Regulation of gene expression

biology
biotechnology

elective courses
elective monographs

General knowledge of issues related to different levels of regulation of gene expression in Eukaryotes and Prokaryotes.

Classroom

All levels of regulation of gene expression in Eukaryotes and Prokaryotes will be presented and discussed: chromatin structure, genomic imprinting, transcription, pre-mRNA splicing, RNA modification, RNA transport and stability, translation, protein modification, folding and degradation. In addition, the role of factors, enzymes, complexes, RNA structure and non-coding RNA molecules in the regulation of gene expression will be discussed. Finally, the significance of alternative processes (transcription initiation, splicing, translation initiation) for transcriptome and translatome diversity will be presented.

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.

L. A. Allison "Fundamental Molecular Biology"

Chosen review and experimental publications.

Having completed the course and the lab the student:

KNOWLEDGE

1. Has broad knowledge in the field of molecular biology with a particular focus on processes related to gene expression and RNA metabolism.

2. Is familiar with the up-to-date knowledge in the main areas of molecular biology and processes concerning operation of gene expression mechanisms in Eukaryotes and Prokaryotes.

3. Is familiar with a variety of modern techniques and research tools in molecular biology, genetics and biochemistry

4. Has a deep understanding of the significance of carrying out basic research in molecular biology for the develompments in applied and medical sciences.

5. Shows caution and criticism when acquiring and interpreting knowledge in the field of molecular biology and its practical application

ABILITIES

1. Is able to study independently in a targeted manner

2. Demonstrates abilities to use electronic resources and published scientific literature in Polish and English concerning advanced aspects of molecular biology

3. Demonstrates ability to critically assess and analyze published scientific data.

SOCIAL AWARENESS

1. Understands the need to provide information on new developments in molecular biology

2. Shows caution and criticism during the acquisition and interpretation of knowledge in the field of molecular biology and its application in practice

Written examination based on lecture material (51% passes)

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