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PhD topics for academic year 2021/2022

Department of Biochemistry and Microbiology

Faculty of Food and Biochemical Technology

Retrovirus integration and epigenetic provirus silencing

Hejnar Jiří, RNDr. CSc. ( hej...@img.cas.cz)
Autonomous transcription of integrated retroviruses and retrotransposons is affected by genetic and epigenetic features of respective sites of integration. These, mostly suppressive effects silence proviral transcription activity by mechanisms such as DNA methylation and posttranslation modifications of adjacent histone molecules. Provirus silencing is a general feature of integrated retroviruses, but its extent and kinetics vary among different retrovirus species. We studied the role of integration site using single cell clones bearing the unique integrations of reporter vectors derived mostly from avian leukosis virus (ALV) or human immunodefficiency virus (HIV). This appproach enabled us to correlate expression of reporter gene and the epigenomic landscape at the site of integration.
The topic to be open for one doctoral student will be the immediate early silencing of proviruses, which occurs quickly after integration or even during the integration event due to the extensive epigenomic shift and DNA repair processes. For this type of studies, it will be necessary to establish a special dual reporter system of vectors, which records the narrow and quickly vanishing pulses of transcriptional activity during and shortly after integration. Furthermore, integration preference or various retroviruses will be studied at the level of primary DNA sequence, epigenomic landscape, functional chromosomal segments and 3D genome structure. It is expected that this study will finish with alterations of chromatin contacts and topologically associated domains (TAD) of chromatin at the site of retrovirus integration.
Institute of Molecular Genetics of the CAS, v. v. i.

Department of Informatics and Chemistry

Bioinformatics

Faculty of Chemical Technology

Cellular heterogeneity of the tumour microenvironment

Kolář Michal, Mgr. Ph.D. ( kol...@img.cas.cz)
The tumour microenvironment significantly influences the behaviour of tumours from their origin, through proliferation, to the development of metastases. The dissertation will deal with the heterogeneity of cell types present in the tumour microenvironment and the heterogeneity of cells of individual types, such as cancer-associated fibroblasts, using functional genomic tools at the whole genome level and at the level of individual cells. The results of the analyzes will be statistically processed and interpreted in the context of cellular signaling pathways in order to find new tumour markers or therapeutic targets.
Institute of Molecular Genetics of the CAS, v. v. i.
Faculty of Chemical Technology

Epigenetic changes in malignancies

Kolář Michal, Mgr. Ph.D. ( kol...@img.cas.cz)
The tumour microenvironment significantly influences the behaviour of tumours from their origin, through proliferation to the development of metastases. Epigenetic changes, which are very often observed in tumour cells, are very likely to affect the behavior of other components of the tumour microenvironment, such as cancer-associated fibroblasts. The proposed work will deal with epigenetic changes in cells of the tumour microenvironment, description of changes in chromatin accessibility at the whole genome level, their statistical processing and interpretation of changes in the context of cellular signaling pathways in order to find new tumour markers or therapeutic targets.
Institute of Molecular Genetics of the CAS, v. v. i.
Faculty of Chemical Technology

Genetic recombination and reproductive isolation on Mus musculus model

Forejt Jiří, prof. MUDr. DrSc.
Kolář Michal, Mgr. Ph.D. ( kol...@img.cas.cz)
The aim of the proposed dissertation project is to elucidate the epistatic interaction of the PRDM9 histone methyltransferase gene with the X-linked Hstx2 genetic factor in meiotic recombination and male infertility of intersubspecific hybrids. Our laboratory identified the Prdm9 as the first gene in vertebrates engaged in reproductive isolation between species. PRDM9 protein predetermines the meiotic recombination hotspots within species to ensure meiotic cross-overs, chromosome pairing and differentiation of germ cells, but in intersubspecific hybrids the same gene product causes meiotic arrest and hybrid sterility due to persistence of DNA double-strand breaks, recombination failure and subsequent failure of chromosome pairing. The process is modulated by the Hstx2 genetic factor, localized in a 2.7 Mb interval on the chromosome X. The main task of the project is to identify the genomic sequence responsible for the Hstx2 effect using a panel of bioinformatics tools for mRNA expression profiling using next generation RNA sequencing (RNA-seq), for chromatin immunoprecipitation sequencing (ChIP-seq) and for quantitative trait loci (QTL) mapping.
Institute of Molecular Genetics of the CAS, v. v. i.
Faculty of Chemical Technology

