Genomics and Proteomics

What will you learn?

The aim of the Genomics and Proteomics program is to train top class specialist in these subjects. Students will acquire extensive and in-depth knowledge about the structure and function of the genome at all basic levels of living systems ( i.e., the viral genome, the genome of bacteria, protozoa, fungi and yeasts, algae, higher plants, animals and human genome in more detail). They will deepen their knowledge and skills in basic biological disciplines (especially genetics, molecular biology, microbiology, immunology, biostatistics, physiology of organisms), in biochemistry and proteomics (general biochemistry, enzymology, biochemical proteomic methods) and in biophysics (biophysical methods).

In addition to the theoretical principles of the discipline, students are also closely acquainted with performing basic and advanced methods used in various disciplines. Graduates of this field of study will find jobs in various fields: particularly in research focused on the analysis of genomes (basic research as well as applied research), in bioinformatics (including evolutionary aspects), in the field of molecular medicine (cancer, familial and hereditary diseases, gene therapy), in genetic engineering of microorganisms, plants, and animals, in the development of new biotechnologies, in pharmacogenomics, and in analyzing the proteome of individual groups of organisms, including humans.

Practical training

Students conduct their research activities in the laboratories of their supervisors, where they acquire practical skills essential for their research topics. Further practical skills can be acquired via collaborative frameworks of their labs (either in Czech Republic or abroad).

Further information

http://www.sci.muni.cz/en/DoktorskeStudium/Prehled-programu-a-oboru/obor/Genomika-a-proteomika

Career opportunities

Graduates of this doctorate program are qualified to run a research activities at research institutions and biotech companies, and teach at universities. They will find jobs in various fields, particularly in research focused on the analysis of genomes (basic research as well as applied research), on bioinformatics, molecular medicine, genetic engineering of microorganisms, plants, and animals, on the development of new biotechnologies, and on the analysis of the proteome of individual groups of organisms. In wider sense, they can conduct research and research-related activities like experimental work, project management, etc.

Admission requirements

Data from the previous admission procedure (1 Jan – 30 Apr 2021)

The applicant have to obtain 180 out of the 300 points: field of expertise 60 points/100 language skills 60 points/100 formal criteria 60 points/100 Formal criteria will include assessment of previous education and practice (based on master diploma and reference letter)


Application guide

Dissertation topics

Single-subject studies

Application of tumour biomarkers in gynecological precancer diagnostics
Supervisor: MUDr. Milan Anton, CSc.

Téma zahrnuje dva studované okruhy:
A. Testování molekulárně biologických změn genomové DNA pocházející z děložní sliznice (normální, prekancerózy, nádoru) a z nebuněčné frakce periferní krve s cílem nalezení prognostického markeru.
Provedeme retrospektivní analýzu panelu molekulárně-genetických změn na základě analýzy vybraných mutací, změn počtu somatických kopií, mikrosatelitové nestability a metylace DNA u karcinomů a prekanceróz endometria
Následně ověříme prognostický význam vybraných molekulárně-biologických změn na klinickém souboru, tvořeném genomovou DNA z buněk získaných při výplachu dělohy a ctDNA z nebuněčné frakce periferní krve


B. Využití elektrodového biočipu v detekci lidského papilomaviru u prekanceróz děložního čípku s cílem vyvinout jednodušší a levnější technologii jako alternativu komerčních HPV testů
Projekt bude rozdělen do následujících okruhů:
1. výběr souboru, histologická analýza a validace komerčními HPV testy
2. příprava vhodných sond, výběr a optimalizace amplifikačních technik
3. zjednodušení a zrychlení testu a aplikace na klinický materiál.

Práce bude probíhat v moderně vybavených laboratořích RECAMO Masarykova onkologického ústavu. Napojení na grantové projekty zajištěno, možnost úvazku po domluvě se školitelem.

Supervisor

MUDr. Milan Anton, CSc.

