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RNA structure and function - MB150P91E

Title:	RNA structure and function
Czech title:	Struktura a funkce RNA
Guaranteed by:	Department of Cell Biology (31-151)
Faculty:	Faculty of Science
Actual:	from 2023
Semester:	summer
E-Credits:	3
Examination process:	summer s.:oral
Hours per week, examination:	summer s.:2/0, Ex [HT]
Capacity:	25
Min. number of students:	unlimited
4EU+:	no
Virtual mobility / capacity:	no
State of the course:	taught
Language:	English
Additional information:	http://www.img.cas.cz/public/skupiny/Stanek.html
Note:	enabled for web enrollment

Guarantor:	prof. Mgr. David Staněk, Ph.D.
Teacher(s):	prof. Mgr. David Staněk, Ph.D.

Opinion survey results SS schedule E-learning course

Annotation -

The course "RNA Structure and Function" is planned for master and PhD students and extends basic molecular and cell biology courses. The course is intended mainly for students who want to extend their knowledge about regulation of gene expression and about the ever-growing world of RNA. Individual lectures are focused on transcripts of RNA polymerases I, II and II, their synthesis, processing and function. We will also discuss function of non-coding RNAs, riboswitches and ribozymes. The majority of discoveries about RNAs is documented by original scientific publications with a description of key experiments.

Last update: Staněk David, prof. Mgr., Ph.D. (31.05.2019)

Literature -

Genes IX, autor: Benjamin Lewin, (available on-line: http://biology.jbpub.com/book/genes/index.cfm)

Molecular Cell Biology. 5th edition. autor: Lodis, et al. New York: W. H. Freeman; 2003. ISBN-10 0-71674366-3

RNA World 3rd edition, CSHL Press, ISBN 978-087969739-6

Presentations, slides and notes can be also found at https://dl2.cuni.cz/course/view.php?id=326

Last update: Staněk David, prof. Mgr., Ph.D. (05.04.2022)

Requirements to the exam -

Requirements for the exam

The oral exam covers 3-4 topics presented during the course. At least three days before the exam, students must submit a short (1-2 page) essay or review on a topic in RNA biology of their choice. This may also be a summary of a recent paper focusing on RNA. Students may choose the language in which the essay will be written (English or Czech), and the same language will be used in the oral exam.

Last update: Staněk David, prof. Mgr., Ph.D. (05.04.2022)

Syllabus -

Syllabus "Structure and function of RNA"

Introduction

RNA polymerase I transcripts

Synthesis and processing of ribosomal RNA, nuclear structure and function, structure and function of ribosomes

RNA polymerase II transcripts

- regulation of transcription by non-coding RNAs, links between transcription and processing

- long non-coding RNAs, their transcription, processing and function of specific lncRNAs (XIST, HOTAIR, AIR, MALAT1, etc.)

- short non-coding RNAs, snRNA and snoRNA biogenesis, scaRNA. telomerase structure and function

- pre-mRNA processing (processing at 5' and 3' ends, editing, polyA), mRNA localization and stability

- RNA splicing

- regulation of alternative splicing

- cellular structures involved in RNA metabolism

RNA polymerase III transcripts

Transcription, processing and function of tRNA, 7SK, SRP, U6, RNA P and MRP

Catalytic RNAs

ribozymes and ribosomes, spliceosome and ribosome as ribozymes

RNAi

Synthesis, processing and function of miRNA, piwiRNA, siRNA

Translated with www.DeepL.com/Translator (free version)

Last update: Staněk David, prof. Mgr., Ph.D. (05.04.2022)

