Synergistic DNA and RNA binding of the Hox transcription factor Ultrabithorax coordinates splicing and shapes in vivo homeotic functions
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ABSTRACT:
PROVIDER: PRJNA1258180 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR33409460_1.fastq.gz | Fastqsanger.gz | |||
| SRR33409460_2.fastq.gz | Fastqsanger.gz | |||
| SRR33409462_1.fastq.gz | Fastqsanger.gz | |||
| SRR33409462_2.fastq.gz | Fastqsanger.gz |
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Project description:The dual interaction of many transcription factors (TFs) with both DNA and RNA is an underexplored issue that could fundamentally reshape our understanding of gene regulation. We address this central issue by investigating the RNA binding activity of the Drosophila Hox TF Ultrabithorax (Ubx) in alternative splicing and morphogenesis. Relying on molecular and genetic interactions, we uncover a homodimerization-dependent mechanism by which Ubx regulates splicing. Notably, this mechanism enables the decoupling of Ubx-DNA and -RNA binding activity in splicing. We identify a critical residue for Ubx-RNA binding and demonstrate the essential role of Ubx-RNA binding ability for its homeotic functions. Overall, we uncover a unique mechanism for Ubx-mediated splicing and underscore the critical contribution of synergistic DNA/RNA binding for its morphogenetic functions. These findings advance our understanding of co-transcriptional regulation and highlight the significance of TF-DNA/RNA synergistic function in shaping gene regulatory networks in living organisms.
2025-06-08 | GSE296189 | GEO
Project description:The identity of every segment in the fruitfly Drosophila melanogaster is determined by the action of one or more homeotic selector genes. These genes encode proteins containing DNA-binding domains and function by regulating downstream target genes. The structure and function of homeotic genes are highly conserved across a wide range of animals including human. Although much information is available on the molecular and biochemical nature of homeotic genes, comparatively little is known regarding the mechanism/s that are used to generate segmental diversity. This series of experiments were carried out to determine targets of the homeotic gene Ultrabithorax.
2010-06-10 | E-GEOD-1412 | biostudies-arrayexpress
Project description:The identity of every segment in the fruitfly Drosophila melanogaster is determined by the action of one or more homeotic selector genes. These genes encode proteins containing DNA-binding domains and function by regulating downstream target genes. The structure and function of homeotic genes are highly conserved across a wide range of animals including human. Although much information is available on the molecular and biochemical nature of homeotic genes, comparatively little is known regarding the mechanism/s that are used to generate segmental diversity. This series of experiments were carried out to determine targets of the homeotic gene Ultrabithorax. Keywords: other
2005-05-17 | GSE1412 | GEO
Project description:Hox genes regionalize the animal body axis by modifying complex morphogenetic and differentiation processes during development. The transformation of wings into halteres by the Hox gene Ultrabithorax (Ubx) in Drosophila melanogaster presents an excellent model system to study the transcriptional networks that control such complex developmental programmes. We have employed an inducible misexpression system to switch on Ubx in the wing epithelium at successive larval, prepupal and pupal stages, and have used microarray expression profiling to identify the primary transcriptional responses to Ubx. We find that Ubx regulates hundreds of downstream genes, mostly in a subtle manner. These targets are largely distinct at the different stages of appendage development and diversification.
2010-12-31 | GSE22354 | GEO
Project description:Hox genes encode a family of transcription factors that are key developmental regulators with a highly conserved role in specifying segmental diversity along the metazoan body axis. Although they have been shown to regulate a wide variety of downstream processes, direct transcriptional targets have been difficult to identify and this has been a major obstacle to our understanding of Hox gene function. Here we report the use of a YFP-tagged Drosophila protein-trap line together with chromatin immunoprecipitation and microarray analysis to identify genome-wide binding sites for the Hox protein Ultrabithorax (Ubx). We find 1,147 genes bound by Ubx in chromatin from the haltere imaginal disc, a prominent site of Ubx function where it specifies haltere versus wing development. The functional relevance of these genes is supported by their overlap with genes showing differential expression between wing and haltere imaginal discs. The Ubx-bound genes are highly enriched in genes involved in developmental processes. They contain both high-level regulatory genes as well as genes involved in more basic cell functions supporting the idea that Hox genes regulate many levels of developmental pathways. Several signalling pathways are highly enriched and within these pathways Ubx target genes occur at multiple level from ligands to transcriptional effectors. We also performed genome-wide analysis of the binding sites for the Hox cofactor Homothorax (Hth), revealing a striking similarity in the binding profiles of Hth and Ubx. We suggest that these binding profiles may be strongly influenced by chromatin accessibility and we provide evidence of a clear link between Ubx/Hth binding and the chromatin state at genes regulated by Polycomb silencing. The role of chromatin accessibility has important implications for Hox gene function and for genomic target selection by transcription factors in general.
