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

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. Author summaryLong non-coding RNA (lncRNA) genes are often co-expressed in the brain with neighbouring protein coding genes involved in gene expression control. Such lncRNA-protein coding gene pairs are predicted to work together to regulate neuronal development and function. Despite this, the regulatory mechanisms controlling their co-expression is poorly understood. Here, we identify the chromatin interactions and DNA sequences controlling expression of the Paupar-Pax6 lncRNA-protein coding locus in the brain. We show that the Wnt signalling pathway, a key regulator of development and disease, acts through the TCF7L2 transcription factor to co-ordinate their expression. We find that Paupar DNA contains sequences that silence Pax6 whilst the Paupar RNA can act as an activator of Pax6. Our work generates new insights into the complex regulatory relationship controlling the function of neighbouring lncRNA-protein coding genes and is important for understanding development of the brain.