DNA damage repair of DNA-protein crosslinks in Arabidopsis thaliana
Supervisor: doc. Mgr. Aleš Pečinka, Ph.D.

Cellular processes and external factors generate stress that can damage nuclear DNA. Proteins covalently bound to DNA represent a little-studied but serious type of DNA damage – DNA-protein crosslinks (DPCs). DPCs block transcription and DNA replication and therefore need to be repaired. We have developed a highly efficient genetic screen for the identification of genes involved in DPC repair. Using the candidates from this genetic screen, we aim to reconstruct molecular pathways protecting the plant genome against DPCs. This will help to understand an important mechanism ensuring plant fitness and fertility.

Notes

This work will be realized at the Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics in Olomouc.

Supervisor

doc. Mgr. Aleš Pečinka, Ph.D.

Exploring of glycosylation towards diagnosis and prognosis of malignancies via mass spectrometry-based approaches.
Supervisor: RNDr. Erika Lattová, PhD.

Glycosylation as one of the major posttranslational modification (PTM) of proteins is involved in a wide range of fundamental molecular processes. Variations in oligosaccharide (glycan) structures have been also shown in association with different pathological events. Glycans are extraordinarily complex molecules and unlike other oligomers, they are synthesized through interaction with a complex biochemical environment comprising hundreds of glycosyltransferases. Consequently, glycans possess significant structural heterogeneity. In addition, proteins may carry several different glycans, displaying a wide range of site occupancy, which could dynamically change. These facts make investigation of oligosaccharides rather demanding and usually require the sequential employment of several approaches. On the other hand, the above-mentioned characteristics make glycans particularly attractive candidates in medical studies.
Although a number of methods have been developed for identification of glycans, the investigation of glycoconjugate structures and understanding their roles in living systems represents tremendous challenges in the field of proteomics. Mass spectrometry (MS) is one the most sensitive and fast technique for the analysis of biomolecules. The information gained by MS allows to assign putative monosaccharide structures present in detected glycans since the mass of a monosaccharide is measured with a high degree of accuracy. Moreover, tandem MS experiments enable more detailed information and in conjunction with oligosaccharide dissection using exoglycosidase enzyme arrays can provide structural analysis and confirm the types of linkages. Therefore, one of the crucial tasks of the thesis will be the investigation of glycosylation in association with pathological events employing MS based proteomic methodology. Experimental work will be performed in laboratories of RG and CF Proteomics, CEITEC, building E26.

Lattová E., Skřičková J., Hausnerová J., Frola L., Křen L., Zdráhal Z., Bryant J., Popovic M. Ihnátová I.:
N-Glycan profiling of lung adenocarcinoma in patients at different stages of disease
Mod. Pathol., 33 (6), 1146-1156 (2020)

Notes

It is necessary to contact Dr. Lattova (or prof. Zdrahal) for informal introduction of the topic before a formal application.

Supervisor

RNDr. Erika Lattová, PhD.

Hormonal regulations of <I>de novo</I> organogenesis in plants
Supervisor: Mgr. Markéta Pernisová, Ph.D.
Plants, unlike animals, possess the unique developmental plasticity that enables them to develop or regenerate organs throughout their whole life. This ability requires the presence of regulators that trigger specific spatiotemporal changes in developmental programs. The phytohormones auxin and cytokinin are thought to be major regulators of plant organogenesis. Auxin is necessary to induce de novo organ development, while cytokinins modulate the organogenic response resulting in root or shoot formation. The project aims to study molecular mechanisms regulating de novo organogenesis both in planta and in vitro. The principal focus will be on changes in the metabolism, signalling and differential regulation of gene expression. A wide range of molecular biology methods will be used, e.g., DNA and RNA manipulation, CRISPR/Cas9 approach, and luciferase assays, as well as microscopy, image analysis and in vitro cultivation.
Supervisor

Mgr. Markéta Pernisová, Ph.D.

