Pasieka, R. | bioRxiv Science

bioRxiv2026

Waking the sleepers: lincRNA overexpression compromises DHX36 activity and global protein synthesis

Transposable element-derived long intergenic noncoding RNAs (lincRNAs) are increasingly recognized as context-dependent regulators of gene expression; however, the functional consequences of their ectopic activation in somatic cells remain poorly understood. We previously showed that U7 snRNA represses a subset of LTR12-associated lincRNAs, including lnc-ARRDC4-1 and lnc-ADCYAP1-2, two testis-enriched lincRNAs with minimal expression in somatic cells. Here, we examined the consequences of their increased expression in somatic cells. We showed that overexpression of either lincRNA led to common transcriptomic changes, proteomic changes, impaired migration, altered adhesion and proliferation, and a ~50% reduction in protein synthesis. Furthermore, we identified lnc-ARRDC4-1 as an upstream regulator of lnc-ADCYAP1-2 transcription. Downstream of this event, lnc-ADCYAP1-2 interacts with the RNA helicase DHX36, a regulator of G-quadruplex-containing mRNAs. lnc-ADCYAP1-2 activation reduces DHX36 protein levels, which is accompanied by decreased protein output from a subset of DHX36 mRNA targets. At the cellular level, these effects correlate with cellular disfunction and altered global translation. Our results suggest a lnc-ARRDC4-1:lnc-ADCYAP1-2:DHX36 regulatory cascade linking the derepression of LTR12-containing lincRNAs to reduced protein synthesis and altered cellular processes in somatic cells.

Molecular Biology↗

bioRxiv2023

Novel function of U7 snRNA in the repression of HERV1/LTR12s and lincRNAs in human cells

U7 snRNA is part of U7 snRNP, a complex required for the 3end processing of replication-dependent histone pre-mRNAs in the S phase of the cell cycle. During this maturation event, the 5 region of U7 snRNA hybridizes with the highly complementary sequence present in the 3UTR of histone pre-mRNAs, called histone downstream element, HDE. This base-pair interaction triggers subsequent reactions that eventually result in cleavage and release of mature histone transcripts. Intriguingly, U7 snRNP is constitutively expressed throughout the cell cycle and in nondividing cells, suggesting another function of U7 snRNA/snRNP in cells. Here, we show that several human endogenous retroviruses (HERVs) are significantly upregulated in HEK293T cells with U7 snRNA knockdown. They predominantly belong to the LTR12 class. Interestingly, some of them are located within long intergenic noncoding RNAs (lincRNAs), which in turn are upregulated in U7 snRNA knockdown cells as well. Significantly, both these HERV1/LTR12s and lincRNAs contain two or more sequence motifs that perfectly match the 5 end of U7 snRNA, which we called HDE-like motifs. We confirmed that mutations within the HDE-like motifs abrogate U7 snRNA regulatory function and stimulate the expression of selected lincRNAs. Furthermore, we demonstrate that U7 snRNA inhibits HERV1/LTR12 and lincRNA expression at the transcription level. We propose a mechanism in which U7 snRNA hampers binding/activity of NF-Y transcription factor to CCAAT motifs that are frequently found in LTRs as well as in a close proximity to HDE-like motifs. The expression of many HERV1/LTR12s and lincRNAs regulated by U7 snRNA seems to be tissue specific, therefore, we suggest that U7 snRNA plays a protective role in keeping deleterious genetic elements in silence in selected types of cells.

molecular biology↗