Dataset Information

U1 snRNP and RNA polymerase II interaction is predominantly mediated by Prp40 rather than U1-70K in yeast

ABSTRACT: Transcription and splicing are coupled both temporally and physically. A previous cryo-EM structure of the human U1 snRNP and RNA polymerase pol II complex has shown that U1 snRNP uses predominantly the RRM domain of U1-70K to directly interact with the RPB2 subunit of pol II. However, residues on U1-70K involved in the interaction with pol II are not conserved in yeast U1-70K, raising the question whether yeast U1 snRNP interacts with pol II in a similar manner. We found that yeast pol II associates with both U1 and U2 snRNPs, but U1-70K makes a minimal contribution to U1 snRNP’s interaction with pol II. On the other hand, multiple domains of yeast Prp40 interact with pol II and the removal of the C-terminal domain (CTD) of pol II does not affect this interaction. Although yeast Prp40 is stably associated with U1 snRNP, its human homologs, PRPF40a and PRPF40b, are alternative splicing factors that are not integral components of U1 snRNP. This shift of function of Prp40 homologs may have led to the evolution of U1-70K to be the main interactor with pol II in the human system.

INSTRUMENT(S):

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Aaron Issaian

LAB HEAD: Rui, Zhao

PROVIDER: PXD078573 | Pride | 2026-05-20

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20250305_AI_Rui_Xlink_F10_Slot1-19_1_9616.d.zip	Other
	20250305_AI_Rui_Xlink_F11_Slot1-20_1_9621.d.zip	Other
	20250305_AI_Rui_Xlink_F12_Slot1-21_1_9622.d.zip	Other
	20250305_AI_Rui_Xlink_F13_Slot1-22_1_9623.d.zip	Other
	20250305_AI_Rui_Xlink_F14_Slot1-23_1_9624.d.zip	Other

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Publications

U1 snRNP and RNA polymerase II interaction is predominantly mediated by Prp40 rather than U1-70K in yeast.

Li Xueni X Li Jiaqin J Srivastava Pankaj P Shi Shasha S Issaian Aaron A Bevers Shaun S Wagner Marisa Elise ME D'Alessandro Angelo A Zhao Rui R

bioRxiv : the preprint server for biology 20250830

Transcription and splicing are coupled both temporally and physically. A previous cryo-EM structure of the human U1 snRNP and RNA polymerase pol II complex has shown that U1 snRNP uses predominantly the RRM domain of U1-70K to directly interact with the RPB2 subunit of pol II. However, residues on U1-70K involved in the interaction with pol II are not conserved in yeast U1-70K, raising the question whether yeast U1 snRNP interacts with pol II in a similar manner. We found that yeast pol II assoc ...[more]

PMID: 40909591

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Project description:Pervasive transcription in the mammalian genome produces thousands of long noncoding RNAs (lncRNAs) and promoter- or enhancer-associated unstable transcripts. They preferentially locate to chromatin, at which some regulate chromatin structure, transcription and RNA processing. While several RNA sequences responsible for nuclear localization have been identified, such as repeats in the lncRNA Xist and Alu-like elements for long RNAs, how lncRNAs as a class are enriched on chromatin remains elusive. To screen for cis-elements that contribute to RNA-chromatin localization, we developed a high-throughput method named RNA elements for subcellular localization by sequencing (REL-seq), and discovered a U1 small nuclear ribonucleoprotein (snRNP)-recognition motif being critical for chromatin localization of reporter RNAs. Across the genome, chromatin-bound lncRNAs, which are enriched with 5’ splice sites and depleted of 3’ splice sites, exhibit high levels of U1 snRNA binding compared to cytoplasm-localized protein-coding mRNAs. Acute depletion of U1 snRNA, or U1 snRNP protein component SNRNP70, drastically reduces the chromatin association of hundreds of lncRNAs and unstable transcripts without altering the overall transcription rate in cells. In addition, rapid degradation of SNRNP70 reduces the localization of both nascent and polyadenylated lncRNA transcripts to chromatin, and disrupts the nuclear-speckles and genome-wide localization of Malat1, a highly conserved and abundant lncRNA. Moreover, chromatin-bound U1 snRNP interacts with transcriptionally engaged RNA polymerase (Pol) II. Together, these results demonstrate that U1 snRNP acts widely to tether and mobilize lncRNAs to chromatin in a Pol II transcription-dependent manner. Our findings uncover a novel role of U1 snRNP beyond pre-mRNA processing and provide molecular insights into how lncRNAs are recruited to Pol II-transcribed genes and have a propensity for chromatin-associated functions.