THREE-DIMENSIONAL MODELING

Course objectives

General skills The course of Genomics is designed to provide students with an introduction to the structure, function and evolution of genomes and transcripts in humans and in other model organisms. Topics discussed will include modern genome sequencing technologies, as well the recent in silico and in vivo approaches used for functional genomics and for the functional role of emerging non-coding RNA classes (practical examples taken from recent literature will be used). The course also provides students with basic knowledge for accessing browsers and public databases for the analysis of gene expression data, GO and miRNA target prediction software. By the end of the course, students will be able to apply the acquired knowledge to the study of the basic mechanisms of gene expression, as well as of complex processes such as development, cell division and differentiation, and to exploit them for a practical use in both basic and applied research. Specific skills The students who have passed the exam will be able to know and to understand (acquired knowledge) - the origin and the maintenance of the biological complexity; - the paradigm shift introduced by genomics in genetic analysis: from forward to reverse genetics. - structure and function of the genome in humans and in the main model systems; - problems and technologies of genome-wide analyses applied to biological processes; - the influence of the modern sequencing technologies for a better description and for the study of transcriptome dynamics in humans and in the main model systems; - the complex networks of interaction between the biological molecules in the mechanisms of regulation of gene expression. The students who have passed the exam will be able to (acquired expertise): - interpret the biological phenomena in a multi-scale and multi-factorial context; - interpret the results of genomic studies and to discriminate which techniques to apply according to the different problems to be dealt with in the genomic field.

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Program - Frequency - Exams

Course program
This is an introduction to Genomics where the main methodologies underlying genomics, transcriptomics and proteomics and their practical use in basic and applied research are provided. Structural Genomics Evolution of the concept of gene: from Darwin's theories of heredity to the post-genomic era; the Human Genome Project. The Encode project. DNA (Sanger method, Maxam-Gilbert, BAC) and genome sequencing technologies. Automated sequencing. The Next-Generation Sequencing (NGS). The "Illumina" technology. Anatomy of genomes, genome size and number of genes. The non-coding DNA (ncDNA). RNA sequencing technologies. The transcriptome and high-throughput analysis of gene expression; WET lab and DRYLAB for a typical RNA-seq analysis (FASTQ, PHRED quality score, FASTQC). De-novo identification and differential expression analysis of mRNA and non-coding RNAs (ncRNA). Genetic and biochemical approaches to the study of the Interactome. The yeast two-hybrid system. Immunoprecipitation, Co-immunoprecipitation, Protein tagging and pull-down assays. Studying the interaction between PROTEIN (ChIP) and RNA (ChIRP) with the chromatin: the i) Chromatin Immunoprecipitation (ChIP) and the ii) Chromatin Isolation by RNA Purification (ChIRP). Functional Genomics "forward" and "reverse" genetics approaches. RNA interference (RNAi). Genomic editing: the CRISPR/CAS9 system. Functional analysis of mRNA and non-coding RNAs (ncRNA) in muscular and neuronal (mouse and human) differentiation systems. Web tools for genomics resources search and analysis Exercises in the computerized classroom. Elaboration and interpretation of genomic data. Biological databases (primary, secondary, specialized); the FLAT format; NCBI and resources: access via Taxonomy, Gene; Protein Map Viewer, Pubmed and Pubmed MeSH, Entrez; Genome browsers (UCSC), Ensembl, DDBJ, UniProt; Basics of gene ontology (GO). TARGETSCAN and miRTARBASE.
Books
For news on textbooks and teaching materials see: https://elearning2.uniroma1.it
  • Academic year2025/2026
  • CourseBiology
  • CurriculumGenetico-molecolare
  • Year3rd year
  • Semester2nd semester
  • SSDBIO/11
  • CFU3