title: Comprehensive characterization of erythroid-specific enhancers in the genomic regions of human Krüppel-like factors.
abstract: BACKGROUND
  Mapping of DNase I hypersensitive sites (DHSs) is a powerful tool to experimentally identify cis-regulatory elements (CREs). Among CREs, enhancers are abundant and predominantly act in driving cell-specific gene expression. Krüppel-like factors (KLFs) are a family of eukaryotic transcription factors. Several KLFs have been demonstrated to play important roles in hematopoiesis. However, transcriptional regulation of KLFs via CREs, particularly enhancers, in erythroid cells has been poorly understood.
  
  
  RESULTS
  In this study, 23 erythroid-specific or putative erythroid-specific DHSs were identified by DNase-seq in the genomic regions of 17 human KLFs, and their enhancer activities were evaluated using dual-luciferase reporter (DLR) assay. Of the 23 erythroid-specific DHSs, the enhancer activities of 15 DHSs were comparable to that of the classical enhancer HS2 in driving minimal promoter (minP). Fifteen DHSs, some overlapping those that increased minP activities, acted as enhancers when driving the corresponding KLF promoters (KLF-Ps) in erythroid cells; of these, 10 DHSs were finally characterized as erythroid-specific KLF enhancers. These 10 erythroid-specific KLF enhancers were further confirmed using chromatin immunoprecipitation coupled to sequencing (ChIP-seq) data-based bioinformatic and biochemical analyses.
  
  
  CONCLUSIONS
  Our present findings provide a feasible strategy to extensively identify gene- and cell-specific enhancers from DHSs obtained by high-throughput sequencing, which will help reveal the transcriptional regulation and biological functions of genes in some specific cells.
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P,R, China. jstam@u.washington.edu.
authors.forename: Qian
authors.initials: Q
authors.lastname: Xiong
authors.forename: Zhaojun
authors.initials: Z
authors.lastname: Zhang
authors.forename: Kai-Hsin
authors.initials: KH
authors.lastname: Chang
authors.forename: Hongzhu
authors.initials: H
authors.lastname: Qu
authors.forename: Hai
authors.initials: H
authors.lastname: Wang
authors.forename: Heyuan
authors.initials: H
authors.lastname: Qi
authors.forename: Yajuan
authors.initials: Y
authors.lastname: Li
authors.forename: Xiuyan
authors.initials: X
authors.lastname: Ruan
authors.forename: Yaran
authors.initials: Y
authors.lastname: Yang
authors.forename: Yadong
authors.initials: Y
authors.lastname: Yang
authors.forename: Yanming
authors.initials: Y
authors.lastname: Li
authors.forename: Richard
authors.initials: R
authors.lastname: Sandstrom
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Sabo
authors.forename: Qiliang
authors.initials: Q
authors.lastname: Li
authors.forename: George
authors.initials: G
authors.lastname: Stamatoyannopoulos
authors.forename: John A
authors.initials: JA
authors.lastname: Stamatoyannopoulos
authors.forename: Xiangdong
authors.initials: X
authors.lastname: Fang
mesh_terms: D001665:Binding Sites; D002874:Chromosome Mapping; D003850:Deoxyribonuclease I / Q000737:chemistry; D053595:Embryonic Stem Cells / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D041905:Erythroid Cells / Q000378:metabolism*; D015894:Genome, Human; D057809:HEK293 Cells; D006367:HeLa Cells; D006801:Humans; D020014:K562 Cells; D051741:Kruppel-Like Transcription Factors / Q000235:genetics* / Q000378:metabolism; D009928:Organ Specificity; D011485:Protein Binding; D059467:Transcriptome; D015854:Up-Regulation
chemical_list: D051741:Kruppel-Like Transcription Factors; D003850:Deoxyribonuclease I