c-Myb Binding Sites in Haematopoietic Chromatin Landscapes

Abstract

Strict control of tissue-specific gene expression plays a pivotal role during lineage commitment. The transcription factor c-Myb has an essential role in adult haematopoiesis and functions as an oncogene when rearranged in human cancers. Here we have exploited digital genomic footprinting analysis to obtain a global picture of c-Myb occupancy in the genome of six different haematopoietic cell-types. We have biologically validated several c-Myb footprints using c-Myb knockdown data, reporter assays and DamID analysis. We show that our predicted conserved c-Myb footprints are highly dependent on the haematopoietic cell type, but that there is a group of gene targets common to all cell-types analysed. Furthermore, we find that c-Myb footprints co-localise with active histone mark H3K4me3 and are significantly enriched at exons. We analysed co-localisation of c-Myb footprints with 104 chromatin regulatory factors in K562 cells, and identified nine proteins that are enriched together with c-Myb footprints on genes positively regulated by c-Myb and one protein enriched on negatively regulated genes. Our data suggest that c-Myb is a transcription factor with multifaceted target regulation depending on cell type.

MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism

“…Results from the MYB ChIP-seq were validated in three ways. First, we performed MYB ChIP-seq in K562 cells and confirmed enrichment at genes reported to be target genes in a prior study of these cells ( Supplementary Figure 9 ) 29 . Second, we used Homer 30 to perform an unbiased motif analysis across peaks identified (peak detection threshold 10 −7 ) in mNSC over-expressing MYBQKI, and identified MYB motifs to be the most enriched motifs across all peaks (p= 1 −681 ) ( Supplementary Figure 10a ).…”

Transcription factor motif quality assessment requires systematic comparative analysis

“…However, the scores from the two sets of negative sequences used are not significantly different (p=0.484, Wilcoxon rank-sum test). For Myb, the low correlation could be attributed to how it binds, indirectly 59 .…”

Dual Mechanism of Rag Gene Repression by c-Myb during Pre-B Cell Proliferation

“…Unfortunately, were unable to extend our c-Myb ChIP experiments to endogenous c-Myb in either Abelson pre-B cells or primary B-lineage progenitors. Difficulty with endogenous c-Myb ChIP in murine cells has been noted in the literature (29) but was performed by others (30). Thus, optimizing c-Myb ChIP conditions in these contexts will be an important step toward support of a model where c-Myb antagonizes Foxo1 Erag binding during pre-B cell development in vivo.…”