Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing

Baolei Yuan; Xuan Zhou; Keiichiro Suzuki; Gerardo Ramos-Mandujano; Mengge Wang; Muhammad Tehseen; Lorena V. Cortés-Medina; James J. Moresco; Sarah Dunn; Reyna Hernandez-Benitez; Tomoaki Hishida; Na Young Kim; Manal M. Andijani; Chongwei Bi; Manching Ku; Yuta Takahashi; Jinna Xu; Jinsong Qiu; Ling Huang; Christopher Benner; Emi Aizawa; Jing Qu; Guang Hui Liu; Zhongwei Li; Fei Yi; Yanal Ghosheh; Changwei Shao; Maxim Shokhirev; Patrizia Comoli; Francesco Frassoni; John R. Yates; Xiang Dong Fu; Concepcion Rodriguez Esteban; Samir Hamdan; Mo Li; Juan Carlos Izpisua Belmonte

doi:10.1038/s41467-022-31220-8

Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing

Baolei Yuan, Xuan Zhou, Keiichiro Suzuki, Gerardo Ramos-Mandujano, Mengge Wang, Muhammad Tehseen, Lorena V. Cortés-Medina, James J. Moresco, Sarah Dunn, Reyna Hernandez-Benitez, Tomoaki Hishida, Na Young Kim, Manal M. Andijani, Chongwei Bi, Manching Ku, Yuta Takahashi, Jinna Xu, Jinsong Qiu, Ling Huang, Christopher BennerEmi Aizawa, Jing Qu, Guang Hui Liu, Zhongwei Li, Fei Yi, Yanal Ghosheh, Changwei Shao, Maxim Shokhirev, Patrizia Comoli, Francesco Frassoni, John R. Yates, Xiang Dong Fu, Concepcion Rodriguez Esteban, Samir Hamdan, Mo Li^*, Juan Carlos Izpisua Belmonte^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

10 Scopus citations

Abstract

The diverse functions of WASP, the deficiency of which causes Wiskott-Aldrich syndrome (WAS), remain poorly defined. We generated three isogenic WAS models using patient induced pluripotent stem cells and genome editing. These models recapitulated WAS phenotypes and revealed that WASP deficiency causes an upregulation of numerous RNA splicing factors and widespread altered splicing. Loss of WASP binding to splicing factor gene promoters frequently leads to aberrant epigenetic activation. WASP interacts with dozens of nuclear speckle constituents and constrains SRSF2 mobility. Using an optogenetic system, we showed that WASP forms phase-separated condensates that encompasses SRSF2, nascent RNA and active Pol II. The role of WASP in gene body condensates is corroborated by ChIPseq and RIPseq. Together our data reveal that WASP is a nexus regulator of RNA splicing that controls the transcription of splicing factors epigenetically and the dynamics of the splicing machinery through liquid-liquid phase separation.

Original language	English (US)
Article number	3646
Journal	Nature Communications
Volume	13
Issue number	1
DOIs	https://doi.org/10.1038/s41467-022-31220-8
State	Published - Dec 2022

