C7201 Basic Genomics

Faculty of Science
Autumn 2024
Extent and Intensity
2/0/0. 2 credit(s) (plus 2 credits for an exam). Type of Completion: zk (examination).
Teacher(s)
doc. Mgr. Petra Procházková Schrumpfová, Ph.D. (lecturer)
Guaranteed by
doc. Mgr. Petra Procházková Schrumpfová, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: doc. Mgr. Petra Procházková Schrumpfová, Ph.D.
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Prerequisites
No prerequisites are required. Basic knowledge of biochemistry, genetics, or molecular biology is welcome.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
The aim of the course is to provide a theoretical overview of the basic approaches to contemporary genomics. Students will gain an understanding of the factors that can influence the analysis of genomic data. They will become familiar with genome variability and regulatory mechanisms that control not only individual genes but also entire gene families. The role of non-coding regions of genomes and their significance will also be described. Students will learn about the connection between genomes, transcriptomes, and epigenomes.


All topics listed in the syllabus will be discussed with the aim of enabling students to understand the fundamental principles of genomics and their interconnections. The course does not emphasise a detailed mastery of all the terms covered but rather focuses on understanding underlying mechanisms and their relationships.
Learning outcomes
By the end of the lectures, students will have a comprehensive understanding of modern approaches to genomics. They will be able to use and interpret information stored in genomic databases and navigate the main methodologies used for genome analysis in different organisms.
Syllabus
  • Introduction to Genomics: Definition of genetic and genomic terms; gene location on chromosomes; recombination; gene variants; autosomal and gonosomal inheritance; genetic and physical maps of genome organization.
  • Genome Variability in Evolution: Genomes of viruses, prokaryotes, archaea, fungi, plants, and animals; C-value paradox; metagenomics; whole-genome and segmental duplications; gene families; organelle genomes (nucleus, mitochondria, chloroplasts) and the evolution of eukaryotic genomes.
  • Structure of Eukaryotic Genes: Structure of protein-coding genes; functional and regulatory parts of genes; basic processes of gene expression (transcription, translation); gene nomenclature; DNA regulatory motifs and their identification; comparative genomics.
  • Structure of Prokaryotic Genes: Operons; functional and regulatory parts of prokaryotic genes; genomes with linear and circular chromosomes.
  • Genome Sections Related to Genes: Pseudogenes; retrogenes; incomplete genes; introns; insertions/deletions, minimal genome.
  • Non-coding Sections of Genomes: Repetitive sequences (tandem, retrotransposed) and genome plasticity; 3D genomics.
  • Genetic Engineering: Introduction of genes of interest into the genome; insertions, deletions, translocations; fusion genes.
  • Transcriptomics: Classification of RNA types; transcriptome of coding and non-coding parts of genomes and its analysis.
  • Epigenomics: The genome including epigenetic changes at the DNA and histone level; remodeling factors; the impact of the epigenome on the transcriptome.
  • Genome Browsers: Genome assembly and annotation; visualization and integration of genomic data, functional genomics.
  • Basic Methods in Genomics: 1D genomic methods (first, second, and third-generation sequencing; bisulfite sequencing / TET enzyme sequencing, ChIP-seq, etc.); methods analyzing chromatin status (MNase-seq, DNase-seq, FAIRE-seq, ATAC-seq, etc.); methods for determining 3D genomic architecture (3C, 4C, 5C, Hi-C, ChIP-loop, TADs, etc.).
Literature
  • Genomics: A Very Short Introduction, Archibald, John M.,Oxford University Press, 2018, ISBN 9780198786207
  • Genomes, Brown TA, Genomes, ISBN 0367674076, 2023
  • SNUSTAD, D. Peter and Michael J. SIMMONS. Genetika. Translated by Jiřina Relichová. Druhé, aktualizované vydá. Brno: Masarykova univerzita, 2017, xix, 844. ISBN 9788021086135. info
  • ALBERTS, Bruce. Molecular biology of the cell. 5th ed. New York, N.Y.: Garland science, 2008, xxxiii, 12. ISBN 9780815341062. info
Teaching methods
The main teaching method consists of lectures that present general examples and principles, which will be placed in a broader context. Special emphasis will be placed on the connections that can facilitate the understanding of genomic data analysis.
Assessment methods
Type of exam: Written exam.
Náhradní absolvování
Knowledge of the course material can be verified by completing a written test after returning from abroad.
Language of instruction
Czech
Further Comments
The course is taught annually.
The course is taught every week.
The course is also listed under the following terms Autumn 2013, Autumn 2014, Autumn 2015.
  • Enrolment Statistics (recent)
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