3D genome organization around nuclear speckles drives mRNA splicing efficiency

Creators: Bhat, Prashant; Chow, Amy; Emert, Benjamin; Ettlin, Olivia; Quinodoz, Sofia A.; Takei, Yodai; Huang, Wesley; Blanco, Mario R.; Guttman, Mitchell

Abstract

The nucleus is highly organized such that factors involved in transcription and processing of distinct classes of RNA are organized within specific nuclear bodies. One such nuclear body is the nuclear speckle, which is defined by high concentrations of protein and non-coding RNA regulators of pre-mRNA splicing. What functional role, if any, speckles might play in the process of mRNA splicing remains unknown. Here we show that genes localized near nuclear speckles display higher spliceosome concentrations, increased spliceosome binding to their pre-mRNAs, and higher co-transcriptional splicing levels relative to genes that are located farther from nuclear speckles. We show that directed recruitment of a pre-mRNA to nuclear speckles is sufficient to drive increased mRNA splicing levels. Finally, we show that gene organization around nuclear speckles is highly dynamic with differential localization between cell types corresponding to differences in Pol II occupancy. Together, our results integrate the longstanding observations of nuclear speckles with the biochemistry of mRNA splicing and demonstrate a critical role for dynamic 3D spatial organization of genomic DNA in driving spliceosome concentrations and controlling the efficiency of mRNA splicing.

Additional Information

The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. We thank Allen Chen, Mackenzie Strehle, Drew Honson, Elizabeth Soehalim, Elizabeth Detmar, Say-Tar Goh, and Drew Perez for experimental help; Isabel Goronzy for computational assignment of speckle hubs; Lior Pachter, Tara Chari, Ben Riviere, Delaney Sullivan, and Noah Ollikainen for computational help; Michael Elowitz, Barbara Wold, Long Cai, Arjun Raj for reagents; Fangyuan Ding, Hong Yin, Joanna Jachowicz, Luke Frankiw, Yicheng Luo for helpful discussions; Igor Antoshechkin for sequencing; Aaron Lin for sequencing advice; Mackenzie Strehle, Drew Honson and Kent Leslie for critical comments on the manuscript; Job Dekker and Johan Gibcus for HFFc6 cell lines, Rene Maehr and Krishan Mohan Parsi for H1 ESC and H1 endoderm cell lines. Inna-Marie Strazhnik for illustrations and Shawna Hiley for editing. Imaging was performed in the Biological Imaging Facility with the support of the Caltech Beckman Institute and the Arnold and Mabel Beckman Foundation. This work was funded by NIH T32 GM 7616-40, NIH NRSA CA247447, the UCLA-Caltech Medical Scientist Training Program, a Chen Graduate Innovator Grant, and the Josephine De Karman Fellowship Trust (P.B.); an HHMI Gilliam Fellowship, NSF GRFP Fellowship, and the HHMI Hanna H. Gray Fellows Program (S.A.Q.). This work was funded by the NIH 4DN program (U01 DK127420), NIH Directors' Transformative Research Award (R01 DA053178), the NYSCF, CZI Ben Barres Early Career Acceleration Award, and funds from Caltech. AUTHOR CONTRIBUTIONS: P.B. and M.G. conceived the study, analyzed data, interpreted results, and wrote the manuscript. P.B., A.C., and M.G. designed experiments. P.B., A.C., O.E., S.A.Q., W.H., and M.R.B. performed experiments. B.E. performed RNA FISH and image analysis including nuclear segmentation and spot detection. Y.T analyzed seqFISH+ data. P.B. and M.G. supervised the work and M.G. acquired funding. The authors have declared no competing interest.

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