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
Epigenetic modifications work with genetic mechanisms to control gene expression
and chromatin structure in normal cells [1]. Disruption of epigenetic regulatory
processes results in abnormal gene function and/or alterations in cellular signalling
pathways, leading to several pathological states such as cancer [2]. Unlike most
genetic mutations, epigenetic abnormalities are reversible and potentially good
targets for deriving therapeutic strategies. Global changes in the epigenetic landscape can precede genetic alterations at early stages of disease development, making
them suitable predictive biomarkers for clinical diagnosis [3]. Furthermore, several
studies have identified defects in epigenetic modulators as indicators of both progression and outcome of a disease, as well as biomarkers of patient response to
therapy and early detection of recurrence, suggesting a prospective translational
application in clinical practice to improve prognosis [4–7]. Advanced technologies
able to rapidly analyse epigenetic changes have revealed a challenging scenario and
provide an accurate detection of new key epi-targets in pathological states and
several multifactorial complex diseases, including cancer. This chapter will describe
the most innovative epigenomic technologies and will be divided into three main
sections: (1) assays, in vitro and in cell, useful to define the activity and binding of
epigenetic modulators; (2) genome-wide approaches used to determine the chromatin modification status of cells at nucleotide resolution level and to detect the binding
sites of DNA-associated proteins; and (3) methodologies for miRNA expression and
functional analysis. The advantages, limitations, cost-effectiveness and therapeutic
perspectives of each technique will also be discussed. Further work improving the
Advanced Assays in Epigenetics
525
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
Epigenetic modifications work with genetic mechanisms to control gene expression
and chromatin structure in normal cells [1]. Disruption of epigenetic regulatory
processes results in abnormal gene function and/or alterations in cellular signalling
pathways, leading to several pathological states such as cancer [2]. Unlike most
genetic mutations, epigenetic abnormalities are reversible and potentially good
targets for deriving therapeutic strategies. Global changes in the epigenetic landscape can precede genetic alterations at early stages of disease development, making
them suitable predictive biomarkers for clinical diagnosis [3]. Furthermore, several
studies have identified defects in epigenetic modulators as indicators of both progression and outcome of a disease, as well as biomarkers of patient response to
therapy and early detection of recurrence, suggesting a prospective translational
application in clinical practice to improve prognosis [4–7]. Advanced technologies
able to rapidly analyse epigenetic changes have revealed a challenging scenario and
provide an accurate detection of new key epi-targets in pathological states and
several multifactorial complex diseases, including cancer. This chapter will describe
the most innovative epigenomic technologies and will be divided into three main
sections: (1) assays, in vitro and in cell, useful to define the activity and binding of
epigenetic modulators; (2) genome-wide approaches used to determine the chromatin modification status of cells at nucleotide resolution level and to detect the binding
sites of DNA-associated proteins; and (3) methodologies for miRNA expression and
functional analysis. The advantages, limitations, cost-effectiveness and therapeutic
perspectives of each technique will also be discussed. Further work improving the
Advanced Assays in Epigenetics
525