دورية أكاديمية
Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart.
| العنوان: | Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart. |
|---|---|
| المؤلفون: | Pandi B, Brenman S, Black A, Ng DCM, Lau E, Lam MPY |
| المصدر: | Journal of proteome research [J Proteome Res] 2024 Aug 02; Vol. 23 (8), pp. 3161-3173. Date of Electronic Publication: 2024 Mar 08. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: American Chemical Society Country of Publication: United States NLM ID: 101128775 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1535-3907 (Electronic) Linking ISSN: 15353893 NLM ISO Abbreviation: J Proteome Res Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Washington, D.C. : American Chemical Society, c2002- |
| مواضيع طبية MeSH: | Alternative Splicing* , Protein Isoforms*/genetics , Protein Isoforms*/metabolism , Intrinsically Disordered Proteins*/genetics , Intrinsically Disordered Proteins*/metabolism , Intrinsically Disordered Proteins*/chemistry, Humans ; Heart Ventricles/metabolism ; Proteome/genetics ; Proteome/metabolism ; Heart Atria/metabolism ; Myocardium/metabolism ; Myocardium/chemistry ; LIM Domain Proteins/genetics ; LIM Domain Proteins/metabolism ; LIM Domain Proteins/chemistry ; Mass Spectrometry ; Tensins/metabolism ; Tensins/genetics ; Organ Specificity ; Protein Binding |
| مستخلص: | A computational analysis of mass spectrometry data was performed to uncover alternative splicing derived protein variants across chambers of the human heart. Evidence for 216 non-canonical isoforms was apparent in the atrium and the ventricle, including 52 isoforms not documented on SwissProt and recovered using an RNA sequencing derived database. Among non-canonical isoforms, 29 show signs of regulation based on statistically significant preferences in tissue usage, including a ventricular enriched protein isoform of tensin-1 (TNS1) and an atrium-enriched PDZ and LIM Domain 3 (PDLIM3) isoform 2 (PDLIM3-2/ALP-H). Examined variant regions that differ between alternative and canonical isoforms are highly enriched with intrinsically disordered regions. Moreover, over two-thirds of such regions are predicted to function in protein binding and RNA binding. The analysis here lends further credence to the notion that alternative splicing diversifies the proteome by rewiring intrinsically disordered regions, which are increasingly recognized to play important roles in the generation of biological function from protein sequences. |
| التعليقات: | Update of: bioRxiv. 2023 Oct 09:2023.10.08.561375. doi: 10.1101/2023.10.08.561375. (PMID: 37873130) |
| References: | Nucleic Acids Res. 2015 Apr 20;43(7):e47. (PMID: 25605792) Dev Cell. 2022 Apr 25;57(8):959-973.e7. (PMID: 35472321) Protein Sci. 2021 Jan;30(1):70-82. (PMID: 32881101) Elife. 2022 Dec 15;11:. (PMID: 36519529) J Mol Cell Cardiol. 2015 Apr;81:107-13. (PMID: 25683494) Am J Physiol Heart Circ Physiol. 2022 Feb 1;322(2):H181-H233. (PMID: 34797172) Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):E5593-601. (PMID: 25480548) Nat Methods. 2020 Sep;17(9):869-870. (PMID: 32669682) Nat Methods. 2017 May;14(5):513-520. (PMID: 28394336) J Biol Chem. 2004 Jun 18;279(25):26402-10. (PMID: 15084604) Proteomics. 2010 Mar;10(6):1127-40. (PMID: 20077415) Nat Commun. 