Call us toll-free

Cis-regulatory module - Wikipedia

T1 - Independent effects of cis- and trans-regulatory variation on gene expression in Drosophila melanogaster

Approximate price

Pages:

275 Words

$19,50

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA ..

AB - Biochemical interactions between cis-regulatory DNA sequences and trans-regulatory gene products suggest that cis- and trans-acting polymorphisms may interact genetically. Here we present a strategy to test this hypothesis by comparing the relative cis-regulatory activity of two alleles in different genetic backgrounds. Of the eight genes surveyed in this study, five were affected by trans-acting variation that altered total transcript levels, two of which were also affected by differences in cis-regulation. The presence of trans-acting variation had no effect on relative cis-regulatory activity, showing that cis-regulatory polymorphisms can function independently of trans-regulatory variation. The frequency of such independent interactions on a genomic scale is yet to be determined.

Computational discovery of cis-regulatory sequences



The X inactive-specific transcript (Xist) gene is expressed exclusively from the inactive X chromosome, producing a 17-kb spliced, polyadenylated transcript that is retained in the nucleus. The Xist transcript seems to be the primary signal for spreading the inactive state along the chromosome. But Xist itself does not seem to be involved in counting. Some of the elements lying outside Xist that influence counting and choice in X inactivation (see Xic) might be involved in regulating its expression.

The X chromosome-inactivation centre (Xic) was originally defined through studies on structurally abnormal X chromosomes as a master control region, the presence of which is essential for X inactivation to occur. It is responsible for initiating X inactivation : an X- chromosome fragment that carries a Xic can become inactivated, whereas one in which the Xic is missing cannot. The Xic is also involved in counting, whereby only a single X is kept active per two sets of autosomes in a cell, and all other Xic -carrying chromosomes are inactivated.

The X chromosome-controlling element (Xce) affects the choice of X to be inactivated (or to remain active). In females heterozygous for different Xce alleles, an X chromosome that carries a strong Xce allele is more likely to remain active than one that carries a weak Xce allele, thereby leading to . The degree of skewing is rarely more than 70:30%.Refined genetic mapping using microsatellite markers indicate that the Xce locus might be distinct from Xist, lying distal and 3' to Xist (38).

TsiX is an element transcribed from the antisense strand relative to Xist. Tsix is expressed in undifferentiated ES cells and early embryos, and has been proposed to control Xist expression at the onset of X inactivation (3, 35). TsiX antisense transcription spans the whole of the Xist gene, extending well over 40 kb. The 5' end and promoter of the TsiX gene has been proposed to be closely associated with the DXPas34 locus, although other (weaker) promoters might be scattered across a large region 3' to Xist (34). Targeted deletion of the 5' end of TsiX/DXPas34 leads to nonrandom inactivation of the deleted X chromosome (35) and a failure of imprinted X inactivation (52). This might indicate that this locus and/or the transcript that it produces influences X chromosome choice and imprinting of the X chromosome.

The DXPas34 locus is a 3 kb CpG-rich region, containing a 34-mer minisatellite repeat lying roughly 15 kb downstream of the 3' end of Xist. DXPas34 is hypermethylated on the active X chromosome in somatic cells. The degree of hypermethylation was thought to correlate with allelism at the Xce locus, although Xce lies outside the DXPas34 region (2). The principal initiation site for TsiX transcription has been reported to lie within DXPas34 (3).

and classifying candidate cis-regulatory sequences sites in ..

T1 - Prediction of cis-regulatory elements controlling genes differentially expressed by retinal and choroidal vascular endothelial cells

The greatest risk factor for kidney stones is hypercalciuria, the etiology of which is largely unknown. A recent genome-wide association study (GWAS) linked hypercalciuria and kidney stones to a claudin-14 (CLDN14) risk haplotype. However, the underlying molecular mechanism was not delineated. Recently, renal CLDN14 expression was found to increase in response to increased plasma calcium, thereby inducing calciuria. We hypothesized therefore that some children with hypercalciuria and kidney stones harbor a CLDN14 variant that inappropriately increases gene expression. To test this hypothesis, we sequenced the CLDN14 risk haplotype in a cohort of children with idiopathic hypercalciuria and kidney stones. An intronic single nucleotide polymorphism (SNP) was more frequent in affected children. Dual luciferase and cell based assays demonstrated increased reporter or CLDN14 expression when this polymorphism was introduced. In silico studies predicted the SNP introduced a novel insulinoma-associated 1 (INSM1) transcription factor binding site. Consistent with this, repeating the dual luciferase assay in the presence of INSM1, further increased reporter expression. Our data suggest that children with the INSM1 binding site within the CLDN14 risk haplotype have a higher likelihood of hypercalciruia and kidney stones. Enhanced CLDN14 expression may play a role in the pathophysiology of their hypercalciuria. This article is protected by copyright. All rights reserved.

