Everything you wanted to know about gene expression but were afraid to ask - MB140P27
Title: Everything you wanted to know about gene expression but were afraid to ask
Czech title: Vše, co jste chtěli vědět o genové expresi, ale báli jste se zeptat
Guaranteed by: Department of Genetics and Microbiology (31-140)
Faculty: Faculty of Science
Actual: from 2025
Semester: summer
E-Credits: 3
Examination process: summer s.:combined
Hours per week, examination: summer s.:2/0, Ex [HT]
Capacity: 20
Min. number of students: unlimited
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: English
Level: specialized
Note: enabled for web enrollment
Guarantor: RNDr. Leoš Valášek, DSc., Ph.D.
Opinion survey results   Examination dates   
Annotation -
While the central dogma of molecular biology still somehow stands,
many other dogmas in the field of gene expression are falling like ripe pears from a
pear tree. Indeed, much of what appeared to be indisputable truth when we were
students like you, has fallen into oblivion over time. But, is it really the case that much
of the old knowledge is simply no longer valid? Or is it also partly a matter of the
"publish or perish" competition and the pursuit of sensationalism in science at any
cost? Let’s look at the new discoveries in the field of gene expression regulation, the
underlying cutting-edge methodology, the old dogmas falling and new ones
emerging. However, let’s be critical, let’s be interactive, let’s learn together.

- this is an advanced course for MSc. and PhD students including Erasmus (in English)
- signing up for the course is HIGHLY recommended only after the completion of the bachelor program
- limit is 20 students per class
contacts: Leos Valasek (724731661; valasekl@biomed.cas.cz)
Adriana Roithova (739679009; adriana.roithova@biomed.cas.cz)
Last update: Marková Hana, RNDr., Ph.D. (25.04.2025)
Course completion requirements -

Exam: combination of written and oral

Part A (20 mins); In a form of a journal club; we will pick a few recent, high profile

papers on exciting topics pertinent to regulation of gene expression for you to choose

from - well in advance of the exam. Your goal will be to introduce the topic of one of

them in a broader perspective, present and critically comment on the results, discuss

the proposed model, suggest alternative ways to prove or disprove the presented

findings, indicate of what you as the first author of this paper would do next.

Part B (25 mins); We will provide a brief introduction into some problem plus a set of

figures on separate sheets (either from our own work or from a published work of

others) - well in advance of the exam. Your task will be to create the story of the

paper in a form of the ppt and present it: i.e. to assemble the figs into a logical order,

to briefly describe the methods used, to write a few concluding words about a

particular figure and a connecting sentence to the next figure, to pick the most

appropriate topics for discussion, and as a bonus, to discuss these.

We do not really care how deep your theoretical knowledge is, we care about how

you can translate your theoretical knowledge into the ultimate goal/practical skill of

each researcher - writing a paper.

Do not get intimidated, this should be fun that will come very handy when you start

working seriously in a lab.

Last update: Marková Hana, RNDr., Ph.D. (27.04.2023)
Literature -

Not specified - we will try to follow the most recent progress of the field of

regulation of gene expression.

Last update: Marková Hana, RNDr., Ph.D. (27.04.2023)
Requirements to the exam -

combination of written and oral

Part A (30 mins); in a form of a journal club. We will pick two recent, high profile papers on exciting topics pertinent to regulation of gene expression for you to choose from - exactly one week in advance of the exam. Your goal will be to introduce the topic of one of them in a broad perspective, present and critically comment on the results, discuss the proposed model, suggest alternative ways to prove or disprove the presented findings, indicate of what you, as the first author of this paper, would do next.

Part B (15 mins); we will provide a brief introduction into some problem in a form of an abstract plus a set of unlabeled figures on separate sheets including figure legends (either from our own work or from a published work of others) - right after the part A is finished. You will have 10 min in privacy to re-create the story of that

paper and present it to us in 5 min. That is to assemble the figs into a logical order and describe briefly what was done first and why, what was done next, etc., and what is most likely a take home message. We do not really care how deep your theoretical knowledge is, we care about how smoothly you can translate your theoretical knowledge into the ultimate goal/practical skill of a researcher - reading, analyzing and writing a paper.

