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Letters to the Editor
sequencing (ChIP-Seq). Neither 4C-Seq nor ChIP-Seq revealed an impact of RE deletion on the interaction fre- quency of G2DHE with the EVI1 promoter or on the dep- osition of active chromatin marks, such as H3K27ac and H3K4me3, in any of the two edited cell lines (results for MOLM-1 shown in the Online Supplementary Figure S2A), making it unlikely that the expression changes in EVI1
are caused by changes in the regulatory function of G2DHE.
Since the reduction of EVI1 expression was specific only to the MOLM-1, but not UCSD-AML1 deletion clones, we speculated that this effect might be due to other features present in the sequence deleted in MOLM- 1, rather than the consequence of the breakpoint-RE-
A
B
Figure 1. Chromosomal breakpoints in acute myeloid leukemia inv(3)/t(3;3) (3q-AML) are enriched in retroelements. (A) 3q-capture sequencing revealed a char- acteristic breakpoint pattern (red and black arrowheads) at 3q21.3 (upper tracks) and 3q26.2 (lower tracks). At 3q21.3, a breakpoint-free region downstream (left) of RPN1 was identified as a commonly translocated segment containing G2DHE. At 3q26.2, breakpoints of inversion cases map exclusively downstream (left) or within the last EVI1 intron, whereas translocation cases have breakpoints upstream of EVI1. Color-coded diamonds indicate the position of RE: long inter- spersed elements (LINE), short interspersed elements (SINE) or long terminal repeats (LTR), annotated by RepeatMasker. (B) RNA sequencing of 3q-AML samples revealed a characteristic RNA readthrough signature at 3q21.3. Bisulfite amplicon sequencing on representative 3q-AML samples showed focal hypomethylation of breakpoint regions (red arrowheads) on the rearranged allele but not on the normal allele and non-3q samples.
haematologica | 2021; 106(8)