scholarly journals Redundant enhancers in the iab-5 domain cooperatively activate Abd-B in the A5 and A6 abdominal segments of Drosophila

2021 ◽  
Author(s):  
Nikolay Postika ◽  
Paul Schedl ◽  
Pavel Georgiev ◽  
Olga Kyrchanova
Keyword(s):  
Regulatory Elements ◽  
Regulatory Domain ◽  
Bithorax Complex ◽  
Tissue Specific ◽  
Regulatory Domains ◽  
Male Specific ◽  
Necessary And Sufficient

The homeotic Abdominal-B (Abd-B) gene belongs to Bithorax complex and is regulated by four regulatory domains named iab-5, iab-6, iab-7 and iab-8, each of which is thought to be responsible for directing the expression of Abd-B in one of the abdominal segments from A5 to A8. It is assumed that male specific features of the adult cuticle in A5 is solely dependent on regulatory elements located in iab-5, while the regulatory elements in the iab-6 are both necessary and sufficient for the proper differentiation of the A6 cuticle. Unexpectedly, we found that this long held assumption is not correct. Instead, redundant tissue-specific enhancers located in the iab-5 domain are required for the proper activation of Abd-B not only in A5 but also in A6. Our study of deletions shows that the iab-5 initiator is essential for the functioning of the iab-5 enhancers in A5, as well as for the correct differentiation of A6. This requirement is circumvented by deletions that remove the initiator and most of the iab-5 regulatory domain sequences. While the remaining iab-5 enhancers are inactive in A5, they are activated in A6 and contribute to the differentiation of this segment. In this case, Abd-B stimulation by the iab-5 enhancers in A6 depends on the initiators in the iab-4 and iab-6 domains.

scholarly journals Redundant enhancers in the iab-5 domain cooperatively activate Abd-B in the A5 and A6 abdominal segments of Drosophila

Development ◽  
2021 ◽  
Author(s):  
Nikolay Postika ◽  
Paul Schedl ◽  
Pavel Georgiev ◽  
Olga Kyrchanova
Keyword(s):  
Additive Model ◽  
Bithorax Complex ◽  
Tissue Specific ◽  
Regulatory Domains ◽  
Necessary And Sufficient

The Abdominal-B (Abd-B) gene belongs to Bithorax complex and its expression is controlled by four regulatory domains, iab-5, iab-6, iab-7 and iab-8, each of which is thought to be responsible for directing the expression of Abd-B in one of the abdominal segments from A5 to A8. A variety of experiments have supported the idea that BX-C regulatory domains are functionally autonomous and that each domain is both necessary and sufficient to orchestrate the development of the segment they specify. Unexpectedly, we discovered that this model does not always hold. Instead, we find that tissue-specific enhancers located in the iab-5 domain are required for the proper activation of Abd-B not only in A5 but also in A6. Our findings indicate that the functioning of the iab-5 and iab-6 domains in development of the adult cuticle A5 and A6 in males fit better with an additive model much like that first envisioned by Ed Lewis.

scholarly journals Hepatic-Specific Accessibility of Igf1 Gene Enhancers Is Independent of Growth Hormone Signaling

2013 ◽  
Vol 27 (12) ◽  
pp. 2080-2092 ◽  
Author(s):  
Mahalakshmi Santhanam ◽  
Dennis J. Chia
Keyword(s):  
Gene Regulation ◽  
Gene Transcription ◽  
Tissue Expression ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Binding Motifs ◽  
Tissue Specific ◽  
Regulatory Domains ◽  
Binding Domains

The diverse roles of IGF-1 in physiology include acting as the endocrine intermediate to elicit the anabolic actions of GH. The majority of serum IGF-1 is synthesized in liver, where GH stimulates Igf1 gene transcription via the transcription factor, signal transducer and activator of transcription (Stat)5b. We and others have identified multiple Stat5-binding domains at the Igf1 locus that function in gene regulation, but it remains unclear whether the roles of these domains are tissue specific. Survey of the chromatin landscape of regulatory domains can provide insight about mechanisms of gene regulation, with chromatin accessibility regarded as a hallmark feature of regulatory domains. We prepared chromatin from liver, kidney, and spleen of C57BL/6 mice, and used formaldehyde-associated isolation of regulatory elements to assess chromatin accessibility at the major Igf1 promoter and 7 -binding enhancers. Whereas the promoters of other prototypical tissue-specific genes are open in a tissue-specific way, the major Igf1 promoter is open in all 3 tissues, albeit moderately more so in liver. In contrast, chromatin accessibility at Igf1 Stat5-binding domains is essentially restricted to liver, indicating that the enhancers are driving extensive differences in tissue expression. Furthermore, studies with Ghrhrlit/lit mice reveal that prior GH exposure is not necessary to establish open chromatin at these domains. Lastly, formaldehyde-associated isolation of regulatory elements of human liver samples confirms open chromatin at IGF1 Promoter 1, but unexpectedly, homologous Stat5-binding motifs are not accessible. We conclude that robust GH-stimulated hepatic Igf1 gene transcription utilizes tissue-specific mechanisms of epigenetic regulation that are established independent of GH signaling.

