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Matrin3 binds directly to intronic pyrimidine-rich sequences and controls alternative splicing.
Genes Cells. 2017 Sep; 22(9):785-798.GC

Abstract

Matrin3 is an RNA-binding protein that is localized in the nuclear matrix. Although various roles in RNA metabolism have been reported for Matrin3, in vivo target RNAs to which Matrin3 binds directly have not been investigated comprehensively so far. Here, we show that Matrin3 binds predominantly to intronic regions of pre-mRNAs. Photoactivatable Ribonucleoside-Enhanced Cross-linking and Immunoprecipitation (PAR-CLIP) analysis using human neuronal cells showed that Matrin3 recognized pyrimidine-rich sequences as binding motifs, including the polypyrimidine tract, a splicing regulatory element. Splicing-sensitive microarray analysis showed that depletion of Matrin3 preferentially increased the inclusion of cassette exons that were adjacent to introns that contained Matrin3-binding sites. We further found that although most of the genes targeted by polypyrimidine tract binding protein 1 (PTBP1) were also bound by Matrin3, Matrin3 could control alternative splicing in a PTBP1-independent manner, at least in part. These findings suggest that Matrin3 is a splicing regulator that targets intronic pyrimidine-rich sequences.

Authors+Show Affiliations

Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan. Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

28695676

Citation

Uemura, Yuri, et al. "Matrin3 Binds Directly to Intronic Pyrimidine-rich Sequences and Controls Alternative Splicing." Genes to Cells : Devoted to Molecular & Cellular Mechanisms, vol. 22, no. 9, 2017, pp. 785-798.
Uemura Y, Oshima T, Yamamoto M, et al. Matrin3 binds directly to intronic pyrimidine-rich sequences and controls alternative splicing. Genes Cells. 2017;22(9):785-798.
Uemura, Y., Oshima, T., Yamamoto, M., Reyes, C. J., Costa Cruz, P. H., Shibuya, T., & Kawahara, Y. (2017). Matrin3 binds directly to intronic pyrimidine-rich sequences and controls alternative splicing. Genes to Cells : Devoted to Molecular & Cellular Mechanisms, 22(9), 785-798. https://doi.org/10.1111/gtc.12512
Uemura Y, et al. Matrin3 Binds Directly to Intronic Pyrimidine-rich Sequences and Controls Alternative Splicing. Genes Cells. 2017;22(9):785-798. PubMed PMID: 28695676.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Matrin3 binds directly to intronic pyrimidine-rich sequences and controls alternative splicing. AU - Uemura,Yuri, AU - Oshima,Takuya, AU - Yamamoto,Munetaka, AU - Reyes,Charles Jourdan, AU - Costa Cruz,Pedro Henrique, AU - Shibuya,Toshiharu, AU - Kawahara,Yukio, Y1 - 2017/07/11/ PY - 2017/01/09/received PY - 2017/06/11/accepted PY - 2017/7/12/pubmed PY - 2018/1/13/medline PY - 2017/7/12/entrez SP - 785 EP - 798 JF - Genes to cells : devoted to molecular & cellular mechanisms JO - Genes Cells VL - 22 IS - 9 N2 - Matrin3 is an RNA-binding protein that is localized in the nuclear matrix. Although various roles in RNA metabolism have been reported for Matrin3, in vivo target RNAs to which Matrin3 binds directly have not been investigated comprehensively so far. Here, we show that Matrin3 binds predominantly to intronic regions of pre-mRNAs. Photoactivatable Ribonucleoside-Enhanced Cross-linking and Immunoprecipitation (PAR-CLIP) analysis using human neuronal cells showed that Matrin3 recognized pyrimidine-rich sequences as binding motifs, including the polypyrimidine tract, a splicing regulatory element. Splicing-sensitive microarray analysis showed that depletion of Matrin3 preferentially increased the inclusion of cassette exons that were adjacent to introns that contained Matrin3-binding sites. We further found that although most of the genes targeted by polypyrimidine tract binding protein 1 (PTBP1) were also bound by Matrin3, Matrin3 could control alternative splicing in a PTBP1-independent manner, at least in part. These findings suggest that Matrin3 is a splicing regulator that targets intronic pyrimidine-rich sequences. SN - 1365-2443 UR - https://www.unboundmedicine.com/medline/citation/28695676/Matrin3_binds_directly_to_intronic_pyrimidine_rich_sequences_and_controls_alternative_splicing_ L2 - https://doi.org/10.1111/gtc.12512 DB - PRIME DP - Unbound Medicine ER -