Genome organization around nuclear speckles drives mRNA splicing efficiency

We thank D. Honson, E. Detmar and D. Perez for experimental help; B. Riviere, L. Pachter and N. Ollikainen for computational help; M. Flynn for the bidirectional reporter plasmid; L. Cai, M. Elowitz and A. Raj for reagents; F. Ding, H. Yin, J. Jachowicz, L. Frankiw and Y. Luo for discussions; B. Yeh for discussions about splicing efficiency calculations; I. Antoshechkin for sequencing; G. Spigola for microscopy advice; A. Lin for sequencing advice; B. Yeh, D. Honson and K. Leslie for critical comments on the manuscript; R. Maehr and K. Mohan Parsi for H1 ES cell lines; B. Wold and B. Williams for myocyte cell lines; and S. Hiley for editing. Illustrations in Figs. 1a,c–d,e,g2a,b, 3a,b, 4a, 5a–c and 6 and Extended Data Figs. 4b and 9 were created by I.-M. Strazhnik, Caltech. Imaging was performed at 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.); and a 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.

Sequencing datasets have been deposited into the GEO with accession identifier GSE247833.

Extended Data Fig. 1 Correlation between speckle proximity scores between SPRITE datasets and TSA-seq for SON.

Additional scripts and data are available at GitHub (https://github.com/GuttmanLab/speckle).

S.A.Q. and M.G. are inventors on a patent covering the SPRITE method.