85299 - Epigenomics

Course Unit Page

Academic Year 2021/2022

Learning outcomes

By the end of the course the student is familiar with the mechanisms underlying epigenetic phenomena pertaining gene regulation and genome organization. The student is able to frame the adaptation of genomic high-throughput assays to the study of the complete set of epigenetic modifications on the genetic material of a cell, and their impact on gene expression, genome stability, cellular differentiation and tumorigenesis.

Course contents

Lecture 1: Historical notes about the birth of Epigenetics as a new  scientific discipline. Basic concepts and analysis of phenomena that  apparently do not follow mendelian laws. 

Lecture 2: Epigenome: Expressivity of the genome independent from DNA sequence. Analysing genetic inheritance beyond DNA sequence.

Lecture 3: Defining multiple transcriptomes from the same informational DNA sequence. Understanding how transcription works: Basal transcription:

Lecture 4: Defining multiple transcriptomes from the same informational DNA sequence. Understanding how transcription works:Regulated transcription: 

Lecture 5: Genome wide analyses of the transcriptome from sequence of bulk biological material

Lecture 6:Genome wide analyses of the transcriptome from single cell sequencing.

Lecture 7: Defining multiple transcriptomes from the same informational DNA sequence. Understanding how transcription works: Histones and transcription.

Lecture 8: Histones as targets of DNA re-modeling complexes. 

Lecture 9: Histones as targets of multiple post-translational modifications.

Lecture 10: Modifiers, Readers and Erasers of epigenetic marks.

Lecture 11: Genome wide analyses of chromatin architecture: ChIP and ChIP-seq

Lecture 12:Genome wide analyses of chromatin architecture: 3C, 5C, iC.

Lecture 13:  The DNA methylation problem. CpGs or not CpGs. CpG islands.

Lecture 14: De novo or maintenance of DNA methylation. DNMTs and their function during development.

Lecture 15: Analyses of the DNA methylation status: use of methylation sensitive REs; MS-PCR bisulfite sequencing, COBRA.

Lecture 16: Genome wide DNA methylation: Methyl-DIP; definition of the methylome by NGS.

Lecture 17: Histone modifications meet DNA methylation

Lecture 18: Molecular epigenetic memory.

Lecture 19: Case study 1: What is known/posing questions

Lecture 20: Case study 1: Brain storming/ problem solving

Lecture 21: Case study 2: What is known/posing questions

Lecture 22: Case study 2: Brain storming/ problem solving

Lecture 21: Case study 3: What is known/posing questions

Lecture 22: Case study 3: Brain storming/ problem solving

 

 

 

Readings/Bibliography

EPIGENETICS II edition CSHL edited by D. Allis

ISBN 978-1-936113-59-0

papers from scientific literature

Teaching methods

Lectures, group discussion, brain storming, flipped classroom

Assessment methods

Brief written dissertation or ppt presentation describing analyses and possible solutions of relatively simple still unsolved questions that came out during brain storming.

Teaching tools

white board, video-projection,  origami class, pc.

Office hours

See the website of Giovanni Perini