Chromosome organisation in interphase plant nuclei
Supervisor: prof. Mgr. Martin Lysák, Ph.D., DSc.

Jak jsou chromozomy organizovány a uspořádány v buněčném jádru? Něco málo víme, ale víc toho nevím, ani po více než 100 letech výzkumu v této oblasti. Disertační práce je zaměřena na analýzu konfigurace interfáznich chromozomů a tkzv. chromosome territories v jádrech rostlin z různých fylogenetických skupin. K zodpovězení těchto otázek budou využity metody srovnávácí genomiky (např. kontaktní Hi-C mapy) a cytogenomiky (např. malování chromozomů).

Supervisor

prof. Mgr. Martin Lysák, Ph.D., DSc.

Identification and quantification of N-linked glycoproteins presented in sera and tissues of patients with oncological disease
Supervisor: prof. Ing. Lenka Hernychová, Ph.D.

Je známo, že změny glykanových struktur na povrchu nádorových buněk ovlivňují proliferaci, adhezi, migraci i buněčnou signalizaci. Strukturně změněné N-glykany (zvýšená fukosylace, sialylace nebo přítomnost komplexních rozvětvených struktur) byly detekovány v sérech a nádorových tkáních pacientů s různými typy nádorů. Proto glykoproteiny i jejich glykanové části jsou atraktivními markery vhodnými pro diagnostiku onkologických onemocnění.
Cílem dizertační práce bude podílet se na vývoji metod izolace glykoproteinů ze sér a tkání pacientů s nádorem vaječníků nebo nádorem prsu s využitím hydrazidové chemie nebo lektinové chromatografie. Analýza připravených vzorků na hmotnostních spektrometrech, hodnocení dat, selekce markerů a jejich diskuze s dostupnou literaturou.

Doporučená literatura
Zhang H, Li XJ, Martin DB, Aebersold R. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol. 2003 Jun;21(6):660-6. PMID:12754519

Hernychová L, Uhrík L, Nenutil R, Novotný MV. Glycoproteins in the Sera of Oncological Patients. Klin Onkol. 2019 Fall;32(Supplementum 3):39-45. PMID:31627705

Supervisor

prof. Ing. Lenka Hernychová, Ph.D.

Identification of novel molecular components involved in root directional growth.
Supervisor: Tomasz Nodzynski, B.A., M.Sc., Ph.D.

Young seedlings when germinating have at least two key tropic responses to execute, that is reorient the shoot part toward the energy giving light and re-align the root with the gravity vector to be able to grow into the soil that contains moisture and vital minerals. In the case of the root there are more levels of developmental complexity to be taken into consideration as it grows into the mature root system. While the key principles of auxin role in gravitropism have been worked out, the fine-tuning of auxin transport as well as the interlink between auxin and modifications of gravitropic sensing are still not fully understood, and that knowledge gap we want to supplement with this project.
Within this project we plan to address the molecular mechanism(s) underlying the root directional growth as well as how gravitropic sensing is linked and also unlinked with auxin transport enabling main root and lateral roots gravitropism modifications. We will perform gravity sensing-based forward genetic screen to uncover novel molecular regulators involved in gravity perception and execution. Next we will map obtained mutants and characterize physiological and cellular phenotype of mutants and overexpression lines.

Supervisor

Tomasz Nodzynski, B.A., M.Sc., Ph.D.

Mechanisms of effect of LDL receptor genetic variants
Supervisor: Mgr. Lukáš Tichý, Ph.D.

Our workgroup is interested in molecular basis of severe dyslipidemias in human. The most common of dyslipidemias is familial hypercholesterolemia (FH). The frequency of FH in most populations is about 1/200, and so it is possible to predict that about 50,000 people could be affected in the Czech Republic. The clinical phenotype of FH is caused predominantly by mutations in the LDLR gene. LDLR mutations have been reported along the whole length of the gene. Our workgroup focuses on functional assays of LDLR mutations. For further details please refer to our publications (PMIDs: 27175606, 20663204, 28379029, …).

