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 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 H3K27 modifications define segmental regulatory domains in the Drosophila bithorax complex

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Sarah K Bowman ◽  
Aimee M Deaton ◽  
Heber Domingues ◽  
Peggy I Wang ◽  
Ruslan I Sadreyev ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Binding Protein ◽  
Histone H3 ◽  
Polycomb Group ◽  
Homeotic Genes ◽  
Bithorax Complex ◽  
Body Segment ◽  
Regulatory Domains ◽  
Definition Of ◽  
Identity Expression

The bithorax complex (BX-C) in Drosophila melanogaster is a cluster of homeotic genes that determine body segment identity. Expression of these genes is governed by cis-regulatory domains, one for each parasegment. Stable repression of these domains depends on Polycomb Group (PcG) functions, which include trimethylation of lysine 27 of histone H3 (H3K27me3). To search for parasegment-specific signatures that reflect PcG function, chromatin from single parasegments was isolated and profiled. The H3K27me3 profiles across the BX-C in successive parasegments showed a ‘stairstep’ pattern that revealed sharp boundaries of the BX-C regulatory domains. Acetylated H3K27 was broadly enriched across active domains, in a pattern complementary to H3K27me3. The CCCTC-binding protein (CTCF) bound the borders between H3K27 modification domains; it was retained even in parasegments where adjacent domains lack H3K27me3. These findings provide a molecular definition of the homeotic domains, and implicate precisely positioned H3K27 modifications as a central determinant of segment identity.

scholarly journals A Stage-Specific Factor Confers Fab-7 Boundary Activity during Early Embryogenesis in Drosophila

2007 ◽  
Vol 28 (3) ◽  
pp. 1047-1060 ◽  
Author(s):  
Tsutomu Aoki ◽  
Susan Schweinsberg ◽  
Julia Manasson ◽  
Paul Schedl
Keyword(s):  
Adult Stage ◽  
Early Embryogenesis ◽  
Specific Factor ◽  
Bithorax Complex ◽  
Recognition Sequence ◽  
Regulatory Domains ◽  
Nuclear Extracts ◽  
Early Embryos ◽  
Blocking Activity ◽  
Enhancer Blocking

ABSTRACT The Fab-7 boundary is required to ensure that the iab-6 and iab-7 cis-regulatory domains in the Drosophila Bithorax complex can function autonomously. Though Fab-7 functions as a boundary from early embryogenesis through to the adult stage, this constitutive boundary activity depends on subelements whose activity is developmentally restricted. In the studies reported here, we have identified a factor, called early boundary activity (Elba), that confers Fab-7 boundary activity during early embryogenesis. The Elba factor binds to a recognition sequence within a Fab-7 subelement that has enhancer-blocking activity during early embryogenesis, but not during mid-embryogenesis or in the adult. We found that the Elba factor is present in early embryos but largely disappears during mid-embryogenesis. We show that mutations in the Elba recognition sequence that eliminate Elba binding in nuclear extracts disrupt the early boundary activity of the Fab-7 subelement. Conversely, we find that early boundary activity can be reconstituted by multimerizing the Elba recognition site.

scholarly journals Boundaries support specific long-distance interactions between enhancers and promoters in Drosophila Bithorax complex

2018 ◽  
Author(s):  
Nikolay Postika ◽  
Mario Metzler ◽  
Markus Affolter ◽  
Martin Müller ◽  
Paul Schedl ◽  
...  
Keyword(s):  
Target Genes ◽  
Model Systems ◽  
Homeotic Genes ◽  
Bithorax Complex ◽  
Long Distance ◽  
Gene Target ◽  
Regulatory Domains ◽  
Insulator Elements

