Dissecting the temporal requirements for homeotic gene function

Development ◽  
1994 ◽  
Vol 120 (7) ◽  
pp. 1983-1995 ◽  
Author(s):  
J. Castelli-Gair ◽  
S. Greig ◽  
G. Micklem ◽  
M. Akam

Homeotic genes confer identity to the different segments of Drosophila. These genes are expressed in many cell types over long periods of time. To determine when the homeotic genes are required for specific developmental events we have expressed the Ultrabithorax, abdominal-A and Abdominal-Bm proteins at different times during development using the GAL4 targeting technique. We find that early transient homeotic gene expression has no lasting effects on the differentiation of the larval epidermis, but it switches the fate of other cell types irreversibly (e.g. the spiracle primordia). We describe one cell type in the peripheral nervous system that makes sequential, independent responses to homeotic gene expression. We also provide evidence that supports the hypothesis of in vivo competition between the bithorax complex proteins for the regulation of their down-stream targets.

1996 ◽  
Vol 16 (4) ◽  
pp. 1714-1721 ◽  
Author(s):  
F Argenton ◽  
Y Arava ◽  
A Aronheim ◽  
M D Walker

The E2A protein is a mammalian transcription factor of the helix-loop-helix family which is implicated in cell-specific gene expression in several cell lineages. Mouse E2A contains two independent transcription activation domains, ADI and ADII; whereas ADI functions effectively in a variety of cultured cell lines, ADII shows preferential activity in pancreatic beta cells. To analyze this preferential activity in an in vivo setting, we adapted a system involving transient gene expression in microinjected zebra fish embryos. Fertilized one- to four-cell embryos were coinjected with an expression plasmid and a reporter plasmid. The expression plasmids used encode the yeast Gal4 DNA-binding domain (DBD) alone, or Gal4 DBD fused to ADI, ADII, or VP16. The reporter plasmid includes the luciferase gene linked to a promoter containing repeats of UASg, the Gal4-binding site. Embryo extracts prepared 24 h after injection showed significant luciferase activity in response to each of the three activation domains. To determine the cell types in which the activation domains were functioning, a reporter plasmid encoding beta-galactosidase and then in situ staining of whole embryos were used. Expression of ADI led to activation in all major groups of cell types of the embryo (skin, sclerotome, myotome, notochord, and nervous system). On the other hand, ADII led to negligible expression in the sclerotome, notochord, and nervous system and much more frequent expression in the myotome. Parallel experiments conducted with transfected mammalian cells have confirmed that ADII shows significant activity in myoblast cells but little or no activity in neuronal precursor cells, consistent with our observations in zebra fish. This transient-expression approach permits rapid in vivo analysis of the properties of transcription activation domains: the data show that ADII functions preferentially in cells of muscle lineage, consistent with the notion that certain activation domains contribute to selective gene activation in vivo.


Development ◽  
1994 ◽  
Vol 120 (9) ◽  
pp. 2629-2636 ◽  
Author(s):  
A. Lonie ◽  
R. D'Andrea ◽  
R. Paro ◽  
R. Saint

The Polycomblike gene of Drosophila melanogaster, a member of the Polycomb Group of genes, is required for the correct spatial expression of the homeotic genes of the Antennapaedia and Bithorax Complexes. Mutations in Polycomb Group genes result in ectopic homeotic gene expression, indicating that Polycomb Group proteins maintain the transcriptional repression of specific homeotic genes in specific tissues during development. We report here the isolation and molecular characterisation of the Polycomblike gene. The Polycomblike transcript encodes an 857 amino acid protein with no significant homology to other proteins. Antibodies raised against the product of this open reading frame were used to show that the Polycomblike protein is found in all nuclei during embryonic development. Antibody staining also revealed that the Polycomblike protein is found on larval salivary gland polytene chromosomes at about 100 specific loci, the same loci to which the Polycomb and polyhomeotic proteins, two other Polycomb Group proteins, are found. These data add further support for a model in which Polycomb Group proteins form multimeric protein complexes at specific chromosomal loci to repress transcription at those loci.