Supervisor

Mgr. Lukáš Tichý, Ph.D.

Modeling Small RNA binding rules using Machine Learning
Supervisor: Panagiotis Alexiou, PhD

Small RNAs (miRNAs, piRNAs) bind their targets in a sequence and structure dependent manner. The rules of binding for each category of small RNAs have been studied for a long time, but have not to date been clearly identified.

New technological advancements in the fields of Sequencing have allowed the production of 'chimeric' reads that contain both the small RNA and a part of the binding site sequence. Using these type of datasets we can, for the first time, have an unbiased prediction of where small RNAs bind on their targets.

Deep Learning is a field of Machine Learning that has shown great advances in the past decade by using Deep Neural Networks to model complex datasets. In the field of Genomics, it is being increasingly used to identify RNA binding protein sites, Transcription Factor Binding Sites etc.

We will utilize Deep Learning techniques and NGS datasets of small RNA binding to model and interpret the rules of small RNA binding to their targets.

Supervisor

Panagiotis Alexiou, PhD

Plant transposons and "genome landscape"
Supervisor: doc. RNDr. Eduard Kejnovský, CSc.

Genomy eukaryot nejsou neměnnými genetickými entitami. Zejména v poslední době se stále silněji ukazuje, že se jedná o velmi dynamické systémy, generátory vlastních přestaveb, schopné citlivě reagovat na změny prostředí. Většina eukaryotních genomů je z velké části tvořena opakujícími se úseky DNA, tzv. repeticemi. Mezi repetice patří i klíčoví hráči dynamiky genomů - transponovatelné elementy, tzv. transpozony, populárně označované jako „skákající geny“. Transpozony jsou rozptýleny po celém genomu. Přestože transpozony představují významnou část rostlinných genomů, jejich evoluční dynamika a vliv na fungování buňky začínají být teprve chápány.

V rámci navrhované dizertace budeme pomocí bioinformatických nástrojů i experimentů studovat různé aspekty života transpozonů v rostlinných genomech - jejich věk, strukturní rysy, vlny amplifikací, rozsah genové konverze a ektopické rekombinace stejně jako vliv těchto procesů na velikost genomů a účast při tvorbě centromer a formování 3D organizace interfázního jádra. Naše výsledky přispějí k pochopení struktury, funkce a evoluce transpozonů. Doktorská práce předpokládá zvládnutí širokého spektra metod molekulární biologie a genomiky a také řady bioinformatických nástrojů a rovněž práci s odbornou literaturou. Pro bioinformatické analýzy budou využita jak data z dostupných databází, tak i naše vlastní data pocházející ze sekvenování druhé generace (NGS). Student bude používat nejrůznější bioinformatické nástroje dostupné na internetu i vlastnoručně vytvořené. Výsledky analýz budou publikovány v kvalitních impaktovaných časopisech. Pro studenta nabízíme možnost pracovního úvazku. Projekt je financován Grantovou agenturou ČR.

Supervisor

doc. RNDr. Eduard Kejnovský, CSc.

Proteins interactions with DNA, focus on local DNA structures
Supervisor: doc. Mgr. Václav Brázda, Ph.D.

