Identification of a candidate regulatory region in the human CD8 gene complex by colocalization of DNase I hypersensitive sites and matrix attachment regions which bind SATB1 and GATA-3.
To locate elements regulating the human CD8 gene complex, we mapped nuclear matrix attachment regions (MARs) and DNase I hypersensitive (HS) sites over a 100-kb region that included the CD8B gene, the intergenic region, and the CD8A gene. MARs facilitate long-range chromatin remodeling required for enhancer activity and have been found closely linked to several lymphoid enhancers. Within the human CD8 gene complex, we identified six DNase HS clusters, four strong MARs, and several weaker MARs. Three of the strong MARs were closely linked to two tissue-specific DNase HS clusters (III and IV) at the 3' end of the CD8B gene. To further establish the importance of this region, we obtained 19 kb of sequence and screened for potential binding sites for the MAR-binding protein, SATB1, and for GATA-3, both of which are critical for T cell development. By gel shift analysis we identified two strong SATB1 binding sites, located 4.5 kb apart, in strong MARs. We also detected strong GATA-3 binding to an oligonucleotide containing two GATA-3 motifs located at an HS site in cluster IV. This clustering of DNase HS sites and MARs capable of binding SATB1 and GATA-3 at the 3' end of the CD8B gene suggests that this region is an epigenetic regulator of CD8 expression.
Kieffer
Lynda J
LJ
Department of Laboratory Medicine and Department of Genetics and Section of Immunobiology, Yale University, New Haven, CT 06520, USA.
Greally
John M
JM
Landres
Inna
I
Nag
Shanta
S
Nakajima
Yuko
Y
Kohwi-Shigematsu
Terumi
T
Kavathas
Paula B
PB
D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics / Q000276:immunology; D016827:CD8 Antigens / Q000235:genetics* / Q000378:metabolism; D002461:Cell Line, Transformed; D003001:Cloning, Molecular; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D003850:Deoxyribonuclease I / Q000235:genetics* / Q000378:metabolism; D050990:GATA3 Transcription Factor; D006801:Humans; D019169:Jurkat Cells; D036961:Matrix Attachment Region Binding Proteins; D008969:Molecular Sequence Data; D015530:Nuclear Matrix / Q000235:genetics* / Q000378:metabolism; D011485:Protein Binding / Q000235:genetics / Q000276:immunology; D012045:Regulatory Sequences, Nucleic Acid / Q000276:immunology*; D017422:Sequence Analysis, DNA; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic / Q000276:immunology; D014407:Tumor Cells, Cultured
D016827:CD8 Antigens; C431698:CD8alpha antigen; C433839:CD8alphabeta antigen; D004268:DNA-Binding Proteins; D050990:GATA3 Transcription Factor; C494749:GATA3 protein, human; D036961:Matrix Attachment Region Binding Proteins; C076189:SATB1 protein, human; D015534:Trans-Activators; D003850:Deoxyribonuclease I