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Faucillion ML, Johansson AM, Larsson J. Modulation of RNA stability regulates gene expression in two opposite ways: through buffering of RNA levels upon global perturbations and by supporting adapted differential expression. Nucleic Acids Res 2022; 50:4372-4388. [PMID: 35390159 PMCID: PMC9071389 DOI: 10.1093/nar/gkac208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 03/09/2022] [Accepted: 03/17/2022] [Indexed: 01/02/2023] Open
Abstract
The steady state levels of RNAs, often referred to as expression levels, result from a well-balanced combination of RNA transcription and decay. Alterations in RNA levels will therefore result from tight regulation of transcription rates, decay rates or both. Here, we explore the role of RNA stability in achieving balanced gene expression and present genome-wide RNA stabilities in Drosophila melanogaster male and female cells as well as male cells depleted of proteins essential for dosage compensation. We identify two distinct RNA-stability mediated responses involved in regulation of gene expression. The first of these responds to acute and global changes in transcription and thus counteracts potentially harmful gene mis-expression by shifting the RNA stability in the direction opposite to the transcriptional change. The second response enhances inter-individual differential gene expression by adjusting the RNA stability in the same direction as a transcriptional change. Both mechanisms are global, act on housekeeping as well as non-housekeeping genes and were observed in both flies and mammals. Additionally, we show that, in contrast to mammals, modulation of RNA stability does not detectably contribute to dosage compensation of the sex-chromosomes in D. melanogaster.
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Affiliation(s)
| | | | - Jan Larsson
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
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2
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Halievski K, Mo K, Westwood JT, Monks DA. Transcriptional profile of muscle following acute induction of symptoms in a mouse model of Kennedy's disease/spinobulbar muscular atrophy. PLoS One 2015; 10:e0118120. [PMID: 25719894 PMCID: PMC4341878 DOI: 10.1371/journal.pone.0118120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 01/07/2015] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Kennedy's disease/Spinobulbar muscular atrophy (KD/SBMA) is a degenerative neuromuscular disease affecting males. This disease is caused by polyglutamine expansion mutations of the androgen receptor (AR) gene. Although KD/SBMA has been traditionally considered a motor neuron disease, emerging evidence points to a central etiological role of muscle. We previously reported a microarray study of genes differentially expressed in muscle of three genetically unique mouse models of KD/SBMA but were unable to detect those which are androgen-dependent or are associated with onset of symptoms. METHODOLOGY/PRINCIPAL FINDINGS In the current study we examined the time course and androgen-dependence of transcriptional changes in the HSA-AR transgenic (Tg) mouse model, in which females have a severe phenotype after acute testosterone treatment. Using microarray analysis we identified differentially expressed genes at the onset and peak of muscle weakness in testosterone-treated Tg females. We found both transient and persistent groups of differentially expressed genes and analysis of gene function indicated functional groups such as mitochondrion, ion and nucleotide binding, muscle development, and sarcomere maintenance. CONCLUSIONS/SIGNIFICANCE By comparing the current results with those from the three previously reported models we were able to identify KD/SBMA candidate genes that are androgen dependent, and occur early in the disease process, properties which are promising for targeted therapeutics.
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Affiliation(s)
- Katherine Halievski
- Department of Psychology, University of Toronto Mississauga,
Mississauga, Ontario, Canada
| | - Kaiguo Mo
- Department of Psychology, University of Toronto Mississauga,
Mississauga, Ontario, Canada
| | - J. Timothy Westwood
- Department of Psychology, University of Toronto Mississauga,
Mississauga, Ontario, Canada
| | - Douglas A. Monks
- Department of Psychology, University of Toronto Mississauga,
Mississauga, Ontario, Canada
- * E-mail:
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3
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Endogenously imprinted genes in Drosophila melanogaster. Mol Genet Genomics 2014; 289:653-73. [DOI: 10.1007/s00438-014-0840-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 03/04/2014] [Indexed: 12/21/2022]
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4
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Gonsalves SE, Neal SJ, Kehoe AS, Westwood JT. Genome-wide examination of the transcriptional response to ecdysteroids 20-hydroxyecdysone and ponasterone A in Drosophila melanogaster. BMC Genomics 2011; 12:475. [PMID: 21958154 PMCID: PMC3228561 DOI: 10.1186/1471-2164-12-475] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 09/29/2011] [Indexed: 12/19/2022] Open
Abstract
Background The 20-hydroxyecdysone (20E) hierarchy of gene activation serves as an attractive model system for studying the mode of steroid hormone regulated gene expression and development. Many structural analogs of 20E exist in nature and among them the plant-derived ponasterone A (PoA) is the most potent. PoA has a higher affinity for the 20E nuclear receptor, composed of the ecysone receptor (EcR) and Ultraspiracle proteins, than 20E and a comparison of the genes regulated by these hormones has not been performed. Furthermore, in Drosophila different cell types elicit different morphological responses to 20E yet the cell type specificity of the 20E transcriptional response has not been examined on a genome-wide scale. We aim to characterize the transcriptional response to 20E and PoA in Drosophila Kc cells and to 20E in salivary glands and provide a robust comparison of genes involved in each response. Results Our genome-wide microarray analysis of Kc167 cells treated with 20E or PoA revealed that far more genes are regulated by PoA than by 20E (256 vs 148 respectively) and that there is very little overlap between the transcriptional responses to each hormone. Interestingly, genes induced by 20E relative to PoA are enriched in functions related to development. We also find that many genes regulated by 20E in Kc167 cells are not regulated by 20E in salivary glands of wandering 3rd instar larvae and we show that 20E-induced levels of EcR isoforms EcR-RA, ER-RC, and EcR-RD/E differ between Kc cells and salivary glands suggesting a possible cause for the observed differences in 20E-regulated gene transcription between the two cell types. Conclusions We report significant differences in the transcriptional responses of 20E and PoA, two steroid hormones that differ by only a single hydroxyl group. We also provide evidence that suggests that PoA induced death of non-adapted insects may be related to PoA regulating different set of genes when compared to 20E. In addition, we reveal large differences between Kc cells and salivary glands with regard to their genome-wide transcriptional response to 20E and show that the level of induction of certain EcR isoforms differ between Kc cells and salivary glands. We hypothesize that the differences in the transcriptional response may in part be due to differences in the EcR isoforms present in different cell types.