Genome sequencing brings a huge amount of information regarding the genetic basis of life. While this information provides a foundation for our understanding of biology, it has become clear that the DNA code alone does not hold all the answers. Epigenetic modifications and higher order DNA structures beyond the double helix contribute to basic biological processes and maintaining cellular stability. Local alternative DNA structures are known to exist in all organisms. Negative supercoiling induces in vitro local nucleotide sequence-dependent DNA structures such as cruciforms, left-handed DNA, triplex and quadruplex structures etc. The formation of cruciforms requires perfect or imperfect inverted repeats of 6 or more nucleotides in the DNA sequence. Inverted repeats are distributed nonrandomly in the vicinity of breakpoint junctions, promoter regions, and at sites of replication initiation. Cruciform structures could for example affect the degree of DNA supercoiling, the positioning of nucleosomes in vivo, and the formation of other secondary structures of DNA. The three-dimensional molecular structure of DNA, specifically the shape of the backbone and grooves of genomic DNA, can be dramatically affected by nucleotide changes, which can cause differences in protein-binding affinity and phenotype. The recognition of cruciform DNA seems to be critical not only for the stability of the genome, but also for numerous, basic biological processes. As such, it is not surprising that many proteins have been shown to exhibit cruciform structure-specific binding properties [1] or G-quadruplex binding properties [2]. Contemporary we have developed easy accessible web tools for analyses of inverted repeats [3] and G-quadruplexes[4] and we have analyzed the presence of inverted repeats and G-quadruplexes in various genomic datasets, such as all sequences mitochondrial genomes [5], all bacterial genomes [6], in S.cerevisiae (in review), in human genome etc. A deeper understanding of the processes related to the formation and function of alternative DNA structures will be an important component to consider in the post-genomic era.

Supervisor

doc. Mgr. Václav Brázda, Ph.D.

Proteins involved in the regulation of telomeric repeats
Supervisor: Mgr. Petra Procházková Schrumpfová, Ph.D.

Telomeres are the physical ends of linear chromosomes that protect these ends against erroneous recognition as unrepaired chromosomal breaks and regulate the access to Telomerase, a reverse transcriptase that solves the problem terminal DNA loss in each cell cycle. Telomeric structures are known to be composed of short repetitive DNA sequences (telomeric repeats), histone octamers, and number of proteins that bind telomeric DNA, either directly or indirectly, and together, form the protein telomere cap.

Interestingly, telomeric repeats are not exclusively located at the chromosome ends, but they belong among cis-regulatory elements present in promoters of several genes. The distribution of short telomeric motifs (telo-boxes) within the genome is not random, and proteins associated with these telomeric repeats may serve as the epigenetic regulatory mechanisms facilitating metastable changes in gene activity.

The telomeric cap proteins of diverse organisms are less conserved than one might expect. In plants, knowledge of telomere-associated proteins associated with telomeres and regulation of access to telomerase complex is incomplete. The research aims to elucidate the roles of candidate proteins involved in telomerase biogenesis in plants. The outcomes contribute to the characterization of new telomere- or telomerase-associated proteins, complete our knowledge of telomerase assembly or telomere maintenance in plants. In addition, we would like to examine the regulatory factors associated with the telo-boxes present in promoters of the genes active during plant development.

Notes

Poznámky: Práce může být vypracována ve slovenštině či angličtině.

Supervisor

Mgr. Petra Procházková Schrumpfová, Ph.D.

Qualitative and quantitative analysis of selected types of posttranslational modifications
Supervisor: prof. RNDr. Zbyněk Zdráhal, Dr.

Posttranslační modifikace (PTM) významně ovlivňují regulaci buněčných procesů. V současné době je známo více než 400 druhů. Analýza PTM je poměrně složitý proces, jelikož neexistuje jedna univerzální metoda, která by byla schopná detekovat všechny druhy PTM současně, a zpravidla je nutno použít pro každý druh modifikace individuální postup přípravy vzorku, resp. metodu analýzy. Navíc modifikovaných forem proteinů je v rámci proteomu kvantitativně řádově méně než odpovídajících nemodifikovaných proteinů, což také znesnadňuje jejich detekci.

Cílem disertační práce bude vývoj a optimalizace souboru metod pro kvalitativní a kvantitativní charakterizaci vybraných typů posttranslačních modifikací hmotnostní spektrometrií a aplikace těchto metod v rámci řešení probíhajících projektů.

Experimentální část bude probíhat v laboratořích VS/CL Proteomika, CEITEC-MU (budova E26, UKB Bohunice), vybavených špičkovou instrumentací.

Notes

Před podáním přihlášky je nutno se neformálně seznámit s tématem, kontaktujte prof. Zbyňka Zdráhala.

