Wnt and Bmp signalling cooperatively regulate graded Emx2 expression in the dorsal telencephalon

Development ◽  
2002 ◽  
Vol 129 (13) ◽  
pp. 3045-3054 ◽  
Author(s):  
Thomas Theil ◽  
Songül Aydin ◽  
Silke Koch ◽  
Lars Grotewold ◽  
Ulrich Rüther
Keyword(s):  
Binding Sites ◽  
Ectopic Expression ◽  
Gene Families ◽  
Specific Expression ◽  
Enhancer Activity ◽  
Molecular Control ◽  
Smad Proteins ◽  
Ectopic Activation ◽  
Dorsal Telencephalon ◽  
Bmp Signalling

Pattern formation of the dorsal telencephalon is governed by a regionalisation process that leads to the formation of distinct domains, including the future hippocampus and neocortex. Recent studies have implicated signalling proteins of the Wnt and Bmp gene families as well as several transcription factors, including Gli3 and the Emx homeobox genes, in the molecular control of this process. The regulatory relationships between these genes, however, remain largely unknown. We have used transgenic analysis to investigate the upstream mechanisms for regulation of Emx2 in the dorsal telencephalon. We have identified an enhancer from the mouse Emx2 gene that drives specific expression of a lacZ reporter gene in the dorsal telencephalon. This element contains binding sites for Tcf and Smad proteins, transcriptional mediators of the Wnt and Bmp signalling pathway, respectively. Mutations of these binding sites abolish telencephalic enhancer activity, while ectopic expression of these signalling pathways leads to ectopic activation of the enhancer. These results establish Emx2 as a direct transcriptional target of Wnt and Bmp signalling and provide insights into a genetic hierarchy involving Gli3, Emx2 and Bmp and Wnt genes in the control of dorsal telencephalic development.

Segmental expression of the EphA4 (Sek-1) receptor tyrosine kinase in the hindbrain is under direct transcriptional control of Krox-20

Development ◽  
1998 ◽  
Vol 125 (3) ◽  
pp. 443-452 ◽  
Author(s):  
T. Theil ◽  
M. Frain ◽  
P. Gilardi-Hebenstreit ◽  
A. Flenniken ◽  
P. Charnay ◽  
...  
Keyword(s):  
Tyrosine Kinase ◽  
Receptor Tyrosine Kinase ◽  
Binding Sites ◽  
Cell Signalling ◽  
Ectopic Expression ◽  
Regulatory Sequences ◽  
Kinase Gene ◽  
Specific Expression ◽  
Enhancer Activity ◽  
Enhancer Element

Segmentation of the vertebrate hindbrain leads to the formation of a series of rhombomeres (r) with distinct identities. Recent studies have uncovered regulatory links between transcription factors governing this process, but little is known of how these relate to molecules mediating cell-cell signalling. The Eph receptor tyrosine kinase gene EphA4 (Sek-1) is expressed in r3 and r5, and function-blocking experiments suggest that it is involved in restricting intermingling of cells between odd- and even-numbered rhombomeres. We have analysed the cis-acting regulatory sequences of the EphA4 gene in transgenic mice and identified a 470 bp enhancer element that drives specific expression in r3 and r5. Within this element, we have identified eight binding sites for the Krox-20 transcription factor that is also expressed in r3 and r5. Mutation of these binding sites abolishes r3/r5 enhancer activity and ectopic expression of Krox-20 leads to ectopic activation of the enhancer. These data indicate that Krox-20 is a direct transcriptional activator of EphA4. Together with evidence that Krox-20 regulates Hox gene expression, our findings reveal a mechanism by which the identity and movement of cells are coupled such that sharply restricted segmental domains are generated.

scholarly journals Transcription factor GATA-4 regulates cardiac muscle-specific expression of the alpha-myosin heavy-chain gene.

1994 ◽  
Vol 14 (7) ◽  
pp. 4947-4957 ◽  
Author(s):  
J D Molkentin ◽  
D V Kalvakolanu ◽  
B E Markham
Keyword(s):  
Skeletal Muscle ◽  
Transcription Factor ◽  
Retinoic Acid ◽  
Cardiac Muscle ◽  
Myosin Heavy Chain ◽  
Heavy Chain ◽  
Binding Sites ◽  
Ectopic Expression ◽  
Specific Expression ◽  
Cardiac Phenotype

