RNA is essential for cell survival. Not only is it a messenger between the genomes and proteomes but it also carries out, or participates in, many functions such as RNA processing and protein translation, acting as structural scaffolds, transporters, gene regulators and biocatalysts. We will help to clarify molecular mechanisms underlying RNA quality control in eukaryotic cells through the investigation of the detailed biochemical principles of RNA recognition, processing and degradation. We will use a combination of biochemical, genetic, and structural methods to unravel the molecular mechanism of eukaryotic RNA surveillance.
Example of NMR spectroscopy investigation of RNA sequence- and structure-dependent recognition by proteins.
list / cards
Name and position |
Phone |
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Richard Štefl, Ph.D. Research Programme Coordinator, Research Group Leader |
+420 54949 2436 | |
Karel Kubíček Researcher |
+420 54949 3388, +420 54949 5507, +420 54949 3253 | |
Dušan Hemzal, Ph.D. Researcher |
+420 54949 3412 | |
Naděžda Špačková, Ph.D. Researcher |
+420 54949 7561 | |
Veronika Janštová, Ph.D. Postdoctoral Fellow |
+420 54949 6957 | |
Tomáš Klumpler, Ph.D. Postdoctoral Fellow |
+420 54949 7576, +420 54949 3430 | |
Tomasz Kabzinski PhD student |
+420 54949 8147 | |
Aiste Kasiliauskaite PhD student |
+420 54949 8147 | |
Joanna Oniskiewicz PhD student |
+420 54949 6460 | |
Oliver Taltynov PhD student |
+420 54949 8147 | |
Kateřina Linhartová Student |
+420 54949 8147 | |
Hedvika Cimbálníková Project Assistant |
+420 54949 4391 | |
Martin Polák odborný pracovník - PhD student |
+420 54949 4233 | |
Gita Jančaříková Research Project Manager dedicated for Structural biology |
+420 54949 4932 | |
Michaela Twarógová Student |
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Jiří Nováček, Ph.D. Head of Core Facility |
+420 54949 3893 | |
Pavla Myslivcová laborantka |
+420 54949 6489 | |
Crina-Maria Ionescu Postdoctoral Fellow |
+420 54949 6384 | |
Veronika Klápšťová odborná pracovnice - PhD student |
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Jaroslava Urbánková odborná pracovnice, technička |
+420 54949 3590 | |
Jakub Macošek Technician |
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Eliška Šmiřáková PhD student |
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David Zapletal odborný pracovník |
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Pavel Brázda PhD student |
+420 54949 7832 | |
Marek Šebesta odborný pracovník ve výzkumu - postdoc |
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Tomáš Šikorský PhD student |
Supervisor: doc. Mgr. Richard Štefl, Ph.D.
Consultants: Mgr. Karel Kubíček, PhD., doc. Mgr. Štěpánka Vaňáčová, Ph.D.
Chromatin is a highly flexible architecture in which spatially and temporally coordinated changes between structurally condensed states (transcriptionally repressive), and structurally accessible states (transcriptionally active) regulate gene expression. Posttranslational modifications of histones play the fundamental role in maintaining the dynamic equilibrium of these two chromatin states. Individual histone modifications are associated with a given stage of chromatin remodelling and transcriptional cycle. Interestingly, the C-terminal domain (CTD) of RNA polymerase II (RNAPII) is also posttranslationally modified which serves as a signal for the recruitment of appropriate processing factors in coordination with the transcription cycle. Recent findings revealed that these is an overlap between the occurrence of the histone and CTD marks, suggesting the existence of a cross-talk between the chromatin remodelers (orchestrated by histone modifications) and transcription/processing factors (orchestrated by RNAPII CTD modifications). We will identify protein adaptors that spatially and temporally mediate interactions between chromatin and RNAPII. These proteins will be structurally characterized and we will reveal the structural basis for the cross-talk between histones and RNAPII that is orchestrated through their posttranslational modifications.
Keywords: RNA, posttranslational modifications, CTD, RNAPII, histones, chromatin, C-terminal domain, gene expression
Supervisor: doc. Mgr. Richard Štefl, Ph.D.
Consultants: Mgr. Karel Kubíček, PhD., Mgr. Pavel Plevka, Ph.D.
The concept of the CTD code that specifies the position of RNAPII in the transcriptional cycle and thus recruits specific processing factors, was suggested almost a decade ago. However, how the C-terminal domain (CTD) of RNA polymerase II recruits, activates, and displaces appropriate processing factors in coordination with the transcription cycle, remains obscure. Association of specific factors with the CTD is dictated by different post-translational modification patterns and conformational changes in the CTD. To reveal the CTD code, a combination of structural, biochemical, and genetic methods will be used to study important complexes of the CTD with CTD code reader proteins. The project will help to decipher the basic rules that govern the readout of the CTD code.
Keywords: CTD, TNAPII, C-terminal domain, CTD code, post-translational modification
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