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Gene regulatory networks in neural cell fate acquisition from genome-wide chromatin association of Geminin and Zic1

View Article: PubMed Central - PubMed

ABSTRACT

Neural cell fate acquisition is mediated by transcription factors expressed in nascent neuroectoderm, including Geminin and members of the Zic transcription factor family. However, regulatory networks through which this occurs are not well defined. Here, we identified Geminin-associated chromatin locations in embryonic stem cells and Geminin- and Zic1-associated locations during neural fate acquisition at a genome-wide level. We determined how Geminin deficiency affected histone acetylation at gene promoters during this process. We integrated these data to demonstrate that Geminin associates with and promotes histone acetylation at neurodevelopmental genes, while Geminin and Zic1 bind a shared gene subset. Geminin- and Zic1-associated genes exhibit embryonic nervous system-enriched expression and encode other regulators of neural development. Both Geminin and Zic1-associated peaks are enriched for Zic1 consensus binding motifs, while Zic1-bound peaks are also enriched for Sox3 motifs, suggesting co-regulatory potential. Accordingly, we found that Geminin and Zic1 could cooperatively activate the expression of several shared targets encoding transcription factors that control neurogenesis, neural plate patterning, and neuronal differentiation. We used these data to construct gene regulatory networks underlying neural fate acquisition. Establishment of this molecular program in nascent neuroectoderm directly links early neural cell fate acquisition with regulatory control of later neurodevelopment.

No MeSH data available.


Zic1 over-expression during neural fate acquisition promotes the expression of Zic1-associated genes.(A) Browser views of selected Zic1-associated genes, tested below. (B,C) ES cells stably over-express Zic1 (Zic1 OE) after three days of neural cell fate acquisition (D3), as defined by qRTPCR for mRNA (B) and immunoblotting for protein (C). (D) Gene expression levels of Zic1-associated genes were defined by qRTPCR during 3 days of neural fate acquisition (D1-3), with versus without Zic1 overexpression. Gene expression levels on each day of NE fate acquisition are expressed relative to ES = 1.0 and p-values shown (student’s t-test) compare expression with versus without Zic1 OE on each day of the NE fate acquisition: ** =< 0.01, * =< 0.05, ns = not significant. Error bars represent standard deviation for a representative qPCR performed in triplicate.
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f5: Zic1 over-expression during neural fate acquisition promotes the expression of Zic1-associated genes.(A) Browser views of selected Zic1-associated genes, tested below. (B,C) ES cells stably over-express Zic1 (Zic1 OE) after three days of neural cell fate acquisition (D3), as defined by qRTPCR for mRNA (B) and immunoblotting for protein (C). (D) Gene expression levels of Zic1-associated genes were defined by qRTPCR during 3 days of neural fate acquisition (D1-3), with versus without Zic1 overexpression. Gene expression levels on each day of NE fate acquisition are expressed relative to ES = 1.0 and p-values shown (student’s t-test) compare expression with versus without Zic1 OE on each day of the NE fate acquisition: ** =< 0.01, * =< 0.05, ns = not significant. Error bars represent standard deviation for a representative qPCR performed in triplicate.

Mentions: We experimentally tested whether Zic1 over-expression could promote expression of a subset of genes that were predicted to be Zic1 associated in NE in our ChIP-seq data and that exhibited embryonic CNS-enriched expression (Fig. 5A). Expression of these genes increased during neural fate acquisition and Zic1 overexpression further promoted their expression during ES-NE fate acquisition (Fig. 5B–D). Therefore, comparison of Zic1-associated genes defined by ChIP-seq in NE with genes enriched in embryonic CNS in vivo can predict targets of Zic1-dependent activation during neural fate acquisition.


Gene regulatory networks in neural cell fate acquisition from genome-wide chromatin association of Geminin and Zic1
Zic1 over-expression during neural fate acquisition promotes the expression of Zic1-associated genes.(A) Browser views of selected Zic1-associated genes, tested below. (B,C) ES cells stably over-express Zic1 (Zic1 OE) after three days of neural cell fate acquisition (D3), as defined by qRTPCR for mRNA (B) and immunoblotting for protein (C). (D) Gene expression levels of Zic1-associated genes were defined by qRTPCR during 3 days of neural fate acquisition (D1-3), with versus without Zic1 overexpression. Gene expression levels on each day of NE fate acquisition are expressed relative to ES = 1.0 and p-values shown (student’s t-test) compare expression with versus without Zic1 OE on each day of the NE fate acquisition: ** =< 0.01, * =< 0.05, ns = not significant. Error bars represent standard deviation for a representative qPCR performed in triplicate.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5121602&req=5

f5: Zic1 over-expression during neural fate acquisition promotes the expression of Zic1-associated genes.(A) Browser views of selected Zic1-associated genes, tested below. (B,C) ES cells stably over-express Zic1 (Zic1 OE) after three days of neural cell fate acquisition (D3), as defined by qRTPCR for mRNA (B) and immunoblotting for protein (C). (D) Gene expression levels of Zic1-associated genes were defined by qRTPCR during 3 days of neural fate acquisition (D1-3), with versus without Zic1 overexpression. Gene expression levels on each day of NE fate acquisition are expressed relative to ES = 1.0 and p-values shown (student’s t-test) compare expression with versus without Zic1 OE on each day of the NE fate acquisition: ** =< 0.01, * =< 0.05, ns = not significant. Error bars represent standard deviation for a representative qPCR performed in triplicate.
Mentions: We experimentally tested whether Zic1 over-expression could promote expression of a subset of genes that were predicted to be Zic1 associated in NE in our ChIP-seq data and that exhibited embryonic CNS-enriched expression (Fig. 5A). Expression of these genes increased during neural fate acquisition and Zic1 overexpression further promoted their expression during ES-NE fate acquisition (Fig. 5B–D). Therefore, comparison of Zic1-associated genes defined by ChIP-seq in NE with genes enriched in embryonic CNS in vivo can predict targets of Zic1-dependent activation during neural fate acquisition.

View Article: PubMed Central - PubMed

ABSTRACT

Neural cell fate acquisition is mediated by transcription factors expressed in nascent neuroectoderm, including Geminin and members of the Zic transcription factor family. However, regulatory networks through which this occurs are not well defined. Here, we identified Geminin-associated chromatin locations in embryonic stem cells and Geminin- and Zic1-associated locations during neural fate acquisition at a genome-wide level. We determined how Geminin deficiency affected histone acetylation at gene promoters during this process. We integrated these data to demonstrate that Geminin associates with and promotes histone acetylation at neurodevelopmental genes, while Geminin and Zic1 bind a shared gene subset. Geminin- and Zic1-associated genes exhibit embryonic nervous system-enriched expression and encode other regulators of neural development. Both Geminin and Zic1-associated peaks are enriched for Zic1 consensus binding motifs, while Zic1-bound peaks are also enriched for Sox3 motifs, suggesting co-regulatory potential. Accordingly, we found that Geminin and Zic1 could cooperatively activate the expression of several shared targets encoding transcription factors that control neurogenesis, neural plate patterning, and neuronal differentiation. We used these data to construct gene regulatory networks underlying neural fate acquisition. Establishment of this molecular program in nascent neuroectoderm directly links early neural cell fate acquisition with regulatory control of later neurodevelopment.

No MeSH data available.