MOLECULAR BIOLOGY

Course objectives

GENERAL OBJECTIVES: The Molecular Biology course is designed to provide students the conceptual and methodological basis required to study the molecular mechanisms regulating gene expression in physiological and pathological conditions, including epigenetics. In addition to the knowledge on the structure and metabolism of nucleic acids, the course will introduce the most relevant techniques of DNA cloning, DNA and RNA manipulation and the applications of Genetic Engineering to basic research and biomedicine. Topics discussed will also include the recent generation of sequencing technologies in light of their importance for the recent annotation of emerging noncoding RNA genes. The discovery of long noncoding and circular RNAs will be also discussed as well as the in vivo approaches used to study their functional role (practical examples taken from recent literature will be used). The course will include lectures and seminars. 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 OBJECTIVES: A - Knowledge and understanding OF 1) to know the mechanisms of regulation of gene expression and the technological methods available to intervene on it; OF 2) to know the structure and function of the genome in humans and in the main model systems; OF 3) to know the origin and the maintenance of the biological complexity; OF 4) to understand 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; OF 5) to understand the network of interactions between the biological molecules in the mechanisms of regulation of gene expression. B - Application skills OF 6) To be able to discriminate techniques to apply according to the different problems to be dealt with in the molecular biology field C - Autonomy of judgment OF 7) To be able to use the specific terminology; OF 8) To be able to interpret the biological phenomena in a multi-scale and multi-factorial context; OF 9) To be able to interpret the results of genomic studies D - Communication skills OF 10) To know how to report papers already present in the literature in the form of an oral presentation E - Ability to learn OF 11) Have the ability to search and consult the scientific literature in the main biological databases OF 12) Have the ability to evaluate the importance and the stringency of the published data