AbstractDrosophila bithorax complex (BX-C) is one of the best model systems for studying the role of boundaries (insulators) in gene regulation. Expression of three homeotic genes, Ubx, abd-A, and Abd-B, is orchestrated by nine parasegment-specific regulatory domains. These domains are flanked by boundary elements, which function to block crosstalk between adjacent domains, ensuring that they can act autonomously. Paradoxically, seven of the BX-C regulatory domains are separated from their gene target by at least one boundary, and must “jump over” the intervening boundaries. To understand the jumping mechanism, the Mcp boundary was replaced with Fab-7 and Fab-8. Mcp is located between the iab-4 and iab-5 domains, and defines the border between the set of regulatory domains controlling abd-A and Abd-B. When Mcp is replaced by Fab-7 or Fab-8, they direct the iab-4 domain (which regulates abd-A) to inappropriately activate Abd-B in abdominal segment A4. For the Fab-8 replacement, ectopic induction was only observed when it was inserted in the same orientation as the endogenous Fab-8 boundary. A similar orientation dependence for bypass activity was observed when Fab-7 was replaced by Fab-8. Thus, boundaries perform two opposite functions in the context of BX-C – they block crosstalk between neighboring regulatory domains, but at the same time actively facilitate long distance communication between the regulatory domains and their respective target genes.Author SummaryDrosophila bithorax complex (BX-C) is one of a few examples demonstrating in vivo role of boundary/insulator elements in organization of independent chromatin domains. BX-C contains three HOX genes, whose parasegment-specific pattern is controlled by cis-regulatory domains flanked by boundary/insulator elements. Since the boundaries ensure autonomy of adjacent domains, the presence of these elements poses a paradox: how do the domains bypass the intervening boundaries and contact their proper regulatory targets? According to the textbook model, BX-C regulatory domains are able to bypass boundaries because they harbor special promoter targeting sequences. However, contrary to this model, we show here that the boundaries themselves play an active role in directing regulatory domains to their appropriate HOX gene promoter.

The Fab-8 boundary defines the distal limit of the bithorax complex iab-7 domain and insulates iab-7 from initiation elements and a PRE in the adjacent iab-8 domain

Development ◽  
2000 ◽  
Vol 127 (4) ◽  
pp. 779-790 ◽  
Author(s):  
S. Barges ◽  
J. Mihaly ◽  
M. Galloni ◽  
K. Hagstrom ◽  
M. Muller ◽  
...  
Keyword(s):  
Higher Order ◽  
Specific Pattern ◽  
Bithorax Complex ◽  
Response Element ◽  
Regulatory Domains ◽  
Polycomb Response Element ◽  
Distal Side ◽  
Blocking Activity ◽  
Enhancer Blocking ◽  
Order Domain

The Drosophila bithorax complex Abdominal-B (Abd-B) gene specifies parasegmental identity at the posterior end of the fly. The specific pattern of Abd-B expression in each parasegment (PS) determines its identity and, in PS10-13, Abd-B expression is controlled by four parasegment-specific cis-regulatory domains, iab-5 to iab-8, respectively. In order to properly determine parasegmental identity, these four cis-regulatory domains must function autonomously during both the initiation and maintenance phases of BX-C regulation. The studies reported here demonstrate that the (centromere) distal end of iab-7 domain is delimited by the Fab-8 boundary. Initiators that specify PS12 identity are located on the proximal iab-7 side of Fab-8, while initiators that specify PS13 identity are located on the distal side of Fab-8, in iab-8. We use transgene assays to demonstrate that Fab-8 has enhancer blocking activity and that it can insulate reporter constructs from the regulatory action of the iab-7 and iab-8 initiators. We also show that the Fab-8 boundary defines the realm of action of a nearby iab-8 Polycomb Response Element, preventing this element from ectopically silencing the adjacent domain. Finally, we demonstrate that the insulating activity of the Fab-8 boundary in BX-C is absolutely essential for the proper specification of parasegmental identity by the iab-7 and iab-8 cis-regulatory domains. Fab-8 together with the previously identified Fab-7 boundary delimit the first genetically defined higher order domain in a multicellular eukaryote.

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.

scholarly journals McpandFab-7: molecular analysis of putative boundaries of cis-regulatory domains in the bithorax complex ofDrosophila melanogaster

1994 ◽  
Vol 22 (15) ◽  
pp. 3138-3146 ◽  
Author(s):  
FranÇois Karch ◽  
Mireille Galloni ◽  
Làszlò Sipos ◽  
Janos Gausz ◽  
Henrik Gyurkovics ◽  
...  
Keyword(s):  
Molecular Analysis ◽  
Bithorax Complex ◽  
Regulatory Domains

scholarly journals Sustained activation of STAT5 is essential for chromatin remodeling and maintenance of mammary-specific function

2009 ◽  
Vol 184 (1) ◽  
pp. 57-66 ◽  
Author(s):  
Ren Xu ◽  
Celeste M. Nelson ◽  
John L. Muschler ◽  
Mandana Veiseh ◽  
Barbara K. Vonderhaar ◽  
...  
Keyword(s):  
Prolactin Receptor ◽  
Functional Differentiation ◽  
Specific Gene ◽  
Tissue Specific ◽  
Signal Transducers ◽  
Prolactin Signaling ◽  
Transcription Factor Activation ◽  
Mammary Epithelia ◽  
Necessary And Sufficient ◽  
Sustained Activation

