## 2 Results
### Inc-_Nr6a1_ Protein Interactome
A total of 619 LADs were mapped in the control cells, 148 of them were partially lost in _Lnc-Nr6a1_-depleted cells, and 45 new LADS appeared in the _Lnc-Nr6a1_-depleted cells (Figure S10A). Genes associated with these LADs were identified (Table S6) and gene ontology analysis of genes associated to partially lost LADs showed enrichment in genes involved in small sensory perception and chemotaxis (Figure S10B). Moreover, comparison between LADs-associated genes and expression changes detected in _Lnc-Nr6a1_-depleted cells showed a match in only five genes (\(p\)-value = 0.17) (Figure S10C), inferring that the absence of interaction of Inc-_Nr6a1-1_ with lamin A/C is not the direct cause of the gene expression changes in depleted cells. Figure 7: _Cont._  
Our finding that glycolytic proteins ALDOA, ENO1, PKM, GAPDH, along with LDHA, interact with Inc-_Nr6a1-1_ is outstanding. Covalent bonds between Inc-_Nr6a1-1_ and interacting proteins are direct because they were created by UV crosslinking. This result strongly suggested that Inc-_Nr6a1-1_ could act as a scaffold molecule to gather glycolytic proteins to promote glycolysis by substrate channeling. To test this hypothesis, we measured the glycolysis metabolic process in the control and _Luc-Nr6a1-_depleted cells using the Seahorse Analyzer, which provides accurate measurements of glycolytic rates for basal conditions and compensatory glycolysis following mitochondrial inhibition. We found that the knockout of _Luc-Nr6a1_ significantly reduced basal glycolysis and compensatory glycolysis and that these effects were all reverted by overexpression of the Inc-_Nr6a1-1_ isoform (Figure 8A,B). Next, we analyzed whether the interaction of Inc-_Nr6a1-1_ with each of the proteins occurred independently or whether the Inc-_Nr6a1-1_ isoform forms a glycolytic complex with these enzymes. To this end, coimmunoprecipitation experiments were carried out on UV-crosslinked extracts from control cells and _Luc-Nr6a1-_depleted cells using an antibody against ENO-1 and the immunoprecipitated proteins were subjected to quantitative mass spectrometry. The analysis results showed the enrichment of glycolytic enzymes ALDOA, PKM, and GAPDH, along with LDHA previously detected by theiDRIP technique, in addition to the enrichment of the glycolytic enzymes TP1, PGAM1 and PGK1 (Table S7). Furthermore, quantification of immunoprecipitated proteins revealed a markedly lower amount of immunoprecipitated glycolytic enzymes in _Luc-Nr6a1-_depleted cells (Figure 8C). These data indicate that Inc-_Nr6a1-1_ may function as a molecular scaffold for glycolytic multi-enzymatic complex formation (Figure 8D) and this promotes enhanced catalytic efficiency. Figure 7: iDRIP-MS reveals direct Inc-_Nr6a1-1_-interacting proteins. (**A**) A schematic overview of the iDRIP-MS method. (**B**) Retrieval of RNA by iDRIP using Inc-_Nr6a1-1_ and _LacZ_ probes measured by RT-qPCR. Efficiency of Inc-_Nr6a1-1_ pulldown was determined by comparing to a standard curve generated using serial dilutions of input. Error bars S.D. (**C**) Selected Inc-_Nr6a1-1_-interacting proteins identified by iDRIP are grouped into functional classes. (**D**) Physical association of Inc-_Nr6a1-1_ with Lamin A/C, g-catenin (Plakoglobin), ENO1, ALDOA and GAPDH was confirmed by RNA immunoprecipitation (RIP). ENO1, enolase; ALDOA, aldolase; GAPDH, glyceraldehyde 3-phophatedeshydrogenase. The results are the median of three technical replicates; error bars represent S.D. (**E**) Subcellular localization of Inc-_Nr6a1_ isoforms. Expression of _Hprt_, Inc-_Nr6a1-1_, Inc-_Nr6a1-2_, _U3_ and _Xist_ in cytoplasmic, nuclear soluble and nuclear insoluble fractions of NMuMG cells. The graph is an average of three technical replicates; error bars represent S.D.