Dynamic in vivo binding of transcription factors to cis-regulatory modules of cer and gsc in the stepwise formation of the Spemann-Mangold organizer

ABSTRACTTranscription factors (TFs) are often used repeatedly during development and homeostasis to control distinct processes in the same and/or different cellular contexts. Considering the limited number of TFs in the genome and the tremendous number of events that need to be regulated, re-use of TFs is necessary. We analyzed how the expression of the homeobox TF, orthodenticle homeobox 2 (Otx2), is regulated in a cell type- and stage-specific manner during development in the mouse retina. We identified seven Otx2 cis-regulatory modules (CRMs), among which the O5, O7 and O9 CRMs mark three distinct cellular contexts of Otx2 expression. We discovered that Otx2, Crx and Sox2, which are well-known TFs regulating retinal development, bind to and activate the O5, O7 or O9 CRMs, respectively. The chromatin status of these three CRMs was found to be distinct in vivo in different retinal cell types and at different stages. We conclude that retinal cells use a cohort of TFs with different expression patterns and multiple CRMs with different chromatin configurations to regulate the expression of Otx2 precisely.

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Cell type- and stage-specific expression of Otx2 is coordinated by a cohort of transcription factors and multiple cis-regulatory modules in the retina

10.1101/2019.12.19.882969 ◽

2019 ◽

Cited By ~ 2

Author(s):

Candace Chan ◽

Nicolas Lonfat ◽

Rong Zhao ◽

Alexander Davis ◽

Liang Li ◽

...

Keyword(s):

Transcription Factors ◽

Expression Patterns ◽

Cell Types ◽

Retinal Cell ◽

Cell Type ◽

Specific Expression ◽

Regulatory Modules ◽

Specific Manner ◽

A Cell

AbstractTranscription factors (TFs) are often used repeatedly during development and homeostasis to control distinct processes in the same and/or different cellular contexts. Considering the limited number of TFs in the genome and the tremendous number of events that need to be regulated, re-use of TFs is an advantageous strategy. However, the mechanisms that control the activation of TFs in different cell types and at different stages of development remain unclear. The neural retina serves as a model of the development of a complex tissue. We used this system to analyze how expression of the homeobox TF, Orthodenticle homeobox 2 (Otx2), is regulated in a cell type- and stage-specific manner during retinogenesis. We identified seven Otx2 cis-regulatory modules (CRMs), among which the O5, O7 and O9 CRMs mark three distinct cellular contexts of Otx2 expression. These include mature bipolar interneurons, photoreceptors, and retinal progenitor/precursor cells. We discovered that Otx2, Crx and Sox2, which are well-known TFs regulating retinal development, bind to and activate the O5, O7 or O9 CRMs respectively. The chromatin status of these three CRMs was found to be distinct in vivo in different retinal cell types and at different stages, as revealed by ATAC-seq and DNase-seq analyses. We conclude that retinal cells utilize a cohort of TFs with different expression patterns, and multiple CRMs with different chromatin configurations, to precisely regulate the expression of Otx2 in a cell type- and stage-specific manner in the retina.

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Chromatin Immunoprecipitation Experiments to Investigate In Vivo Binding of Arabidopsis Transcription Factors to Target Sequences

Plant Signal Transduction - Methods in Molecular Biology ◽

10.1007/978-1-59745-289-2_17 ◽

2009 ◽

pp. 261-272 ◽

Cited By ~ 5

Author(s):

Benjamin Fode ◽

Christiane Gatz

Keyword(s):

Transcription Factors ◽

Chromatin Immunoprecipitation ◽

In Vivo Binding ◽

Target Sequences

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Faculty Opinions recommendation of Intrinsically disordered regions direct transcription factor in vivo binding specificity.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.738147787.793576666 ◽

2020 ◽

Author(s):

Andrew D Sharrocks

Keyword(s):

Transcription Factor ◽

Binding Specificity ◽

Direct Transcription ◽

In Vivo Binding ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Disordered Regions