Epithelial cells, once dissociated and placed in two-dimensional (2D) cultures, rapidly lose tissue-specific functions. We showed previously that in addition to prolactin, signaling by laminin-111 was necessary to restore functional differentiation of mammary epithelia. Here, we elucidate two additional aspects of laminin-111 action. We show that in 2D cultures, the prolactin receptor is basolaterally localized and physically segregated from its apically placed ligand. Detachment of the cells exposes the receptor to ligation by prolactin leading to signal transducers and activators of transcription protein 5 (STAT5) activation, but only transiently and not sufficiently for induction of milk protein expression. We show that laminin-111 reorganizes mammary cells into polarized acini, allowing both the exposure of the prolactin receptor and sustained activation of STAT5. The use of constitutively active STAT5 constructs showed that the latter is necessary and sufficient for chromatin reorganization and β-casein transcription. These results underscore the crucial role of continuous laminin signaling and polarized tissue architecture in maintenance of transcription factor activation, chromatin organization, and tissue-specific gene expression.

scholarly journals Complete reconstitution of bypass and blocking functions in a minimal artificial Fab-7 insulator from Drosophila bithorax complex

2019 ◽  
Vol 116 (27) ◽  
pp. 13462-13467 ◽  
Author(s):  
Olga Kyrchanova ◽  
Marat Sabirov ◽  
Vladic Mogila ◽  
Amina Kurbidaeva ◽  
Nikolay Postika ◽  
...  
Keyword(s):  
Cross Talk ◽  
Binding Sites ◽  
Multiprotein Complex ◽  
Bithorax Complex ◽  
Artificial Boundary ◽  
Long Distance ◽  
Specific Expression ◽  
Regulatory Domains ◽  
Architectural Proteins ◽  
Distance Communication

Boundaries in the bithorax complex (BX-C) delimit autonomous regulatory domains that drive parasegment-specific expression of the Hox genes Ubx, abd-A, and Abd-B. The Fab-7 boundary is located between the iab-6 and iab-7 domains and has two key functions: blocking cross-talk between these domains and at the same time promoting communication (boundary bypass) between iab-6 and the Abd-B promoter. Using a replacement strategy, we found that multimerized binding sites for the architectural proteins Pita, Su(Hw), and dCTCF function as conventional insulators and block cross-talk between the iab-6 and iab-7 domains; however, they lack bypass activity, and iab-6 is unable to regulate Abd-B. Here we show that an ∼200-bp sequence of dHS1 from the Fab-7 boundary rescues the bypass defects of these multimerized binding sites. The dHS1 sequence is bound in embryos by a large multiprotein complex, Late Boundary Complex (LBC), that contains the zinc finger proteins CLAMP and GAF. Using deletions and mutations in critical GAGAG motifs, we show that bypass activity correlates with the efficiency of recruitment of LBC components CLAMP and GAF to the artificial boundary. These results indicate that LBC orchestrates long-distance communication between the iab-6 regulatory domain and the Abd-B gene, while the Pita, Su(Hw), and dCTCF proteins function to block local cross-talk between the neighboring regulatory domains iab-6 and iab-7.

scholarly journals Modeling tissue-specific breakpoint proximity of structural variations from 2,382 whole-genomes to identify cancer drivers

2021 ◽  
Author(s):  
Alexander Martinez-Fundichely ◽  
Austin Dixon ◽  
Ekta Khurana
Keyword(s):  
Three Dimensional ◽  
Additive Model ◽  
Neutral Evolution ◽  
Cancer Genes ◽  
Structural Variations ◽  
Tissue Specific ◽  
Genomic Features ◽  
Interaction Terms ◽  
Whole Genomes ◽  
Genomic Regions

AbstractStructural variations (SVs) in cancer cells often impact large genomic regions with functional consequences. However, little is known about the genomic features related to the breakpoint distribution of SVs in different cancers, a prerequisite to distinguish loci under positive selection from those with neutral evolution. We developed a method that uses a generalized additive model to investigate the breakpoint proximity curves from 2,382 whole-genomes of 32 cancer types. We find that a multivariate model, which includes linear and nonlinear partial contributions of various tissue-specific features and their interaction terms, can explain up to 57% of the observed deviance of breakpoint proximity. In particular, three-dimensional genomic features such as topologically associating domains (TADs), TAD-boundaries and their interaction with other features show significant contributions. The model is validated by identification of known cancer genes and revealed putative drivers in novel cancers that have previous evidence of therapeutic relevance in other cancers.

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