Open Access Research article

Comprehensive characterization of erythroid-specific enhancers in the genomic regions of human Krüppel-like factors

Qian Xiong12, Zhaojun Zhang1, Kai-Hsin Chang3, Hongzhu Qu14, Hai Wang123, Heyuan Qi12, Yajuan Li1, Xiuyan Ruan1, Yaran Yang1, Yadong Yang1, Yanming Li12, Richard Sandstrom4, Peter J Sabo4, Qiliang Li5, George Stamatoyannopoulos5, John A Stamatoyannopoulos4* and Xiangdong Fang15*

Author Affiliations

1 CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P.R. China

2 University of Chinese Academy of Sciences, Beijing 100049, P.R. China

3 Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA

4 Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA

5 Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA

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BMC Genomics 2013, 14:587  doi:10.1186/1471-2164-14-587

Published: 28 August 2013



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.


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.


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.

DHS profiling; High-throughput sequencing; Erythroid; Enhancer; Krüppel-like factors