Channel 1
MONICA BALLARINO Lecturers' profile

Program - Frequency - Exams

Course program
Course program The course includes 60 hours of theoretical lectures, visits to the laboratories and student seminars. Updated information is available on the e-learning page of the course: https://elearning.uniroma1.it/course/view.php?id=8419 Evolution of the concept of gene: from Darwin's theories of heredity to the post-genomic era; the Human Genome Project. Anatomy of genomes, genome size and number of genes. Fantom and Encode projects. The non-coding DNA (ncDNA). DNA structure and replication. Chromatin structure and histone modifications. mRNA transcription and maturation: capping, splicing and polyadenylation; the “RNA Factory” model: coupling between transcriptional and post-transcriptional processes. Alternative splicing and human diseases. Protein translation. RNA interference. Main classes of noncoding RNAs: microRNAs (miRNAs), nuclear biogenesis (miRNA Factories); long non-coding RNAs (lncRNAs), nuclear and cytoplasmic species (biogenesis and function); circular RNAs (circRNAs), biogenesis and function. Functional analysis of noncoding RNAs in cell differentiation (myogenesis). Genomic editing: the CRISPR/CAS9 system. Generation of mouse models (Knock-IN/Knock-OUT). Outline of the main technologies for the study and manipulation of DNA and RNA: labeling of nucleic acids and hybridization assays (Southern/Northern Blot, microarray), PCR, RT-PCR, DNA cloning. Next-Generation RNA Sequencing (NGS) and Bioinformatics in Molecular Biology. Genetic and biochemical approaches to the study of the Interactome: yeast two-hybrid, Immunoprecipitation, Co-immunoprecipitation, Protein tagging and pull-down assays. Protein and RNA chromatin interactions: the i) Chromatin Immunoprecipitation (ChIP) and the ii) Chromatin Isolation by RNA Purification (ChIRP). Identification and study of sub-topological domains (TADs): 3C, 4C, 5C, Hi-C e ChIA-PET. Cell and tissue imaging.
Prerequisites
The course of Molecular Biology is taught in the 2nd semester of the 1st year of the Master’s Degree Programme in Physics (LM-17 class) and it is included among the optional courses. Basic prerequisites for understanding the topics covered by the course are a basic knowledge of Biology. Both the written and oral comprehension of the English language is essential to take advantage of the oral lessons and the scientific articles proposed by the teachers in addition to textbooks as didactic material.
Books
The didactic material adopted is described from the first lesson and consists of: One textbook at student’s choice among the followings: - Biologia Molecolare del gene – VII edizione – Watson et al., Ed. Zanichelli - Biologia Molecolare – R.F. Weaver – Mc Graw Hill –Il gene X – B. Lewin et al. (Zanichelli) Scientific articles in .pdf format (provided by the teacher at the end of each lesson) Lesson slides Practice test on the main topics of the course For news on textbooks and teaching materials see: https://elearning.uniroma1.it/course/view.php?id=8419
Teaching mode
The course is structured in frontal theoretical lectures. In particular, there are 60 hours of total teaching (6 CFU). Lectures are held 2 times per week and presented by the use of slides on Power-Point.
Frequency
Lectures are not mandatory but strongly recommended.
Exam mode
The exam aims at verifying the level of knowledge and in-depth examination of the topics of the teaching program and the reasoning skills developed by the student. The evaluation is expressed in thirtieths (minimum grade 18/30, maximum mark 30/30 with summa cum laude). The overall exam allows verifying the achievement of the objectives in terms of knowledge and skills acquired, as well as communication skills. During the oral tests property of language, clarity of exposition and critical capacity to solve biological problems are also evaluated. The time required for oral interviews is 40 minutes.
Bibliography
The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions. Cipriano A, Ballarino M. Front Mol Biosci. 2018 Mar 6;5:20. doi: 10.3389/fmolb.2018.00020. eCollection 2018. Review. RNA regulation: a new genetics? Mattick JS. Nat Rev Genet. 2004 Apr;5(4):316-23. Review. The relationship between non-protein-coding DNA and eukaryotic complexity. Taft RJ, Pheasant M, Mattick JS. Bioessays. 2007 Mar;29(3):288-99. Next-generation sequencing: from basic research to diagnostics. Voelkerding KV, Dames SA, Durtschi JD. Clin Chem. 2009 Apr;55(4):641-58. doi: 10.1373/clinchem.2008.112789. Epub 2009 Feb 26. Review. What is bioinformatics? A proposed definition and overview of the field. Luscombe NM, Greenbaum D, Gerstein M. Methods Inf Med. 2001;40(4):346-58. Review. A survey of best practices for RNA-seq data analysis. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A. Genome Biol. 2016 Jan 26;17:13. doi: 10.1186/s13059-016-0881-8. Review. Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells. Zhao S, Fung-Leung WP, Bittner A, Ngo K, Liu X. PLoS One. 2014 Jan 16;9(1):e78644. doi: 10.1371/journal.pone.0078644. eCollection 2014. Next-generation sequencing: from basic research to diagnostics. Voelkerding KV, Dames SA, Durtschi JD. Clin Chem. 2009 Apr;55(4):641-58. doi: 10.1373/clinchem.2008.112789. Epub 2009 Feb 26. Review. Library construction for next-generation sequencing: Overviews and challenges. Steven R. Head, H. Kiyomi Komori, Sarah A. LaMere, Thomas Whisenant, Filip Van Nieuwerburgh, Daniel R. Salomon, Phillip Ordoukhanian. Biotechniques. 2014; 56(2): 61–passim. doi: 10.2144/000114133 A Mouse Geneticist’s Practical Guide to CRISPR Applications. Priti Singh, John C. Schimenti, Ewelina Bolcun-Filas. Genetics. 2015 Jan; 199(1): 1–15. doi: 10.1534/genetics.114.169771 Prevention of muscular dystrophy in mice by CRISPR/Cas9–mediated editing of germline DNA. Chengzu Long, John R. McAnally, John M. Shelton, Alex A. Mireault, Rhonda Bassel-Duby, Eric N. Olson. Science. 2014 Sep 5; 345(6201): 1184–1188. doi: 10.1126/science.1254445 Yeast Two-Hybrid Screen. Lauren Makuch. Methods in Enzymology, Volume 539, Chapter III.
Lesson mode
The course is structured in frontal theoretical lectures. In particular, there are 60 hours of total teaching (6 CFU). Lectures are held 2 times per week and presented by the use of slides on Power-Point.
MONICA BALLARINO Lecturers' profile

