Abstract
BackgroundHuman RUNX1 gene is one of the most frequent target for chromosomal translocations associated with acute myeloid leukemia (AML) and acute lymphoid leukemia (ALL). The highest prevalence in AML is noted with (8; 21) translocation; which represents 12 to 15% of all AML cases. Interestingly, all the breakpoints mapped to date in t(8;21) are clustered in intron 5 of the RUNX1 gene and intron 1 of the ETO gene. No homologous sequences have been found at the recombination regions; but DNase I hypersensitive sites (DHS) have been mapped to the areas of the genes involved in t(8;21). Presence of DHS sites is commonly associated with regulatory elements such as promoters, enhancers and silencers, among others.ResultsIn this study we used a combination of comparative genomics, cloning and transfection assays to evaluate potential regulatory elements located in intron 5 of the RUNX1 gene. Our genomic analysis identified nine conserved non-coding sequences that are evolutionarily conserved among rat, mouse and human. We cloned two of these regions in pGL-3 Promoter plasmid in order to analyze their transcriptional regulatory activity. Our results demonstrate that the identified regions can indeed regulate transcription of a reporter gene in a distance and position independent manner; moreover, their transcriptional effect is cell type specific.ConclusionsWe have identified nine conserved non coding sequence that are harbored in intron 5 of the RUNX1 gene. We have also demonstrated that two of these regions can regulate transcriptional activity in vitro. Taken together our results suggest that intron 5 of the RUNX1 gene contains multiple potential cis-regulatory elements.
Highlights
Human RUNX1 gene is one of the most frequent target for chromosomal translocations associated with acute myeloid leukemia (AML) and acute lymphoid leukemia (ALL)
The transcription factor RUNX1/AML1 is an important regulator of hematopoiesis and RUNX1 gene is one of the most frequent target of chromosomal translocations in cells of the myeloid lineage [1]
Identification of Conserved Non Coding Sequences (CNS) in intron 5 of the RUNX1 gene All the breakpoints mapped for the (8;21) and (3;21) translocations are restricted to intron 5 of the RUNX1 gene (Figure 1)
Summary
Human RUNX1 gene is one of the most frequent target for chromosomal translocations associated with acute myeloid leukemia (AML) and acute lymphoid leukemia (ALL). No homologous sequences have been found at the recombination regions; but DNase I hypersensitive sites (DHS) have been mapped to the areas of the genes involved in t(8;21). The transcription factor RUNX1/AML1 is an important regulator of hematopoiesis and RUNX1 gene is one of the most frequent target of chromosomal translocations in cells of the myeloid lineage [1]. Genomic comparison of diverse set of vertebrate species revealed many genomic intervals that have remained conserved throughout the vertebrate lineage [10]. Some of these sequences correspond to coding genes and non-coding RNAs, two third of them are unlikely to produce a functional transcript. Comparative genomics based strategies are being employed to predict genomic regions involved in transcriptional regulation, even in the absence of knowledge about the specific characteristics of individual cis-regulatory element [13]
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