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

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. Here, we present Tiled-C, a low-input chromosome conformation capture (3C) technique. We use this approach to study chromatin architecture at high spatial and temporal resolution through in vivo mouse erythroid differentiation. Integrated analysis of 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 reorganization within the TAD and formation of specific contacts between enhancers and promoters. 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.

A functional overlap between actively transcribed genes and chromatin boundary elements

“…The borders of the TAD are created when cohesin is stalled and stabilised by its interaction with the N-terminal region of CTCF. Our previous studies of the mouse α-globin sub-TAD using chromosome conformation capture (26,(39)(40)(41)(42)(43)(44) and super-resolution imaging (39) are entirely consistent with this model involving the interplay between enhancers, promoters, and boundary elements. Here, we have identified the precise elements responsible for forming the boundaries of the sub-TAD and contributing to the differential interactions between the enhancers and the promoters.…”

“…The duplicated mouse α-like globin genes (Hba-α1 and Hba-α2) and their five enhancers (R1, R2, R3, Rm, and R4) form a very well-characterised, small ~70 kb tissue-specific sub-TAD in erythroid cells, arranged 5'-R1-R2-R3-Rm-R4-Hba-α1-Hba-α2-3'. In the past, this locus has been extensively used to establish the principles underpinning mammalian gene regulation and relating genome structure to function (26,(39)(40)(41)(42)(43)(44). The α-globin sub-TAD is flanked by several, largely convergent CTCF binding sites (26).…”

Independence of 3D chromatin conformation and gene regulation during Drosophila dorsoventral patterning

“…Previous studies have produced conflicting results about whether tissue-specific enhancer-promoter interactions are correlated with tissue-specific activation of gene expression. Studies using 3C approaches have found evidence of enriched enhancer-promoter interactions Jin et al, 2013;Krietenstein et al, 2020;Li et al, 2012;Sanyal et al, 2012), which may precede (Cruz-Molina et al, 2017;Ghavi-Helm et al, 2014) or correlate with (Bonev et al, 2017;Oudelaar et al, 2020) transcriptional activation. However, several recent studies in mammals as well as Drosophila provide evidence that stable enhancer-promoter contacts are not required for gene activation (Alexander et al, 2019;Benabdallah et al, 2019;Chen et al, 2018;Heist et al, 2019;Mir et al, 2018).…”

“…multiple studies have shown differences in chromatin conformation between different cell types or tissues (Bonev et al, 2017;Chathoth and Zabet, 2019;Joshi et al, 2015;Kragesteen et al, 2018;Le Dily et al, 2014;Oudelaar et al, 2020;Schmitt et al, 2016), whether these changes are the cause or consequence of changes in gene expression is unclear. Therefore, a fundamental question arises as to whether changes in gene expression and chromatin state drive chromatin reorganisation, or whether changes in chromatin organisation facilitate cell typespecific activation of genes and their regulatory elements.…”

Suv39h-catalysed H3K9me3 is critical for euchromatic genome organisation and the maintenance of gene transcription

“…The temporal or causal relationship between chromatin interactivity and gene transcription has been challenging to untangle due to the complex interdependency between the two processes. Some groups propose that genome reorganisation often precedes gene expression changes (Stadhouders et al, 2018), whereas others propose that these interactions form concomitant with gene expression (Oudelaar et al, 2020). Here, we propose that the structural alterations in chromatin organisation caused by a loss of LADs in the Suv39DKO are the driving force for the transcriptional change, and are not a consequence of transcriptional alterations.…”