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Multiple Layers of Complexity in the Regulation of the Bithorax Complex in Drosophila

English title Multiple Layers of Complexity in the Regulation of the Bithorax Complex in Drosophila
Applicant Nagoshi Emi
Number 170179
Funding scheme Project funding (Div. I-III)
Research institution Département de Génétique et Evolution Faculté des Sciences Université de Genève
Institution of higher education University of Geneva - GE
Main discipline Genetics
Start/End 01.01.2017 - 31.12.2019
Approved amount 535'535.00
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All Disciplines (3)

Discipline
Genetics
Molecular Biology
Embryology, Developmental Biology

Keywords (9)

ncRNA; Chromatin; Boundary; Post-Mating-Response; Insulator; microRNAs; micro peptides; Cis-regulation; Homeotic gene

Lay Summary (French)

Lead
Influence de l'architecture chromosomique dans la régulation des gènes sous-jacants.
Lay summary

Bien qu'il soit maintenant possible de créer des organismes vivants exprimant tout gène d’intérêt d'une manière contrôlée, nous restons encore assez ignorants des processus qui régissant la communication entre les régions régulatrices des gènes et leurs promoteurs cibles.  Une des difficultés réside dans le fait que les gènes sont souvent de grande taille et que leurs éléments régulateurs se trouvent très éloignés de leurs promoteurs cible.  Il devient ainsi difficile d'effectuer une dissection fonctionnelle dans le contexte chromosomique natif. Pour répondre à cette question, nous étudions la régulation des gènes homéotiques (gènes Hox) du complexe bithorax (BX-C) chez la drosophile. Les gènes homéotiques sont remarquablement conservés entre les invertébrés et les vertébré : ils sont organisés en «complexes» et sont disposés le long du chromosome dans le même ordre que les structures qu’ils spécifient le long de l'axe antéropostérieu. Cette correspondance entre organisation génomique et axe antéro-postérieur fournit une occasion unique d'étudier la régulation des gènes dans leur contexte chromosomique. Nous avons identifié certains éléments régulateurs comprenant des « enhancers » capables de détecter leur position le long de l'axe AP, des « enhancers » tissus-spécifiques et des éléments régulateurs capables de véhiculer le maintien épigénétique de l'état d'activité des gènes hox.  Nous avons également identifié des éléments frontières qui jouent un rôle fondamental dans l'activation séquentielle des gènes homéotiques le long du chromosome. Nous essayons de comprendre comment l’activité de ces éléments régulateurs est coordonnée en accordant une attention particulière aux nombreux transcrits non-codants qui émanent des régions régulatrices. 

 

Nous étudions également un nouveau gène du BX-C qui code pour un micro-ARN et un micro-peptide et qui est impliqué dans le comportement reproductif.

 

 

Direct link to Lay Summary Last update: 03.11.2016

Responsible applicant and co-applicants

Employees

Publications

Publication
Vps11 and Vps18 of Vps-C membrane traffic complexes are E3 ubiquitin ligases and fine-tune signalling
Segala Gregory, Bennesch Marcela A., Ghahhari Nastaran Mohammadi, Pandey Deo Prakash, Echeverria Pablo C., Karch François, Maeda Robert K., Picard Didier (2019), Vps11 and Vps18 of Vps-C membrane traffic complexes are E3 ubiquitin ligases and fine-tune signalling, in Nature Communications, 10(1), 1833-1833.
A FACS-based Protocol to Isolate RNA from the Secondary Cells of Drosophila Male Accessory Glands
Immarigeon Clément, Karch François, Maeda Robert K. (2019), A FACS-based Protocol to Isolate RNA from the Secondary Cells of Drosophila Male Accessory Glands, in Journal of Visualized Experiments, (151), 75-81.
Rab-mediated trafficking in the secondary cells of Drosophila male accessory glands and its role in fecundity
Prince Elodie, Kroeger Benjamin, Gligorov Dragan, Wilson Clive, Eaton Suzanne, Karch François, Brankatschk Marko, Maeda Robert K. (2019), Rab-mediated trafficking in the secondary cells of Drosophila male accessory glands and its role in fecundity, in Traffic, 20(2), 137-151.
Using a phiC31 “Disintegrase” to make new attP sites in the Drosophila genome at locations showing chromosomal position effects
Maharjan Mukesh, Maeda Robert K., Karch François, Hart Craig M. (2018), Using a phiC31 “Disintegrase” to make new attP sites in the Drosophila genome at locations showing chromosomal position effects, in PLOS ONE, 13(10), e0205538-e0205538.
The BEN Domain Protein Insensitive Binds to the Fab-7 Chromatin Boundary To Establish Proper Segmental Identity in Drosophila
Fedotova Anna, Aoki Tsutomu, Rossier Mikaël, Mishra Rakesh Kumar, Clendinen Chaevia, Kyrchanova Olga, Wolle Daniel, Bonchuk Artem, Maeda Robert K., Mutero Annick, Cleard Fabienne, Mogila Vladic, Karch François, Georgiev Pavel, Schedl Paul (2018), The BEN Domain Protein Insensitive Binds to the Fab-7 Chromatin Boundary To Establish Proper Segmental Identity in Drosophila, in Genetics, 210(2), 573-585.
The lncRNA male-specific abdominal plays a critical role in Drosophila accessory gland development and male fertility
Maeda Robert K., Sitnik Jessica L., Frei Yohan, Prince Elodie, Gligorov Dragan, Wolfner Mariana F., Karch François (2018), The lncRNA male-specific abdominal plays a critical role in Drosophila accessory gland development and male fertility, in PLOS Genetics, 14(7), e1007519-e1007519.
Different Evolutionary Strategies To Conserve Chromatin Boundary Function in the Bithorax Complex
Cleard Fabienne, Wolle Daniel, Taverner Andrew M., Aoki Tsutomu, Deshpande Girish, Andolfatto Peter, Karch Francois, Schedl Paul (2017), Different Evolutionary Strategies To Conserve Chromatin Boundary Function in the Bithorax Complex, in Genetics, 205(2), 589-603.

