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Advanced Assays in Epigenetics

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Book cover Chemical Epigenetics

Part of the book series: Topics in Medicinal Chemistry ((TMC,volume 33))

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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.

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Abbreviations

5caC:

5-Carboxylcytosine

5fC:

5-Formylcytosine

5hmC:

5-Hydroxymethylcytosine

5mC:

5-Methylcytosine

AlphaScreen:

Amplified Luminescent Proximity Homogeneous Assay Screen

BRET:

Bioluminescence resonance energy transfer

BS-seq:

Bisulfite sequencing

CAB-seq:

Chemical modification-assisted bisulfite sequencing

CE-SSCP:

Capillary electrophoresis single-strand conformation polymorphism

CETSA:

Cellular thermal shift assay

ChIP:

Chromatin immunoprecipitation

ChroP:

Chromatin proteomics

ddPCR:

Droplet digital PCR

EDC:

1-Ethyl-3(3-dimethylaminoproyl)-carbodiimide hydrochloride

EnIGMA:

Enzyme-assisted identification of genome modification assay

ePL:

Enhanced ProLabel

ES:

Embryonic stem

EWAS:

Epigenome-wide association studies

EXPAR:

Exponential amplification reaction

fCAB-seq:

5-Formylcytosine chemical modification-assisted bisulfite sequencing

FISH:

Fluorescent in situ hybridization

FLIM:

Fluorescence lifetime microscopy

FRET:

Förster resonance energy transfer

G4:

G-quadruplex

HATs:

Histone acetyltransferases

HMTs:

Histone methyltransferases

HTDR:

High-throughput dose-response

HTS:

High-throughput screening

HT-seq:

High-throughput sequencing

ISH:

In situ hybridization

ITC:

Isothermal titration colorimetry

LC-MS:

Liquid chromatography-mass spectrometry

LNA:

Locked nucleic acid

miRNA:

microRNA

miR-TRAP:

miRNA trapping

MPS:

Massive parallel sequencing

MS:

Mass spectrometry

MST:

Microscale thermophoresis

NGS:

Next-generation sequencing

Nluc:

NanoLuc luciferase

PAR-CLIP:

Photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation

QD:

Quantum dot

RBPs:

RNA binding proteins

RIME:

Rapid immunoprecipitation mass spectrometry of endogenous protein

Rluc:

Renilla luciferase

RRBS:

Reduced representation bisulfite sequencing

scBS-seq:

Single-cell bisulfite sequencing

scM&T-seq:

Single-cell genome-wide methylome and transcriptome sequencing

scRRBS:

Single-cell reduced representation bisulfite sequencing

snmC-seq:

Single-nucleus methylcytosine sequencing

SNPs:

Single-nucleotide polymorphisms

SPR:

Surface plasmon resonance

TAB-seq:

Tet-assisted bisulfite sequencing

TCL:

Targeted chromatin ligation

Tm:

Melting temperature

TR-FRET:

Time-resolved fluorescent energy transfer

UV:

Ultraviolet

YFP:

Yellow fluorescent protein

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Authors and Affiliations

  1. Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Napoli, Italy

    Carmela Dell’Aversana, Federica Sarno, Cristina Giorgio & Lucia Altucci

  2. IRCCS, SDN, Naples, Italy

    Mariarosaria Conte

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  1. Carmela Dell’Aversana
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  2. Federica Sarno
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  3. Mariarosaria Conte
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  4. Cristina Giorgio
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  5. Lucia Altucci
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Correspondence to Lucia Altucci .

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  1. Sapienza University of Rome, Rome, Italy

    Antonello Mai

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Funding: The authors acknowledge AIRC17217; PON_0101227; VALERE: Vanvitelli per la Ricerca; Regione Campania lotta alle patologie oncologiche: iCURE (CUP B21C17000030007); and Regione Campania FASE2: IDEAL (CUP B53D18000080007). We thank C. Fisher for linguistic editing.

Conflict of Interest: The authors declare no competing interests.

Ethical Statement: This article does not contain any studies with human participants or animals performed by any of the authors.

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Dell’Aversana, C., Sarno, F., Conte, M., Giorgio, C., Altucci, L. (2019). Advanced Assays in Epigenetics. In: Mai, A. (eds) Chemical Epigenetics. Topics in Medicinal Chemistry, vol 33. Springer, Cham. https://doi.org/10.1007/7355_2019_82

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