Supervisor

prof. RNDr. Zbyněk Zdráhal, Dr.

Real-Time Cellular Structural Biology: Nucleic Acids
Supervisor: doc. Mgr. Lukáš Trantírek, Ph.D.

Objectives: Develop and apply novel in-cell NMR-based approaches that monitor structural transitions in regulatory DNA regions during biological processes.

Focus: Doctoral research projects focus on the time-resolved
characterization of conformational transitions of selected DNA motifs in vivo during cell-cycle progression or upon activation of a signaling cascade. Students will acquire experience with: UV/CD/NMR spectroscopy knowledge, chemical modifications of
nucleic acids, DNA cloning, human cell culture manipulations, or work with
alternative biological models (Xenopus laevis).


Examples of potential student doctoral thesis:
A] De novo folding of DNA G-quadruplex in the intracellular space
B] Local conformational equilibria in DNA in the course of cell-cycle and meiosis

Supervisor

doc. Mgr. Lukáš Trantírek, Ph.D.

Regulation of transposons in dioecious plants
Supervisor: RNDr. Roman Hobza, Ph.D.

Transpozony jsou mobilní genetické elementy schopné samostatné replikace v rámci genomů většiny organismů. Transpozony mohou být domestikovány, podílejí se na tvorbě funkčních strukur genomů a genových regulačních sítí, ale jejich inzerční aktivita může způsobovat škodlivé mutace. Pro přežití hostitele je proto důležitá existence mechanizmů bránících nadměrné aktivitě transpozonů. Tyto obranné mechanizmy jsou založeny především na RNA interferenci (RNAi) využívající krátké molekuly RNA (sRNA) k cílenému umlčení transpozonů na transkripční (epigenetické modifikace chromatinu) nebo posttranskripční úrovni. U dvoudomých rostlin byly objeveny transpozony s velmi odlišnou distribucí na pohlavních chromozomech, což naznačuje, že jsou transpozony různě aktivní v samčí a samičí linii. Předmětem doktorské práce je charakterizace repetitivních sekvencí a transpozonů u vybraných dvoudomých rostlin a následně studium mechanizmů regulujících aktivitu transpozonů. Doktorská práce předpokládá zvládnutí širokého spektra metod molekulární biologie a cytologie, přípravu transgenních a mutantních rostlin, práci s tkáňovými kulturami, zvládnutí mikroskopických technik a analýzy obrazu, některých bioinformatických nástrojů a práci s odbornou literaturou. Výsledky budou prezentovány formou plakátových sdělení nebo přednášek na mezinárodních konferencích a článků v impaktovaných časopisech.

Supervisor

RNDr. Roman Hobza, Ph.D.

Structural Maintenance of Chromosomes (SMC) complexes
Supervisor: doc. Mgr. Jan Paleček, Dr. rer. nat.

Our lab is interested in the chromatin structure and dynamics. The chromatin structure must be not only maintained through the cell cycle, but also dynamically modulated during processes like mitosis and replication. Amongst the chromatin-associated complexes, the SMC (Structural Maintenance of Chromosomes) complexes play the central role. Two of them, Cohesin and Condensin, facilitate chromosome segregation and condensation, respectively. Third, the most enigmatic SMC5/6 complex is involved in the DNA damage repair and replication restart, however its essential chromatin-modulating function is still unclear. Our laboratory focuses on the SMC5/6 architecture and functions using state-of-the-art structural biology approaches and various molecular biology tools. For further details please refer to our website (http://www.ncbr.muni.cz/SPEC/) and our publications (https://orcid.org/0000-0002-6223-5169).

Supervisor

doc. Mgr. Jan Paleček, Dr. rer. nat.

Structure-functional relationship of telomeres and telomerases
Supervisor: Mgr. Eva Sýkorová, CSc.

