ArticleGenome research2015
Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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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.
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Who cites it
32 citing papers in PubMed, 72 citations in OpenAlex.
- Biology of Hox Genes: Questions and Technological Challenges.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Transcription ofJournal of developmental biology · 2023Article
- Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube.Development (Cambridge, England) · 2023Article
- A conservedRNA biology · 2023Article
- Exploring differential exon usage via short- and long-read RNA sequencing strategies.Open biology · 2022Article
- Sex-biased and parental allele-specific gene regulation by KDM6A.Biology of sex differences · 2022Article
- Synthetic regulatory reconstitution reveals principles of mammalianScience (New York, N.Y.) · 2022Article
- Transcriptional Regulation and Implications for ControllingJournal of developmental biology · 2022Review
- Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq.Nucleic acids research · 2021Article
- Pontin Functions as A Transcriptional Co-activator for Retinoic Acid-induced HOX Gene Expression.Journal of molecular biology · 2021Article
- Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature.Epigenetics & chromatin · 2021Article
- Genome-Wide Binding Analyses of HOXB1 Revealed a Novel DNA Binding Motif Associated with Gene Repression.Journal of developmental biology · 2021Article
- Gene- and Species-Specific Hox mRNA Translation by Ribosome Expansion Segments.Molecular cell · 2020Article
- lncRNA HotairM1 Depletion Promotes Self-Renewal of Cancer Stem Cells through HOXA1-Nanog Regulation Loop.Molecular therapy. Nucleic acids · 2020Article
- A six-amino-acid motif is a major determinant in functional evolution of HOX1 proteins.Genes & development · 2020Article
- Evolving Role of RING1 and YY1 Binding Protein in the Regulation of Germ-Cell-Specific Transcription.Genes · 2019Review
- Hematopoietic Differentiation of Human Pluripotent Stem Cells: HOX and GATA Transcription Factors as Master Regulators.Current genomics · 2019Review
- Abnormal level of CUL4B-mediated histone H2A ubiquitination causes disruptive HOX gene expression.Epigenetics & chromatin · 2019Article
- A Hox-TALE regulatory circuit for neural crest patterning is conserved across vertebrates.Nature communications · 2019Article
- First report case with negative genetic study (array CGH, exome sequencing) in patients with vertical transmission of Zika virus infection and associated brain abnormalities.The application of clinical genetics · 2019Article
Corrections and comments
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Authors and funding
17 authors at 1 institution in 1 country.
Funding
Abstract
The clustered Hox genes, which are highly conserved across metazoans, encode homeodomain-containing transcription factors that provide a blueprint for segmental identity along the body axis. Recent studies have underscored that in addition to encoding Hox genes, the homeotic clusters contain key noncoding RNA genes that play a central role in development. In this study, we have taken advantage of genome-wide approaches to provide a detailed analysis of retinoic acid (RA)-induced transcriptional and epigenetic changes within the homeotic clusters of mouse embryonic stem cells. Although there is a general colinear response, our analyses suggest a lack of strict colinearity for several genes in the HoxA and HoxB clusters. We have identified transcribed novel noncoding RNAs (ncRNAs) and their cis-regulatory elements that function in response to RA and demonstrated that the expression of these ncRNAs from both strands represent some of the most rapidly induced transcripts in ES cells. Finally, we have provided dynamic analyses of chromatin modifications for the coding and noncoding genes expressed upon activation and suggest that active transcription can occur in the presence of chromatin modifications and machineries associated with repressed transcription state over the clusters. Overall, our data provide a resource for a better understanding of the dynamic nature of the coding and noncoding transcripts and their associated chromatin marks in the regulation of homeotic gene transcription during development.
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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.