Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The emergence of the stem cell-associated Sox and POU transcription factors predates animal origins (Spec-Seq)

ABSTRACT: The emergence of the stem cell-associated Sox and POU transcription factors predates animal origins (Spec-Seq)

PROVIDER: PRJNA1067621 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR27682408_1.fastq.gz	Fastqsanger.gz
	SRR27682408_2.fastq.gz	Fastqsanger.gz
	SRR27682409_1.fastq.gz	Fastqsanger.gz
	SRR27682409_2.fastq.gz	Fastqsanger.gz
	SRR27682410_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 68

Similar Datasets

The emergence of the stem cell-associated Sox and POU transcription factors predates animal origins (Spec-Seq)

Project description:Pluripotent stem cells are a hallmark of animal multicellularity. Sox and POU family transcription factors are pivotal for stemness and were believed to be animal innovations as they were reported absent from the genomes of their unicellular relatives. Here we describe new unicellular holozoan orthologues to Sox and POU families, indicating that they emerged before the appearance of animals. We show that choanoflagellate and filasterean Sox genes have DNA binding specificity similar to Sox2. Choanoflagellate Sox can partner with the POU member Oct4 on DNA elements found in pluripotency enhancers. Consistently, choanoflagellate – but not filasterean – Sox genes can replace Sox2 to reprogram mouse somatic cells into induced pluripotent stem cells (iPSC). In contrast, choanoflagellate POU harbors a unique DNA-binding profile that differs from Oct4 and cannot generate iPSCs. Pluripotency reprogramming with reconstructed ancestral Sox genes shows that their molecular ability to induce stemness was already present in the last common ancestor of animals and their unicellular relatives. Our findings imply that the evolution of stem cells exploited a pre-existing set of transcription factors, where the critical innovation involved an initial change in DNA specificity of POU and the exaptation of the ancestral capacity to interact with Sox transcription factors.

2024-10-23 | GSE253886 | GEO

The emergence of the stem cell-associated Sox and POU transcription factors predates animal origins (SELEX)

2024-10-23 | GSE253887 | GEO

The emergence of the stem cell-associated Sox and POU transcription factors predates animal origins

Project description:The emergence of the stem cell-associated Sox and POU transcription factors predates animal origins

| PRJNA1067618 | ENA

The emergence of the stem cell-associated Sox and POU transcription factors predates animal origins (SELEX)

Project description:The emergence of the stem cell-associated Sox and POU transcription factors predates animal origins (SELEX)

| PRJNA1067620 | ENA

The emergence of the stem cell-associated Sox and POU transcription factors predates animal origins

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-10-23 | GSE253888 | GEO

Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells

Project description:Embryonic stem cell (ESCs) identity is orchestrated by co-operativity between the transcription factors (TFs) Sox2 and the class V POU-TF, Oct4 at composite Sox/Oct motifs. Neural stem cells (NSCs) lack Oct4 but express Sox2 and class III POU-TFs. This raises the question of how Sox2 interacts with POU-TFs to transcriptionally specify ESCs or NSCs. Here we show that Oct4 alone binds the Sox/Oct motif and the octamer-containing palindromic MORE equally well. Sox2 binding selectively increases the affinity of Oct4 for the Sox/Oct motif. In contrast, Oct6 binds preferentially to the MORE, and is unaffected by Sox2. ChIP-seq in NSCs shows the MORE to be the most enriched motif for class III POU-TFs, with MORE sub-types apparent, but no Sox/Oct motif enrichment. These results suggest that in NSCs, co-operativity between Sox2 and class III POU-TFs may not occur and that POU-TF driven transcription uses predominantly the MORE cis architecture. Thus, distinct interactions between Sox2 and POU-TF subclasses distinguish pluripotent ESCs from multipotent NSCs, providing molecular insight into how Oct4 alone can convert NSCs to pluripotency.

2015-08-21 | GSE69859 | GEO

CTCF Spec-seq

Project description:CTCF Spec-seq

| PRJNA777865 | ENA

Spec-seq sequencing data for CTCF [2021 series]

Project description:This series is an updated dataset consisting of the Spec-seq and Methyl-Spec-seq samples for human CTCF with a bigger sequencing libraries and different epigenetic modifications. Each sample has replicate to gurantee the reproducibility for each measurement.

2021-11-06 | GSE188164 | GEO

Methyl-Spec-seq control data sets

Project description:We developed a novel in-vitro experimental method to characterize the protein-DNA interaction specificity and methylation sensitivity, we called Methyl-Spec-seq. In this data set, mouse ZFP57 (F1-F3) was used as a positive control example to show that Methyl-Spec-seq can determine the relative binding energy for variants with different methylation property, i.e., unmethylated, top hemimethylated, bottom hemimethylated, duplex methylated by either chemical synthesis or enzymatic treatment.

2017-05-10 | GSE98542 | GEO

Methyl-Spec-seq control data sets

2017-08-31 | GSE98686 | GEO