相关论文: A model for codon position bias in RNA editing
Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than…
A-to-I RNA editing by ADARs is a post-transcriptional mechanism for expanding the proteomic repertoire. Genetic recoding by editing was so far observed for only a few mammalian RNAs that are predominantly expressed in nervous tissues.…
Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a model that unifies four possible mechanisms for reassignment,…
Evolving genomes increase a number of their genes by gene duplications. To escape degradation in a functionless pseudogene, any gene duplicate needs to be guarded by negative (purifying) selection from otherwise inevitable fixation of…
Messenger RNA encodes a sequence of amino acids by using codons. For most amino acids there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for…
mRNA editing of sequences of many species is analyzed. The nature of the inserted nucleotides and the position of the insertion sites, once fixed the edited peptide chain, are explained by introducing a minimum principle in the framework of…
A self-organizing approach is proposed for gene finding based on the model of codon usage for coding regions and positional preference for noncoding regions. The symmetry between the direct and reverse coding regions is adopted for reducing…
The relationship between sequences and secondary structures or shapes in RNA exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (that among all sequences of fixed length certain shapes are…
We address the question, related with the origin of the genetic code, of why are there three bases per codon in the translation to protein process. As a followup to our previous work, we approach this problem by considering the…
This paper uses a recently presented abstract, tuneable Boolean regulatory network model extended to consider aspects of mobile DNA, such as transposons. The significant role of mobile DNA in the evolution of natural systems is becoming…
Co-localization of networks of genes in the nucleus is thought to play an important role in determining gene expression patterns. Based upon experimental data, we built a dynamical model to test whether pure diffusion could account for the…
Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino acid, are used differently across the variety of living organisms. The biological meaning of this phenomenon, known as codon usage bias, is still controversial. In…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…
Background: The evolution of microRNA regulation in metazoans is a mysterious process: MicroRNA sequences are highly conserved among distal organisms, but on the other hand, there is no evident conservation of their targets. Results: We…
Human genetic diseases often arise from point mutations, emphasizing the critical need for precise genome editing techniques. Among these, base editing stands out as it allows targeted alterations at the single nucleotide level. However,…
Human genetic diseases often arise from point mutations, emphasizing the critical need for precise genome editing techniques. Among these, base editing stands out as it allows targeted alterations at the single nucleotide level. However,…
The neutral mutation rate is known to vary widely along human chromosomes, leading to mutational hot and cold regions. We provide evidence that categories of functionally-related genes reside preferentially in mutationally hot or cold…
Background: There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information…
Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of…
Using the shape space of codons and tRNAs we give a physical description of the genetic code evolution on the basis of the codon capture and ambiguous intermediate scenarios in a consistent manner. In the lowest dimensional version of our…