Our research focuses on the characterization and modeling of post-transcriptional regulatory networks involved in the coordination of gene expression programs in vertebrates, using a combination of cell and molecular biology studies with genomics and bioinformatics approaches. We are particularly interested in regulatory events determined by small non-coding RNAs and the interaction of RNA binding proteins with mRNA untranslated sequence elements (UTRs)and how they can be targeted to influence on gene expression outputs for therapeutic applications. ...
An example of underestimating the probability of frequent word occurrences is apparent in a recent study by Rigoutsos et al [16]. They reported that certain DNA words, termed pyknons, appear frequently in human gene-related sequences andin noncoding regions, in restricted configurations, and presented many arguments for the pyknon s functionality. By relying on a Bernoulli model, they reasoned that 16-mers should appear in a random genome sequence more than forty times with a probability ,10-32. Such a word frequency, however, is not as extraordinary if we take into account the universal shape of genomic spectra. A DPL distribution fitted to the human genome spectrum yields a P-value of 0.001 (see Supplementary Material).This latter translates to about four million 16-mers that are expected to occur at least forty times in a random genome-sized sequence. Strikingly, at least 460 thousand frequent words appear already in the repeat-masked sequence as accidental constituents of the fitted ...
An example of underestimating the probability of frequent word occurrences is apparent in a recent study by Rigoutsos et al [16]. They reported that certain DNA words, termed pyknons, appear frequently in human gene-related sequences andin noncoding regions, in restricted configurations, and presented many arguments for the pyknon s functionality. By relying on a Bernoulli model, they reasoned that 16-mers should appear in a random genome sequence more than forty times with a probability ,10-32. Such a word frequency, however, is not as extraordinary if we take into account the universal shape of genomic spectra. A DPL distribution fitted to the human genome spectrum yields a P-value of 0.001 (see Supplementary Material).This latter translates to about four million 16-mers that are expected to occur at least forty times in a random genome-sized sequence. Strikingly, at least 460 thousand frequent words appear already in the repeat-masked sequence as accidental constituents of the fitted ...
Hagai, T.; Chen, X.; Miragaia, R. J.; Rostom, R.; Gomes, T.; Kunowska, N.; Henriksson, J.; Park, J. E.; Proserpio, V.; Donati, G. et al.; Bossini-Castillo, L.; Vieira Braga, F. A.; Naamati, G.; Fletcher, J.; Stephenson, E.; Vegh, P.; Trynka, G.; Kondova, I.; Dennis, M.; Haniffa, M.; Nourmohammad, A.; Lässig, M.; Teichmann, S. A.: Gene expression variability across cells and species shapes innate immunity. Nature 563 (7730), pp. 197 - 202 (2018 ...
Pos found in: POS-16, POS-5, POS-8LA, POS-8A, Rod End, Metric, Male, Right Thread, Lubricant Type RE (METRIC, MALE, RIGHT THREAD, LUBRICAN, Rod End,..
TY - JOUR. T1 - Gene expression variability as a unifying element of the pluripotency network. AU - Mason, Elizabeth A.. AU - Mar, Jessica C.. AU - Laslett, Andrew L.. AU - Pera, Martin F.. AU - Quackenbush, John. AU - Wolvetang, Ernst. AU - Wells, Christine A.. PY - 2014/8/12. Y1 - 2014/8/12. N2 - Heterogeneity is a hallmark of stem cell populations, in part due to the molecular differences between cells undergoing self-renewal and those poised to differentiate. We examined phenotypic and molecular heterogeneity in pluripotent stem cell populations, using public gene expression data sets. A high degree of concordance was observed between global gene expression variability and the reported heterogeneity of different human pluripotent lines. Network analysis demonstrated that low-variability genes were the most highly connected, suggesting that these are the most stable elements of the gene regulatory network and are under the highest regulatory constraints. Known drivers of pluripotency were ...
The 3 untranslated region (3 UTR) of mRNA contains elements that play regulatory roles in polyadenylation, localization, translation efficiency, and mRNA stability. Despite the significance of the 3 UTR, there is no popular method for annotating 3 UTRs and for profiling their isoforms. Recently, poly(A)-position profiling by sequencing (3P-seq) and other similar methods have successfully been used to annotate 3 UTRs; however, they contain complex RNA-biochemical experimental steps, resulting in a low yield of products. Now, researchers from Hanyang University, Korea have developed heuristic and regression methods to estimate and quantify the usage of 3 UTRs with widely profiled RNA sequencing (RNA-seq) data. With this approach, the 3 UTR usage estimated from RNA-seq was found to be highly correlated to that of 3P-seq, and poly(A) cleavage signals of 3 UTRs were detected upstream of the predicted poly(A) cleavage sites. These methods predicted greater number of 3 UTRs than 3P-seq, which allows
The present invention describes the use of hybrid short 3′ untranslated (3′UTR) regions which are composed of two regions, one region from an 3′ untranslated region of a stable eukaryotic mRNA, and an
The three prime untranslated region (3′-UTR) is known to play a pivotal role in modulating gene expression by determining the fate of mRNA...
