RNA decay rate as a control point for long non-coding RNA function: a BRIC-based causal analysis of NEAT1

The abundance of a long non-coding RNA (lncRNA) is set by both its synthesis and its decay, yet for nuclear lncRNAs the contribution of decay - and whether decay rate is a determinant of function - has been little explored. I addressed this for NEAT1, the architectural scaffold of paraspeckles. By genome-wide half-life measurement (5'-bromouridine immunoprecipitation chase, BRIC), NEAT1 is a representative short-lived lncRNA at the median of the lncRNA half-life distribution (∼3.3 h), unlike the stable MALAT1. Using inhibitor-free decay measurement and bidirectional perturbation, I show that the core nuclear exosome (EXOSC5, EXOSC2), but not the 5'→3' exonuclease XRN2, the exosome-associated 3'→5' exonuclease EXOSC10, or the deadenylase PARN, sets the NEAT1 decay rate: exosome depletion lengthened the NEAT1 half-life (7.8 → 15.1 h) and raised its abundance; reciprocally, EXOSC5 over-expression shortened the NEAT1 half-life and EXOSC2 over-expression reduced its abundance. The resulting changes in NEAT1 abundance scaled the number and size of paraspeckles without increasing paraspeckle-protein mRNA levels, and changed the expression of candidate PSF/NONO target genes: across three orthogonal NEAT1 manipulations, increased NEAT1 abundance was associated with repression of RAP1A and TCF3 and activation of the NONO-regulated gene GJA1, without changing those mRNAs' own stabilities (under EXOSC5 depletion). These results, which complement the subsequently established exosome-adaptor mechanism of NEAT1 turnover by adding a direct decay-rate measurement and a functional read-out, identify RNA decay rate as a control point - a throttle - on lncRNA function, supported through bidirectional perturbation for NEAT1 in HeLa cells.