Learning outcomes -

Learning outcomes
After successful completion of the course RNA Structure and Function, the student will be
able to:
1. Explain the structural diversity of RNA molecules and relate RNA structure to
function in cellular processes.
(Understanding)
2. Describe the synthesis, processing, and functional organization of RNA polymerase I
transcripts, including ribosomal RNA biogenesis, nucleolar structure, and ribosome
assembly.
(Understanding)
3. Analyze the molecular architecture and function of ribosomes and evaluate their role
as ribozymes in protein synthesis.
(Analysis – Evaluation)
4. Explain the mechanisms of transcription and co-transcriptional processing of RNA
polymerase II transcripts and discuss the functional coupling between transcription
and RNA processing.
(Understanding – Analysis)
5. Describe and compare classes of long non-coding RNAs and evaluate the biological
functions of selected lncRNAs (e.g. XIST, HOTAIR, AIR, MALAT1) in gene
regulation and nuclear organization.
(Analysis – Evaluation)
6. Explain the biogenesis, processing, and function of short non-coding RNAs,
including snRNAs, snoRNAs, scaRNAs, and describe the structure and function of
telomerase.
(Understanding – Analysis)
7. Describe the molecular mechanisms of pre-mRNA processing, including 5′ and 3′ end
formation, RNA editing, polyadenylation, and explain how these processes affect
mRNA localization and stability.
(Understanding)
8. Analyze the mechanism of RNA splicing and evaluate the role of the spliceosome as
a catalytic ribonucleoprotein complex.
(Analysis – Evaluation)
9. Explain the regulatory principles of alternative splicing and assess its impact on
transcriptome and proteome diversity.
(Analysis – Evaluation)
10. Describe and compare RNA polymerase III transcripts and explain the transcription,
processing, and cellular functions of several RNA polymerase III transcripts
(Understanding – Analysis)
11. Explain the principles of catalytic RNAs and compare ribozymes, ribosomes, and the
spliceosome with respect to RNA-based catalysis.
(Analysis)
12. Analyze and evaluate RNA interference pathways and explain the biogenesis and
function of miRNAs, siRNAs, and piRNAs in post-transcriptional gene regulation.
(Analysis – Evaluation)

Last update: Šebková Nataša, RNDr., Ph.D. (03.02.2026)

Výsledky učení
Po úspěšném absolvování kurzu Struktura a funkce RNA bude student schopen:
1. Vysvětlit strukturní rozmanitost molekul RNA a dát do souvislosti strukturu RNA s funkcí
v buněčných procesech.
(Porozumění)
2. Popsat syntézu, zpracování a funkční uspořádání transkriptů RNA polymerázy I, včetně
biogeneze ribozomální RNA, struktury jádra a sestavení ribozomu.
(Porozumění)
3. Analyzovat molekulární architekturu a funkci ribozomů a zhodnotit jejich úlohu jako
ribozymů při syntéze bílkovin.
(Analýza - hodnocení)
4. Vysvětlit mechanismy transkripce a ko-transkripčního zpracování transkriptů RNA
polymerázy II a diskutovat o funkčním propojení mezi transkripcí a zpracováním RNA.
(Porozumění - Analýza)
5. Vysvětlit, co je to transkripce a popsat a porovnat třídy dlouhých nekódujících RNA a
zhodnotit biologické funkce vybraných lncRNA (např. XIST, HOTAIR, AIR, MALAT1) v
genové regulaci a jaderné organizaci.
(Analýza - hodnocení)
6. Vysvětlit biogenezi, zpracování a funkci krátkých nekódujících RNA, včetně snRNA,
snoRNA, scaRNA, a popsat strukturu a funkci telomerázy.
(Porozumění - analýza)
7. Popsat molekulární mechanismy zpracování pre-mRNA, včetně tvorby 5′ a 3′ konce,
editace RNA, polyadenylace, a vysvětlit, jak tyto procesy ovlivňují lokalizaci a stabilitu
mRNA.
(Porozumění)
8. Analyzovat mechanismus sestřihu RNA a zhodnotit úlohu spliceosomu jako
katalytického ribonukleoproteinového komplexu.
(Analýza - hodnocení)
9. Vysvětlit regulační principy alternativního sestřihu a zhodnotit jeho vliv na rozmanitost
transkriptomu a proteomu.
(Analýza - hodnocení)
10. Popsat a porovnat transkripty RNA polymerázy III a vysvětlit transkripci, zpracování a
buněčné funkce několika transkriptů RNA polymerázy III.
(Porozumění - Analýza)
11. Popsat vlastnosti transkriptů RNA polymerázy III a vysvětlit principy katalytických
RNA a porovnejte ribozymy, ribosomy a spliceosom s ohledem na katalýzu na bázi RNA.
(Analýza)
12. Analyzovat a zhodnotit dráhy RNA interference a vysvětlit biogenezi a funkci miRNA,
siRNA a piRNA v posttranskripční genové regulaci.
(Analýza - hodnocení)

Last update: Šebková Nataša, RNDr., Ph.D. (03.02.2026)