Sequence provided by depositing laboratory may be theoretical/predicted or based on Sanger/NGS sequencing results. Discrepancies between sequencing results obtained by Addgene and the original sequence provided by the depositor may be present. ...
Mori Y, Imaizumi K, Katayama T, Yoneda T, Tohyama M. Two cis-acting elements in the 3 untranslated region of alpha-CaMKII regulate its dendritic targeting ...
Ophthalmol. OOmm 00 35 CtI. Prepare 7 to 9 days after administration a suspension from the liver of Tadalis-Sx chick cna pool these samples. The probe for hoxa4 was then synthesized from the extremity of the 3 untranslated region of the gene until Vali BglII site located in the second exon.
Advances in single-cell technologies have revealed vast differences between cells once thought to be in the same category, calling into question how we define cell type in the first place ...
The mouse Tcp10 genes are transcribed exclusively in male germ cells and display multiple 5 and 3 untranslated variations generated by alternative splicing and polyadenylation signal usage. To investigate the possible role of untranslated sequences in the regulation of these genes, chimeric expression constructs with or without endogenous 5 and 3 untranslated sequences were generated and used to make transgenic mice. Analysis of these animals showed that the untranslated sequences have no effect on the transcription or translation of an attached lacZ reporter gene, thereby implying these sequences are dispensible. However, the endogenous pattern of polyadenylation site usage was altered when Tcp10 3 untranslated sequences were linked to lacZ, indicating that internal coding sequence can influence recognition of polyadenylation signals in testis. The characteristics of alternative splicing and polyadenylation signal variability reflects a common theme of promiscuity in testicular gene
Untranslated regions (UTRs) are sections of the RNA before the start codon and after the stop codon that are not translated, termed the five prime untranslated region (5 UTR) and three prime untranslated region (3 UTR), respectively. These regions are transcribed as part of the same transcript as the coding region. Several roles in gene expression have been attributed to the untranslated regions, including mRNA stability, mRNA localization, and translational efficiency. The ability of a UTR to perform these functions depends on the sequence of the UTR and can differ between mRNAs. The stability of mRNAs may be controlled by the 5 UTR and/or 3 UTR due to varying affinity for RNA degrading enzymes called ribonucleases and for ancillary proteins that can promote or inhibit RNA degradation. Translational efficiency, including sometimes the complete inhibition of translation, can be controlled by UTRs. Proteins that bind to either the 3 or 5 UTR may affect translation by influencing the ...
Sigma-Aldrich offers abstracts and full-text articles by [Spenser S Smith, Catherine B Kessler, Vikram Shenoy, Clifford J Rosen, Anne M Delany].
Pippucci T, Savoia A, Perrotta S, Pujol-Moix N, Noris P, Castegnaro G, Pecci A, Gnan C, Punzo F, Marconi C, Gherardi S, Loffredo G, De Rocco D, Scianguetta S, Barozzi S, Magini P, Bozzi V, Dezzani L, Di Stazio M, Ferraro M, Perini G, Seri M, Balduini CL (2011) Mutations in the 5 UTR of ANKRD26, the ankirin repeat domain 26 gene, cause an autosomal-dominant form of inherited thrombocytopenia, THC2. Am J Hum Genet 88(1):115-120. https://​doi.​org/​10.​1016/​j.​ajhg.​2010.​12.​006 CrossRefPubMedPubMedCentral ...
Absolute number of identified transcription start sites in correlation to the length of their 5′-untranslated regions (5′-UTRs). The 1,642 TSSs located upst
In molecular genetics, the three prime untranslated region (3-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codon. An mRNA molecule is transcribed from the DNA sequence and is later translated into protein. Several regions of the mRNA molecule are not translated into protein including the 5 cap, 5 untranslated region, 3 untranslated region, and the poly(A) tail. The 3-UTR often contains regulatory regions that post-transcriptionally influence gene expression. Regulatory regions within the 3-untranslated region can influence polyadenylation, translation efficiency, localization, and stability of the mRNA. The 3-UTR contains both binding sites for regulatory proteins as well as microRNAs (miRNAs). By binding to specific sites within the 3-UTR, miRNAs can decrease gene expression of various mRNAs by either inhibiting translation or directly causing degradation of the transcript. The 3-UTR also has silencer regions which bind to repressor ...
Untranslated regions (UTRs) are sections of the mRNA before the start codon and after the stop codon that are not translated, termed the five prime untranslated region (5 UTR) and three prime untranslated region (3 UTR), respectively. These regions are transcribed with the coding region and thus are exonic as they are present in the mature mRNA. Several roles in gene expression have been attributed to the untranslated regions, including mRNA stability, mRNA localization, and translational efficiency. The ability of a UTR to perform these functions depends on the sequence of the UTR and can differ between mRNAs. Genetic variants in 3 UTR have also been implicated in disease susceptibility because of the change in RNA structure and protein translation.[16]. The stability of mRNAs may be controlled by the 5 UTR and/or 3 UTR due to varying affinity for RNA degrading enzymes called ribonucleases and for ancillary proteins that can promote or inhibit RNA degradation. (See also, C-rich stability ...
