NA-Seq: a discovery tool for the analysis of chromatin structure and dynamics during differentiation.
It is well established that epigenetic modulation of genome accessibility in chromatin occurs during biological processes. Here we describe a method based on restriction enzymes and next-generation sequencing for identifying accessible DNA elements using a small amount of starting material, and use it to examine myeloid differentiation of primary human CD34+ cells. The accessibility of several classes of cis-regulatory elements was a predictive marker of in vivo DNA binding by transcription factors, and was associated with distinct patterns of histone posttranslational modifications. We also mapped large chromosomal domains with differential accessibility in progenitors and maturing cells. Accessibility became restricted during differentiation, correlating with a decreased number of expressed genes and loss of regulatory potential. Our data suggest that a permissive chromatin structure in multipotent cells is progressively and selectively closed during differentiation, and illustrate the use of our method for the identification of functional cis-regulatory elements.
Gargiulo
Gaetano
G
Department of Experimental Oncology, IFOM-IEO Campus, European Institute of Oncology (IEO), Via Ripamonti 435, 20141 Milan, Italy.
Levy
Samuel
S
Bucci
Gabriele
G
Romanenghi
Mauro
M
Fornasari
Lorenzo
L
Beeson
Karen Y
KY
Goldberg
Susanne M
SM
Cesaroni
Matteo
M
Ballarini
Marco
M
Santoro
Fabio
F
Bezman
Natalie
N
Frigè
Gianmaria
G
Gregory
Philip D
PD
Holmes
Michael C
MC
Strausberg
Robert L
RL
Pelicci
Pier Giuseppe
PG
Urnov
Fyodor D
FD
Minucci
Saverio
S
D018952:Antigens, CD34 / Q000378:metabolism; D002454:Cell Differentiation / Q000235:genetics*; D002478:Cells, Cultured; D002843:Chromatin / Q000235:genetics*; D004262:DNA Restriction Enzymes; D044127:Epigenesis, Genetic; D018507:Gene Expression Regulation, Developmental; D055106:Genome-Wide Association Study / Q000379:methods*; D006412:Hematopoietic Stem Cells / Q000166:cytology / Q000378:metabolism; D006657:Histones / Q000378:metabolism; D006801:Humans; D038042:Myelopoiesis / Q000235:genetics; D014157:Transcription Factors / Q000378:metabolism
D018952:Antigens, CD34; D002843:Chromatin; D006657:Histones; D014157:Transcription Factors; D004262:DNA Restriction Enzymes