We explore if there exist universal statistical patterns that are different in coding and noncoding DNA and can be found in all living organisms, regardless of their phylogenetic origin. We find that (i) the mutual in...
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We explore if there exist universal statistical patterns that are different in coding and noncoding DNA and can be found in all living organisms, regardless of their phylogenetic origin. We find that (i) the mutual information function I has a significantly different functional form in coding and noncoding DNA. We further find that (ii) the probability distributions of the average mutual information Ī are significantly different in coding and noncoding DNA, while (iii) they are almost the same for organisms of all taxonomic classes. Surprisingly, we find that Ī is capable of predicting coding regions as accurately as organism-specific coding measures.
We analyze the histograms for the lengths of the 16 possible distinct repeats of identical dimers, known as dimeric tandem repeats, in DNA sequences. For coding regions, the probability of finding a repetitive sequenc...
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We analyze the histograms for the lengths of the 16 possible distinct repeats of identical dimers, known as dimeric tandem repeats, in DNA sequences. For coding regions, the probability of finding a repetitive sequence of ℓ copies of a particular dimer decreases exponentially as ℓ increases. For the noncoding regions, the distribution functions for most of the 16 dimers have long tails and can be approximated by power-law functions, while for coding DNA, they can be well fit by a first-order Markov process. We propose a model, based on known biophysical processes, which leads to the observed probability distribution functions for noncoding DNA. We argue that this difference in the shape of the distribution functions between coding and noncoding DNA arises from the fact that noncoding DNA is more tolerant to evolutionary mutational alterations than coding DNA.
Yeast (Saccharomyces cerevisiae) histone mRNA synthesis is tightly regulated to the S phase of the cell division cycle as a result of both transcriptional and posttranscriptional regulation. We focused on the role of ...
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Yeast (Saccharomyces cerevisiae) histone mRNA synthesis is tightly regulated to the S phase of the cell division cycle as a result of both transcriptional and posttranscriptional regulation. We focused on the role of posttranscriptional control in histone H2B1 gene (HTB1) regulation and studied a portion of the HTB1 message required for cell-cycle-specific accumulation. The 3'' end of the HTB1 gene containing a 17-amino-acid coding sequence and entire noncoding sequence was fused to the bacterial neomycin phosphotransferase II gene (neo) under control of the GAL1 promoter. The expression of the endogenous and chimeric HTB1 genes was analyzed during the yeast cell cycle. As yeast cells entered a synchronous cell cycle following release from .alpha.-factor arrest, the level of GAL1-promoter-controlled neo-HTB1 message increased approximately 12-fold during S phase and dropped to basal level when the cells left S phase. This indicates that the 3'' end of the HTB1 mRNA is capable of conferring cycle-specific regulation on a heterologous message. Deletion analysis of the 3'' end showed that the signal for cell cycle control of HTB1 mRNA includes contiguous coding and noncoding sequences surrounding the stop codon. This differs fromthe situation in mammalian cells, whose posttranscriptional regulation of histone genes is mediated through a short sequence containing a stem-loop structure near the very terminus of the untranslated 3'' end.
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