhancers, whereas species with larger populations will be expected to evolve their enhancers at much higher rates. We propose that the different degree of conservation seen in vertebrate and Drosophila enhancers may be explained solely by differences in their population sizes and generation times.

Animals↗

PubMed2005

Transgenes as screening tools to probe and manipulate the zebrafish genome.

The zebrafish, originally an object of study as an inexpensive and prolific vertebrate embryological model with a plethora of genetic tricks, has over the past decade moved to large-scale chemical mutagenesis and recently came of age as a high throughput transgenic model with a sequenced genome nearing completion. Insertional mutagenesis, gene trapping and enhancer detection are all contributing to the increasing speed with which research in this biomedical model is progressing. We review here some of the recent developments in the emerging field of zebrafish developmental genomics and transgenesis.

Animals↗

PubMed2027

Mapping Stage-Specific Enhancer Dynamics During the Specification of Human Trophoblast Lineage.

Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is a powerful technique for mapping cis-acting regulatory elements in DNA regions, such as enhancers and promoters, that are associated with specific histone modification marks or bound by transcription factors (TFs). By systematically mapping enhancer landscapes across various cell types or differentiation trajectories, this methodology facilitates the discovery of highly regulated genes specific to certain cell types, as well as the underlying transcriptional and epigenetic regulatory mechanisms that establish cellular identity and function. Particular emphasis has been placed on mapping large clusters of enhancers known as super-enhancers (SEs), which are often associated with cell-type-specific master TFs. Unlike typical enhancers, SEs can help to identify previously unknown key TFs specific to certain cell types. Follow-up studies can systematically validate these master regulators and their mechanisms of action, providing a comprehensive framework for deciphering the regulatory architecture underlying cellular identity. This protocol outlines how to map dynamic changes in enhancer and SE usage during human trophoblast differentiation using human trophoblast stem cells (TSCs) and their subsequent differentiation into more specialized cell types.

Humans↗

PubMed1995

Molecular and genetic analysis of nitrite reductase co-suppression in transgenic tobacco plants.

Silencing of Nia host genes and transgenes (encoding nitrate reductase) was previously achieved by introducing into tobacco plants the tobacco Nia2 cDNA cloned downstream of the cauliflower mosaic virus (CaMV) 35S promoter. To check whether Nii host genes and transgenes (encoding nitrite reductase, the second enzyme of the nitrate assimilation pathway) were also susceptible to silencing, a transgene consisting of the tobacco Nii1 gene with two copies of the enhancer of the 35S promoter cloned 1 kb upstream of the Nii promoter region was introduced into tobacco plants. Among nine independent transformants analysed, two showed silencing of Nii host genes and transgenes in some descendants after selfing, but never after back-crossing with wild-type plants, suggesting that silencing depends on the number of transgene loci and/or on certain allelic or ectopic combinations of transgene loci. In one transformant carrying a single transgene locus in a homozygous state, silencing was triggered in all progeny plants of each generation, 20 to 50 days after germination. Field trial analysis confirmed that silencing was not triggered when the transgene locus of this latter line was present in a hemizygous state. In addition, it was revealed that silencing can be triggered, albeit at low frequency and later during the development, when this transgene locus is brought into the presence of a non-allelic transgene locus by crossing, suggesting that a homozygous state is not absolutely required.

Cloning, Molecular↗

PubMedDate not supplied

Promoter inactivation or inhibition by sequence-specific methylation and mechanisms of reactivation.

In studies on adenovirus promoters, predominantly on the late E2A promoter of adenovirus type 2 (Ad2), we have demonstrated by a number of experimental approaches that the sequence-specific methylation of three 5'-CCGG-3' sequences inactivates this promoter. Recently, we have developed a cell-free transcription system in which the methylation-inactivation of eukaryotic promoters can be studied in detail. It has also been shown that methylation-caused promoter inactivation can be reversed by the 289 amino acid E1A protein of Ad2 or of adenovirus type 5. In the presence of this protein with a transactivating effect, transcription is initiated at the authentic cap site of the methylated late E2A promoter. A similar reactivation of the methylated late E2A promoter can also be effected by a cis-acting genetic element, i.e., the strong enhancer of human cytomegalovirus. Further studies will be directed toward the biochemical mechanisms of promoter silencing by sequence-specific methylations.

Adenoviruses, Human↗

PubMed1993

Selection is not required to produce invariant T-cell receptor gamma-gene junctional sequences.

Recombination of V-, D- and J-gene segments can generate an enormous diversity of T-cell antigen receptor (TCR) gene sequences. Although many gamma delta T cells fully exploit this diversification process, those in the epidermal and vaginal epithelium do not, predominantly expressing invariant gamma delta receptors in which the V-(D)-J junctional sequences in almost all the productive rearrangements are identical. The almost exclusive use of identical TCRs by cells in these sites is thought to reflect recognition of a stress-induced autologous antigen. To explain the prevalence of the invariant junctional sequences, it has been proposed that thymic selection operates on a population of originally diverse progenitor cells, resulting in a homogeneous repertoire. Alternatively the invariant sequences may result from biases in the recombination machinery in the fetal thymic progenitors of these cells. We report here the use of mice into which mutated TCR gamma-gene rearrangement substrates have been introduced as transgenes to demonstrate directly that the canonical TCR V gamma 3-J gamma 1 and V gamma 4-J gamma 1 sequences occur at high frequency in the absence of the possibility of selection for the protein products.

Animals↗