Development ◽  
1993 ◽  
Vol 117 (1) ◽  
pp. 119-134 ◽  
Author(s):  
T.R. Breen ◽  
P.J. Harte

The trithorax (trx) gene is required for normal development of the body plan in Drosophila embryos and adults. Mutations in trx cause homeotic transformations throughout the body. Genetic studies suggest that trx encodes a positive regulatory factor required throughout development for normal expression of multiple homeotic genes of the bithorax and Antennapedia complexes (BX-C and ANT-C). To determine how trx influences homeotic gene expression, we examined the expression of the BX-C genes Ultrabithorax, abdominal-A, Abdominal-B and the ANT-C genes Antennapedia, Sex combs reduced and Deformed in trx embryos. We show that trx does indeed exert its effects by positively regulating homeotic gene expression and that its effects on expression of individual homeotic genes are complex: each of the BX-C and ANT-C genes examined exhibits different tissue-specific, parasegment-specific and promoter-specific reductions in their expression. This implies that each of these genes have different requirements for trx in different spatial contexts in order to achieve normal expression levels, presumably depending on the promoters involved and the other regulatory factors bound at each of their multiple tissue- and parasegment-specific cis-regulatory sites in different regions of the embryo. These results also imply that those components of homeotic gene expression patterns for which trx is dispensable, require other factors, possibly those encoded by other trithorax-like genes.


Science ◽  
2020 ◽  
Vol 370 (6518) ◽  
pp. eaba7612 ◽  
Author(s):  
Silvia Domcke ◽  
Andrew J. Hill ◽  
Riza M. Daza ◽  
Junyue Cao ◽  
Diana R. O’Day ◽  
...  

The chromatin landscape underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of chromatin accessibility and gene expression in fetal tissues. For chromatin accessibility, we devised a three-level combinatorial indexing assay and applied it to 53 samples representing 15 organs, profiling ~800,000 single cells. We leveraged cell types defined by gene expression to annotate these data and cataloged hundreds of thousands of candidate regulatory elements that exhibit cell type–specific chromatin accessibility. We investigated the properties of lineage-specific transcription factors (such as POU2F1 in neurons), organ-specific specializations of broadly distributed cell types (such as blood and endothelial), and cell type–specific enrichments of complex trait heritability. These data represent a rich resource for the exploration of in vivo human gene regulation in diverse tissues and cell types.


1997 ◽  
Vol 17 (8) ◽  
pp. 4707-4717 ◽  
Author(s):  
O N Denisenko ◽  
K Bomsztyk

The heterogeneous nuclear ribonucleoprotein K protein represents a novel class of proteins that may act as docking platforms that orchestrate cross-talk among molecules involved in signal transduction and gene expression. Using a fragment of K protein as bait in the yeast two-hybrid screen, we isolated a cDNA that encodes a protein whose primary structure has extensive similarity to the Drosophila melanogaster extra sex combs (esc) gene product, Esc, a putative silencer of homeotic genes. The cDNA that we isolated is identical to the cDNA of the recently positionally cloned mouse embryonic ectoderm development gene, eed. Like Esc, Eed contains six WD-40 repeats in the C-terminal half of the protein and is thought to repress homeotic gene expression during mouse embryogenesis. Eed binds to K protein through a domain in its N terminus, but interestingly, this domain is not found in the Drosophila Esc. Gal4-Eed fusion protein represses transcription of a reporter gene driven by a promoter that contains Gal4-binding DNA elements. Eed also represses transcription when recruited to a target promoter by Gal4-K protein. Point mutations within the eed gene that are responsible for severe embryonic development abnormalities abolished the transcriptional repressor activity of Eed. Results of this study suggest that Eed-restricted homeotic gene expression during embryogenesis reflects the action of Eed as a transcriptional repressor. The Eed-mediated transcriptional effects are likely to reflect the interaction of Eed with multiple molecular partners, including K protein.


2021 ◽  
Author(s):  
Hao-Shan Chen ◽  
Xiao-Long Zhang ◽  
Rong-Rong Yang ◽  
Guang-Ling Wang ◽  
Xin-Yue Zhu ◽  
...  