AB - Cultured endothelial cells of the human retina and choroid demonstrate distinct patterns of gene expression. We hypothesized that differential gene expression reflected differences in the interactions of transcription factors and respective cis-regulatory motifs(s) in these two endothelial cell subpopulations, recognizing that motifs often exist as modules. We tested this hypothesis in silico by using TRANSFAC Professional and CisModule to identify cis-regulatory motifs and modules in genes that were differentially expressed by human retinal versus choroidal endothelial cells, as identified by analysis of a microarray data set. Motifs corresponding to eight transcription factors were significantly (p

Independent effects of cis- and trans-regulatory …

Orrenius S, Thor H, McConkey D, Nicotera P, & Bellomo G (1989) Mechanism of cell toxicity: the thiol/calcium hypothesis.

The course presents computational and statistical methods for gene and protein networks and structural proteomics; it emphasizes: (1) Probablistic models for gene regulatory networks via microarray, chromatin immune-precipitation, and cis-regulatory data; (2) Signal transduction pathways via tandem mass spectrometry data; (3) Molecular Modeling forligand-receptor coupling and docking. The course is recommended for graduate students.

There are as wide a variety of presentations of manifesting carriers as there are of males with DMD and BMD. Some girls may have a muscular dystrophy that is as severe as boys with DMD. Other women may only have very mild problems with muscle weakness late in adult life. Some women get aches and pains in their muscles as their first complaint and may notice enlargement of their calves and other muscles. There are other manifestations of Duchenne muscular dystrophy, for example involvement of intellectual function and of heart muscle. Problems in these areas can be the only signs that someone is a manifesting carrier. These presentations are less common than a woman noticing a mild but progressive weakness involving usually first her legs but later on the arms as well. Most manifesting carriers notice some progression of their muscle problem with time; however it is rare for there to be any sudden deterioration.

KW - cis-Regulatory module
Order now
  • the hypothesis that such local, cis regulatory networks may ..

    Cis-regulatory elements (CREs) are regions of non-coding DNA which regulate the transcription of neighboring genes

  • Divergence in cis-regulatory sequences surrounding the opsin gene ..

    18/01/2011 · Divergence within cis-regulatory sequences may ..

  • To characterize the cis -regulatory elements ..

    Here we present a strategy to test this hypothesis by comparing the relative cis-regulatory activity of two ..

Order now

Cis-regulatory mechanisms of left/right asymmetric …

Biochemical interactions between cis-regulatory DNA sequences and trans-regulatory gene products suggest that cis- and trans-acting polymorphisms may interact genetically. Here we present a strategy to test this hypothesis by comparing the relative cis-regulatory activity of two alleles in different genetic backgrounds. Of the eight genes surveyed in this study, five were affected by trans-acting variation that altered total transcript levels, two of which were also affected by differences in cis-regulation. The presence of trans-acting variation had no effect on relative cis-regulatory activity, showing that cis-regulatory polymorphisms can function independently of trans-regulatory variation. The frequency of such independent interactions on a genomic scale is yet to be determined.

The activity of these L/R asymmetric cis-regulatory elements is ..

The underlying hypothesis is that functional non-coding sequences - particularly those governing a set of tissue-specific genes - will evince common features at the sequence level that can be identified computationally and modeled with sufficient precision to enable accurate de novo predictions.

it was hypothesized that it functions as a cis-regulatory element

Cultured endothelial cells of the human retina and choroid demonstrate distinct patterns of gene expression. We hypothesized that differential gene expression reflected differences in the interactions of transcription factors and respective cis-regulatory motifs(s) in these two endothelial cell subpopulations, recognizing that motifs often exist as modules. We tested this hypothesis in silico by using TRANSFAC Professional and CisModule to identify cis-regulatory motifs and modules in genes that were differentially expressed by human retinal versus choroidal endothelial cells, as identified by analysis of a microarray data set. Motifs corresponding to eight transcription factors were significantly (p

Order now
  • Kim

    "I have always been impressed by the quick turnaround and your thoroughness. Easily the most professional essay writing service on the web."

  • Paul

    "Your assistance and the first class service is much appreciated. My essay reads so well and without your help I'm sure I would have been marked down again on grammar and syntax."

  • Ellen

    "Thanks again for your excellent work with my assignments. No doubts you're true experts at what you do and very approachable."

  • Joyce

    "Very professional, cheap and friendly service. Thanks for writing two important essays for me, I wouldn't have written it myself because of the tight deadline."

  • Albert

    "Thanks for your cautious eye, attention to detail and overall superb service. Thanks to you, now I am confident that I can submit my term paper on time."

  • Mary

    "Thank you for the GREAT work you have done. Just wanted to tell that I'm very happy with my essay and will get back with more assignments soon."

Ready to tackle your homework?

Place an order