Transcription through the iab-7 cis-regulatory domain of the bithorax complex interferes with maintenance of Polycomb-mediated silencing

Development ◽  
2002 ◽  
Vol 129 (21) ◽  
pp. 4915-4922 ◽  
Author(s):  
Ilham Hogga ◽  
François Karch
Keyword(s):  
Domain Boundary ◽  
Regulatory Region ◽  
Chromatin Domain ◽  
Dependent Manner ◽  
Regulatory Domain ◽  
Bithorax Complex ◽  
Regulatory Domains ◽  
Repression Complex ◽  
Ectopic Activation ◽  
Functional Autonomy

The Fab-7 chromatin domain boundary insures functional autonomy of the iab-6 and iab-7 cis-regulatory domains in the bithorax complex (BX-C). We have previously shown that chromatin insulators such asgypsy or scsmin are potent insulators that cannot substitute for Fab-7 function within the BX-C. During the early stages of these swapping experiments, we initially used a fragment of scs that was slightly larger than a minimal scs element (scsmin). We report that this scs fragment, unlike scsmin, interferes in an orientation-dependent manner with the output of a regulatory region covering 80 kb of DNA (from iab-4 to iab-8). At the core of this orientation-dependent phenotype is a promoter located immediately adjacent to the scs insulator. In one orientation, the promoter traps the activity of theiab-3 through iab-5 cis-regulatory domains, diverting them from the abd-A gene. In the opposite orientation, the promoter is transcribing the iab-7 cis-regulatory domain, resulting in ectopic activation of the latter. Our data suggest that transcription through aPolycomb-Response Element (PRE) interferes with the maintenance of aPolycomb repression complex.

scholarly journals Sir3p Domains Involved in the Initiation of Telomeric Silencing in Saccharomyces cerevisiae

Genetics ◽  
1998 ◽  
Vol 150 (3) ◽  
pp. 977-986 ◽  
Author(s):  
Yangsuk Park ◽  
John Hanish ◽  
Arthur J Lustig
Keyword(s):  
Amino Acids ◽  
Active Site ◽  
Fusion Proteins ◽  
Initiation Site ◽  
Negative Control ◽  
Model System ◽  
Mutant Protein ◽  
Regulatory Domain ◽  
C Terminus ◽  
Necessary And Sufficient

Abstract Previous studies from our laboratory have demonstrated that tethering of Sir3p at the subtelomeric/telomeric junction restores silencing in strains containing Rap1-17p, a mutant protein unable to recruit Sir3p. This tethered silencing assay serves as a model system for the early events that follow recruitment of silencing factors, a process we term initiation. A series of LexA fusion proteins in-frame with various Sir3p fragments were constructed and tested for their ability to support tethered silencing. Interestingly, a region comprising only the C-terminal 144 amino acids, termed the C-terminal domain (CTD), is both necessary and sufficient for restoration of silencing. Curiously, the LexA-Sir3N205 mutant protein overcomes the requirement for the CTD, possibly by unmasking a cryptic initiation site. A second domain spanning amino acids 481-835, termed the nonessential for initiation domain (NID), is dispensable for the Sir3p function in initiation, but is required for the recruitment of the Sir4p C terminus. In addition, in the absence of the N-terminal 481 amino acids, the NID negatively influences CTD activity. This suggests the presence of a third region, consisting of the N-terminal half (1-481) of Sir3p, termed the positive regulatory domain (PRD), which is required to initiate silencing in the presence of the NID. These data suggest that the CTD “active” site is under both positive and negative control mediated by multiple Sir3p domains.

