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Lecturer(s)
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Šebela Marek, prof. Mgr. Dr.
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Frébort Ivo, prof. RNDr. CSc., Ph.D.
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Course content
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Genome and chromosome structure. Genetic, cytological and physical maps. Contig maps and clone banks. Genes and accompanying sequences. Pseudogenes. Intergenic DNA. Repetitive sequences and mobile elements. Human genome. Mapping of human genome. Sequencing of human genome. Genes and non-coding DNA in human genome. Repetitive sequences in human genome. Single nucleotide polymorphism. HapMap and Genome 1000 projects. Comparative genomics. Syntheny. Paleogenomics. Matagenomics. Sequencing methods of 2nd and 3rd generation. Pyrosequencing. Reversible cyclic termination. SMRT (single molecule real-time) sequencing. Sequencing principles of following companies: Illumina, Roche, PacBio, SOLiD, Ion Torrent, Oxford Nanopores. Functional genome testing based on RNA analysis. DNA arrays and gene chips. Affymetrix chips. RNA-seq. Chip-seq. Methyl-seq. Genome databases: GeneBank, EMBL-bank, Ensembl, TAIR (Arabidopsis). BLAST/BLAT.
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Learning activities and teaching methods
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Dialogic Lecture (Discussion, Dialog, Brainstorming)
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Learning outcomes
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Subject content is focused on description of genome structure. Emphasis is paid above all to methodology how to obtain information about genome structure with focus on parallel sequencing methods, genetic mapping, annotation of genes and other functional elements, databases of DNA sequences, description of chromosome structure and its parts. Functional parts of genome: coding sequences and repetitive sequences. Comparative genomics with focus on model organisms: Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana a Homo sapiens. DNA polymorfismus. Methods of whole genome and whole transcriptome approaches: Affymetrix, RNAseq, ChiP-Seq.
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Prerequisites
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Successful graduated studium of Bachelor of Science and Magister of Science in Biochemistry.
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Assessment methods and criteria
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Oral exam
Oral examination - successfuly answered three questions of general knowledge.
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Recommended literature
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Alberts, B. Molecular Biology of Cell, 6th edition, Garland Publishing (2015)..
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Brown, T.A. Genomes. John Wiley and Sons, Inc., New York, 1999..
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Gibson, C, Muse, S.V. A Primer Of Genome Science, Sinauer Associate (2009).
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Snustad, D. P., Simmons, M. J. (2017). Genetika. Brno: Munipress.
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Snustad D.P. a Simmons M.J. Principles of Genetics, 7th edition, John Wiley and Sons (2016).
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