A distinct epigenetic signature at targets of a leukemia protein.
BACKGROUND
Human myelogenous leukemia characterized by either the non random t(8; 21)(q22; q22) or t(16; 21)(q24; q22) chromosome translocations differ for both their biological and clinical features. Some of these features could be consequent to differential epigenetic transcriptional deregulation at AML1 targets imposed by AML1-MTG8 and AML1-MTG16, the fusion proteins deriving from the two translocations. Preliminary findings showing that these fusion proteins lead to transcriptional downregulation of AML1 targets, marked by repressive chromatin changes, would support this hypothesis. Here we show that combining conventional global gene expression arrays with the power of bioinformatic genomic survey of AML1-consensus sequences is an effective strategy to identify AML1 targets whose transcription is epigenetically downregulated by the leukemia-associated AML1-MTG16 protein.


RESULTS
We interrogated mouse gene expression microarrays with probes generated either from 32D cells infected with a retroviral vector carrying AML1-MTG16 and unable of granulocyte differentiation and proliferation in response to the granulocyte colony stimulating factor (G-CSF), or from 32D cells infected with the cognate empty vector. From the analysis of differential gene expression alone (using as criteria a p value < 0.01 and an absolute fold change > 3), we were unable to conclude which of the 37 genes downregulated by AML1-MTG16 were, or not, direct AML1 targets. However, when we applied a bioinformatic approach to search for AML1-consensus sequences in the 10 Kb around the gene transcription start sites, we closed on 17 potential direct AML1 targets. By focusing on the most significantly downregulated genes, we found that both the AML1-consensus and the transcription start site chromatin regions were significantly marked by aberrant repressive histone tail changes. Further, the promoter of one of these genes, containing a CpG island, was aberrantly methylated.


CONCLUSIONS
This study shows that a leukemia-associated fusion protein can impose a distinct epigenetic repressive signature at specific sites in the genome. These findings strengthen the conclusion that leukemia-specific oncoproteins can induce non-random epigenetic changes.
Rossetti
Stefano
S
Department of Cancer Genetics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA. stefano.rossetti@roswellpark.org <stefano.rossetti@roswellpark.org>
Hoogeveen
André T
AT
Liang
Ping
P
Stanciu
Cornel
C
van der Spek
Peter
P
Sacchi
Nicoletta
N
D000818:Animals; D002478:Cells, Cultured / Q000187:drug effects / Q000378:metabolism; D002843:Chromatin / Q000235:genetics; D002885:Chromosomes, Human, Pair 16 / Q000235:genetics / Q000648:ultrastructure; D002891:Chromosomes, Human, Pair 21 / Q000235:genetics / Q000648:ultrastructure; D016384:Consensus Sequence; D050676:Core Binding Factor Alpha 2 Subunit / Q000235:genetics / Q000502:physiology*; D018899:CpG Islands; D015536:Down-Regulation / Q000235:genetics; D044127:Epigenesis, Genetic / Q000235:genetics*; D020869:Gene Expression Profiling; D015973:Gene Expression Regulation, Leukemic / Q000235:genetics*; D020868:Gene Silencing; D016179:Granulocyte Colony-Stimulating Factor / Q000494:pharmacology; D006657:Histones / Q000378:metabolism; D006801:Humans; D007377:Interleukin-3 / Q000494:pharmacology; D007951:Leukemia, Myeloid / Q000235:genetics* / Q000378:metabolism; D051379:Mice; D022423:Myeloid Cells / Q000187:drug effects / Q000378:metabolism; D009363:Neoplasm Proteins / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D015514:Oncogene Proteins, Fusion / Q000235:genetics / Q000502:physiology; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D011993:Recombinant Fusion Proteins / Q000502:physiology; D012097:Repressor Proteins / Q000235:genetics / Q000502:physiology*; D024363:Transcription Initiation Site; D014162:Transfection; D014178:Translocation, Genetic
C112643:AML1-MTG16 protein, human; D002843:Chromatin; D050676:Core Binding Factor Alpha 2 Subunit; D006657:Histones; D007377:Interleukin-3; D009363:Neoplasm Proteins; D015514:Oncogene Proteins, Fusion; C493728:RUNX1 protein, human; D011993:Recombinant Fusion Proteins; D012097:Repressor Proteins; D016179:Granulocyte Colony-Stimulating Factor