Chromatin interaction maps identify Wnt responsive cis-regulatory elements coordinating Paupar-Pax6 expression in neuronal cells

Abstract

Central nervous system-expressed long non-coding RNAs (lncRNAs) are often located in the genome close to protein coding genes involved in transcriptional control. Such lncRNA-protein coding gene pairs are frequently temporally and spatially co-expressed in the nervous system and are predicted to act together to regulate neuronal development and function. Although some of these lncRNAs also bind and modulate the activity of the encoded transcription factors, the regulatory mechanisms controlling co-expression of neighbouring lncRNA-protein coding genes remain unclear. Here, we used high resolution NG Capture-C to map the cis-regulatory interaction landscape of the key neuro-developmental Paupar-Pax6 lncRNA-mRNA locus. The results define chromatin architecture changes associated with high Paupar-Pax6 expression in neurons and identify both promoter selective as well as shared cis-regulatory-promoter interactions involved in regulating Paupar-Pax6 co-expression. We discovered that the TCF7L2 transcription factor, a regulator of chromatin architecture and major effector of the Wnt signalling pathway, binds to a subset of these candidate cis-regulatory elements to coordinate Paupar and Pax6 co-expression. We describe distinct roles for Paupar in Pax6 expression control and show that the Paupar DNA locus contains a TCF7L2 bound transcriptional silencer whilst the Paupar transcript can act as an activator of Pax6. Our work provides important insights into the chromatin interactions, signalling pathways and transcription factors controlling co-expression of adjacent lncRNAs and protein coding genes in the brain.

Ganglioglioma deep transcriptomics reveals primitive neuroectoderm neural precursor-like population

“…Top candidate transcription factors for both cluster 6 and neoplastic CD34 + cells included paired box 6 (PAX6) and its transcriptional activators myeloid ectopic viral integration site homeobox 1 (MEIS1) and transcription factor 7 like 2 (TCF7L2; Additional file 1 : Fig. S5A–D) [ 55 , 59 ]. In the healthy adult brain, these transcription factors are not normally coexpressed [ 35 , 65 ].…”

“…More interestingly, PAX6 is a neuroectodermal neural precursor cell marker, and the MEIS1-PAX6 cascade appears critical to early neuroectodermal cell fate determination [ 24 , 55 , 91 ]. In addition, TCF7L2 coordinates PAX6 activation in neural cells and modulates MYC as part of the WNT pathway [ 59 ]. PAX6 , MEIS1 , and TCF7L2 concentrations as well as SCENIC-calculated regulon scores correlated strongly with ganglioglioma neoplastic cell stemness by CellRank/CytoTRACE pseudotime or SCENT signaling entropy rate (Fig.…”

Ganglioglioma deep transcriptomics reveals primitive neuroectoderm neural precursor-like population

“…To do so, gene regulatory networks were reconstructed in an unbiased manner using SCENIC 66 . Top candidate transcription factors for both cluster 6 and CD34 -expressing neoplastic cells included paired box 6 (PAX6) and its transcriptional activators myeloid ectopic viral integration site homeobox 1 (MEIS1) and transcription factor 7 like 2 (TCF7L2; sFigure 5A-D ) 67,68 . In the healthy adult brain, these transcription factors are not normally coexpressed 29,30 .…”

“…More interestingly, PAX6 is a neuroectodermal neural precursor cell marker, and the MEIS1-PAX6 cascade appears critical to early neuroectodermal cell fate determination[25, 53, 88]. In addition, TCF7L2 coordinates PAX6 activation in neural cells and modulates MYC as part of the WNT pathway[57]. PAX6 , MEIS1 , and TCF7L2 concentrations as well as SCENIC-calculated regulon scores correlated strongly with ganglioglioma neoplastic cell stemness by CellRank/CytoTRACE pseudotime or SCENT signaling entropy rate ( Figure 5A and sFigure 5E-F ).…”

Endogenous neural stem cells characterization using omics approaches: Current knowledge in health and disease

“…LncRNAs have been also assessed by applying a novel technique for chromatin conformation capture, named NG Capture-C, which allows to simultaneously reconstruct gene networks in multiple cell types, and to reveal how chromatin conformations shape gene activity (Davies et al, 2016(Davies et al, , 2017. This technique has been specifically applied to the lncRNAs that are co-expressed with their near protein-coding genes, specifically the Paupar lncRNA-Pax6 gene pair (Pavlaki et al, 2022). Data revealed complex cis-regulatory interactions in both Paupar and Pax6 promoter regions related to their paired co-expression in the brain.…”