The alpha-myosin heavy-chain (alpha-MHC) gene is the major structural protein in the adult rodent myocardium. Its expression is restricted to the heart by a complex interplay of trans-acting factors and their cis-acting sites. However, to date, the factors that have been shown to regulate expression of this gene have also been found in skeletal muscle cells. Recently, transcription factor GATA-4, which has a tissue distribution limited to the heart and endodermally derived tissues, was identified. We recently found two putative GATA-binding sites within the proximal enhancer of the alpha-MHC gene, suggesting that GATA-4 might regulate its expression. In this study, we establish that GATA-4 interacts with the alpha-MHC GATA sites to stimulate cardiac muscle-specific expression. Mutation of the GATA-4-binding sites either individually or together decreased activity by 50 and 88% in the adult myocardium, respectively. GATA-4-dependent enhancement of activity from a heterologous promoter was mediated through the alpha-MHC GATA sites. Coinjection of an alpha-MHC promoter construct with a GATA-4 expression vector permitted ectopic expression in skeletal muscle but not in fibroblasts. Thus, the lack of alpha-MHC expression in skeletal muscle correlates with a lack of GATA-4. GATA-4 DNA binding activity was significantly up-regulated in triiodothyronine- or retinoic acid-treated cardiomyocytes. Putative GATA-4-binding sites are also found in the regulatory regions of other cardiac muscle-expressed structural genes. This indicates a mechanism whereby triiodothyronine and retinoic acid can exert coordinate control of the cardiac phenotype through a trans-acting regulatory factor.

Notch signaling is required for arterial-venous differentiation during embryonic vascular development

Development ◽  
2001 ◽  
Vol 128 (19) ◽  
pp. 3675-3683 ◽  
Author(s):  
Nathan D. Lawson ◽  
Nico Scheer ◽  
Van N. Pham ◽  
Cheol-Hee Kim ◽  
Ajay B. Chitnis ◽  
...  
Keyword(s):  
Notch Signaling ◽  
Blood Vessels ◽  
Cell Fate ◽  
Venous Blood ◽  
Vascular Development ◽  
Ectopic Expression ◽  
Specific Expression ◽  
Ectopic Activation ◽  
On Line ◽  
Embryonic Vascular Development

Recent evidence indicates that acquisition of artery or vein identity during vascular development is governed, in part, by genetic mechanisms. The artery-specific expression of a number of Notch signaling genes in mouse and zebrafish suggests that this pathway may play a role in arterial-venous cell fate determination during vascular development. We show that loss of Notch signaling in zebrafish embryos leads to molecular defects in arterial-venous differentiation, including loss of artery-specific markers and ectopic expression of venous markers within the dorsal aorta. Conversely, we find that ectopic activation of Notch signaling leads to repression of venous cell fate. Finally, embryos lacking Notch function exhibit defects in blood vessel formation similar to those associated with improper arterial-venous specification. Our results suggest that Notch signaling is required for the proper development of arterial and venous blood vessels, and that a major role of Notch signaling in blood vessels is to repress venous differentiation within developing arteries.Movies available on-line

Spatially specific expression of Hoxb4 is dependent on the ubiquitous transcription factor NFY

Development ◽  
2002 ◽  
Vol 129 (16) ◽  
pp. 3887-3899 ◽  
Author(s):  
Jonathan Gilthorpe ◽  
Marie Vandromme ◽  
Tim Brend ◽  
Alejandro Gutman ◽  
Dennis Summerbell ◽  
...  
Keyword(s):  
Gene Expression ◽  
Binding Sites ◽  
Specific Interaction ◽  
Transcriptional Regulators ◽  
Heterologous Promoter ◽  
Specific Expression ◽  
Enhancer Activity ◽  
Hox Gene ◽  
Two Factors ◽  
Enhancer Function

Understanding how boundaries and domains of Hox gene expression are determined is critical to elucidating the means by which the embryo is patterned along the anteroposterior axis. We have performed a detailed analysis of the mouse Hoxb4 intron enhancer to identify upstream transcriptional regulators. In the context of an heterologous promoter, this enhancer can establish the appropriate anterior boundary of mesodermal expression but is unable to maintain it, showing that a specific interaction with its own promoter is important for maintenance. Enhancer function depends on a motif that contains overlapping binding sites for the transcription factors NFY and YY1. Specific mutations that either abolish or reduce NFY binding show that it is crucial for enhancer activity. The NFY/YY1 motif is reiterated in the Hoxb4 promoter and is known to be required for its activity. As these two factors are able to mediate opposing transcriptional effects by reorganizing the local chromatin environment, the relative levels of NFY and YY1 binding could represent a mechanism for balancing activation and repression of Hoxb4 through the same site.

scholarly journals Annotation and analysis of yellow genes in Diaphorina citri, vector for the Huanglongbing disease

