BACKGROUND: Transcriptional hotspots are defined as genomic regions bound by multiple factors. They have been identified recently as cell type specific enhancers regulating developmentally essential genes in many species such as worm, @entity238 and @entity1 . The in-depth analysis of hotspots across multiple cell types in same species still remains to be explored and can bring new biological insights. RESULTS: We therefore collected 108 transcription-related factor (TF) ChIP sequencing data sets in ten @entity19 cell types and classified the peaks in each cell type in three groups according to binding occupancy as singletons (low-occupancy), combinatorials (mid-occupancy) and hotspots (high-occupancy). The peaks in the three groups clustered largely according to the occupancy, suggesting priming of genomic loci for mid occupancy irrespective of cell type. We then characterized hotspots for diverse structural functional properties. The genes neighbouring hotspots had a small overlap with hotspot genes in other cell types and were highly enriched for cell type specific function. Hotspots were enriched for sequence motifs of key TFs in that cell type and more than 90% of hotspots were occupied by pioneering factors. Though we did not find any sequence signature in the three groups, the H3K4me1 binding profile had bimodal peaks at hotspots, distinguishing hotspots from mono-modal H3K4 @entity19 singletons. In @entity2828 cells, differentially expressed genes after perturbation of activators were enriched for hotspot genes suggesting hotspots primarily act as transcriptional activator hubs. Finally, we proposed that @entity2828 hotspots might be under control of @entity32772 and not DNMT for silencing. CONCLUSION: Transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes. In @entity2828 cells, they are predicted to act as transcriptional activator hubs and might be under @entity32772 control for silencing.

XXXX transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs.

@entity1 :: ('9606', 'Species') :: ['humans'] @entity2828 :: ('MESH:D012512', 'Disease') :: ['ES'] @entity19 :: ('10090', 'Species') :: ['me1', 'murine'] @entity238 :: ('7227', 'Species') :: ['fly'] @entity32772 :: ('9869', 'Gene') :: ['SetDB1']
@entity1 :: (9606,Species) :: ['Mammalian']
