Distinct global binding patterns of the Wilms tumor gene 1 (WT1) -KTS and +KTS isoforms in leukemic cells.
The zinc finger transcription factor Wilms tumor gene 1 (WT1) acts as an oncogene in acute myeloid leukemia. A naturally occurring alternative splice event between zinc fingers three and four, removing or retaining three amino acids (±KTS), is believed to change the DNA binding affinity of WT1, although there are conflicting data regarding the binding affinity and motifs of the different isoforms. Increased expression of the WT1 -KTS isoform at the expense of the WT1 +KTS isoform is associated with poor prognosis in acute myeloid leukemia. We determined the genome-wide binding pattern of WT1 -KTS and WT1 +KTS in leukemic K562 cells by chromatin immunoprecipitation and deep sequencing. We discovered that the WT1 -KTS isoform predominantly binds close to transcription start sites and to enhancers, in a similar fashion to other transcription factors, whereas WT1 +KTS binding is enriched within gene bodies. We observed a significant overlap between WT1 -KTS and WT1 +KTS target genes, despite the binding sites being distinct. Motif discovery revealed distinct binding motifs for the isoforms, some of which have been previously reported as WT1 binding sites. Additional analyses showed that both WT1 -KTS and WT1 +KTS target genes are more likely to be transcribed than non-targets, and are involved in cell proliferation, cell death, and development. Our study provides evidence that WT1 -KTS and WT1 +KTS share target genes yet still bind distinct locations, indicating isoform-specific regulation in transcription of genes related to cell proliferation and differentiation, consistent with the involvement of WT1 in acute myeloid leukemia.
Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Huddinge, Sweden.
Tove
T
Ullmark
Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Huddinge, Sweden.
Linnea
L
Järvstråt
Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Huddinge, Sweden.
Carl
C
Sandén
Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Huddinge, Sweden.
Giorgia
G
Montano
Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Huddinge, Sweden.
Helena
H
Jernmark-Nilsson
Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Huddinge, Sweden.
Henrik
H
Lilljebjörn
Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
Andreas
A
Lennartsson
Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Huddinge, Sweden.
Thoas
T
Fioretos
Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Huddinge, Sweden.
Kristina
K
Drott
Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Huddinge, Sweden.
Karina
K
Vidovic
Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Huddinge, Sweden.
Björn
B
Nilsson
Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Huddinge, Sweden urban.gullberg@med.lu.se.
Urban
U
Gullberg
D017398:Alternative Splicing; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D015973:Gene Expression Regulation, Leukemic; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007938:Leukemia / Q000235:genetics* / Q000378:metabolism*; D059372:Nucleotide Motifs; D011485:Protein Binding; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D024363:Transcription Initiation Site; D025721:WT1 Proteins / Q000235:genetics* / Q000378:metabolism*
D014157:Transcription Factors; D025721:WT1 Proteins