Program - Frequency - Exams

Course program
Course program The course includes 60 hours of theoretical lectures, visits to the laboratories and student seminars. Updated information is available on the e-learning page of the course: https://elearning.uniroma1.it/course/view.php?id=8419 Evolution of the concept of gene: from Darwin's theories of heredity to the post-genomic era; the Human Genome Project. Anatomy of genomes, genome size and number of genes. Fantom and Encode projects. The non-coding DNA (ncDNA). DNA structure and replication. Chromatin structure and histone modifications. mRNA transcription and maturation: capping, splicing and polyadenylation; the “RNA Factory” model: coupling between transcriptional and post-transcriptional processes. Alternative splicing and human diseases. Protein translation. RNA interference. Main classes of noncoding RNAs: microRNAs (miRNAs), nuclear biogenesis (miRNA Factories); long non-coding RNAs (lncRNAs), nuclear and cytoplasmic species (biogenesis and function); circular RNAs (circRNAs), biogenesis and function. Functional analysis of noncoding RNAs in cell differentiation (myogenesis). Genomic editing: the CRISPR/CAS9 system. Generation of mouse models (Knock-IN/Knock-OUT). Outline of the main technologies for the study and manipulation of DNA and RNA: labeling of nucleic acids and hybridization assays (Southern/Northern Blot, microarray), PCR, RT-PCR, DNA cloning. Next-Generation RNA Sequencing (NGS) and Bioinformatics in Molecular Biology. Genetic and biochemical approaches to the study of the Interactome: yeast two-hybrid, Immunoprecipitation, Co-immunoprecipitation, Protein tagging and pull-down assays. Protein and RNA chromatin interactions: the i) Chromatin Immunoprecipitation (ChIP) and the ii) Chromatin Isolation by RNA Purification (ChIRP). Identification and study of sub-topological domains (TADs): 3C, 4C, 5C, Hi-C e ChIA-PET. Cell and tissue imaging.
Prerequisites
The course of Molecular Biology is taught in the 2nd semester of the 1st year of the Master’s Degree Programme in Physics (LM-17 class) and it is included among the optional courses. Basic prerequisites for understanding the topics covered by the course are a basic knowledge of Biology. Both the written and oral comprehension of the English language is essential to take advantage of the oral lessons and the scientific articles proposed by the teachers in addition to textbooks as didactic material.
Books
The didactic material adopted is described from the first lesson and consists of: One textbook at student’s choice among the followings: - Biologia Molecolare del gene – VII edizione – Watson et al., Ed. Zanichelli - Biologia Molecolare – R.F. Weaver – Mc Graw Hill –Il gene X – B. Lewin et al. (Zanichelli) Scientific articles in .pdf format (provided by the teacher at the end of each lesson) Lesson slides Practice test on the main topics of the course For news on textbooks and teaching materials see: https://elearning.uniroma1.it/course/view.php?id=8419
Teaching mode
The course is structured in frontal theoretical lectures. In particular, there are 60 hours of total teaching (6 CFU). Lectures are held 2 times per week and presented by the use of slides on Power-Point.
Frequency
Lectures are not mandatory but strongly recommended.
Exam mode
The exam aims at verifying the level of knowledge and in-depth examination of the topics of the teaching program and the reasoning skills developed by the student. The evaluation is expressed in thirtieths (minimum grade 18/30, maximum mark 30/30 with summa cum laude). The overall exam allows verifying the achievement of the objectives in terms of knowledge and skills acquired, as well as communication skills. During the oral tests property of language, clarity of exposition and critical capacity to solve biological problems are also evaluated. The time required for oral interviews is 40 minutes.
Bibliography
The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions. Cipriano A, Ballarino M. Front Mol Biosci. 2018 Mar 6;5:20. doi: 10.3389/fmolb.2018.00020. eCollection 2018. Review. RNA regulation: a new genetics? Mattick JS. Nat Rev Genet. 2004 Apr;5(4):316-23. Review. The relationship between non-protein-coding DNA and eukaryotic complexity. Taft RJ, Pheasant M, Mattick JS. Bioessays. 2007 Mar;29(3):288-99. Next-generation sequencing: from basic research to diagnostics. Voelkerding KV, Dames SA, Durtschi JD. Clin Chem. 2009 Apr;55(4):641-58. doi: 10.1373/clinchem.2008.112789. Epub 2009 Feb 26. Review. What is bioinformatics? A proposed definition and overview of the field. Luscombe NM, Greenbaum D, Gerstein M. Methods Inf Med. 2001;40(4):346-58. Review. A survey of best practices for RNA-seq data analysis. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A. Genome Biol. 2016 Jan 26;17:13. doi: 10.1186/s13059-016-0881-8. Review. Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells. Zhao S, Fung-Leung WP, Bittner A, Ngo K, Liu X. PLoS One. 2014 Jan 16;9(1):e78644. doi: 10.1371/journal.pone.0078644. eCollection 2014. Next-generation sequencing: from basic research to diagnostics. Voelkerding KV, Dames SA, Durtschi JD. Clin Chem. 2009 Apr;55(4):641-58. doi: 10.1373/clinchem.2008.112789. Epub 2009 Feb 26. Review. Library construction for next-generation sequencing: Overviews and challenges. Steven R. Head, H. Kiyomi Komori, Sarah A. LaMere, Thomas Whisenant, Filip Van Nieuwerburgh, Daniel R. Salomon, Phillip Ordoukhanian. Biotechniques. 2014; 56(2): 61–passim. doi: 10.2144/000114133 A Mouse Geneticist’s Practical Guide to CRISPR Applications. Priti Singh, John C. Schimenti, Ewelina Bolcun-Filas. Genetics. 2015 Jan; 199(1): 1–15. doi: 10.1534/genetics.114.169771 Prevention of muscular dystrophy in mice by CRISPR/Cas9–mediated editing of germline DNA. Chengzu Long, John R. McAnally, John M. Shelton, Alex A. Mireault, Rhonda Bassel-Duby, Eric N. Olson. Science. 2014 Sep 5; 345(6201): 1184–1188. doi: 10.1126/science.1254445 Yeast Two-Hybrid Screen. Lauren Makuch. Methods in Enzymology, Volume 539, Chapter III.
Lesson mode
The course is structured in frontal theoretical lectures. In particular, there are 60 hours of total teaching (6 CFU). Lectures are held 2 times per week and presented by the use of slides on Power-Point.
  • Lesson code1044546
  • Academic year2025/2026
  • CoursePhysics
  • CurriculumPhysics of Biological Systems
  • Year1st year
  • Semester2nd semester
  • SSDBIO/11
  • CFU6