{"doi":"10.1093/nar/gkaf784","title":"MALAT1 regulates mRNA processing through sequence dependent RNA–RNA and RNA–protein interactions","abstract":"Messenger RNAs (mRNAs) are subject to multiple layers of gene expression regulation, enabling the production of a large diversity of RNA transcripts and encoded proteins from a smaller number of genes in the human genome. We find that the metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) non-coding RNA regulates mRNA processing through direct RNA-RNA and RNA-protein interactions. MALAT1 interacts with both the TAR DNA binding protein (TDP-43) and the spermine/spermidine acetyltransferase SAT1 pre-mRNA to enhance alternative splicing of SAT1 through direct, sequence-specific interactions. MALAT1 interaction with TDP-43 and SAT1 increases TDP-43 binding affinity for SAT1 pre-mRNA by coordinating tripartite RNA-RNA-protein interactions. These tripartite interactions enhance SAT1 alternative splicing. This mechanism of pre-mRNA processing may not be limited to MALAT1, TDP-43, and SAT1. Similarly, alternative splicing of the liprin-α3 PPFIA3 pre-mRNA at exon 16 by the cleavage stimulation factor subunit 2 protein is enhanced by sequence-specific interactions with MALAT1 RNA. We conclude that the abundant MALAT1 non-coding RNA contains modular RNA-RNA and RNA-protein binding regions that facilitate the processing of mRNA transcripts relevant for neuronal function.","journal":"Nucleic Acids Research","year":2025,"id":518658,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9598,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1386549,"name":"Simone Hall","orcid":null,"position":1,"is_corresponding":false},{"id":1386550,"name":"Raul Johnson","orcid":null,"position":2,"is_corresponding":false},{"id":1172146,"name":"Jonathan Zhu","orcid":"0000-0001-7074-0459","position":3,"is_corresponding":false},{"id":1172474,"name":"Lauren Ellis","orcid":null,"position":4,"is_corresponding":false},{"id":1117347,"name":"Colleen A. McHugh","orcid":"0000-0001-6008-2640","position":5,"is_corresponding":false},{"id":1243328,"name":"Adarsh Balaji","orcid":"0009-0007-3295-9936","position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":null,"created_at":"2026-07-19T02:49:09.679930Z","pmid":"40808300","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}