Bibliographical note

Funding Information:
We would like to thank B. Lubin for advice on hematopoiesis and assistance in cord blood unit procurement; C. Cole, R. Walker, J. Lieu, R. Tonai, and M. Swearingen for providing cord blood samples; Y. Zheng and Y. Tian for assistance on hematopoietic differentiation and flow cytometry; A. Shirbini for assistance on MST experiment and analysis; members of the Belmonte and Li lab for helpful discussions; Y. Zhang, A.T. Gutiérrez, A. Geobl, R.D. Soligalla and Y. Hishida for technical assistance, J.H. Xiong for help with MATLAB. L. Mack, J. Olvera, C. O’Connor, E. O’Connor and K. Marquez for help with flow cytometry; D. O’Keefe and M. Wang for critical reading of the manuscript; M. Schwarz, P. Schwarz, C. Xia, X. Zhang, and M.K.Y. Sicat for administrative help. We thank KAUST Visualization Core Lab for Avizo software support. We also thank KAUST Bioscience core lab for sequencing support and KAUST Imaging and Characterization core lab for help with confocal microscopy. The research of the Li laboratory was supported by KAUST Office of Sponsored Research (OSR), under award numbers BAS/1/1080-01 and URF/1/4716-01. This work was supported by the Waitt Advanced Biophotonics Core Facility of the Salk Institute with funding from NIH-NCI CCSG: P30 014195, NINDS Neuroscience Core Grant, and the Waitt Foundation. G.H.L. was supported by the National Key Research and Development Program of China (2020YFA0804000), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16010000), the National Natural Science Foundation of China (Grant Nos. 81921006, 92149301, 92168201). J.C.I.B. was supported by grants from The Moxie Foundation, G. Harold and Leila Y. Mathers Charitable Foundation.

Publisher Copyright:
© 2022, The Author(s).

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

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10.1038/s41467-022-31220-8

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Yuan, B., Zhou, X., Suzuki, K., Ramos-Mandujano, G., Wang, M., Tehseen, M., Cortés-Medina, L. V., Moresco, J. J., Dunn, S., Hernandez-Benitez, R., Hishida, T., Kim, N. Y., Andijani, M. M., Bi, C., Ku, M., Takahashi, Y., Xu, J., Qiu, J., Huang, L., ... Izpisua Belmonte, J. C. (2022). Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing. Nature Communications, 13(1), Article 3646. https://doi.org/10.1038/s41467-022-31220-8

@article{faba6bee258b4e32b2cd760c1d012157,

title = "Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing",

abstract = "The diverse functions of WASP, the deficiency of which causes Wiskott-Aldrich syndrome (WAS), remain poorly defined. We generated three isogenic WAS models using patient induced pluripotent stem cells and genome editing. These models recapitulated WAS phenotypes and revealed that WASP deficiency causes an upregulation of numerous RNA splicing factors and widespread altered splicing. Loss of WASP binding to splicing factor gene promoters frequently leads to aberrant epigenetic activation. WASP interacts with dozens of nuclear speckle constituents and constrains SRSF2 mobility. Using an optogenetic system, we showed that WASP forms phase-separated condensates that encompasses SRSF2, nascent RNA and active Pol II. The role of WASP in gene body condensates is corroborated by ChIPseq and RIPseq. Together our data reveal that WASP is a nexus regulator of RNA splicing that controls the transcription of splicing factors epigenetically and the dynamics of the splicing machinery through liquid-liquid phase separation.",

author = "Baolei Yuan and Xuan Zhou and Keiichiro Suzuki and Gerardo Ramos-Mandujano and Mengge Wang and Muhammad Tehseen and Cort{\'e}s-Medina, {Lorena V.} and Moresco, {James J.} and Sarah Dunn and Reyna Hernandez-Benitez and Tomoaki Hishida and Kim, {Na Young} and Andijani, {Manal M.} and Chongwei Bi and Manching Ku and Yuta Takahashi and Jinna Xu and Jinsong Qiu and Ling Huang and Christopher Benner and Emi Aizawa and Jing Qu and Liu, {Guang Hui} and Zhongwei Li and Fei Yi and Yanal Ghosheh and Changwei Shao and Maxim Shokhirev and Patrizia Comoli and Francesco Frassoni and Yates, {John R.} and Fu, {Xiang Dong} and Esteban, {Concepcion Rodriguez} and Samir Hamdan and Mo Li and {Izpisua Belmonte}, {Juan Carlos}",

