LDB1-mediated enhancer looping can be established independent of mediator and cohesin

Abstract

Mechanistic studies in erythroid cells indicate that LDB1, as part of a GATA1/TAL1/LMO2 complex, brings erythroid-expressed genes into proximity with enhancers for transcription activation. The role of co-activators in establishing this long-range interaction is poorly understood. Here we tested the contributions of the RNA Pol II pre-initiation complex (PIC), mediator and cohesin to establishment of locus control region (LCR)/β-globin proximity. CRISPR/Cas9 editing of the β-globin promoter to eliminate the RNA Pol II PIC by deleting the TATA-box resulted in loss of transcription, but enhancer–promoter interaction was unaffected. Additional deletion of the promoter GATA1 site eliminated LDB1 complex and mediator occupancy and resulted in loss of LCR/β-globin proximity. To separate the roles of LDB1 and mediator in LCR looping, we expressed a looping-competent but transcription-activation deficient form of LDB1 in LDB1 knock down cells: LCR/β-globin proximity was restored without mediator core occupancy. Further, Cas9-directed tethering of mutant LDB1 to the β-globin promoter forced LCR loop formation in the absence of mediator or cohesin occupancy. Moreover, ENCODE data and our chromatin immunoprecipitation results indicate that cohesin is almost completely absent from validated and predicted LDB1-regulated erythroid enhancer-gene pairs. Thus, lineage specific factors largely mediate enhancer–promoter looping in erythroid cells independent of mediator and cohesin.

Chromatin interactions and expression quantitative trait loci reveal genetic drivers of multimorbidities

“…Collectively, these results suggest that the frequency of spatial eQTL-eGene contact in cell lines are relatively uniform across tissues but the eQTL effects in the cell lines are tissue specific. This is consistent with previous results that show that transcription is not necessary for the formation and maintenance of a spatial connection 39,40…”

Cohesin-dependent and independent mechanisms support chromosomal contacts between promoters and enhancers

“…The Mediator complex has long been proposed to physically link enhancers and promoters (Malik and Roeder, 2010), but deletion of its core subunit MED14 did not induce major changes in promoter-enhancer interactions (El Khattabi et al, 2019). Other potential candidates include the LDB1 complex that has been shown to facilitate promoter-enhancer interactions in some systems (Deng et al, 2012;Krivega and Dean, 2017;Song et al, 2007), as well as eRNAs that may be involved in chromatin loop stabilisation (Matharu and Ahituv, 2015).…”

Predicting Enhancer-Promoter Interaction from Genomic Sequence with Deep Neural Networks

“…SPEID also ranks ZIC4, E2F3 and FOXK1 motifs as having top 5%, top 10%, and top 5% feature importance, respectively, in enhancer regions. ZIC4 and E2F3 are factors known to interact with enhancers [32], and their motifs are both found to be enriched in cohesin-occupied enhancers together with the CTCF motif [33]. FOXK1 has been shown to localize in both enhancers and promoters [34].…”