Functional analysis of the zinc finger modules of the Saccharomyces cerevisiae splicing factor Luc7.

Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9509184 Publication Model: Electronic Cited Medium: Internet ISSN: 1469-9001 (Electronic) Linking ISSN: 13558382 NLM ISO Abbreviation: RNA Subsets: MEDLINE

Publication: <2003->: Cold Spring Harbor, NY : Cold Spring Harbor Laboratory Press
Original Publication: New York, NY : Cambridge University Press, c1995-

Saccharomyces cerevisiae Proteins*/genetics ; Saccharomyces cerevisiae Proteins*/metabolism ; Saccharomyces cerevisiae*/genetics ; Saccharomyces cerevisiae*/metabolism ; Zinc Fingers*; RNA, Small Nuclear/genetics ; RNA, Small Nuclear/metabolism ; RNA Splicing Factors/metabolism ; RNA Splicing Factors/genetics ; RNA Splice Sites ; Humans ; RNA-Binding Proteins/metabolism ; RNA-Binding Proteins/genetics ; RNA Splicing ; RNA Precursors/genetics ; RNA Precursors/metabolism ; Alternative Splicing ; Ribonucleoprotein, U1 Small Nuclear/metabolism ; Ribonucleoprotein, U1 Small Nuclear/genetics ; Introns/genetics

Identification of splice sites is a critical step in pre-messenger RNA (pre-mRNA) splicing because the definition of the exon/intron boundaries controls what nucleotides are incorporated into mature mRNAs. The intron boundary with the upstream exon is initially identified through interactions with the U1 small nuclear ribonucleoprotein (snRNP). This involves both base-pairing between the U1 snRNA and the pre-mRNA as well as snRNP proteins interacting with the 5' splice site (5'ss)/snRNA duplex. In yeast, this duplex is buttressed by two conserved protein factors, Yhc1 and Luc7. Luc7 has three human paralogs (LUC7L, LUC7L2, and LUC7L3), which play roles in alternative splicing. What domains of these paralogs promote splicing at particular sites is not yet clear. Here, we humanized the zinc finger (ZnF) domains of the yeast Luc7 protein in order to understand their roles in splice site selection using reporter assays, transcriptome analysis, and genetic interactions. Although we were unable to determine a function for the first ZnF domain, humanization of the second ZnF domain to mirror that found in LUC7L or LUC7L2 resulted in altered usage of nonconsensus 5'ss. In contrast, the corresponding ZnF domain of LUC7L3 could not support yeast viability. Further, humanization of Luc7 can suppress mutation of the ATPase Prp28, which is involved in U1 release and exchange for U6 at the 5'ss. Our work reveals a role for the second ZnF of Luc7 in splice site selection and suggests that different ZnF domains may have different ATPase requirements for release by Prp28.
(© 2024 Carrocci et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.)

Update of: bioRxiv. 2024 Feb 04:2024.02.04.578419. doi: 10.1101/2024.02.04.578419. (PMID: 38352541)

Genes Dev. 2013 Jan 15;27(2):129-44. (PMID: 23348838)
Elife. 2015 Jan 02;4:. (PMID: 25555158)
RNA. 1999 Feb;5(2):221-34. (PMID: 10024174)
Science. 1993 Dec 24;262(5142):2035-9. (PMID: 8266100)
Nature. 2019 Sep;573(7774):375-380. (PMID: 31485080)
Nucleic Acids Res. 2007;35(17):5874-85. (PMID: 17726058)
Genome Res. 2017 Mar;27(3):491-499. (PMID: 28100584)
Cell Rep. 2021 Apr 13;35(2):108989. (PMID: 33852859)
Curr Opin Struct Biol. 2020 Dec;65:139-148. (PMID: 32717639)
Annu Rev Biochem. 2020 Jun 20;89:359-388. (PMID: 31794245)
Cell Rep. 2013 Oct 17;5(1):151-65. (PMID: 24075986)
Science. 1988 Nov 18;242(4881):1028-35. (PMID: 2973660)
Elife. 2022 Aug 12;11:. (PMID: 35959885)
Mol Cell. 2013 Aug 8;51(3):338-48. (PMID: 23891561)
Bioinformatics. 2017 Apr 15;33(8):1216-1217. (PMID: 28110292)
Mol Cell. 2005 Jul 1;19(1):53-63. (PMID: 15989964)
Genes Dev. 1999 Sep 15;13(18):2425-38. (PMID: 10500099)
RNA Biol. 2023 Jan;20(1):525-538. (PMID: 37528617)
Nat Commun. 2014;5:3123. (PMID: 24452287)
Bioinformatics. 2017 Nov 15;33(22):3645-3647. (PMID: 29036507)
Genome Biol. 2014;15(12):550. (PMID: 25516281)
RNA. 2016 Sep;22(9):1302-10. (PMID: 27354704)
Science. 1993 Dec 24;262(5142):1982-8. (PMID: 8266093)
Nat Biotechnol. 2019 Aug;37(8):907-915. (PMID: 31375807)
Mol Cell. 2021 May 6;81(9):1905-1919.e12. (PMID: 33852893)
Methods Enzymol. 2002;350:380-92. (PMID: 12073325)
Elife. 2017 Aug 22;6:. (PMID: 28829039)
Nucleic Acids Res. 2012 Jan;40(Database issue):D700-5. (PMID: 22110037)
Mol Cell. 1999 Jan;3(1):55-64. (PMID: 10024879)
Nat Commun. 2017 Oct 19;8(1):1035. (PMID: 29051543)
Nature. 2018 Jul;559(7714):419-422. (PMID: 29995849)
Nucleic Acids Res. 2019 May 7;47(8):e47. (PMID: 30783653)
G3 (Bethesda). 2014 Mar 20;4(3):389-98. (PMID: 24374639)
Nat Struct Mol Biol. 2024 May;31(5):835-845. (PMID: 38196034)
Nucleic Acids Res. 2014 Apr;42(7):4697-711. (PMID: 24497193)
RNA. 2024 Jul 16;30(8):1070-1088. (PMID: 38688558)
Mol Cell. 2008 Aug 8;31(3):360-70. (PMID: 18691968)
Methods Mol Biol. 2014;1079:105-16. (PMID: 24170397)
PLoS Genet. 2014 Apr 10;10(4):e1004249. (PMID: 24722551)
RNA. 2022 Oct 31;:. (PMID: 36316087)
Nucleic Acids Res. 2017 May 5;45(8):4837-4852. (PMID: 28062854)
Cell Rep. 2020 Jun 9;31(10):107754. (PMID: 32521279)
Genetics. 1993 Apr;133(4):851-63. (PMID: 8462846)
Nat Rev Mol Cell Biol. 2005 May;6(5):386-98. (PMID: 15956978)

R35 GM130370 United States GM NIGMS NIH HHS; R35 GM136261 United States GM NIGMS NIH HHS; T32 GM132046 United States GM NIGMS NIH HHS

Keywords: Luc7; RNA; snRNP; spliceosome; splicing

0 (Saccharomyces cerevisiae Proteins)
0 (Luc7 protein, S cerevisiae)
0 (RNA, Small Nuclear)
0 (RNA Splicing Factors)
0 (RNA Splice Sites)
0 (RNA-Binding Proteins)
0 (RNA Precursors)
0 (Ribonucleoprotein, U1 Small Nuclear)

Date Created: 20240508 Date Completed: 20240716 Latest Revision: 20241024

20241024

PMC11251517

10.1261/rna.079956.124

38719745