note = "Funding Information: We would like to thank B. Lubin for advice on hematopoiesis and assistance in cord blood unit procurement; C. Cole, R. Walker, J. Lieu, R. Tonai, and M. Swearingen for providing cord blood samples; Y. Zheng and Y. Tian for assistance on hematopoietic differentiation and flow cytometry; A. Shirbini for assistance on MST experiment and analysis; members of the Belmonte and Li lab for helpful discussions; Y. Zhang, A.T. Guti{\'e}rrez, A. Geobl, R.D. Soligalla and Y. Hishida for technical assistance, J.H. Xiong for help with MATLAB. L. Mack, J. Olvera, C. O{\textquoteright}Connor, E. O{\textquoteright}Connor and K. Marquez for help with flow cytometry; D. O{\textquoteright}Keefe and M. Wang for critical reading of the manuscript; M. Schwarz, P. Schwarz, C. Xia, X. Zhang, and M.K.Y. Sicat for administrative help. We thank KAUST Visualization Core Lab for Avizo software support. We also thank KAUST Bioscience core lab for sequencing support and KAUST Imaging and Characterization core lab for help with confocal microscopy. The research of the Li laboratory was supported by KAUST Office of Sponsored Research (OSR), under award numbers BAS/1/1080-01 and URF/1/4716-01. This work was supported by the Waitt Advanced Biophotonics Core Facility of the Salk Institute with funding from NIH-NCI CCSG: P30 014195, NINDS Neuroscience Core Grant, and the Waitt Foundation. G.H.L. was supported by the National Key Research and Development Program of China (2020YFA0804000), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16010000), the National Natural Science Foundation of China (Grant Nos. 81921006, 92149301, 92168201). J.C.I.B. was supported by grants from The Moxie Foundation, G. Harold and Leila Y. Mathers Charitable Foundation. Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = dec,

doi = "10.1038/s41467-022-31220-8",

language = "English (US)",

volume = "13",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Research",

number = "1",

}

Yuan, B, Zhou, X, Suzuki, K, Ramos-Mandujano, G, Wang, M , Tehseen, M, Cortés-Medina, LV, Moresco, JJ, Dunn, S, Hernandez-Benitez, R, Hishida, T, Kim, NY, Andijani, MM, Bi, C, Ku, M, Takahashi, Y, Xu, J, Qiu, J, Huang, L, Benner, C, Aizawa, E, Qu, J, Liu, GH, Li, Z, Yi, F, Ghosheh, Y, Shao, C, Shokhirev, M, Comoli, P, Frassoni, F, Yates, JR, Fu, XD, Esteban, CR, Hamdan, S , Li, M & Izpisua Belmonte, JC 2022, 'Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing', Nature Communications, vol. 13, no. 1, 3646. https://doi.org/10.1038/s41467-022-31220-8

TY - JOUR

T1 - Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing

AU - Yuan, Baolei

AU - Zhou, Xuan

AU - Suzuki, Keiichiro

AU - Ramos-Mandujano, Gerardo

AU - Wang, Mengge

AU - Tehseen, Muhammad

AU - Cortés-Medina, Lorena V.

AU - Moresco, James J.

AU - Dunn, Sarah

AU - Hernandez-Benitez, Reyna

AU - Hishida, Tomoaki

AU - Kim, Na Young

AU - Andijani, Manal M.

AU - Bi, Chongwei

AU - Ku, Manching

AU - Takahashi, Yuta

AU - Xu, Jinna

AU - Qiu, Jinsong

AU - Huang, Ling

AU - Benner, Christopher

AU - Aizawa, Emi

AU - Qu, Jing

AU - Liu, Guang Hui

AU - Li, Zhongwei

AU - Yi, Fei

AU - Ghosheh, Yanal

AU - Shao, Changwei

AU - Shokhirev, Maxim

AU - Comoli, Patrizia

AU - Frassoni, Francesco

AU - Yates, John R.

