The identification and quantification of highly stable ‘common hairpin’ in the dynamic process of co-transcriptional mRNA folding

Zhou, Wei; Chen, Xuefeng; Zhang, Kun-Lin; Liu, Ciquan

doi:10.1016/j.theochem.2004.11.042

Cited by 4 publications

(2 citation statements)

References 24 publications

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“…Our previous work [10,11] showed that the mRNA sequence is increased on the same step. The dynamically extended folding process starts from 90 nucleotide (1-90 nt), and then extends 30 nt in turn until the full length (1-90 nt, 1-120 nt, 1-150 nt, …, entire sequence).…”

Section: Methodsmentioning

confidence: 99%

Secondary structural analysis of the mRNA regions encoding the hemagglutinin cleavage site basic amino acids of the avian influenza virus H5N1 subtype samples

et al. 2008

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Here we report the codon bias and the mRNA secondary structural features of the hemagglutinin (HA) cleavage site basic amino acid regions of avian influenza virus H5N1 subtypes. We have developed a dynamic extended folding strategy to predict RNA secondary structure with RNAstructure 4.1 program in an iterative extension process. Statistical analysis of the sequences showed that the HA cleavage site basic amino acids favor the adenine-rich codons, and the corresponding mRNA fragments are mainly in the folding states of single-stranded loops. Our sequential and structural analyses showed that to prevent and control these highly pathogenic viruses, that is, to inhibit the gene expression of avian influenza virus H5N1 subtypes, we should consider the single-stranded loop regions of the HA cleavage site-coding sequences as the targets of RNA interference.

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Section: Methodsmentioning

confidence: 99%

Secondary structural analysis of the mRNA regions encoding the hemagglutinin cleavage site basic amino acids of the avian influenza virus H5N1 subtype samples

et al. 2008

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“…We applied the dynamic extended folding approach to analyze the structures of the human Hb premRNAs [13,16,17] . Taking the dynamic extended folding process of HBB pre-mRNA as an example, there were 78 hairpins appearing during the 54 simulations.…”

Section: Framework Structures Of the Human Hb Pre-mrnasmentioning

confidence: 99%

Splicing signals in the human hemoglobin genes at the sequence and folding levels

Zhang

Xie

et al. 2011

Wuhan Univ. J. Nat. Sci.

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Identification of the splice sites is a critical and tough issue in eukaryotic genome annotation. Here, a statistical study is introduced for detecting the splicing signals in the human hemoglobin (Hb) pre-mRNAs by using the approaches of regional pairwise alignment, splicing weight matrix scoring, and dynamic extended folding. First, the regional pairwise alignment results show that the coding regions of the human Hb genes are at a high level for both conservation and fluctuation. Second, the weighted matrix scoring results indicate that, although the authentic splicing motifs are always scored the highest in a sequence, the sequence motif alone is inadequate to precisely define the splice sites. Finally, we deduce the RNA frame structures by applying an extended folding approach to analyze the stable folding elements. We find out that the splice sequences tend to take stretching and partially paired conformations, which benefit recognition and competitive binding of the splicing factors. These results indicate that precise splicing is an integrated effect of multiple mechanisms of signal recognition at the level of sequence and structure.Splice site prediction is a critical and tough issue for defining the protein-coding sequences in eukaryotic genome sequences [1,2] . Although more than 98% of the introns start at GU and end at AG, the problem lies in selecting the correct splice sites from many GUs and AGs in a pre-mRNA [3] . For example, there are 87 GUs and 81 AGs in HBB pre-mRNAs, but only two GU-AG pairs are the authentic splice sites. Given the advances in splicing motif, branch site, and splicing enhancers and silencers, it is still unclear how to recognize the splice sites precisely.A good candidate for exploring the mechanisms of splice site recognition is the human hemoglobin (Hb) gene family, which comprises ten genes in two clusters: all the five α-type genes cluster tightly at the chromosome position 16p13.3 in the order of HBZ, HBM, HBA2, HBA1, and HBQ1 [4,5] and the other five β-type genes at 11p15.5, in the order of HBE1, HBG2, HBG1, HBD, and HBB. These short genes contain two introns, dividing the coding sequences into three parts, as well as the two terminal non-translational regions, where we denoted the seven regions as 5'u, cd1, in1, cd2, in2, cd3, and 3'u, for the 5'-untranslated region, coding sequence 1, intron 1, coding sequence 2, intron 2, coding sequence 3, and 3'-untranslated region, respectively.Recognition of the human Hb pre-mRNA splice

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Dynamic extended folding: Modeling the RNA secondary structures during co-transcriptional folding

Cao

Xie

Zhang

et al. 2009

Journal of Theoretical Biology

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The identification and quantification of highly stable ‘common hairpin’ in the dynamic process of co-transcriptional mRNA folding

Cited by 4 publications

References 24 publications

Secondary structural analysis of the mRNA regions encoding the hemagglutinin cleavage site basic amino acids of the avian influenza virus H5N1 subtype samples

Secondary structural analysis of the mRNA regions encoding the hemagglutinin cleavage site basic amino acids of the avian influenza virus H5N1 subtype samples

Splicing signals in the human hemoglobin genes at the sequence and folding levels

Dynamic extended folding: Modeling the RNA secondary structures during co-transcriptional folding

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