The mammalian genome is transcribed into large numbers of long noncoding RNAs (lncRNAs), but definition of functional lncRNA groups has proven difficult. Here we consider positional conservation as an indicator of functional relatedness across species. We identify 665 positionally conserved lncRNA (pcRNAs) promoters in the mouse and human genomes that are preserved in genomic position relative to orthologous protein coding genes. We find that pcRNAs are genomically associated with developmental transcription factors, with which they are co-expressed in a tissue specific manner. Interestingly, the majority of pcRNAs are linked to chromatin organisation structures, overlapping binding sites for CTCF and residing at the anchor points of chromatin loops. We named this group of RNAs topological anchor point (tap)RNAs and we show that they possess short stretches of highly conserved sequence that are enriched in binding motifs for Zinc Finger proteins. Knock down experiments revealed that tapRNAs and their neighbouring protein-coding genes are functionally connected, regulating each other’s expression and similarly influencing the metastatic phenotype of cancer cells in vitro.  This work identifies tapRNAs as a sub-group of lncRNAs with potential importance in genome organization, development and disease.