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Non-Coding Functional Regions in Gene Regulation and Splicing Mechanisms

This journal club article delves into the intricate world of non-coding functional regions, such as cis-regulation of pre-mRNA splicing and post-splicing events. It discusses the impact of synonymous codon choice on translational efficiency and accuracy, emphasizing the importance of CRUNCS and selective pressure in maintaining protein function and regulatory roles. Various methods, including sequence conservation metrics and Fitch’s algorithm, are explored for analyzing these regions.

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Non-Coding Functional Regions in Gene Regulation and Splicing Mechanisms

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Presentation Transcript

  1. Journal club 06/27/08

  2. Non-coding functional regions • Cis-regulation of pre-mRNA splicing • Post-splicing (mature mRNA) – degradation, localization • Translational efficiency & accuracy – Choice of synonymous codon Secondary structure elements

  3. CRUNCS • Coding regions under non-coding selection • Are not located in non-functional sequences as are, ex: most known transcription factors binding sites, but rather in coding regions

  4. Mixture selective pressure • Maintain the function of the protein encoded by the gene (AA selecvtive pressure) • Maintain their regulatory role (CRUNCS) – ex: regulatory factors binding sites

  5. Methods • Sequence conservation: • Entropy score • Parsimony score • Conservation p-value (mixture models) • Posterior distributions of conservation scores • Conditional p-values

  6. Fitch’s algorithm

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