Advanced genomics and epigenomics

EPIGENOMICS (6 CFU)

Introduction to epigenetics.
The DNA and the chromatin structure.
The nucleosome
Histone Post-translational modifications.
The Writers
The Readers
The biochemistry of DNA Methylation
The Yamanaka experiments and the role of Transcription Factors

Genome-wide assays and bioinformatic analysis protocols for the characterization of genetic and epigenetic regulation of gene transcription:
· Nucleosome occupancy and DNA accessibility (e.g. ATAC-Seq)
· DNA Methylation (e.g. BS-Seq)
· Chromatin conformation capture assays (e.g. Hi-C, ChIA-Pet)
· ChiP-Seq for Transcription Factors
· ChiP-Seq for histone modifications and chromatin states
· DAP-Seq
Computational approaches for the reconstruction of gene regulatory networks with DNA pattern scanning (Information Theory, Position weight matrices), gene expression compendia (CLR and similar), and integration of ChIP-Seq data.
Case studies examples (ChIP-Seq analysis with identification of transcription factor binding sites, CLR on a gene expression compendium of E. coli).

ADVANCED GENOMICS
Tn-mutagenesis for the discovery of essential genes or genes involved in specific processes, with high fitness cost - experimental approaches (Tn-Seq, Tn-seq circle, TraDIS, Rb-Tn-seq...) and bioinformatic analysis
Iso-seq for full transcriptome characterization
The small RNA (sRNA) world:
- RNA in Bacteria, bioinformatic prediction of sRNAs. Dynamical properties of genetic circuits with sRNA-dependent regulation. Case studies: Quorum sensing regulation in Vibrio fischeri and in Vibrio cholerae
- sRNA in Plants and their pathogens. Experimental approaches, sequencing and the quest for targets aided by PARE (degradome sequencing) in plants. Immuno-precipitation of Ago1 protein. Bioinformatic approaches to target prediction. Phasing pattern identification. Mobile sRNAs in patho-systems: the Cuscuta case study.
Meta-taxonomics, meta-genomics, meta-transcriptomics for the characterization and the engineering of microbial communities e.g.
Metabolic engineering: basics of metabolic networks and FBA modelling
Quantitative Trait Loci in Plants and Animals
Evolutionary genomics, the pangenome concept, orthologs, paralogs and orthogroups, phylogenetic profiles;
Pathogens and the prediction of antibiotic resistance genes.
Predictive models based on genomic properties, DNA compositional models.