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RNA-sequencing of LEUTX-inducible H9 human embryonic stem cells

ABSTRACT: RNA-sequencing of LEUTX-inducible H9 human embryonic stem cells

PROVIDER: PRJEB45411 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR5992820.fastq.gz	Fastqsanger.gz
	ERR5992830.fastq.gz	Fastqsanger.gz
	ERR5992840.fastq.gz	Fastqsanger.gz
	ERR5992850.fastq.gz	Fastqsanger.gz
	ERR5992821.fastq.gz	Fastqsanger.gz

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RNA-sequencing of LEUTX-inducible H9 human embryonic stem cells

Project description:We generated an inducible DDdCas9VP192 activator cell line in H9 human embryonic stem cells using the Sleeping beauty transposition system. The guides targeting a LEUTX promoter and enhancers were introduced by PiggyBac transposition. Three sample types were generated: Promoter only, Promoter+Enhancer1, Promoter+Enhancer2. Cells were collected before and at 24 h, 48 h, and 72 h after doxycycline treatment, and subjected to STRT RNA-sequencing.

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Project description:TCF7L1 is a member of the T cell factor/Lymphoid enhancer factor (TCF/LEF) family of tran-scription factors that are part of the WNT/beta-CATENIN signaling pathway. TCF7L1 modulates transcription by interacting with other regulators on chromatin. TCF7L1 has been shown to be one of the key factors in maintaining pluripotency in human embryonic stem cells (ESCs). We previously demonstrated that the absence of TCF71 causes H9 hESCs to differentiate sponta-neously (Sierra et al., 2018 Development 145(4).pii:dev161075). Mechanistically, how TCF7L1 inhibits differentiation and keeps cells in the pluripotent state is not clear. Identifying transcrip-tional regulators on chromatin is a critical step to elucidating one of several molecular mecha-nisms controlled by TCF7L1. We previously developed a FLAG tagged TCF7L1 transgene that is controlled by a doxycycline-inducible TET-ON system and generated the H9-TCF7L1 line (Sier-ra et al., 2018 Development 145(4).pii:dev161075). Here we used the H9-TCF7L1 line and em-ployed the method called rapid immunoprecipitation (IP) mass spectrometry of endogenous pro-tein (RIME) (Mohammed et al., 2016 Nat Protoc 11(2):316-26) to identify TCF7L1-associated proteins on chromatin. Coupling of these two methods (the FLAG tagged TETON inducible sys-tem and RIME) allowed us to control the level of TCF7L1 expression in hESCs, immunopreci-pate TCF7L1 using an anti-FLAG antibody and capture TCF7L1-bound associated complexes on chromatin. Our MS analysis identified some known proteins that have been shown to associate with the WNT/beta-CATENIN/TCF/LEF pathway, as well as novel complexes that have not been linked with TCF7L1. Gene Ontology analysis suggest these proteins function in chromatin modi-fication, splicing, and RNA processing. Our data could create new ideas for in-depth studies of TCF7L1 controlling pluripotency in human ESCs and for understanding how TCF7L1 may act in other cell types.

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