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The TFIID subunit Taf13 is dispensable for RNA polymerase II transcription, but essential for early embryogenesis (RNA-Seq)

ABSTRACT: The TFIID subunit Taf13 is dispensable for RNA polymerase II transcription, but essential for early embryogenesis (RNA-Seq)

PROVIDER: PRJNA1068142 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27699714.fastq.gz	Fastqsanger.gz
	SRR27699715.fastq.gz	Fastqsanger.gz
	SRR27699716.fastq.gz	Fastqsanger.gz
	SRR27699717.fastq.gz	Fastqsanger.gz
	SRR27699718.fastq.gz	Fastqsanger.gz

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The TFIID subunit Taf13 is dispensable for RNA polymerase II transcription, but essential for early embryogenesis

Project description:The TFIID subunit Taf13 is dispensable for RNA polymerase II transcription, but essential for early embryogenesis

| PRJNA1068141 | ENA

The TFIID subunit Taf13 is dispensable for RNA polymerase II transcription, but essential for early embryogenesis [CUT&TAG]

Project description:The TFIID subunit Taf13 is dispensable for RNA polymerase II transcription, but essential for early embryogenesis [CUT&TAG]

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The TFIID subunit Taf13 is dispensable for RNA polymerase II transcription, but essential for early embryogenesis (ChIP-Seq)

Project description:The TFIID subunit Taf13 is dispensable for RNA polymerase II transcription, but essential for early embryogenesis (ChIP-Seq)

| PRJNA1068143 | ENA

The TFIID subunit Taf13 is dispensable for RNA polymerase II transcription, but essential for early embryogenesis (ChIP-Seq)

Project description:RNA polymerase II transcription initiation requires assembly of a preinitiation complex (PIC). According to the stepwise model of PIC assembly, TFIID is the first GTF to be recruited. TFIID comprises TBP and 13 TBP-associated factors (TAFs). We focused on TAF13, the smallest subunit of TFIID. Taf13 has a histone-like domain that heterodimerizes with its partner Taf11. Recently published structures of TFIID place the Taf13-Taf11 heterodimer in lobe A where it forms a “bridge” between TBP and TFIID. According to this structure, the Taf11-Taf13 heterodimer has been suggested to be critical for TBP deposition at promoters. To better address this question, we generated mouse Embryonic Stem Cells (ESCs) cell lines and genetically modified mice where the gene coding for Taf13 was inactivated. Taf13-null mice died at E6.5-E7.5, whereas ESCs survived up to 15 days after inactivation of Taf13, but showed slower growth as compared to controls. To understand how Taf13 inactivation impacts TFIID and RNA polymerase II (Pol II) recruitment, we performed ChIP seq for the TBP and Taf1 subunits of TFIID along with PolII on ESC lines expressing or not Taf13. ChIP seq for histone marks H3K4Me3 and H3K27ac were also performed. Taf13 inactivation does not impair TBP recruitment at promoters, while that of Pol II was reduced both at the promoter and gene body. Surprisingly, recruitment of Taf1 was increased and while the H3K4Me3 mark was not affected, H3K27ac was notably increased in the absence of Taf13. Taken together, these data showed that loss of the Taf11-Taf13 heterodimer did not strongly impact TBP recruitment to promoters, but led to increased Taf1 and H3K27ac levels, but reduced paused and elongating Pol II.

2025-06-18 | GSE254023 | GEO

The TFIID subunit Taf13 is dispensable for RNA polymerase II transcription, but essential for early embryogenesis (RNA-Seq)

Project description:RNA polymerase II transcription initiation requires assembly of a preinitiation complex (PIC). According to the stepwise model of PIC assembly, TFIID is the first GTF to be recruited. TFIID comprises TBP and 13 TBP-associated factors (TAFs). We focused on TAF13, the smallest subunit of TFIID. Taf13 has a histone-like domain that heterodimerizes with its partner Taf11. Recently published structures of TFIID place the Taf13-Taf11 heterodimer in lobe A where it forms a “bridge” between TBP and TFIID. According to this structure, the Taf11-Taf13 heterodimer has been suggested to be critical for TBP deposition at promoters. To better address this question, we generated mouse Embryonic Stem Cells (ESCs) cell lines and genetically modified mice where the gene coding for Taf13 was inactivated. Taf13-null mice died at E6.5-E7.5, whereas ESCs survived up to 15 days after inactivation of Taf13, but showed slower growth as compared to controls. In order to understand how inactivation of Taf13 impact the genes expressions we performed bulk mRNA-seq from the Taf13 expressing and null lines. This analysis showed that loss of TAF13 resulted in a greater than two-fold upregulation of 562 genes but only 41 of them were up-regulated more than four-fold. On the other hand, 382 genes were down-regulated, 34 of which showed more than a four-fold repression. Ontology analyses showed that the affected genes did not belong to any specific pathway, but we noticed that many primitive endoderm markers were up-regulated by TAF13 deficiency (Sox7, Sox17, Gata4, Gata6) and some ESC markers were downregulated (Nanog, Klf4, Zfp42) while the pluripotency markers Sox2 and Oct3/4 were unchanged.

2025-06-18 | GSE254024 | GEO

The TFIID subunit Taf13 is dispensable for RNA polymerase II transcription, but essential for early embryogenesis [CUT&TAG]

Project description:RNA polymerase II (Pol II) transcription initiation requires assembly of a preinitiation complex (PIC) comprising the general transcription factors amongst which the multiprotein complex TFIID. TFIID comprises the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). Recent cryo-electron microscopy studies reported topological reorganization of TFIID upon promoter binding with the TAF11-TAF13 heterodimer as the last TFIID subunits directly contacting TBP prior to deposition on promoter DNA upstream of the transcription start site. To challenge the role of the TAF11-TAF13 heterodimer, we inactivated the gene encoding Taf13 both in mice and embryonic stem cells (ESCs). Taf13 inactivation in mice is embryonic lethal with null embryos implanting but surviving only until E6.5. Taf13-null ESCs are viable, but show slower proliferation and fail to form embryoid bodies and differentiate. Biochemical analyses from these ESCs show that Taf13 loss had minimal effect on TFIID integrity, and genomic profiling shows only a mild reduction of promoter recruitment of TBP and Taf4 while that of Taf1 is increased. Moreover, while TFIIH recruitment is unaffected indicating normal PIC formation, that of Pol II is globally diminished. These data indicate that the Taf11-Taf13 heterodimer is not essential for TBP/TFIID recruitment and PIC formation, but is specifically required for normal Pol II recruitment.

2025-06-18 | GSE282035 | GEO

TAF1, the largest subunit of TFIID, is dispensable for adult hematopoiesis [RNA-Seq]

Project description:TAF1, the largest subunit of TFIID, is dispensable for adult hematopoiesis [RNA-Seq]

| PRJNA1045523 | ENA

TAF1, the largest subunit of TFIID, is dispensable for adult hematopoiesis [ATAC-Seq]

Project description:TAF1, the largest subunit of TFIID, is dispensable for adult hematopoiesis [ATAC-Seq]

| PRJNA1045513 | ENA

TAF1, the largest subunit of TFIID, is dispensable for adult hematopoiesis [scRNA-Seq]

Project description:TAF1, the largest subunit of TFIID, is dispensable for adult hematopoiesis [scRNA-Seq]

| PRJNA1045526 | ENA

TAF1, the largest subunit of TFIID, is dispensable for adult hematopoiesis [ChIP-Seq]

Project description:TAF1, the largest subunit of TFIID, is dispensable for adult hematopoiesis [ChIP-Seq]