Dynamics of the 4D genome during lineage specification, differentiation and maturation in vivo

Abstract

Mammalian gene expression patterns are controlled by regulatory elements, which interact within Topologically Associating Domains (TADs). The relationship between activation of regulatory elements, formation of structural chromatin interactions and gene expression during development is unclear. We developed Tiled-C, a low-input Chromosome Conformation Capture (3C) approach, to study chromatin architecture at high spatial and temporal resolution through in vivo mouse erythroid differentiation. Integrated analysis of matched chromatin accessibility and single-cell expression data shows that regulatory elements gradually become accessible within pre-existing TADs during early differentiation. This is followed by structural re-organization within the TAD and formation of specific contacts between enhancers and promoters. In contrast to previous reports, our high-resolution data show that these enhancer-promoter interactions are not established prior to gene expression, but formed gradually during differentiation, concomitant with progressive upregulation of gene activity. Together, these results provide new insight into the close, interdependent relationship between chromatin architecture and gene regulation during development.

Rewiring of the epigenome and chromatin architecture by retinoic acid signaling during zebrafish embryonic development

“…Promoter loops that change intensity by RA signaling are connected to genes whose transcriptional response to RA goes in the same direction, indicating a consistent connection between enhancer-promoter interactions and target gene expression. This has been previously shown for other differentiation processes in vitro, including neural and erythroid differentiation (37,38). Regarding TF binding, we detect a higher enrichment of RARaa BSs at the anchors of loops induced by RA, suggesting a connection between TF binding and target gene expression by the establishment of chromatin 3D interactions.…”

“…Previous studies indicate that active enhancers are engaged in chromatin 3D interactions with target promoters, being established either before or concomitant with gene activation, depending on the context (34,35). While poised enhancers are already interacting with target promoters in mouse embryonic stem cells (mESCs) (36), enhancer-promoter interactions involving lineage-specific genes are established during neural or erythroid differentiation (37,38). In the case of RA-induced differentiation, changes in interactions between the RA target gene Hoxa1 and three nearby enhancers have been recently reported in mESCs (39).…”

Targeted high-resolution chromosome conformation capture at genome-wide scale

“…Table 1) were sourced from IDT, Sigma or synthesized in house or had been previously reported 8, 21, 34 . We synthesized biotinylated oligonucleotides on a Combimatrix CustomArray B3 DNA synthesiser (B3Synth_v25.1 software) using CustomArray 12K Blank Slides (CustomArray Inc., PN: 2000100-Oligo pool Application) as described 42 . Oligonucleotide pull down for single and double capture of multiplexed 3C libraries was performed using the Nimblegen SeqCap EZ kit as previously described 8 with various masses of oligonucleotides with 10 cycles of DNA amplification.…”