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Faculty Opinions recommendation of Intrinsically disordered regions direct transcription factor in vivo binding specificity.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.738147787.793575950 ◽

2020 ◽

Author(s):

Vladimir Uversky

Keyword(s):

Transcription Factor ◽

Binding Specificity ◽

Direct Transcription ◽

In Vivo Binding ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Disordered Regions

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Subnuclear compartmentalization of sequence-specific transcription factors and regulation of eukaryotic gene expression

Biochemistry and Cell Biology ◽

10.1139/o05-062 ◽

2005 ◽

Vol 83 (4) ◽

pp. 535-547 ◽

Cited By ~ 7

Author(s):

Gareth N Corry ◽

D Alan Underhill

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Transcription Factors ◽

Transcriptional Activation ◽

Current Knowledge ◽

Nuclear Architecture ◽

Subnuclear Localization ◽

Modular Structures

To date, the majority of the research regarding eukaryotic transcription factors has focused on characterizing their function primarily through in vitro methods. These studies have revealed that transcription factors are essentially modular structures, containing separate regions that participate in such activities as DNA binding, protein–protein interaction, and transcriptional activation or repression. To fully comprehend the behavior of a given transcription factor, however, these domains must be analyzed in the context of the entire protein, and in certain cases the context of a multiprotein complex. Furthermore, it must be appreciated that transcription factors function in the nucleus, where they must contend with a variety of factors, including the nuclear architecture, chromatin domains, chromosome territories, and cell-cycle-associated processes. Recent examinations of transcription factors in the nucleus have clarified the behavior of these proteins in vivo and have increased our understanding of how gene expression is regulated in eukaryotes. Here, we review the current knowledge regarding sequence-specific transcription factor compartmentalization within the nucleus and discuss its impact on the regulation of such processes as activation or repression of gene expression and interaction with coregulatory factors.Key words: transcription, subnuclear localization, chromatin, gene expression, nuclear architecture.

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Regulation of sarcomagenesis by the empty spiracles homeobox genes EMX1 and EMX2

Cell Death and Disease ◽

10.1038/s41419-021-03801-w ◽

2021 ◽

Vol 12 (6) ◽

Author(s):

Manuel Pedro Jimenez-García ◽

Antonio Lucena-Cacace ◽

Daniel Otero-Albiol ◽

Amancio Carnero

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Transcription Factors ◽

Neural Crest ◽

Tumor Suppressors ◽

Homeobox Genes ◽

Neuronal Cell ◽

Cell Gene Expression

AbstractThe EMX (Empty Spiracles Homeobox) genes EMX1 and EMX2 are two homeodomain gene members of the EMX family of transcription factors involved in the regulation of various biological processes, such as cell proliferation, migration, and differentiation, during brain development and neural crest migration. They play a role in the specification of positional identity, the proliferation of neural stem cells, and the differentiation of certain neuronal cell phenotypes. In general, they act as transcription factors in early embryogenesis and neuroembryogenesis from metazoans to higher vertebrates. The EMX1 and EMX2’s potential as tumor suppressor genes has been suggested in some cancers. Our work showed that EMX1/EMX2 act as tumor suppressors in sarcomas by repressing the activity of stem cell regulatory genes (OCT4, SOX2, KLF4, MYC, NANOG, NES, and PROM1). EMX protein downregulation, therefore, induced the malignance and stemness of cells both in vitro and in vivo. In murine knockout (KO) models lacking Emx genes, 3MC-induced sarcomas were more aggressive and infiltrative, had a greater capacity for tumor self-renewal, and had higher stem cell gene expression and nestin expression than those in wild-type models. These results showing that EMX genes acted as stemness regulators were reproduced in different subtypes of sarcoma. Therefore, it is possible that the EMX genes could have a generalized behavior regulating proliferation of neural crest-derived progenitors. Together, these results indicate that the EMX1 and EMX2 genes negatively regulate these tumor-altering populations or cancer stem cells, acting as tumor suppressors in sarcoma.

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