ArticlePLoS genetics2007
Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells.
Article in PLoS genetics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
58 citing papers in PubMed, 1 synthesis or guideline pooled it, 88 citations in OpenAlex.
- A meta-analysis of microarray gene expression in mouse stem cells: redefining stemness.PloS one · 2008Pooled it
- 20 years of stemness: From stem cells to hypertranscription and back.Stem cell reports · 2025Review
- The role(s) of NF-Y in development and differentiation.Cell death and differentiation · 2025Review
- The lysine methyltransferase SMYD5 amplifies HIV-1 transcription and is post-transcriptionally upregulated by Tat and USP11.Cell reports · 2023Article
- Identification ofGenes · 2022Article
- The transcription factor NF-Y participates to stem cell fate decision and regeneration in adult skeletal muscle.Nature communications · 2021Article
- Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y.Scientific reports · 2020Article
- Sexually dimorphic DNA damage responses and mutation avoidance in the mouse germline.Genes & development · 2020Article
- Application of the RBBP9 Serine Hydrolase Inhibitor, ML114, Decouples Human Pluripotent Stem Cell Proliferation and Differentiation.International journal of molecular sciences · 2020Article
- Chromatin accessibility in canine stromal cells and its implications for canine somatic cell reprogramming.Stem cells translational medicine · 2020Article
- Discovery, characterization and potential roles of a novel NF-YAx splice variant in human neuroblastoma.Journal of experimental & clinical cancer research : CR · 2019Article
- Germline genome protection: implications for gamete quality and germ cell tumorigenesis.Andrology · 2019Review
- In silico design of context-responsive mammalian promoters with user-defined functionality.Nucleic acids research · 2017Article
- Global Hypertranscription in the Mouse Embryonic Germline.Cell reports · 2017Article
- NF-Y (CBF) regulation in specific cell types and mouse models.Biochimica et biophysica acta. Gene regulatory mechanisms · 2017Review
- Prognostic role of NF-YA splicing isoforms and Lamin A status in low grade endometrial cancer.Oncotarget · 2017Article
- Differential roles of NF-Y transcription factor in ER chaperone expression and neuronal maintenance in the CNS.Scientific reports · 2016Article
- The NSL Chromatin-Modifying Complex Subunit KANSL2 Regulates Cancer Stem-like Properties in Glioblastoma That Contribute to Tumorigenesis.Cancer research · 2016Article
- NF-YB Regulates Spermatogonial Stem Cell Self-Renewal and Proliferation in the Planarian Schmidtea mediterranea.PLoS genetics · 2016Article
- Specification and function of hemogenic endothelium during embryogenesis.Cellular and molecular life sciences : CMLS · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 3 countries.
Funding
Abstract
Understanding the transcriptional regulation of pluripotent cells is of fundamental interest and will greatly inform efforts aimed at directing differentiation of embryonic stem (ES) cells or reprogramming somatic cells. We first analyzed the transcriptional profiles of mouse ES cells and primordial germ cells and identified genes upregulated in pluripotent cells both in vitro and in vivo. These genes are enriched for roles in transcription, chromatin remodeling, cell cycle, and DNA repair. We developed a novel computational algorithm, CompMoby, which combines analyses of sequences both aligned and non-aligned between different genomes with a probabilistic segmentation model to systematically predict short DNA motifs that regulate gene expression. CompMoby was used to identify conserved overrepresented motifs in genes upregulated in pluripotent cells. We show that the motifs are preferentially active in undifferentiated mouse ES and embryonic germ cells in a sequence-specific manner, and that they can act as enhancers in the context of an endogenous promoter. Importantly, the activity of the motifs is conserved in human ES cells. We further show that the transcription factor NF-Y specifically binds to one of the motifs, is differentially expressed during ES cell differentiation, and is required for ES cell proliferation. This study provides novel insights into the transcriptional regulatory networks of pluripotent cells. Our results suggest that this systematic approach can be broadly applied to understanding transcriptional networks in mammalian species.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.