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Affiliation(s)
- Sarah E Gonsalves
- Department of Cell & Systems Biology, University of Toronto, Mississauga, Ontario, Canada
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5
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Gonsalves SE, Moses AM, Razak Z, Robert F, Westwood JT. Whole-genome analysis reveals that active heat shock factor binding sites are mostly associated with non-heat shock genes in Drosophila melanogaster. PLoS One 2011; 6:e15934. [PMID: 21264254 PMCID: PMC3021535 DOI: 10.1371/journal.pone.0015934] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 12/01/2010] [Indexed: 11/19/2022] Open
Abstract
During heat shock (HS) and other stresses, HS gene transcription in eukaryotes is up-regulated by the transcription factor heat shock factor (HSF). While the identities of the major HS genes have been known for more than 30 years, it has been suspected that HSF binds to numerous other genes and potentially regulates their transcription. In this study, we have used a chromatin immunoprecipitation and microarray (ChIP-chip) approach to identify 434 regions in the Drosophila genome that are bound by HSF. We have also performed a transcript analysis of heat shocked Kc167 cells and third instar larvae and compared them to HSF binding sites. The heat-induced transcription profiles were quite different between cells and larvae and surprisingly only about 10% of the genes associated with HSF binding sites show changed transcription. There were also genes that showed changes in transcript levels that did not appear to correlate with HSF binding sites. Analysis of the locations of the HSF binding sites revealed that 57% were contained within genes with approximately 2/3rds of these sites being in introns. We also found that the insulator protein, BEAF, has enriched binding prior to HS to promoters of genes that are bound by HSF upon HS but that are not transcriptionally induced during HS. When the genes associated with HSF binding sites in promoters were analyzed for gene ontology terms, categories such as stress response and transferase activity were enriched whereas analysis of genes having HSF binding sites in introns identified those categories plus ones related to developmental processes and reproduction. These results suggest that Drosophila HSF may be regulating many genes besides the known HS genes and that some of these genes may be regulated during non-stress conditions.
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Affiliation(s)
- Sarah E. Gonsalves
- Department of Cell and Systems Biology, University of Toronto, Mississauga, Canada
| | - Alan M. Moses
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - Zak Razak
- Department of Cell and Systems Biology, University of Toronto, Mississauga, Canada
| | - Francois Robert
- Institut de Recherches Cliniques de Montréal, Montréal, Canada
- Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, Canada
| | - J. Timothy Westwood
- Department of Cell and Systems Biology, University of Toronto, Mississauga, Canada
- * E-mail:
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6
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Kramer JM, Kochinke K, Oortveld MAW, Marks H, Kramer D, de Jong EK, Asztalos Z, Westwood JT, Stunnenberg HG, Sokolowski MB, Keleman K, Zhou H, van Bokhoven H, Schenck A. Epigenetic regulation of learning and memory by Drosophila EHMT/G9a. PLoS Biol 2011; 9:e1000569. [PMID: 21245904 PMCID: PMC3014924 DOI: 10.1371/journal.pbio.1000569] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 11/10/2010] [Indexed: 11/18/2022] Open
Abstract
The epigenetic modification of chromatin structure and its effect on complex neuronal processes like learning and memory is an emerging field in neuroscience. However, little is known about the "writers" of the neuronal epigenome and how they lay down the basis for proper cognition. Here, we have dissected the neuronal function of the Drosophila euchromatin histone methyltransferase (EHMT), a member of a conserved protein family that methylates histone 3 at lysine 9 (H3K9). EHMT is widely expressed in the nervous system and other tissues, yet EHMT mutant flies are viable. Neurodevelopmental and behavioral analyses identified EHMT as a regulator of peripheral dendrite development, larval locomotor behavior, non-associative learning, and courtship memory. The requirement for EHMT in memory was mapped to 7B-Gal4 positive cells, which are, in adult brains, predominantly mushroom body neurons. Moreover, memory was restored by EHMT re-expression during adulthood, indicating that cognitive defects are reversible in EHMT mutants. To uncover the underlying molecular mechanisms, we generated genome-wide H3K9 dimethylation profiles by ChIP-seq. Loss of H3K9 dimethylation in EHMT mutants occurs at 5% of the euchromatic genome and is enriched at the 5' and 3' ends of distinct classes of genes that control neuronal and behavioral processes that are corrupted in EHMT mutants. Our study identifies Drosophila EHMT as a key regulator of cognition that orchestrates an epigenetic program featuring classic learning and memory genes. Our findings are relevant to the pathophysiological mechanisms underlying Kleefstra Syndrome, a severe form of intellectual disability caused by mutations in human EHMT1, and have potential therapeutic implications. Our work thus provides novel insights into the epigenetic control of cognition in health and disease.