Do not get intimidated, this should be fun that will come very handy when you start

working seriously in a lab.

Last update: Marková Hana, RNDr., Ph.D. (25.04.2025)
Syllabus -

1) A Khunian revolution in science

  • science set in the sociological context
  • a Khunian revolution in science
  • a Khunian revolution in molecular biology
  • protein =>; RNA paradigm change
  • “new” RNA world full of surprises and rich in regulatory potential

2) What does it really take to become (and stay) a scientist?

  • publish or perish curse
  • what to expect at individual steps of your scientific career
  • scientific publishing business - misdemeanors & solutions?
  • danger of predatory journals
  • open access publishing
  • IF & H-index madness
  • chasing funds for your own research
  • what makes people to become and stay researches

3) Critical reading of literature, wise writing/structuring and “selling” your own

work

  • what to focus on when reading a paper
  • identifying a knowledge gap
  • asking a right question
  • selecting the optimal methods to answer the given question
  • critical evaluation of the obtained answers
  • discussing the gained knowledge and proposing the next step(s)
  • introduction into a proper structuring and writing your own paper

4) RNA structure and RNPs

  • function
  • methods for RNA structure determination (SHAPE-seq, DMS-seq, LIGR-seq)
  • the computational methods for RNA secondary structure modeling (RNAfold, iFOLD, Ufold,…)
  • advances in experimental RNA structure determination
  • RNP (domains, helicases)
  • first guided journal club on some relevant topic

5) modifications of RNAs

  • biogenesis (how they are formed)
  • detection
  • function
  • diseases
  • second guided journal club on some relevant topic

6) circRNAs and their metabolism

  • types of modifications
  • function
  • detection (m6A-seq, capture-seq, mass-spec, Nanopore DNA sequencing)
  • readers, erasers
  • challenges
  • third guided journal club on some relevant topic

7) The power of tRNAs and their fragments & RNAs as a tool for therapy

  • canonical versus non-canonical roles of tRNAs and their fragments and their

prospective exploitation in medicine

  • history
  • advantages of RNA therapy
  • types of RNA therapy
  • types of RNA delivery methods
  • future of RNA therapy
  • fourth guided journal club on some relevant topic

8) degradation and visualization of RNA in cells

  • mechanisms
  • how to study the RNA turnover (in vivo metabolic labelling, Akron-seq, PARE-seq, degradome-seq, TAIL-seq, SLAM-seq)
  • degron systems, siRNA
  • FISH, molecular beacon, FIT
  • visualization techniques - pros and cons - for living cells (aptamers - protein based, fluorophore-aptamer pair, dye and quencher)
  • fifth guided journal club on some relevant topic

9) Translational control

  • history and what it teaches us
  • a genius of the past that has not yet been surpassed!
  • presence and future - have we really learnt anything?
  • new advances in translational control research: riboseq, single molecule/cells assays, other cutting-edge technology
  • sixth guided journal club on some relevant topic

10) the power of Sel-TCP-seq & CRISPr & reporter assays.

  • history and introduction into (pros and cons of) translational complex sequencing
  • new approaches of data analysis or riboSeq assays
  • differences in CRISPR types (pros and cons of)
  • knock-down, -out, -ins
  • activation and inhibition of gene expression with CRISPR
  • CRISPR and modifying of the genome
  • visualization of the genome with CRISPR
  • targeting into cell compartments using CRISPR
  • everything about reporter assays

11) Ribosome Rescue Complexes and Pathways

  • everything about RQC
  • seventh guided journal club on some relevant topic

12) Guided “paper creating process” student’s flash talks

  • preparation for the exam
  • students can present their own work and get feedback

Last update: Marková Hana, RNDr., Ph.D. (25.04.2025)