2020 ◽  
Author(s):  
Crissy Massimino ◽  
Chad Vosburg ◽  
Teresa Shippy ◽  
Prashant S. Hosmani ◽  
Mirella Flores-Gonzalez ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Life Stage ◽  
Genomic Analysis ◽  
Gene Families ◽  
Manual Annotation ◽  
Diaphorina Citri ◽  
In Planta ◽  
Specific Expression ◽  
Molecular Control ◽  
Depth Analysis

ABSTRACTHuanglongbing (HLB), also known as citrus greening disease, is caused by the bacterium Candidatus Liberibacter asiaticus (CLas) and represents a serious threat to global citrus production. This bacteria is transmitted by the Asian citrus psyllid, Diaphorina citri (Hemiptera) and there are no effective in-planta treatments for CLas. Therefore, one strategy is to manage the psyllid population. Manual annotation of the D. citri genome can identify and characterize gene families that could serve as novel targets for psyllid control. The yellow gene family represents an excellent target as yellow genes are linked to development and immunity due to their roles in melanization. Combined analysis of the genome with RNA-seq datasets, sequence homology, and phylogenetic trees were used to identify and annotate nine yellow genes for the D. citri genome. Phylogenetic analysis shows a unique duplication of yellow-y in D. citri, with life stage specific expression for these two genes. Genomic analysis also indicated the loss of a gene vital to the process of melanization, yellow-f, and the gain of a gene which seems to be unique to hemipterans, yellow 9. We suggest that yellow 9 or the gene yellow 8 (c), which consistently groups closely to yellow-f, may take on this role. Manual curation of genes in D. citri has provided an in-depth analysis of the yellow family among hemipteran insects and provides new targets for molecular control of this psyllid pest. Manual annotation was done as part of a collaborative community annotation project (https://citrusgreening.org/annotation/index).

scholarly journals Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers

2016 ◽  
Vol 113 (23) ◽  
pp. 6508-6513 ◽  
Author(s):  
Emma K. Farley ◽  
Katrina M. Olson ◽  
Wei Zhang ◽  
Daniel S. Rokhsar ◽  
Michael S. Levine
Keyword(s):  
Binding Sites ◽  
Detection Methods ◽  
Affinity Binding ◽  
Binding Affinities ◽  
Specific Expression ◽  
Enhancer Activity ◽  
Binding Motifs ◽  
Weak Binding ◽  
Bona Fide ◽  
Enhancer Detection

Transcriptional enhancers are short segments of DNA that switch genes on and off in response to a variety of intrinsic and extrinsic signals. Despite the discovery of the first enhancer more than 30 y ago, the relationship between primary DNA sequence and enhancer activity remains obscure. In particular, the importance of “syntax” (the order, orientation, and spacing of binding sites) is unclear. A high-throughput screen identified synthetic notochord enhancers that are activated by the combination of ZicL and ETS transcription factors in Ciona embryos. Manipulation of these enhancers elucidated a “regulatory code” of sequence and syntax features for notochord-specific expression. This code enabled in silico discovery of bona fide notochord enhancers, including those containing low-affinity binding sites that would be excluded by standard motif identification methods. One of the newly identified enhancers maps upstream of the known enhancer that regulates Brachyury (Ci-Bra), a key determinant of notochord specification. This newly identified Ci-Bra shadow enhancer contains binding sites with very low affinity, but optimal syntax, and therefore mediates surprisingly strong expression in the notochord. Weak binding sites are compensated by optimal syntax, whereas enhancers containing high-affinity binding affinities possess suboptimal syntax. We suggest this balance has obscured the importance of regulatory syntax, as noncanonical binding motifs are typically disregarded by enhancer detection methods. As a result, enhancers with low binding affinities but optimal syntax may be a vastly underappreciated feature of the regulatory genome.

scholarly journals Molecular analysis of the zeste-white interaction reveals a promoter-proximal element essential for distant enhancer-promoter communication.

Genetics ◽  
1992 ◽  
Vol 131 (1) ◽  
pp. 79-90 ◽  
Author(s):  
S Qian ◽  
B Varjavand ◽  
V Pirrotta
Keyword(s):  
Transcription Start Site ◽  
Binding Sites ◽  
Start Site ◽  
Transcription Start ◽  
Heterologous Promoter ◽  
Specific Expression ◽  
Enhancer Activity ◽  
Directed Mutation ◽  
Sequence Deletion ◽  
Promoter Interaction

