An Integrated Computational and Laboratory Approach for Selective Amplification of mRNAs Containing the Adenylate Uridylate-Rich Element Consensus Sequence

Khabar, Khalid S.A.; Dhalla, Mohammed; Bakheet, Tala; Sy, Cheikh Tidiane; Al‐Haj, Latifa

doi:10.1101/gr.204902

Cited by 8 publications

(4 citation statements)

References 36 publications

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“…Another example of the utility of the ARED is our integrated computational and laboratory approach for selective amplification of ARE-mRNAs (8) in which statistical analysis of the initiation regions in the 5 0 UTR of ARE-mRNAs was performed and accordingly, several 5 0 primers and a single universal 3 0 primer that targeted the initiation consensuses and ARE regions, respectively, were designed. This resulted in selective amplification of ARE-mRNA, many of which are present in ARED.…”

Section: The Database and Biological Applicationsmentioning

confidence: 99%

ARED 2.0: an update of AU-rich element mRNA database

Bakheet¹,

Williams

Khabar³

2003

Nucleic Acids Research

153

138

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The Adenylate Uridylate (AU)-Rich Element Database, ARED-mRNA version 2.0, contains information not present in the previous ARED. This includes additional data entries, new information and links to Unigene, LocusLink, RefSeq records and mouse homologue data. An ARE consensus sequence specific to the 3'UTR is the basis of ARED that demonstrated two important findings: (i) AREs are present in a large, previously unrecognized set of human mRNAs; and (ii) ARE-mRNAs encode proteins of diverse functions which are largely involved in early and transient biological responses. In this update, we have modified the strategy for identifying ARE-mRNA in order to systematically deal with inconsistencies of molecule type and mRNA region in GenBank records. Potential uses for the ARED in functional genomics are also given. The database is accessible via the web, http://rc.kfshrc.edu.sa/ared, with a new querying system that allows searching ARE-mRNAs by any public database identifier or name. The ARED website also contains relevant links to uses for the ARED.

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Section: The Database and Biological Applicationsmentioning

confidence: 99%

ARED 2.0: an update of AU-rich element mRNA database

Bakheet¹,

Williams

Khabar³

2003

Nucleic Acids Research

153

138

View full text Add to dashboard Cite

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“…The structure of AREs is defined as a repeating pentamer (AUUUA) with 1 or 2 A to U substitutions [9]. Bioinformatic searches throughout the human transcriptome have provided computational estimation of sequence characteristics and nucleotide lengths of ARE sequences required for mRNA to be unstable [30,31]. The number of pentamers has an additive effect on mRNA decay and deadenylation processes.…”

Section: Au-rich Element (Are)mentioning

confidence: 99%

Mammalian Cis-Acting RNA Sequence Elements

Louis¹,

Sagarsky²

2018

Gene Expression and Regulation in Mammalian Cells - Transcription From General Aspects

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Cis-acting regulatory sequence elements are sequences contained in the 3 0 and 5 0 untranslated region, introns, or coding regions of precursor RNAs and mature mRNAs that are selectively recognized by a complementary set of one or more trans-acting factors to regulate posttranscriptional gene expression. This chapter focuses on mammalian cis-acting regulatory elements that had been recently discovered in different regions: pre-processed and mature. The chapter begins with an overview of two large networks of mRNAs that contain conserved AU-rich elements (AREs) or GU-rich elements (GREs), and their role in mammalian cell physiology. Other, less conserved, cisacting elements and their functional role in different steps of RNA maturation and metabolism will be discussed. The molecular characteristics of pathological cis-acting sequences that rose from gene mutations or transcriptional aberrations are briefly outlined, with the proposed approach to restore normal gene expression. Concise models of the function of posttranscriptional regulatory networks within different cellular compartments conclude this chapter.

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“…[ 27 ] Khabar et al . [ 28 ] assessed the annealing specificity of primers in PCR reactions under different annealing temperatures (35°C, 40°C, and 45°C) and found perfect matches between at least eight bases at the 3’-end of the 5’-primers and the target region, whereas mispriming occurred only toward the 5’-end. Therefore it is critical to include 8–10 unique bases at the 3’-end of the primer.…”

Section: Introductionmentioning

confidence: 99%

Mining of simple sequence repeats in the Genome of Gentianaceae

et al. 2011

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Simple sequence repeats (SSRs) or short tandem repeats are short repeat motifs that show high level of length polymorphism due to insertion or deletion mutations of one or more repeat types. Here, we present the detection and abundance of microsatellites or SSRs in nucleotide sequences of Gentianaceae family. A total of 545 SSRs were mined in 4698 nucleotide sequences downloaded from the National Center for Biotechnology Information (NCBI). Among the SSR sequences, the frequency of repeat type was about 429 -mono repeats, 99 -di repeats, 15 -tri repeats, and 2 --hexa repeats. Mononucleotide repeats were found to be abundant repeat types, about 78%, followed by dinucleotide repeats (18.16%) among the SSR sequences. An attempt was made to design primer pairs for 545 identified SSRs but these were found only for 169 sequences.

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An Integrated Computational and Laboratory Approach for Selective Amplification of mRNAs Containing the Adenylate Uridylate-Rich Element Consensus Sequence

Cited by 8 publications

References 36 publications

ARED 2.0: an update of AU-rich element mRNA database

ARED 2.0: an update of AU-rich element mRNA database

Mammalian Cis-Acting RNA Sequence Elements

Mining of simple sequence repeats in the Genome of Gentianaceae

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