mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences

Seffens, William

doi:10.1093/nar/27.7.1578

Cited by 183 publications

(151 citation statements)

References 18 publications

Supporting

Mentioning

137

Contrasting

Order By: Relevance

“…However, minimal folding free energy depends on the length of the RNA sequence (Seffens and Digby, 1999). Thus, to avoid the effect of using minimal folding free energy as the one and only criterion to identify new miRNAs (Adai et al, 2005), MFEI was used to distinguish miRNAs from other non-coding and coding RNAs.…”

Section: A B Cmentioning

confidence: 99%

Identification and Validation of Potential Conserved microRNAs and Their Targets in Peach (Prunus persica)

Gao

Luo

Shi

et al. 2012

Molecules and Cells

View full text Add to dashboard Cite

1MicroRNAs are a class of small, endogenous, non-coding RNA molecules that negatively regulate gene expression at the transcriptional or the post-transcriptional level. Although a large number of miRNAs have been identified in many plant species, especially from model plants and crops, they remain largely unknown in peach. In this study, 110 potential miRNAs belonging to 37 families were identified using computational methods. A total of 43 potential targets were found for 21 families based on near-perfect or perfect complementarity between the plant miRNA and the target sequences. A majority of the targets were transcription factors which play important roles in peach development. qRT-PCR analysis of RNA samples prepared from different peach tissues for 25 miRNA families revealed that miRNAs were differentially expressed in different tissues. Furthermore, two target genes were experimentally verified by detection of the miRNA-mediated mRNA cleavage sites in peach using RNA ligase-mediated 5' rapid amplification of cDNA ends (RLM-RACE). Finally, we studied the expression pattern of the two target genes in three different tissues of peach to further understand the mechanism of the interaction between miRNAs and their target genes.

show abstract

Section: A B Cmentioning

confidence: 99%

Identification and Validation of Potential Conserved microRNAs and Their Targets in Peach (Prunus persica)

Gao

Luo

Shi

et al. 2012

Molecules and Cells

View full text Add to dashboard Cite

show abstract

“…For rapidly propagating organisms such as E.coli, selection against wasted ribosomal time would be important (11). The nucleotide distribution and synonymous codon choice will also influence secondary structure in the mRNA (12). Shifting secondary structure requirements along the messenger could therefore also give rise to nucleotide gradients.…”

Section: Introductionmentioning

confidence: 99%

Gradients in nucleotide and codon usage along Escherichia coli genes

Hooper

Berg

2000

Nucleic Acids Research

View full text Add to dashboard Cite

The usage of codons and nucleotide combinations varies along genes and systematic variation causes gradients in usage. We have studied such gradients of nucleotides and nucleotide combinations and their immediate context in Escherichia coli. To distinguish mutational and selectional effects, the genes were subdivided into three groups with different codon usage bias and the gradients of nucleotide usage were studied in each group. Some combinations that can be associated with a propensity for processivity errors show strong negative gradients that become weaker in genes with low codon bias, consistent with a selection on translational efficiency. One of the strongest gradients is for third position G, which shows a pervasive positive gradient in usage in most contexts of surrounding bases.

show abstract

“…This is an interesting observation because this phenomena might not only distinguish between exons and introns on a physicochemical basis, but it might even clearly define the trinucleotide codons and thus the phase of the translation. This codon-related phase-specific variation in FFE may explain why mRNAs have greater negative free folding energies than shuffled or codon choice randomized sequences [23].…”

Section: Resultsmentioning

confidence: 99%

“…In the two optimal codes, all three codon residues (123) were complementary (C) or reverse complementary (RC) to each other. In the suboptimal codes, only two of three codon residues were C or RC to each other (12,13,23), while the third was not necessarily complementary (X).…”

Section: Resultsmentioning

confidence: 99%

The Meaning of a Redundant Codon: There is Protein Folding Information in Nucleic Acids in Addition to the Genetic Code

Biro¹,

Biro²

2006

American J. of Biochemistry and Biotechnology

View full text Add to dashboard Cite

All the information necessary for protein folding is supposed to be present in the amino acid sequence. It is still not possible to provide specific ab initio structure predictions by bioinformatical methods. It is suspected that additional folding information is present in protein coding nucleic acid sequences, which is not represented by the known genetic code. Nucleic acid subsequences comprising the 1st and/or 3rd codon residues in mRNAs express significantly higher free folding energy (FFE) than the subsequence containing only the 2nd residues (p<0.0001, n=81). This periodic FFE difference is not present in introns and therefore it is a specific physico-chemical characteristic of coding sequences and it might contribute to unambiguous definition of codon boundaries during translation. The FFE in the 1st and 3rd residues is additive, which suggests that these residues contain a significant number of complementary bases and contribute to selection for local RNA secondary structures in coding regions. This periodic, codon-related structure-forming of mRNAs indicates a connection between the structure of exons and the corresponding (translated) proteins. The folding energy dot plots of RNAs and the residue contact maps of the coded proteins are indeed similar. Residue contact statistics using 81 different protein structures confirmed that amino acids that are coded by partially reverse and complementary codons (Watson-Crick (WC) base pairs at the 1st and 3rd codon positions and translated in reverse orientation) are preferentially co-located in protein structures. Exons are distinguished from introns and codon boundaries are physico-chemically defined by periodically distributed FFE differences between codon positions. There is a selection for local RNA secondary structures in coding regions and this nucleic acid structure resembles the folding profiles of the coded proteins. The preferentially (specifically) interacting amino acids are coded by partially complementary codons, which strongly supports the connection between mRNA and the corresponding protein structures and indicates that there is protein folding information in nucleic acids that is not present in the genetic code. This might give some additional explanation of codon redundancy.

show abstract

mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences

Cited by 183 publications

References 18 publications

Identification and Validation of Potential Conserved microRNAs and Their Targets in Peach (Prunus persica)

Identification and Validation of Potential Conserved microRNAs and Their Targets in Peach (Prunus persica)

Gradients in nucleotide and codon usage along Escherichia coli genes

The Meaning of a Redundant Codon: There is Protein Folding Information in Nucleic Acids in Addition to the Genetic Code

Contact Info

Product

Resources

About