Integrator restrains paraspeckles assembly by promoting isoform switching of the lncRNA NEAT1

Abstract

<jats:p>RNA 3′ end processing provides a source of transcriptome diversification which affects various (patho)-physiological processes. A prime example is the transcript isoform switch that leads to the read-through expression of the long non-coding RNA <jats:italic>NEAT1_2</jats:italic>, at the expense of the shorter polyadenylated transcript <jats:italic>NEAT1_1</jats:italic>. <jats:italic>NEAT1_2</jats:italic> is required for assembly of paraspeckles (PS), nuclear bodies that protect cancer cells from oncogene-induced replication stress and chemotherapy. Searching for proteins that modulate this event, we identified factors involved in the 3′ end processing of polyadenylated RNA and components of the Integrator complex. Perturbation experiments established that, by promoting the cleavage of <jats:italic>NEAT1_2</jats:italic>, Integrator forces <jats:italic>NEAT1_2</jats:italic> to <jats:italic>NEAT1_1</jats:italic> isoform switching and, thereby, restrains PS assembly. Consistently, low levels of Integrator subunits correlated with poorer prognosis of cancer patients exposed to chemotherapeutics. Our study establishes that Integrator regulates PS biogenesis and a link between Integrator, cancer biology, and chemosensitivity, which may be exploited therapeutically. </jats:p>

Integrator enforces the fidelity of transcriptional termination at protein-coding genes

“…We previously showed that Integrator is involved in the 3′ end processing of multiple classes of noncoding RNAs, including snRNAs, eRNAs, and NEAT1 ( 22 , 23 , 45 ). Moreover, we recently showed that Integrator terminates transcripts associated with paused RNAPII and facilitates transcriptional elongation through the subsequent recruitment of an elongation-competent RNAPII complex ( 28 ).…”

Paraspeckle nuclear condensates: Global sensors of cell stress?

“…[34,37] At the post-transcriptional level, NEAT1 is mainly regulated by altered 3'-end processing to adjust the NEAT1_1:NEAT1_2 ratio. [21,38] Several regions of NEAT1 are important, including near the polyA site of NEAT1_1 where proteins including HNRNPK and TDP43 bind and alter the processing of NEAT1_1 (Figure 2C). [39] When paraspeckles increase a variety of different gene regulatory changes can come into play to aid the cell.…”

Enhancers regulate 3′ end processing activity to control expression of alternative 3′UTR isoforms

“…Finally, the integrator complex has been shown to associate with active enhancers and increases enhancer-promoter communication 77 . Decreased expression of INTS11, the catalytic subunit of the complex, promotes read-through transcription at polyadenylation sites and shifts alternative isoform expression towards the distal isoform 29,78 . This suggests that increased association of integrator at active enhancers could prevent read-through and could increase CPA activity.…”