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

Cao, Huai; Xie, Huazhen; Zhang, Wen; Wang, Kan; Li, Wei; Liu, Ciquan

doi:10.1016/j.jtbi.2009.07.027

Cited by 5 publications

(3 citation statements)

References 37 publications

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“…The dynamic extended folding approach had been described by Cao et al, 2009 [13] . Briefly, the RNA secondary structure of the 5'-terminal 30 nt segment was predicted by using the RNAstructure4.4 program [14] .…”

Section: Dynamic Extended Folding Simulationmentioning

confidence: 99%

“…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%

“…The folding framework structures of the 10 premRNAs were constructed based on the stable and substable hairpins [13] . In Fig.…”

Section: Framework Structures Of the Human Hb Pre-mrnasmentioning

confidence: 99%

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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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Section: Dynamic Extended Folding Simulationmentioning

confidence: 99%

Section: Framework Structures Of the Human Hb Pre-mrnasmentioning

confidence: 99%

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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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Relationships of mRNA-protein secondary structures in the human β-globin gene HBB and four variants

Zhang

et al. 2012

Chin. Sci. Bull.

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Single nucleotide polymorphism is an interesting problem that can alter gene expression, recode amino acids and affect protein function. Protein structural changes have generally been attributed to amino acid replacements, and only a few research efforts have examined the effects of mRNA structural changes to the conformation of the corresponding protein coded by the mRNA. In the present study, the human -globin HBB gene and four variants were examined. The mRNA secondary structures were constructed using the dynamic extended folding method and the encoded protein secondary structures were obtained from related databases. Comparisons were performed between these structures before and after mutations were introduced into the mature mRNAs and the proteins. We focused on the structural changes from mRNA to protein and found that regular protein conformations tend to match stable mRNA regions, whereas irregular protein conformations, such as / turns and random coils, often match unstable mRNA regions. Mutations within unstable regions can alter the mRNA secondary structure and leave footprints in the protein structure. Comparison of the mRNA-protein secondary structure relationships represents a potential strategy to explore protein functional changes.

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Contributions of viroid research to methods for RNA purification, diagnostics, and secondary structure prediction

Steger,

Riesner

2024

Fundamentals of Viroid Biology

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

Cited by 5 publications

References 37 publications

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

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

Relationships of mRNA-protein secondary structures in the human β-globin gene HBB and four variants

Contributions of viroid research to methods for RNA purification, diagnostics, and secondary structure prediction

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