title: NA-Seq: a discovery tool for the analysis of chromatin structure and dynamics during differentiation.
abstract: 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.
authors.affiliation: Department of Experimental Oncology, IFOM-IEO Campus, European Institute of Oncology (IEO), Via Ripamonti 435, 20141 Milan, Italy.
authors.forename: Gaetano
authors.initials: G
authors.lastname: Gargiulo
authors.forename: Samuel
authors.initials: S
authors.lastname: Levy
authors.forename: Gabriele
authors.initials: G
authors.lastname: Bucci
authors.forename: Mauro
authors.initials: M
authors.lastname: Romanenghi
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Fornasari
authors.forename: Karen Y
authors.initials: KY
authors.lastname: Beeson
authors.forename: Susanne M
authors.initials: SM
authors.lastname: Goldberg
authors.forename: Matteo
authors.initials: M
authors.lastname: Cesaroni
authors.forename: Marco
authors.initials: M
authors.lastname: Ballarini
authors.forename: Fabio
authors.initials: F
authors.lastname: Santoro
authors.forename: Natalie
authors.initials: N
authors.lastname: Bezman
authors.forename: Gianmaria
authors.initials: G
authors.lastname: Frigè
authors.forename: Philip D
authors.initials: PD
authors.lastname: Gregory
authors.forename: Michael C
authors.initials: MC
authors.lastname: Holmes
authors.forename: Robert L
authors.initials: RL
authors.lastname: Strausberg
authors.forename: Pier Giuseppe
authors.initials: PG
authors.lastname: Pelicci
authors.forename: Fyodor D
authors.initials: FD
authors.lastname: Urnov
authors.forename: Saverio
authors.initials: S
authors.lastname: Minucci
mesh_terms: 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
chemical_list: D018952:Antigens, CD34; D002843:Chromatin; D006657:Histones; D014157:Transcription Factors; D004262:DNA Restriction Enzymes