2023 Apr 18;14(1):2213. (PMID: 37072382) Nucleic Acids Res. 2021 Jul 2;49(W1):W297-W303. (PMID: 34048569) STAR Protoc. 2020 Oct 21;1(3):100138. (PMID: 33377032) Nucleic Acids Res. 2017 Jan 4;45(D1):D219-D227. (PMID: 27899601) J Am Soc Mass Spectrom. 2016 Nov;27(11):1719-1727. (PMID: 27572102) Science. 2012 Dec 21;338(6114):1587-93. (PMID: 23258890) Front Cell Dev Biol. 2022 Dec 01;10:963608. (PMID: 36531944) PLoS Comput Biol. 2020 Oct 5;16(10):e1008287. (PMID: 33017396) Nat Commun. 2021 Jul 21;12(1):4438. (PMID: 34290238) Biophys J. 2021 Oct 19;120(20):4312-4319. (PMID: 34480923) Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. (PMID: 33270111) Mol Cell Proteomics. 2018 Mar;17(3):422-430. (PMID: 29222161) Nat Methods. 2022 Jun;19(6):730-739. (PMID: 35637310) PLoS Comput Biol. 2015 Jun 10;11(6):e1004325. (PMID: 26061177) Mol Cell. 2012 Jun 29;46(6):884-92. (PMID: 22749401) Genome Biol. 2014;15(12):550. (PMID: 25516281) Genome Biol. 2022 Mar 3;23(1):69. (PMID: 35241129) J Proteome Res. 2020 Jan 3;19(1):537-542. (PMID: 31755270) Trends Biochem Sci. 2017 Jun;42(6):407-408. (PMID: 28483376) Mol Cell. 2012 Jun 29;46(6):871-83. (PMID: 22749400) Trends Cardiovasc Med. 2004 Jan;14(1):13-8. (PMID: 14720469) Nature. 2008 Nov 27;456(7221):470-6. (PMID: 18978772) Nature. 2021 Aug;596(7873):583-589. (PMID: 34265844) Mol Cell Proteomics. 2020 Jul;19(7):1132-1144. (PMID: 32291283) Biochem J. 2000 Oct 15;351 Pt 2:403-11. (PMID: 11023826) J Am Soc Mass Spectrom. 2015 Nov;26(11):1865-74. (PMID: 26115965) Nucleic Acids Res. 2021 Jan 8;49(D1):D605-D612. (PMID: 33237311) PLoS Comput Biol. 2017 Aug 28;13(8):e1005717. (PMID: 28846689) Bioinformatics. 2013 Jan 1;29(1):15-21. (PMID: 23104886) Mol Cell Proteomics. 2020 Sep;19(9):1575-1585. (PMID: 32616513) J Mol Cell Cardiol. 2015 Oct;87:102-12. (PMID: 26268593) J Mol Cell Cardiol. 2023 Aug;181:89-97. (PMID: 37327991) Nat Commun. 2017 Nov 13;8(1):1469. (PMID: 29133944) Nucleic Acids Res. 2023 Jan 6;51(D1):D418-D427. (PMID: 36350672) Trends Biochem Sci. 2017 Feb;42(2):98-110. (PMID: 27712956) Cell Rep. 2019 Dec 10;29(11):3751-3765.e5. (PMID: 31825849) Nat Biotechnol. 2023 Dec;41(12):1776-1786. (PMID: 36959352) Nucleic Acids Res. 2020 Jan 8;48(D1):D1145-D1152. (PMID: 31686107) Cell. 2016 Feb 11;164(4):805-17. (PMID: 26871637) Nat Med. 2012 May;18(5):766-73. (PMID: 22466703) Cell Rep. 2017 Aug 1;20(5):1229-1241. (PMID: 28768205) |
| معلومات مُعتمدة: | R01 GM144456 United States GM NIGMS NIH HHS; R01 HL141278 United States HL NHLBI NIH HHS; R21 HL150456 United States HL NHLBI NIH HHS; R35 GM146815 United States GM NIGMS NIH HHS |
| فهرسة مساهمة: | Keywords: IDR; RBP; alternative splicing; heart tissue usage; intrinsically disordered regions; protein isoforms; protein/RNA binding; proteoform |
| المشرفين على المادة: | 0 (Protein Isoforms) 0 (Intrinsically Disordered Proteins) 0 (Proteome) 0 (LIM Domain Proteins) 0 (Tensins) |
| تواريخ الأحداث: | Date Created: 20240308 Date Completed: 20240802 Latest Revision: 20240808 |
| رمز التحديث: | 20240808 |
| مُعرف محوري في PubMed: | PMC11296937 |
| DOI: | 10.1021/acs.jproteome.3c00789 |
| PMID: | 38456420 |
| قاعدة البيانات: | MEDLINE |
Find this issue from the American Chemical Society | تدمد: | 1535-3907 |
|---|---|
| DOI: | 10.1021/acs.jproteome.3c00789 |