Biology subjects

Munita, R.

Publications and source records attributed to Munita, R..

4 recordsLinked to original sources

bioRxiv2026

Deletion of the MALAT1 RNA 3' end Promotes Transcript Decay, TALAM1 downregulation, and Inhibits Proliferation in Gastric and Breast Cancer Cells

The long non-coding RNA MALAT1 is a conserved oncogenic driver whose function relies on a 3 triple-helix motif. While its biochemistry is well-characterized in vitro, the endogenous requirement for this motif in regulating the stability of the transcript and other genes residing in its locus remains unclear. In this study, we employed a dual-sgRNA CRISPR-Cas9 approach to systematically excise triple-helix-forming sequences from the native MALAT1 locus in gastric (AGS) and breast (MCF7) cancer cells. Our findings demonstrate that the 3 end strongly contributes to MALAT1 stability. Perturbations ranging from genomic deletions to a single-base changes trigger transcript collapse and rapid exonucleolytic decay, while the biogenesis of the small RNA mascRNA (a byproduct of MALAT1, also involved in cancer) remains decoupled and unaffected. In cellulo, DMS probing reveals that edited transcripts retain structural complexity in the 3 region. Phenotypically, structural disruption of the 3 end significantly impairs proliferation of both cancer cellular models. These results identify the 3 triple-helix as a determinant of MALAT1 stability and provide endogenous validation for its role in the analyzed AGS and MCF7 cells.

molecular biology↗

bioRxiv2026

RNA-DNA triplex-forming miRNAs define an evolutionarily recent chromatin regulatory mechanism

MicroRNAs (miRNAs) are best known for their role in post-transcriptional gene regulation in the cytoplasm. However, a subset of miRNAs has been detected in the nucleus, suggesting additional regulatory functions. Here, we systematically characterize chromatin-associated small non-coding RNAs in the human pancreatic cancer cell line PANC-1. Using chromatin RNA immunoprecipitation coupled with small RNA sequencing, we show that the chromatin-associated small RNA population differs markedly from the bulk nuclear RNA pool and is strongly enriched in miRNAs. Among these, miR-21 represents the most abundant chromatin-associated species. Sequence analyses revealed that a subset of these miRNAs fulfills the requirements for RNA-DNA triplex formation at genomic regulatory regions. Gel-shift assays further demonstrate that Argonaute2 (Ago2) directly interacts with triple-helical nucleic acid structures in vitro, suggesting a potential mechanistic link between triplexes and Ago2-chromatin engagement. Evolutionary analyses indicate that these triplex-forming chromatin-associated miRNAs are largely restricted to anthropoid primates, in contrast to broadly conserved non-triplex-forming miRNAs. Together, our results identify a population of chromatin-associated miRNAs and provide evidence for a potential structural mechanism linking miRNAs, Ago2, and chromatin.

molecular biology↗

bioRxiv2020

MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development

Microexons, exons that are [≤]30 nucleotides, were shown to play key roles in neuronal development, but are difficult to detect and quantify using standard RNA-Seq alignment tools. Here, we present MicroExonator, a novel pipeline for reproducible de novo discovery and quantification of microexons. We processed 289 RNA-seq datasets from eighteen mouse tissues corresponding to nine embryonic and postnatal stages, providing the most comprehensive survey of microexons available for mouse. We detected 2,984 microexons, 332 of which are differentially spliced throughout mouse embryonic brain development, including 29 that are not present in mouse transcript annotation databases. Unsupervised clustering of microexons alone segregates brain tissues by developmental time and further analysis suggest a key function for microexon inclusion in axon growth and synapse formation. Finally, we analysed single-cell RNA-seq data from the mouse visual cortex and we report differential inclusion between neuronal subpopulations, suggesting that some microexons could be cell-type specific.

genomics↗

bioRxiv2019

Presence of a D2 receptor truncated protein in the brain of the D2 receptor functional knockout mouse, revisiting its molecular and neurochemical features

Null mice for the dopamine D2 receptor (D2R) have been instrumental in understanding the function of this protein in the central nervous system. Several lines of D2R knockout mice have been generated, which share some characteristics but differ in others. The D2R functional knockout mouse, first described in 1997, is functionally null for D2R-mediated signaling but the Drd2 gene was interrupted at the most extreme distal end leaving open the question about whether transcript and protein are produced. We decided to determine if there are D2R transcripts, the characteristics of these transcripts and whether they are translated in the brain of D2R functional knockout mice. Sequence analysis of 3 Rapid Amplification of cDNA Ends showed that D2R functional knockout mice express transcripts that lack only the exon eight. Immunofluorescence showed D2R-like protein in the brain of the knockout mice. As previously reported, D2R functional knockout mice are hypoactive and insensitive to the D2R agonist quinpirole (QNP). However, the heterozygous showed locomotor activity and response to QNP similar to the wild-type mice. Intriguingly, microdialysis experiments showed that heterozygous mice, such as knockouts, have half the normal levels of synaptic dopamine in the striatum. However, heterozygous mice responded similarly to wild-type mice to an acute injection of QNP, showing a 50% decrease in synaptic dopamine. In conclusion, D2R functional knockout mice express transcripts that lead to a truncated D2R protein that lacks from the sixth transmembrane domain to the C-terminal end but retains the third intracellular loop. We discuss the implications of this truncated D2R coexisting with the native D2R that may explain the unexpected outcomes observed in the heterozygous. Finally, we suggest that the D2R functional knockout mouse can be a useful model for studying protein-protein interaction and trafficking of D2R.

neuroscience↗