2011-04-14 | GSE23864 | GEO
Project description:A comparative genomic analysis of targets of Hox protein Ultrabithorax amongst distant insect species.
| PRJNA292687 | ENA
Project description:Transcription Factors (TFs) play a pivotal role in cell fate decision by coordinating gene expression programs. Although most TFs act at the DNA layer, few TFs bind RNA and modulate splicing. Yet, the mechanistic cues underlying TFs activity in splicing remain elusive. Focusing on the Drosophila Hox TF Ultrabithorax (Ubx), our work shed light on a novel layer of Ubx function at the RNA level. Transcriptome and genome-wide binding profiles in embryonic mesoderm and Drosophila cells indicate that Ubx regulates mRNA expression and splicing to promote distinct outcomes in defined cellular contexts. Our results demonstrate a new RNA-binding ability of Ubx. We find that the N51 amino acid of the DNA-binding Homeodomain is non-essential for RNA interaction in vitro, but is required for RNA interaction in vivo and Ubx splicing activity. Moreover, mutation of the N51 amino acid weakens the interaction between Ubx and active RNA Polymerase II (Pol II). Our results reveal that Ubx regulates elongation-coupled splicing, which could be coordinated by a dynamic interplay with active Pol II on chromatin. Overall, our work uncovered a novel role of the Hox TFs at the mRNA regulatory layer. This could be an essential function for other classes of TFs to control cell diversity.
2021-12-02 | GSE171547 | GEO
Project description:Hox genes regionalize the animal body axis by modifying complex morphogenetic and differentiation processes during development. The transformation of wings into halteres by the Hox gene Ultrabithorax (Ubx) in Drosophila melanogaster presents an excellent model system to study the transcriptional networks that control such complex developmental programmes. We have employed an inducible misexpression system to switch on Ubx in the wing epithelium at successive larval, prepupal and pupal stages, and have used microarray expression profiling to identify the primary transcriptional responses to Ubx. We find that Ubx regulates hundreds of downstream genes, mostly in a subtle manner. These targets are largely distinct at the different stages of appendage development and diversification. We have generated an experimental fly line combining the nabGal4NP3537-driver, a tub-GAL80ts transgene, and a UAS-UbxIa transgene (the control line was carrying a UAS-eGFP transgene instead). Our core microarray analysis has involved comparison of the transcriptional profile of experimental wings carrying the UAS-UbxIa transgene with that of control wings carrying the UAS-eGFP transgene. Pairwise comparisons have been carried out at three successive developmental stages, in particular at (i) the third instar larval wandering stage, about 4hrs before puparium formation at 29˚C, (ii) the prepupal stage, 6hrs after puparium formation (APF) at 29˚C, and (iii) the early pupal stage, 16hrs APF at 29˚C. Moreover, pairwise comparisons have been carried out with samples developed exclusively at 19˚C (UbxIa or eGFP expression OFF), as well as with samples collected at 16hrs after the temperature shift from 19 to 29˚C (UbxIa or eGFP expression ON). This has allowed us to distinguish the Ubx-dependent effects from the intrinsic expression differences between the fly lines used, and from the temperature-induced responses. We have carried out 4 biological replicates for each condition making a total of 48 hybridizations to Affymetrix Drosophila Genome 2.0 arrays.
2010-12-31 | E-GEOD-22354 | biostudies-arrayexpress
Project description:Hox genes impart segment identity to body structures along the anterior-posterior axis and are crucial for the proper development of all organisms. Multiple regulatory elements, best defined in Drosophila melanogaster, ensure that Hox expression patterns follow the spatial and temporal colinearity reflected in their tight genomic organization. However, the precise mechanisms that regulate colinear patterns of Hox gene expression remain unclear, especially in higher vertebrates where it is not fully determined how the distinct activation domains of the tightly clustered Hox genes are defined independent of each other. Here, we report the identification of a large number of novel cis-elements at mammalian Hox clusters that can help in regulating their precise expression pattern.
2013-05-01 | GSE42941 | GEO
Project description:Hox genes impart segment identity to body structures along the anterior-posterior axis and are crucial for the proper development of all organisms. Multiple regulatory elements, best defined in Drosophila melanogaster, ensure that Hox expression patterns follow the spatial and temporal colinearity reflected in their tight genomic organization. However, the precise mechanisms that regulate colinear patterns of Hox gene expression remain unclear, especially in higher vertebrates where it is not fully determined how the distinct activation domains of the tightly clustered Hox genes are defined independent of each other. Here, we report the identification of a large number of novel cis-elements at mammalian Hox clusters that can help in regulating their precise expression pattern. Agilent two-color ChIP-on-Chip experiment, Organism: Mus musculus ,Genotypic Technology designed Custom Mouse 1 million ChIP-on-chip Array (AMADID-0245671)
2013-05-01 | E-GEOD-42941 | biostudies-arrayexpress