Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube Article Swipe
Zainab Afzal
,
Jeffrey J. Lange
,
Christof Nolte
,
Sean McKinney
,
Christopher Wood
,
Ariel Paulson
,
Bony De Kumar
,
Jay R. Unruh
,
Brian D. Slaughter
,
Robb Krumlauf
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1101/2022.08.30.505933
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1101/2022.08.30.505933
Signaling pathways regulate the patterns of Hox gene expression that underlie their functions in specification of axial identity. Little is known about the properties of cis -regulatory elements and underlying transcriptional mechanisms that integrate graded signaling inputs to coordinately control Hox expression. Here we optimized single molecule fluorescent in situ hybridization (smFISH) technique with probes spanning introns to evaluate how three shared retinoic acid response element (RARE)-dependent enhancers in the Hoxb cluster regulate patterns of nascent transcription in vivo at the level of single cells in wild type and mutant embryos. We predominately detect nascent transcription of only a single Hoxb gene in each cell, with no evidence for simultaneous co-transcriptional coupling of all or specific subsets of genes. Single and/or compound RARE mutations indicate each enhancer differentially impacts global and local patterns of nascent transcription, suggesting that selectivity and competitive interactions between these enhancers is important to robustly maintain the proper levels and patterns of nascent Hoxb transcription. This implies rapid and dynamic regulatory interactions potentiate transcription of genes through combined inputs from these enhancers in coordinating the RA response.
Related Topics
Concepts
Enhancer
Hox gene
Retinoic acid
Biology
Transcription (linguistics)
Enhancer RNAs
Transcription factor
Cell biology
Gene
Genetics
Linguistics
Philosophy
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2022.08.30.505933
- https://www.biorxiv.org/content/biorxiv/early/2022/08/30/2022.08.30.505933.full.pdf
- OA Status
- green
- References
- 119
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4293728069
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4293728069Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2022.08.30.505933Digital Object Identifier
- Title
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Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tubeWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2022Year of publication
- Publication date
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2022-08-30Full publication date if available
- Authors
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Zainab Afzal, Jeffrey J. Lange, Christof Nolte, Sean McKinney, Christopher Wood, Ariel Paulson, Bony De Kumar, Jay R. Unruh, Brian D. Slaughter, Robb KrumlaufList of authors in order
- Landing page
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https://doi.org/10.1101/2022.08.30.505933Publisher landing page
- PDF URL
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https://www.biorxiv.org/content/biorxiv/early/2022/08/30/2022.08.30.505933.full.pdfDirect link to full text PDF
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YesWhether a free full text is available
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-
greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2022/08/30/2022.08.30.505933.full.pdfDirect OA link when available
- Concepts
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Enhancer, Hox gene, Retinoic acid, Biology, Transcription (linguistics), Enhancer RNAs, Transcription factor, Cell biology, Gene, Genetics, Linguistics, PhilosophyTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
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119Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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