AU - Fu, Xiang Dong

AU - Esteban, Concepcion Rodriguez

AU - Hamdan, Samir

AU - Li, Mo

AU - Izpisua Belmonte, Juan Carlos

N1 - Funding Information: We would like to thank B. Lubin for advice on hematopoiesis and assistance in cord blood unit procurement; C. Cole, R. Walker, J. Lieu, R. Tonai, and M. Swearingen for providing cord blood samples; Y. Zheng and Y. Tian for assistance on hematopoietic differentiation and flow cytometry; A. Shirbini for assistance on MST experiment and analysis; members of the Belmonte and Li lab for helpful discussions; Y. Zhang, A.T. Gutiérrez, A. Geobl, R.D. Soligalla and Y. Hishida for technical assistance, J.H. Xiong for help with MATLAB. L. Mack, J. Olvera, C. O’Connor, E. O’Connor and K. Marquez for help with flow cytometry; D. O’Keefe and M. Wang for critical reading of the manuscript; M. Schwarz, P. Schwarz, C. Xia, X. Zhang, and M.K.Y. Sicat for administrative help. We thank KAUST Visualization Core Lab for Avizo software support. We also thank KAUST Bioscience core lab for sequencing support and KAUST Imaging and Characterization core lab for help with confocal microscopy. The research of the Li laboratory was supported by KAUST Office of Sponsored Research (OSR), under award numbers BAS/1/1080-01 and URF/1/4716-01. This work was supported by the Waitt Advanced Biophotonics Core Facility of the Salk Institute with funding from NIH-NCI CCSG: P30 014195, NINDS Neuroscience Core Grant, and the Waitt Foundation. G.H.L. was supported by the National Key Research and Development Program of China (2020YFA0804000), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16010000), the National Natural Science Foundation of China (Grant Nos. 81921006, 92149301, 92168201). J.C.I.B. was supported by grants from The Moxie Foundation, G. Harold and Leila Y. Mathers Charitable Foundation. Publisher Copyright: © 2022, The Author(s).

PY - 2022/12

Y1 - 2022/12

N2 - The diverse functions of WASP, the deficiency of which causes Wiskott-Aldrich syndrome (WAS), remain poorly defined. We generated three isogenic WAS models using patient induced pluripotent stem cells and genome editing. These models recapitulated WAS phenotypes and revealed that WASP deficiency causes an upregulation of numerous RNA splicing factors and widespread altered splicing. Loss of WASP binding to splicing factor gene promoters frequently leads to aberrant epigenetic activation. WASP interacts with dozens of nuclear speckle constituents and constrains SRSF2 mobility. Using an optogenetic system, we showed that WASP forms phase-separated condensates that encompasses SRSF2, nascent RNA and active Pol II. The role of WASP in gene body condensates is corroborated by ChIPseq and RIPseq. Together our data reveal that WASP is a nexus regulator of RNA splicing that controls the transcription of splicing factors epigenetically and the dynamics of the splicing machinery through liquid-liquid phase separation.

AB - The diverse functions of WASP, the deficiency of which causes Wiskott-Aldrich syndrome (WAS), remain poorly defined. We generated three isogenic WAS models using patient induced pluripotent stem cells and genome editing. These models recapitulated WAS phenotypes and revealed that WASP deficiency causes an upregulation of numerous RNA splicing factors and widespread altered splicing. Loss of WASP binding to splicing factor gene promoters frequently leads to aberrant epigenetic activation. WASP interacts with dozens of nuclear speckle constituents and constrains SRSF2 mobility. Using an optogenetic system, we showed that WASP forms phase-separated condensates that encompasses SRSF2, nascent RNA and active Pol II. The role of WASP in gene body condensates is corroborated by ChIPseq and RIPseq. Together our data reveal that WASP is a nexus regulator of RNA splicing that controls the transcription of splicing factors epigenetically and the dynamics of the splicing machinery through liquid-liquid phase separation.

UR - http://www.scopus.com/inward/record.url?scp=85132991488&partnerID=8YFLogxK

U2 - 10.1038/s41467-022-31220-8

DO - 10.1038/s41467-022-31220-8

M3 - Article

C2 - 35752626

AN - SCOPUS:85132991488

SN - 2041-1723

VL - 13

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 3646

ER -

Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing

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