WAPL functions as a rheostat of Protocadherin isoform diversity that controls neural wiring

Abstract

Neural type–specific expression of clustered Protocadherin (Pcdh) proteins is essential for the establishment of connectivity patterns during brain development. In mammals, deterministic expression of the same Pcdh isoform promotes minimal overlap of tiled projections of serotonergic neuron axons throughout the brain, while stochastic expression of Pcdh genes allows for convergence of tightly packed, overlapping olfactory sensory neuron axons into targeted structures. How can the same gene locus generate opposite transcriptional programs that orchestrate distinct spatial arrangements of axonal patterns? Here, we reveal that cell type–specific Pcdh expression and axonal behavior depend on the activity of cohesin and its unloader, WAPL (wings apart–like protein homolog). While cohesin erases genomic-distance biases in Pcdh choice, WAPL functions as a rheostat of cohesin processivity that determines Pcdh isoform diversity.

A negatively-charged region within carboxy-terminal domain maintains proper CTCF DNA binding

“…27,[50][51][52][53] This complicated cPcdh expression program is achieved by ATP-dependent active cohesin "loop extrusion" which brings remote super-enhancer in close contacts to target variable promoters via CTCF-mediated anchoring at tandemly-arrayed directional CBS elements. [16][17][18]24,25,28,[54][55][56] . In particular, tandemly-arrayed CTCF sites function as topological chromatin insulators to balance distance-and context-dependent promoter choice to activate cell-specific gene expression in the brain.…”

“…In particular, tandemly-arrayed CTCF sites function as topological chromatin insulators to balance distance- and context-dependent promoter choice to activate cell-specific gene expression in the brain. 17,18,28,54,55 Consequently, the dynamic interactions between CTCF and its recognition sites at variable promoters and super-enhancers are central for establishing cPcdh expression programs during brain development. In this work we systematically investigated the function of CTCF CTD and uncovered a negatively-charged region for maintaining proper CTCF binding to DNA in the large cPCDH gene complex and throughout the entire genome.…”

“…24 In summary, CTCF/cohesin-mediated loop extrusion bridges remote superenhancers in close contact with target variable promoters to form long-distance chromatin loops and this looping is essential for establishing proper expression patterns of the cPCDH genes in the brain. [16][17][18]24,[26][27][28] CTCF contains a central domain of 11 zinc fingers (ZFs) organized in a tandem array flanked by intrinsically disordered regions of the N-terminal domain (NTD) and C-terminal domain (CTD) (Figure 1A). 1,29 The central domain of CTCF binds to DNA directly through ZFs 3-7 and ZFs 9-11.…”

“…24 In summary, CTCF/cohesin-mediated loop extrusion bridges remote super-enhancers in close contact with target variable promoters to form long-distance chromatin loops and this looping is essential for establishing proper expression patterns of the c PCDH genes in the brain. 16–18,24,26–28…”

Mechanism of ZNF143 in chromatin looping and 3D genome organization

“…CTCF/cohesin-mediated directional chromatin contacts between remote super- enhancers and target promoters via continuous active “loop extrusion” determine promoter choice of clustered Pcdh genes 7,16,25 . Developmental regulation of their higher-order chromatin organization in distinct cell-types in the brain enables neurons to achieve proper serotonergic axonal tiling and olfactory sensory neuronal axon convergence, as well as neocortical fine spatial arrangement and connectivity 46,47 . Using the PCDH clusters as model genes, we uncovered that ZNF143 mediates chromatin interactions in both CTCF- dependent and -independent manners.…”