TOBF1 modulates mouse embryonic stem cell fate through regulating alternative splicing of pluripotency genes
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Embryonic stem cells (ESCs) can undergo lineage-specific differentiation, giving rise to different cell types that constitute an organism. Although roles of transcription factors and chromatin modifiers in these cells have been described, how the alternative splicing (AS) machinery regulates their expression has not been sufficiently explored. Here, we show that the long non-coding RNA (lncRNA)-associated protein TOBF1 modulates the AS of transcripts necessary for maintaining stem cell identity in mouse ESCs. Among the genes affected is serine/arginine splicing factor 1 (SRSF1), whose AS leads to global changes in splicing and expression of a large number of downstream genes involved in the maintenance of ESC pluripotency. By overlaying information derived from TOBF1 chromatin occupancy, the distribution of its pluripotency-associated OCT-SOX binding motifs, and transcripts undergoing differential expression and AS upon its knockout, we describe local nuclear territories where these distinct events converge. Collectively, these contribute to the maintenance of mouse ESC identity.
| Originalsprog | Engelsk |
|---|---|
| Artikelnummer | 113177 |
| Tidsskrift | Cell Reports |
| Vol/bind | 42 |
| Udgave nummer | 10 |
| Antal sider | 22 |
| ISSN | 2211-1247 |
| DOI | |
| Status | Udgivet - 2023 |
Bibliografisk note
Funding Information:
The authors thank Dr. Amrita Singh and Ms. Rhythm Phutela from CSIR-IGIB for designing and creating the dual-sgRNA SpCas9 plasmid and the dFnCas9-KRAB plasmid, respectively, which were used for TOBF1 KO and CRISPRi experiments. The authors are grateful to all members of the Chakraborty and Maiti labs for helpful discussions and suggestions and to Dr. Shakti Sagar and Ms. Vandana Singh from CSIR IGIB for help with the microscopy experiments. This study was funded by an EMBO Young Investigator Award (GAP0252) and a Department of Biotechnology grant (GAP0188) to D.C. The mass spectrometry (MS) experiments were funded by EU FP7 grant SyBoSS (242129) to F.B. and C.C. The Novo Nordisk Foundation Center for Protein Research is financially supported by the Novo Nordisk Foundation (NNF14CC0001). M.A. S.M. and D.C. conceived, designed, and interpreted the experiments. A.H.A. analyzed and provided bioinformatics support for data interpretation. L.D. and F.B. analyzed and interpreted data from BAC-tagged cell lines. V.I. and C.C. performed and analyzed data from affinity purification studies. D.P. performed experiments with FUCCI-tagged ESC lines. M.A. and D.C. wrote the manuscript with input from all other authors. The authors declare no competing interests.
Funding Information:
The authors thank Dr. Amrita Singh and Ms. Rhythm Phutela from CSIR-IGIB for designing and creating the dual-sgRNA SpCas9 plasmid and the dFnCas9-KRAB plasmid, respectively, which were used for TOBF1 KO and CRISPRi experiments. The authors are grateful to all members of the Chakraborty and Maiti labs for helpful discussions and suggestions and to Dr. Shakti Sagar and Ms. Vandana Singh from CSIR IGIB for help with the microscopy experiments. This study was funded by an EMBO Young Investigator Award ( GAP0252 ) and a Department of Biotechnology grant ( GAP0188 ) to D.C. The mass spectrometry (MS) experiments were funded by EU FP7 grant SyBoSS ( 242129 ) to F.B. and C.C. The Novo Nordisk Foundation Center for Protein Research is financially supported by the Novo Nordisk Foundation ( NNF14CC0001 ).
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© 2023 The Authors
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