title: Erythroid-induced commitment of K562 cells results in clusters of differentially expressed genes enriched for specific transcription regulatory elements.
abstract: Understanding regulation of fetal and embryonic hemoglobin expression is critical, since their expression decreases clinical severity in sickle cell disease and beta-thalassemia. K562 cells, a human erythroleukemia cell line, can differentiate along erythroid or megakaryocytic lineages and serve as a model for regulation of fetal/embryonic globin expression. We used microarray expression profiling to characterize transcriptomes from K562 cells treated for various times with hemin, an inducer of erythroid commitment. Approximately 5,000 genes were expressed irrespective of treatment. Comparative expression analysis (CEA) identified 899 genes as differentially expressed; analysis by the self-organizing map (SOM) algorithm clustered 425 genes into 8 distinct expression patterns, 322 of which were shared by both analyses. Differential expression of a subset of genes was validated by real-time RT-PCR. Analysis of 5'-flanking regions from differentially expressed genes by PAINT v3.0 software showed enrichment in specific transcription regulatory elements (TREs), some localizing to different expression clusters. This finding suggests coordinate regulation of cluster members by specific TREs. Finally, our findings provide new insights into rate-limiting steps in the appearance of heme-containing hemoglobin tetramers in these cells.
authors.affiliation: The Cardeza Foundation for Hematologic Research and Division of Hematology, Department of Medicine, Jefferson Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.
authors.forename: Sankar
authors.initials: S
authors.lastname: Addya
authors.forename: Margaret A
authors.initials: MA
authors.lastname: Keller
authors.forename: Kathleen
authors.initials: K
authors.lastname: Delgrosso
authors.forename: Christine M
authors.initials: CM
authors.lastname: Ponte
authors.forename: Rajanikanth
authors.initials: R
authors.lastname: Vadigepalli
authors.forename: Gregory E
authors.initials: GE
authors.lastname: Gonye
authors.forename: Saul
authors.initials: S
authors.lastname: Surrey
mesh_terms: D024506:5' Flanking Region / Q000235:genetics; D002454:Cell Differentiation / Q000187:drug effects; D016000:Cluster Analysis; D004912:Erythrocytes / Q000166:cytology* / Q000187:drug effects / Q000378:metabolism*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000187:drug effects / Q000235:genetics*; D006427:Hemin / Q000494:pharmacology; D006801:Humans; D020014:K562 Cells; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000032:analysis / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D015203:Reproducibility of Results; D020218:Response Elements / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013997:Time Factors; D014158:Transcription, Genetic / Q000187:drug effects / Q000235:genetics*
chemical_list: D012333:RNA, Messenger; D006427:Hemin