Genetic recombination and reproductive isolation on Mus musculus model

Forejt Jiří, prof. MUDr. DrSc.
Kolář Michal, Mgr. Ph.D. ( kol...@img.cas.cz)
he aim of the proposed dissertation project is to elucidate the epistatic interaction of the PRDM9 histone methyltransferase gene with the X-linked Hstx2 genetic factor in meiotic recombination and male infertility of intersubspecific hybrids. Our laboratory identified the Prdm9 as the first gene in vertebrates engaged in reproductive isolation between species. PRDM9 protein predetermines the meiotic recombination hotspots within species to ensure meiotic cross-overs, chromosome pairing and differentiation of germ cells, but in intersubspecific hybrids the same gene product causes meiotic arrest and hybrid sterility due to persistence of DNA double-strand breaks, recombination failure and subsequent failure of chromosome pairing. The process is modulated by the Hstx2 genetic factor, localized in a 2.7 Mb interval on the chromosome X. The main task of the project is to identify the genomic sequence responsible for the Hstx2 effect using a panel of bioinformatics tools for mRNA expression profiling using next generation RNA sequencing (RNA-seq), for chromatin immunoprecipitation sequencing (ChIP-seq) and for quantitative trait loci (QTL) mapping.
Institute of Molecular Genetics of the CAS, v. v. i.
Faculty of Chemical Technology

Genome-wide mapping of loci forming genotoxic intermediates associated with collisions between replication and transcription complexes

Dobrovolná Jana, RNDr. Ph.D. ( jan...@img.cas.cz)
Kolář Michal, Mgr. Ph.D. ( kol...@img.cas.cz)
Recent studies have shown that in human precancerous lesions, activated oncogenes induce stalling and collapse of replication forks, leading to genomic instability, a driving force of cancer. The proposed project addresses the hypothesis that oncogene-induced replication stress arises from interference between transcription and replication, which is associated with the formation of genotoxic RNA:DNA hybrids, referred to as R-loops. The project has the following objectives: (i) to identify on genome-wide scale the loci that are prone to R-loop formation under conditions of oncogene-induced replication stress; (ii) to determine basic charateristics of these loci; (iii) to assess whether oncogene activation is associated with R-loop formation at common fragile sites that are preferred target of oncogene-induced replication stress; (iv) to dermine whether R-loop forming loci overlap with the breakpoints of chromosomal rearangements found in cancers.
Institute of Molecular Genetics of the CAS, v. v. i.
Faculty of Chemical Technology

Genome-wide mapping of loci forming genotoxic intermediates associated with collisions between replication and transcription complexes

Dobrovolná Jana, RNDr. Ph.D. ( jan...@img.cas.cz)
Kolář Michal, Mgr. Ph.D. ( kol...@img.cas.cz)
Recent studies have shown that in human precancerous lesions, activated oncogenes induce stalling and collapse of replication forks, leading to genomic instability, a driving force of cancer. The proposed project addresses the hypothesis that oncogene-induced replication stress arises from interference between transcription and replication, which is associated with the formation of genotoxic RNA:DNA hybrids, referred to as R-loops. The project has the following objectives: (i) to identify on genome-wide scale the loci that are prone to R-loop formation under conditions of oncogene-induced replication stress; (ii) to determine basic charateristics of these loci; (iii) to assess whether oncogene activation is associated with R-loop formation at common fragile sites that are preferred target of oncogene-induced replication stress; (iv) to dermine whether R-loop forming loci overlap with the breakpoints of chromosomal rearangements found in cancers.
Institute of Molecular Genetics of the CAS, v. v. i.
Faculty of Chemical Technology

Integration of phenotyping and functional genomic data

Novosadová Vendula, Ing. Ph.D. ( ven...@img.cas.cz)
The position of bioinformatician is becoming necessary for every scientific group. Generating large datasets of omic data makes it necessary to develop new computational algorithms using tools such as machine learning and artificial intelligence, which will also allow the processing of diverse unstructured data. Our group is part of the research infrastructure Czech Centre for Phenogenomics, involved in the systematic annotation of the mouse genome within the International Mouse Phenotyping Consortium (IMPC). We produce mouse lines with one gene deactivated. These lines are further characterized by a standard phenotyping pipeline. The data set from each animal tested has over 700 parameters from different fields. These parameters contain numeric, categorical and image data. We are also collecting metabolomic data for selected lines. The Ph.D. project aims to integrate every data generated both in our center and within the whole IMPC. Linking individual parameters and finding correlations and causality between them and their possible semantic analysis will help to better understand the phenotype. At the same time, knowledge of a given gene function will enable mathematical modeling of the phenotype of genes involved in similar or overlapping regulatory networks.
Institute of Molecular Genetics of the CAS, v. v. i.
Updated: 11.12.2019 11:36, Author: Jan Kříž

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