The complexity of brain circuitry is manifested by numerous cell types based on genetic marker, location and neural connectivity. Cell-type specific recording and manipulation is essential to disentangle causal neural mechanisms in physiology and behavior; however, many current approaches are largely limited by number of intersectional features, incompatibility of common effectors and insufficient gene expression. To tackle these limitations, we devise an intein-based intersectional synthesis of transactivator (IBIST) to selectively control gene expression of common effectors in specific cell types defined by a combination of multiple features. We validate the specificity and sufficiency of IBIST to control common effectors including fluorophores, optogenetic opsins and Ca2+ indicators in various intersectional conditions in vivo. Using IBIST-based Ca2+ imaging, we show that the IBIST can intersect up to five features, and that hippocampal cells tune differently to distinct emotional valences depending on the pattern of projection targets. Collectively, the IBIST multiplexes the capability to intersect cell-type features and is compatible with common effectors to effectively control gene expression, monitor and manipulate neural activities.


2020 ◽  
Author(s):  
Juan A. Sánchez ◽  
Ana L. Gil-Martinez ◽  
Alejandro Cisterna ◽  
Sonia García-Ruíz ◽  
Alicia Gómez ◽  
...  

AbstractMotivationCo-expression networks are a powerful gene expression analysis method to study how genes co-express together in clusters with functional coherence that usually resemble specific cell type behaviour for the genes involved. They can be applied to bulk-tissue gene expression profiling and assign function, and usually cell type specificity, to a high percentage of the gene pool used to construct the network. One of the limitations of this method is that each gene is predicted to play a role in a specific set of coherent functions in a single cell type (i.e. at most we get a single <gene, function, cell type> for each gene). We present here GMSCA (Gene Multifunctionality Secondary Co-expression Analysis), a software tool that exploits the co-expression paradigm to increase the number of functions and cell types ascribed to a gene in bulk-tissue co-expression networks.ResultsWe applied GMSCA to 27 co-expression networks derived from bulk-tissue gene expression profiling of a variety of brain tissues. Neurons and glial cells (microglia, astrocytes and oligodendrocytes) were considered the main cell types. Applying this approach, we increase the overall number of predicted triplets <gene, function, cell type> by 46.73%. Moreover, GMSCA predicts that the SNCA gene, traditionally associated to work mainly in neurons, also plays a relevant function in oligodendrocytes.AvailabilityThe tool is available at GitHub,https://github.com/drlaguna/GMSCA as open source software.ImplementationGSMCA is implemented in R.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 3250-3250
Author(s):  
Eleni-Dimitra Papanagnou ◽  
Tina Bagratuni ◽  
Efstathios Kastritis ◽  
Issidora Papassideri ◽  
Evangelos Terpos ◽  
...  

Abstract Organisms require efficient surveillance of proteome functionality to prevent disruption of proteostasis. Central to the proteostasis ensuring network is the proteasome, which degrades both normal short-lived ubiquitinated proteins and damaged or mutated proteins. Over-activation of the proteasome seems to represent a hallmark of advanced tumors and thus, its selective inhibition provides a strategy for the development of novel anti-tumor therapies. This approach is applied in multiple myeloma (MM) that represents the second most common hematological malignancy. Specifically, proteasome inhibitors have demonstrated clinical efficacy in the treatment of MM and mantle cell lymphoma and are evaluated for the treatment of other malignancies. Nevertheless, the impact of proteasome dysfunction in normal human tissues (which relates to side effects in the clinic) remains poorly understood. By using the fruit fly Drosophila melanogaster as an in vivo experimental platform to study proteasome physiology we found that proteasome functionality is sex-, tissue- and age-dependent. Oral administration of proteasome inhibitors (e.g. Bortezomib or Carfilzomib) in young flies suppressed proteasome activities in the somatic tissues; reduced motor function (recapitulating peripheral neuropathy of Bortezomib treatment in the clinic) and caused premature aging. It also increased oxidative stress and activated an Nrf2-dependent feedback regulatory circuit that upregulated proteasome genes in order to restore normal proteasome functionality. Moreover, in line with observations in the clinic, Carfilzomib was found to cause milder (as compared to Bortezomib) neuromusculatory toxicity and reduction of flies' lifespan. To address the question whether these findings can be translated in humans we started characterizing proteasome physiology in both healthy donors, as well as in MM patients treated with therapeutic proteasome inhibitors. For our studies we used isolated red blood cells (RBCs; represent an anucleate relatively "long-lived" proteome) and peripheral blood mononucleated cells (PBMCs; represent cell lineages with active genomic responses). Our analyses in healthy donors of different ages revealed significant variability of basal proteasome peptidase activities in both cell types. PBMCs expressed (as compared to RBCs) higher basal proteasome activities and RBCs from females had higher chymotrypsin-like activity as compared to RBCs from males of similar age. Furthermore, as in the flies' somatic tissues, proteasome activities were found (independently of sex and cell type) to decline during aging. Studies in RBCs and PBMCs isolated from MM patients treated with Bortezomib revealed donor-, cell type- and drug-specific readouts. In most (but not all) cases proteasome activities were suppressed in both cell types at 24-hrs post-drug administration. RBCs were particularly sensitive to the inhibitor and their proteasome activities remained low during the entire course of treatment. On the contrary, PBMCs were characterized by phases of rebound proteasome activities during the periods of no drug administration; these phases correlated with upregulation of proteasome genes expression, indicating that the feedback regulatory circuit which functions to restore proteasome activities in flies is also operational in humans. Additional gene expression analyses in PBMCs showed that proteasome inhibition also triggers the induction of genes involved in chaperon, autophagy, unfolded protein- and antioxidant-responses pathways; while, as in the fly model, the intensity of genes induction seems to decline during aging. Interestingly, in those patients who (despite treatment) showed no reduction of proteasome activities we found marginal gene expression alterations, suggesting that the observed gene induction largely depends on proteasome loss of function. Importantly, at the clinical level we observed a positive correlation between the degree of proteasome inhibition (in PBMCs or RBCS) and the depth of disease responses. The similarities between the Drosophila pharmacological model and the MM patients indicate that the molecular responses to proteasome malfunction are largely conserved in higher metazoans. We foresee that our ongoing studies will support a more personalized clinical therapeutic approach in hematological malignancies. Disclosures Terpos: Amgen: Honoraria, Other: Travel expenses, Research Funding; Takeda: Honoraria; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel expenses; Novartis: Honoraria; Celgene: Honoraria, Other: Travel expenses. Dimopoulos:Celgene: Honoraria; Onyx: Honoraria; Novartis: Honoraria; Genesis: Honoraria; Janssen-Cilag: Honoraria; Janssen: Honoraria; Amgen: Honoraria.