Abstract We have analyzed the eye and testis enhancers located 1 kb upstream of the transcription start site of the white gene. Both enhancers confer the corresponding tissue-specific expression on a heterologous promoter as well as on the white promoter. The eye determinant consists of multiple elements, each able to stimulate eye-specific expression. It also contains five binding sites for the zeste protein while the immediately adjacent testis element contains none. Site-directed mutation of these zeste binding sites abolishes the zeste-white interaction but does not significantly affect the eye enhancer activity, indicating that they are not important for the eye enhancer activity per se. Other zeste binding sites just upstream of the promoter are not necessary for the zeste-white interaction. We conclude that the overlap of the eye enhancer with the zeste binding sites is responsible for the zeste-white interaction and explains why this interaction affects eye but not testis expression. Sequence deletion or substitution experiments suggested that the white promoter is internal to the transcription start site; the zeste protein is not required for distant enhancer action but a 95-bp promoter-proximal sequence is essential for distant enhancer-promoter interaction. This element may serve as an anchor to stabilize formation of a loop that brings the enhancer to the vicinity of the promoter.

Transcription factor GATA-4 regulates cardiac muscle-specific expression of the alpha-myosin heavy-chain gene

1994 ◽  
Vol 14 (7) ◽  
pp. 4947-4957
Author(s):  
J D Molkentin ◽  
D V Kalvakolanu ◽  
B E Markham
Keyword(s):  
Skeletal Muscle ◽  
Transcription Factor ◽  
Retinoic Acid ◽  
Cardiac Muscle ◽  
Myosin Heavy Chain ◽  
Heavy Chain ◽  
Binding Sites ◽  
Ectopic Expression ◽  
Specific Expression ◽  
Cardiac Phenotype

The alpha-myosin heavy-chain (alpha-MHC) gene is the major structural protein in the adult rodent myocardium. Its expression is restricted to the heart by a complex interplay of trans-acting factors and their cis-acting sites. However, to date, the factors that have been shown to regulate expression of this gene have also been found in skeletal muscle cells. Recently, transcription factor GATA-4, which has a tissue distribution limited to the heart and endodermally derived tissues, was identified. We recently found two putative GATA-binding sites within the proximal enhancer of the alpha-MHC gene, suggesting that GATA-4 might regulate its expression. In this study, we establish that GATA-4 interacts with the alpha-MHC GATA sites to stimulate cardiac muscle-specific expression. Mutation of the GATA-4-binding sites either individually or together decreased activity by 50 and 88% in the adult myocardium, respectively. GATA-4-dependent enhancement of activity from a heterologous promoter was mediated through the alpha-MHC GATA sites. Coinjection of an alpha-MHC promoter construct with a GATA-4 expression vector permitted ectopic expression in skeletal muscle but not in fibroblasts. Thus, the lack of alpha-MHC expression in skeletal muscle correlates with a lack of GATA-4. GATA-4 DNA binding activity was significantly up-regulated in triiodothyronine- or retinoic acid-treated cardiomyocytes. Putative GATA-4-binding sites are also found in the regulatory regions of other cardiac muscle-expressed structural genes. This indicates a mechanism whereby triiodothyronine and retinoic acid can exert coordinate control of the cardiac phenotype through a trans-acting regulatory factor.

scholarly journals Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites

2021 ◽  
Vol 49 (7) ◽  
pp. 3856-3875
Author(s):  
Marina Kulik ◽  
Melissa Bothe ◽  
Gözde Kibar ◽  
Alisa Fuchs ◽  
Stefanie Schöne ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Transcription Factor ◽  
Dna Binding ◽  
Receptor Binding ◽  
Binding Sites ◽  
Specific Gene ◽  
Functional Diversification ◽  
Enhancer Activity ◽  
Sequence Composition

Abstract The glucocorticoid (GR) and androgen (AR) receptors execute unique functions in vivo, yet have nearly identical DNA binding specificities. To identify mechanisms that facilitate functional diversification among these transcription factor paralogs, we studied them in an equivalent cellular context. Analysis of chromatin and sequence suggest that divergent binding, and corresponding gene regulation, are driven by different abilities of AR and GR to interact with relatively inaccessible chromatin. Divergent genomic binding patterns can also be the result of subtle differences in DNA binding preference between AR and GR. Furthermore, the sequence composition of large regions (>10 kb) surrounding selectively occupied binding sites differs significantly, indicating a role for the sequence environment in guiding AR and GR to distinct binding sites. The comparison of binding sites that are shared shows that the specificity paradox can also be resolved by differences in the events that occur downstream of receptor binding. Specifically, shared binding sites display receptor-specific enhancer activity, cofactor recruitment and changes in histone modifications. Genomic deletion of shared binding sites demonstrates their contribution to directing receptor-specific gene regulation. Together, these data suggest that differences in genomic occupancy as well as divergence in the events that occur downstream of receptor binding direct functional diversification among transcription factor paralogs.

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