Untranslated definition, to turn from one language into another or from a foreign language into ones own: to translate Spanish. See more.
Newly found molecular timer stalls ribosomes in the untranslated region of mRNA to limit number of protein molecules synthesized from single mRNA template
Naturally Occurring Human Genetic Variation in the 3′-Untranslated Region of the Secretory Protein Chromogranin A Is Associated With Autonomic Blood Pressure Regulation and Hypertension in a Sex-Dependent Fashion Academic Article ...
Mononucleotide, dinucleotide, hexamer, heptamer, and octamer counts and frequencies were determined for all human 3 UTR sequences. Sets of control sequences were designed for each seed match sequence and each extended-match variant (SeedM + m8, SeedM + t1A, etc.) so as to preserve the expected frequency of random matching between miRNA seed sequences and complementary 3 UTR sequences. All hexamers, heptamers, heptamers, and octamers were examined to identify suitable control sequences for each miRNA seed (or augmented seed) that preserve (1) E(SM), the 1st order Markov probability of the seed match, and (2) O(SM), the observed count of seed matches in human UTRs within a total margin of ±7.5%. As described in Lewis et al. (2003), for a miRNA seed match heptamer S1,S2,S3,S4,S5,S6,S7, E(SM) was equal to (PS1·PS1,S2·PS2,S3·PS3,S4·PS4,S5·PS5,S6·PS6,S7) where PS1 was the frequency of the nucleotide S1 and PSk,Sk+1 was the conditional frequency of the nucleotide Sk+1 given Sk at the previous ...
In Fragile X syndrome-a genetic mishap that results in cognitive delays-the lack of a translation-repressing protein leads to the rampant accumulation of other proteins in the mouse brain.. 0 Comments. ...
HotelsIn Croatia hotels are graded two, three, four or five star.Hotels graded two star are usually managed by the owners, so the advantages include a friendly...
Regulatory RNA regions within a transcript, particularly in the 5′ untranslated region (5′UTR), have been shown in a variety of organisms to control the expression levels of these mRNAs in response to various metabolites or environmental conditions. Considering the unique tolerance of Zymomonas mobilis to ethanol and the growing interest in engineering microbial strains with enhanced tolerance to industrial inhibitors, we searched natural cis-regulatory regions in this microorganism using transcriptomic data and bioinformatics analysis. Potential regulatory 5′UTRs were identified and filtered based on length, gene function, relative gene counts, and conservation in other organisms. An in vivo fluorescence-based screening system was developed to confirm the responsiveness of 36 5′UTR candidates to ethanol, acetate, and xylose stresses. UTR_ZMO0347 (5′UTR of gene ZMO0347 encoding the RNA binding protein Hfq) was found to down-regulate downstream gene expression under ethanol stress. Genomic
Widespread transcription of non-protein-coding DNA suggests that the RNAs produced from such DNA might serve biological functions. Ironically, the suggestion that much non-protein-coding DNA might be functional also comes from evolutionary theory. If two lineages diverge from a common ancestor that possesses regions of non-protein-coding DNA, and these regions are really nonfunctional, then they will accumulate random mutations that are not weeded out by natural selection. Many generations later, the sequences of the corresponding non-protein-coding regions in the two descendant lineages will probably be very different. [Due to fixation by random genetic drift-LAM] On the other hand, if the original non-protein-coding DNA was functional, then natural selection will tend to weed out mutations affecting that function. Many generations later, the sequences of the corresponding non-protein-coding regions in the two descendant lineages will still be similar. (In evolutionary terminology, the ...
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This glyph is used for drawing processed transcripts that have both CDS and UTR segments. The CDS is drawn in the background color, and the UTRs are drawn in an alternate color selected by the utr_color option. In addition, you can make the UTRs thinner than the CDS by setting the thin_utr option.. For this glyph to produce the desired results, you should pass it a compound Bio::SeqFeature that has subfeatures of primary_tag CDS and UTR. In fact, you may give it more specific types of UTR, including 5-UTR, 3-UTR, or the Sequence Ontology terms untranslated_region, five_prime_untranslated_region, and three_prime_untranslated_region.. ...
Question 5 we have another paper to study, about altzeimers and untranslated regions of the mRNA. It looks in detail about mRNA regulation, and that there are mechanisms to stop the translation of mRNA into protein that can react quickly to needs. Anyway, there is a huge number of questions on this - a) to m), and several of these having i) ii) iii) subparts. There are a lot of marks on offer for this (50%). I manage to lose quite a few here though, and nto through not understanding, just being slightly out of kilter with exactly what the question is asking for. I think several of my answers are sort of right, but not what is expected. Grrr. My worst score so far ...