Science ◽  
2020 ◽  
Vol 370 (6514) ◽  
pp. eabb2494 ◽  
Author(s):  
Shengjin Xu ◽  
Hui Yang ◽  
Vilas Menon ◽  
Andrew L. Lemire ◽  
Lihua Wang ◽  
...  

Brains encode behaviors using neurons amenable to systematic classification by gene expression. The contribution of molecular identity to neural coding is not understood because of the challenges involved with measuring neural dynamics and molecular information from the same cells. We developed CaRMA (calcium and RNA multiplexed activity) imaging based on recording in vivo single-neuron calcium dynamics followed by gene expression analysis. We simultaneously monitored activity in hundreds of neurons in mouse paraventricular hypothalamus (PVH). Combinations of cell-type marker genes had predictive power for neuronal responses across 11 behavioral states. The PVH uses combinatorial assemblies of molecularly defined neuron populations for grouped-ensemble coding of survival behaviors. The neuropeptide receptor neuropeptide Y receptor type 1 (Npy1r) amalgamated multiple cell types with similar responses. Our results show that molecularly defined neurons are important processing units for brain function.


Development ◽  
1990 ◽  
Vol 110 (4) ◽  
pp. 1041-1050 ◽  
Author(s):  
G.E. Panganiban ◽  
R. Reuter ◽  
M.P. Scott ◽  
F.M. Hoffmann

The decapentaplegic (dpp) gene product, a member of the transforming growth factor-beta family, is required in Drosophila embryos for normal gastrulation and the establishment of dorsal-ventral polarity in the embryo. dpp is also expressed at specific positions in the visceral mesoderm along the developing midgut. We find that mutations that eliminate the visceral mesoderm expression of dpp lead to defects in midgut morphogenesis and alter the spatially localized expression of the homeotic genes Sex combs reduced (Scr), Ultrabithorax (Ubx), and Antennapedia (Antp) in the visceral mesoderm. The extracellular dpp protein migrates from the visceral mesoderm across the apposing endodermal cell layer in a region of the endoderm that expresses the homeotic gene labial (lab). Mesodermal expression of dpp is required for the expression of lab in these endodermal cells indicating that dpp mediates an inductive interaction between the two germ layers. We propose that extracellular dpp protein regulates gut morphogenesis, in part, by regulating homeotic gene expression in the visceral mesoderm and endoderm of the developing midgut.


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