scholarly journals Tissue‐specific regulatory elements in mammalian promoters

2007 ◽  
Vol 3 (1) ◽  
pp. 73 ◽  
Author(s):  
Andrew D Smith ◽  
Pavel Sumazin ◽  
Michael Q Zhang
Keyword(s):  
Regulatory Elements ◽  
Tissue Specific

scholarly journals Tissue-specific sex differences in human gene expression

2019 ◽  
Vol 28 (17) ◽  
pp. 2976-2986 ◽  
Author(s):  
Irfahan Kassam ◽  
Yang Wu ◽  
Jian Yang ◽  
Peter M Visscher ◽  
Allan F McRae
Keyword(s):  
Gene Expression ◽  
Sex Differences ◽  
Complex Traits ◽  
Tissue Expression ◽  
Regulatory Elements ◽  
Tissue Specific ◽  
Significance Threshold ◽  
Expression Of Genes ◽  
Causal Variants ◽  
Similar Distance

Abstract Despite extensive sex differences in human complex traits and disease, the male and female genomes differ only in the sex chromosomes. This implies that most sex-differentiated traits are the result of differences in the expression of genes that are common to both sexes. While sex differences in gene expression have been observed in a range of different tissues, the biological mechanisms for tissue-specific sex differences (TSSDs) in gene expression are not well understood. A total of 30 640 autosomal and 1021 X-linked transcripts were tested for heterogeneity in sex difference effect sizes in n = 617 individuals across 40 tissue types in Genotype–Tissue Expression (GTEx). This identified 65 autosomal and 66 X-linked TSSD transcripts (corresponding to unique genes) at a stringent significance threshold. Results for X-linked TSSD transcripts showed mainly concordant direction of sex differences across tissues and replicate previous findings. Autosomal TSSD transcripts had mainly discordant direction of sex differences across tissues. The top cis-expression quantitative trait loci (eQTLs) across tissues for autosomal TSSD transcripts are located a similar distance away from the nearest androgen and estrogen binding motifs and the nearest enhancer, as compared to cis-eQTLs for transcripts with stable sex differences in gene expression across tissue types. Enhancer regions that overlap top cis-eQTLs for TSSD transcripts, however, were found to be more dispersed across tissues. These observations suggest that androgen and estrogen regulatory elements in a cis region may play a common role in sex differences in gene expression, but TSSD in gene expression may additionally be due to causal variants located in tissue-specific enhancer regions.

scholarly journals SMAD1 and SMAD5 Expression Is Coordinately Regulated by FLI1 and GATA2 during Endothelial Development

2015 ◽  
Vol 35 (12) ◽  
pp. 2165-2172 ◽  
Author(s):  
Jonathon Marks-Bluth ◽  
Anchit Khanna ◽  
Vashe Chandrakanthan ◽  
Julie Thoms ◽  
Thomas Bee ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Selective Advantage ◽  
Regulatory Elements ◽  
Bmp Signaling ◽  
Tissue Specific ◽  
Morphogenetic Protein ◽  
Smad Signaling Pathway ◽  
Endothelial Development

The bone morphogenetic protein (BMP)/SMAD signaling pathway is a critical regulator of angiogenic sprouting and is involved in vascular development in the embryo. SMAD1 and SMAD5, the core mediators of BMP signaling, are vital for this activity, yet little is known about their transcriptional regulation in endothelial cells. Here, we have integrated multispecies sequence conservation, tissue-specific chromatin,in vitroreporter assay, andin vivotransgenic data to identify and validateSmad1+63 and theSmad5promoter as tissue-specificcis-regulatory elements that are active in the developing endothelium. The activity of these elements in the endothelium was dependent on highly conserved ETS, GATA, and E-box motifs, and chromatin immunoprecipitation showed high levels of enrichment of FLI1, GATA2, and SCL at these sites in endothelial cell lines and E11 dorsal aortasin vivo. Knockdown of FLI1 and GATA2 but not SCL reduced the expression of SMAD1 and SMAD5 in endothelial cellsin vitro. In contrast, CD31+cKit−endothelial cells harvested from embryonic day 9 (E9) aorta-gonad-mesonephros (AGM) regions of GATA2 null embryos showed reducedSmad1but notSmad5transcript levels. This is suggestive of a degree ofin vivoselection where, in the case of reduced SMAD1 levels, endothelial cells with more robust SMAD5 expression have a selective advantage.

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