Top Med Chem (2020) 33: 523–560
DOI: 10.1007/7355_2019_82
© Springer Nature Switzerland AG 2019
Published online: 28 November 2019
Advanced Assays in Epigenetics
Carmela Dell’Aversana, Federica Sarno, Mariarosaria Conte,
Cristina Giorgio, and Lucia Altucci
Contents
1 Epi-proteomic Analyses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 526
1.1 Biochemical Studies: In Vitro Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 526
1.2 Cell-Based Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 530
2 Innovative Genome-Wide Technologies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 536
2.1 ChIP: From Standard Procedures to Innovative Applications . . . . . . . . . . . . . . . . . . . . . . . 536
3 Epigenetic Regulatory Role of miRNA: New Analytical Tools and Technologies . . . . . . . 545
3.1 miRNA Quantification Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 546
3.2 Experimental miRNA Target Identification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 551
4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 554
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 554
Abstract Epigenetic mechanisms orchestrate the finely tuned regulation of genetic
material and play a pivotal role in defining cellular functions and phenotypes. A
growing set of tools supports analysis of the epigenome. This chapter will provide an
overview of the principle methods of studying complex epigenetic machinery,
focusing on recent advancements of tools and techniques in the field of epigenetics.
It will also address the advantages, limitations and perspectives of each approach.
Increasingly, the high sensitivity, specificity, accuracy, precision and reproducibility
of cutting-edge technologies in epigenetics are allowing the identification of new key
targets and molecular mechanisms in healthy and pathological states and are becoming methods of choice for clinical investigations.
Keywords Epigenetics, Genome, Histone modification, Methylation, miRNA
C. Dell’Aversana, F. Sarno, C. Giorgio, and L. Altucci (*)
Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Napoli, Italy
e-mail: lucia.altucci@unicampania.it
M. Conte
IRCCS, SDN, Naples, Italy
DOI: 10.1007/7355_2019_82
© Springer Nature Switzerland AG 2019
Published online: 28 November 2019
Advanced Assays in Epigenetics
Carmela Dell’Aversana, Federica Sarno, Mariarosaria Conte,
Cristina Giorgio, and Lucia Altucci
Contents
1 Epi-proteomic Analyses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 526
1.1 Biochemical Studies: In Vitro Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 526
1.2 Cell-Based Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 530
2 Innovative Genome-Wide Technologies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 536
2.1 ChIP: From Standard Procedures to Innovative Applications . . . . . . . . . . . . . . . . . . . . . . . 536
3 Epigenetic Regulatory Role of miRNA: New Analytical Tools and Technologies . . . . . . . 545
3.1 miRNA Quantification Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 546
3.2 Experimental miRNA Target Identification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 551
4 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 554
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 554
Abstract Epigenetic mechanisms orchestrate the finely tuned regulation of genetic
material and play a pivotal role in defining cellular functions and phenotypes. A
growing set of tools supports analysis of the epigenome. This chapter will provide an
overview of the principle methods of studying complex epigenetic machinery,
focusing on recent advancements of tools and techniques in the field of epigenetics.
It will also address the advantages, limitations and perspectives of each approach.
Increasingly, the high sensitivity, specificity, accuracy, precision and reproducibility
of cutting-edge technologies in epigenetics are allowing the identification of new key
targets and molecular mechanisms in healthy and pathological states and are becoming methods of choice for clinical investigations.
Keywords Epigenetics, Genome, Histone modification, Methylation, miRNA
C. Dell’Aversana, F. Sarno, C. Giorgio, and L. Altucci (*)
Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Napoli, Italy
e-mail: lucia.altucci@unicampania.it
M. Conte
IRCCS, SDN, Naples, Italy