In brief, intracellular life of telomerase is linked to processes of telomerase biogenesis, action at telomeres and degradation. During these processes telomerase interacts with many protein partners that might be essential for particular steps. Highly dynamic nature of telomerase interactome causes difficulty in uncovering functions of telomerase partners that are important for telomerase and those unrelated to telomerase. Using classical experimental methods as well as genomics and proteomics approaches accompained with in silico analyses, we study structure-functional relationship of telomeres and telomerases.

Supervisor

Mgr. Eva Sýkorová, CSc.

Subcellular trafficking in plant survival
Supervisor: Tomasz Nodzynski, B.A., M.Sc., Ph.D.

Endosomal trafficking is vital in plant development both in optimal and stress conditions. This regulated vesicle trafficking is necessary for membrane integrity preservation and therefore plant resistance to acute osmotic stress. We identified proteins differentially localized along the secretory pathway in response to stress indicating their role in cellular stress response. Characterization of those proteins will provide insights into the role of subcellular machinery in plant response to stress and might have potential applications to engineer stress resistant plants that might be curial regarding incoming climate changes.
The PhD student will perform the physiological and cellular phenotype analysis of mutants and overexpression lines. The admitted candidate will perform genetic and molecular biology studies, including in situ protein localization and life confocal imaging techniques. In parallel the student will continue with the characterization of isolated candidate genes interactors.

Supervisor

Tomasz Nodzynski, B.A., M.Sc., Ph.D.

Telomere biology
Supervisor: prof. RNDr. Jiří Fajkus, CSc.

This research direction includes the structure, evolution and maintenance of telomeres and their roles in chromosome stability, DNA repair and plant speciation. A special attention is given to characterisation of telomerase components and interactors.
Further, we investigate epigenetic mechanisms in the regulation of gene expression, chromatin assembly, genome stability and telomere homeostasis. Biochemical, bioinformatic and molecular biology approaches are applied in this research. As model systems, we primarily use plants and plant cell cultures.
For more details, see our web pages: https://www.ceitec.eu/chromatin-molecular-complexes-jiri-fajkus/rg51

Supervisor

prof. RNDr. Jiří Fajkus, CSc.

Tumor biology
Supervisor: doc. Mgr. Roman Hrstka, Ph.D.
Notes

Před podáním přihlášky je vhodné se seznámit s konkrétními tématy pro daný kalendářní rok. Kontakt: doc. Hrstka, MOÚ, Brno.

Supervisor

doc. Mgr. Roman Hrstka, Ph.D.

Y chromosome epigenetic degeneration in dioecious plant Silene latifolia
Supervisor: José Luís Rodríguez Lorenzo, Ph.D.

Silene latifolia is a model organism to study evolutionary young heteromorphic sex chromosomes in plants. S. latifolia sex chromosomes are formed by several regions with ongoing recombination suppression. This recombination suppression triggers Y-allele gene degeneration through accumulation of mutations, chromosome rearrangements and transposable element (TE) insertions. It is known that epigenetic processes can be involved in both gene degeneration and TE regulation. Recent research on maize TEs indicated a new player in TE mobility regulation. This new regulator is another cytosine modification called 5-hydroxymethylcitosine (5-hmC). We aim to analyze methylation and hydroxymethylation of the different TE families and the quantification of these modifications in both sex chromosomes in both sexes separately. We will provide important information about sex chromosome evolution and degeneration processes in plants.

Supervisor

José Luís Rodríguez Lorenzo, Ph.D.

Study information

Provided by Faculty of Science
Type of studies Doctoral
Mode full-time Yes
combined Yes
Study options single-subject studies Yes
single-subject studies with specialization No
major/minor studies No
Standard length of studies 4 years
Language of instruction Czech
Collaborating institutions
  • The Czech Academy of Sciences
  • Biofyzikální ústav AV ČR
Doctoral board and doctoral committees

Do you have any questions?
Send us an e-mail to

doc. Mgr. Jan Paleček, Dr. rer. nat.

Consultant

E‑mail:

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