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The statistical definition of an integration cluster was a critical aspect of this study.
Because miR-155 is localized to a fragile locus (termed the B cell integration cluster BIC) that is an integration site of viral-induced lymphomas, it is possible that expression of miR-155 is regulated differently from other miRNAs.
Interestingly, our microarray screen identified miR-155, the functional product of an exon within the non-protein coding gene bic (B-cell integration cluster) [29], as the only miRNA induced in Jurkat cells.
MiR-155 and its host gene, B-cell integration cluster (BIC), are highly expressed due to MYB regulates BIC in chronic lymphocytic leukemia [ 51].
Among these various miRNAs, miR-155 which initially generated from an exon of a noncoding RNA transcribed from B cell integration cluster located on chromosome 21 is highlighted and widely studied.
Interestingly, miR-155 is of particular interest because of the FOXP3 mediated regulation of the intronic region of B cell integration cluster (Bic), which encodes the gene for miR-155 [ 18]. miR-155 deficient mice showed reduced number of thymus-derived and peripherally induced Treg cells [ 19]; in contrast, Treg suppressive function was unaffected both in vitro and in vivo in these mice [ 20].
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Integration clusters were statistically defined as described in the legend of Figure S1.
A functional classification of the genes annotated within the integration clusters was carried out by the Ingenuity® software.
Conversely, regions heavily targeted by integration clusters in the genome of CD34+ HPCs, such as the LMO2 locus, contained no integration in the T-cell genome (Figure 4A).
Functional annotation of genes targeted by integration clusters were performed by the Ingenuity Pathways Analysis (IPA) tool (Ingenuity Systems, www.ingenuity.com).com
Gene expression profiling and bioinformatics were used to associate integration clusters to transcriptional activity and to genetic and epigenetic features of the T-cell genome.
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