Regulation of gene expression 1400-215REG

1. Stages of regulation of gene expression in Prokaryotes, preliminary comparison with analogous processes in eukaryotes. The interplay of different levels of gene expression.
2. Transcription. Importance of chromatin structure in the regulation of gene expression. Subnuclear structures, nucleosome formation, histones and their modifications (chromatin remodeling factors). The role of chromatin states, euchromatin and heterochromatin, in transcription. Transcriptional machineries of polymerases I, II and III, transcription factors, the mechanisms of transcriptional regulation. Transcriptional silencing of gene expression.
3. RNA maturation, comparisons between Prokaryotes and Eukaryotes. RNA polymerase transcription termination. Pre-mRNA splicing: the catalytic mechanism (comparison with self-splicing introns), description of the process and formation of the active spliceosome, major and minor spliceosomes. Cotranscriptional aspects of splicing, mainly association of complexes and links between transcription, splicing and 3 'end formation. The importance of alternative splicing in development and response to environmental factors. Protein complexes, enzymes and factors involved in RNA maturation.
4. Other processes of RNA maturation: RNA modification, RNA editing, trans-splicing.
5. Localization of proteins and RNA in the cell. RNA export. Structure and composition of the nuclear pore (NP). Export pathways of different RNA classes. Preparation of RNA molecules for export: 3' end, processing, formation of ribonucleoprotein complexes (RNP) competent for export, export progression, remodeling of RNP particles, the first round of translation. The effects of impaired export.
6. RNA decay, part I. General pathways and mechanisms. Enzymes, factors and protein complexes involved RNA degradation. Types of degradation processes and their regulation for various classes of RNA molecules.
7. RNA decay, part II. Specific degradation pathways discussed using chosen examples. Cytoplasmic and nuclear RNA surveillance mechanisms. RNA interference.
8. Translation and its regulation, comparisons between Prokaryotes and Eukaryotes. Protein folding, heat-shock proteins, chaperons. Unfolded Protein Response and resulting ER stress. Unusual amino acids and their incorporation into peptides. Protein recoding. Recognition of amino acids and RNA by aminoacyl-tRNA synthetases.
9. The world of non-coding RNAs. RNA as a versatile molecule: ribozymes, the ribosome, the spliceosome and viral RNAs as
vestiges of "the RNA world". Structure, synthesis and function of ncRNA in regulating gene expression. ncRNA in medicine: human disease correlated with defects in the synthesis and action of ncRNAs. Nobel Prize and RNA.
10. Protein degradation. Protein ubiquitination, structure and function of the proteasome, proteasomal inhibitors.
11. From the gene to its product: effects of synonymous mutations, rare codons, nucleotide sequence diversity and the phenotype.
12. The mitochondrial gene expression. The structure of mitochondria, mitochondrial DNA and RNA. Functions of mitochondria- respiratory chain, apoptosis. Transport into the mitochondria. Mitochondrial replication, transcription, mtRNA processing and translation.