Collaboration

Group / person Country
Types of collaboration
Dr. Stephen Goodwin, Dept of Physiology, Anatomy and Genetics, Oxford University Great Britain and Northern Ireland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Dr. Mariana WOLFNER, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. Welcome BENDER, Dept of Biological Chemistry and Pharmacology, Harvard Medical School, Boston United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Communication with the public

Communication Title Media Place Year
Talks/events/exhibitions Les nuits de la science Western Switzerland 2018

Associated projects

Number Title Start Funding scheme
192621 Molecules and mechanisms regulating the post-mating response in Drosophila 01.09.2020 Project funding (Div. I-III)
149634 Multiple Layers of Complexity in the Regulation of the Bithorax Complex in Drosophila 01.01.2014 Project funding (Div. I-III)

Abstract

1. ABSTRACTAs the regulation of more and more individual genes are studied, a vast complexity is being revealed, showing that gene expression is not simply a matter of enhancers turning on a gene in a specific pattern; it is only through the coordinated action of numerous elements that proper gene expression is realized. This is clearly the case in the Drosophila bithorax complex (BX-C), where many types of key regulatory elements were first discovered and/or characterized. From its conception, our lab has focused on understanding the mechanisms controlling gene expression in the BX-C. Our work, along with the work of others, has led to the discovery of numerous cis-regulatory elements (enhancers, silencers, boundary elements/insulators and initiators) that restrict homeotic gene expression to specific segments along the anterior-posterior axis. Although we are still interested in understanding how these elements function at a molecular level, most of our recent work has led us in a new direction, to study how non-coding RNAs (ncRNAs) and micropeptides (miPEPs) within the BX-C control homeotic gene expression and the development of a specific organ involved in male fertility. For our continuing study of regulatory elements in the BX-C, we are focusing on two types of elements: boundary elements and initiators. Our latest work on boundary elements has indicated that the DNA binding proteins associated with boundary elements are interchangeable and that what really matters is the recruitment of other factors such as CP190 and mod(mdg)4 to give boundaries their function. Using various methods, we would like to test this directly by tethering these molecules to different areas of the genome to see how they modify gene expression. In the process of these experiments, we will make tools that we hope can be used by others to modulate the expression of their genes of interest. Regarding the initiator, much of our current data suggests that initiators function to coordinate enhancer and silencer activity by driving transcription over the regulatory elements. We would like to test this hypothesis by blocking transcription using a new method where RNA polymerase is blocked by the binding of a dead-Cas9 nuclease. During the period of the last grant, we showed that the homeotic gene, Abd-B, is expressed in the Drosophila accessory gland, an organ similar in function to the human prostate gland. The enhancer that drives Abd-B expression in this gland also turns out to be the promoter for a male-specific, long, non-coding RNA called msa. Previously, we showed that the iab-8 variant of this lncRNA regulates abd-A in the CNS via a miRNA. We have shown that like the iab-8 ncRNA, msa is also a template for making the iab-8 miRNA, and that loss of the miRNA causes phenotypes affecting the accessory gland and male fertility. As abd-A is not expressed in the accessory gland, we would now like to determine the targets of the both the miRNA and Abd-B in this gland to account for the resulting mutant phenotypes (ribosome profiling, RNA-seq or DamID followed by validation). In order to interpret the phenotypes better, we have also started a detailed investigation into the unique cell biology of the gland itself. Lastly, we have recently found that a highly conserved sequence within the msa transcript seems to produce a micro-peptide (miPEP). Our preliminary analysis indicates that the expression of this miPEP is tightly controlled at the level of translation to be made only in the male accessory gland. We are now beginning to look for a function for this miPEP. As its expression seems to be limited to the male accessory gland, we are currently concentrating our efforts on phenotypes involving male fertility.
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