Biology subjects

Wanowska, E.

Publications and source records attributed to Wanowska, E..

3 recordsLinked to original sources

bioRxiv2026

Antisense lncRNA transcription promotes A-to-I RNA editing via intermolecular dsRNA in breast cancer

A-to-I RNA editing, catalysed by ADAR enzymes, is the most prevalent post-transcriptional RNA modification in mammals, yet the regulatory inputs shaping cell-type-specific editomes remain incompletely understood. Here we characterise over 2.2 million unique A-to-I editing sites across MCF7 (ER+) and MDA-MB-231 (triple-negative) breast cancer cell lines and 117 patient tumours. MCF7 exhibited substantially more editing per sample, driven by higher ADAR1 expression and a shifted ADAR1/ADAR2 ratio that favoured broad intronic Alu editing in the luminal line versus site-selective synonymous coding editing in the aggressive line. Despite this divergence, approximately 2,500 sites were constitutively edited in both cell lines, defining a conserved core editome. We demonstrate that natural antisense lncRNA transcription constitutes an independent, additive pathway for editing through intermolecular dsRNA formation: editing density at sense-antisense overlaps reversed from depletion to enrichment as a function of balanced co-expression, antisense overlap increased editing probability without affecting density among edited genes, and a factorial analysis across all expressed genes established that inverted Alu pairs are the dominant editing substrate while antisense lncRNA transcription provides an independent contribution whose magnitude scales with overlap length and Alu content. Experimental validation at the NDUFS1/NDUFS1-AS1 locus confirmed co-expression of sense and antisense transcripts, verified editing at computationally predicted positions by Sanger sequencing with genomic DNA controls, and demonstrated differential editing and expression between cell lines. Differentially edited genes included the oncogene VOPP1 and fatty acid metabolism genes at antisense loci, linking epitranscriptomic regulation to the lipid metabolic phenotype of aggressive breast cancer. Our findings establish a two-tier model: a dominant ADAR1-driven programme targeting intramolecular Alu dsRNA, upon which an independent lncRNA antisense pathway is superimposed via intermolecular dsRNA, jointly producing subtype-specific editing landscapes that preserve a constitutive core but diverge in magnitude, functional distribution, and site selection.

cancer biology↗

bioRxiv2023

5' extended protein-coding INO80E transcript regulates expression of two head-to-head overlapping genes: INO80E and HIRIP3

The INO80E gene encodes the protein involved in the chromatin remodeling processes as a part of the multi-subunit INO80-chromatin remodeling complex. The INO80E gene is located on chromosome 16 and overlaps head-to-head with the HIRIP3 gene encoding protein, which binds H2B and H3 core histones and HIRA protein and regulates the chromatin and histone metabolism. Antisense transcription of head-to-head overlapping PC genes may have several consequences and none of them have been comprehensively investigated and explained. Here, we determined that INO80E-201, which overlaps the HIRIP3 gene transcripts, forms an R-loop at its 5 end. We also demonstrated that overlapping transcripts of INO80E and HIRIP3 form an RNA:RNA duplex that has the stabilizing effect on the involved mRNAs. Our results confirmed that this stabilization could be mediated by the ELAVL1 protein. We additionally introduced de novo methylation using the CRISPR/Cas system into the promoter sequence of INO80E gene. As a result of the introduced changes, reduced expression of HIRIP3 and INO80E gene transcripts was observed. It was determined that methylated cytosines were located in the binding sites for four transcription factors including RARG, which was further confirmed to be important in the transcription of both studied genes. Our results strongly suggest that the formation of an RNA:RNA duplex is necessary for stable simultaneous expression of both genes. Lack of this dsRNA structure results in a loss of a wider DNA opening and in consequence transcriptional interference. We also concluded that forming R-loops probably plays only a supplementary role and is not required for proper expression of HIRIP3 and INO80E gene transcripts.

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↗