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Affiliation(s)
- Jamie M. Kramer
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Korinna Kochinke
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Merel A. W. Oortveld
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Hendrik Marks
- Radboud University Nijmegen, Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Faculty of Science, Nijmegen, The Netherlands
| | - Daniela Kramer
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Eiko K. de Jong
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Zoltan Asztalos
- Aktogen Ltd., Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Institute of Biochemistry, Biological Research Center of Hungarian Academy of Sciences, Szeged, Hungary
| | | | - Hendrik G. Stunnenberg
- Radboud University Nijmegen, Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Faculty of Science, Nijmegen, The Netherlands
| | | | | | - Huiqing Zhou
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- Department of Cognitive Neurosciences, Donders Institute for Brain, Cognition and Behavior; Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- * E-mail: (AS); (HvB)
| | - Annette Schenck
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- * E-mail: (AS); (HvB)
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Cherbas L, Willingham A, Zhang D, Yang L, Zou Y, Eads BD, Carlson JW, Landolin JM, Kapranov P, Dumais J, Samsonova A, Choi JH, Roberts J, Davis CA, Tang H, van Baren MJ, Ghosh S, Dobin A, Bell K, Lin W, Langton L, Duff MO, Tenney AE, Zaleski C, Brent MR, Hoskins RA, Kaufman TC, Andrews J, Graveley BR, Perrimon N, Celniker SE, Gingeras TR, Cherbas P. The transcriptional diversity of 25 Drosophila cell lines. Genome Res 2010; 21:301-14. [PMID: 21177962 DOI: 10.1101/gr.112961.110] [Citation(s) in RCA: 191] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Drosophila melanogaster cell lines are important resources for cell biologists. Here, we catalog the expression of exons, genes, and unannotated transcriptional signals for 25 lines. Unannotated transcription is substantial (typically 19% of euchromatic signal). Conservatively, we identify 1405 novel transcribed regions; 684 of these appear to be new exons of neighboring, often distant, genes. Sixty-four percent of genes are expressed detectably in at least one line, but only 21% are detected in all lines. Each cell line expresses, on average, 5885 genes, including a common set of 3109. Expression levels vary over several orders of magnitude. Major signaling pathways are well represented: most differentiation pathways are "off" and survival/growth pathways "on." Roughly 50% of the genes expressed by each line are not part of the common set, and these show considerable individuality. Thirty-one percent are expressed at a higher level in at least one cell line than in any single developmental stage, suggesting that each line is enriched for genes characteristic of small sets of cells. Most remarkable is that imaginal disc-derived lines can generally be assigned, on the basis of expression, to small territories within developing discs. These mappings reveal unexpected stability of even fine-grained spatial determination. No two cell lines show identical transcription factor expression. We conclude that each line has retained features of an individual founder cell superimposed on a common "cell line" gene expression pattern.
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Affiliation(s)
- Lucy Cherbas
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana 47405, USA.
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8
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Papaconstantinou M, Pepper AN, Wu Y, Kasimer D, Westwood T, Campos AR, Bédard PA. Menin links the stress response to genome stability in Drosophila melanogaster. PLoS One 2010; 5:e14049. [PMID: 21124979 PMCID: PMC2987805 DOI: 10.1371/journal.pone.0014049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 10/01/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The multiple endocrine neoplasia type I gene functions as a tumor suppressor gene in humans and mouse models. In Drosophila melanogaster, mutants of the menin gene (Mnn1) are hypersensitive to mutagens or gamma irradiation and have profound defects in the response to several stresses including heat shock, hypoxia, hyperosmolarity and oxidative stress. However, it is not known if the function of menin in the stress response contributes to genome stability. The objective of this study was to examine the role of menin in the control of the stress response and genome stability. METHODOLOGY/PRINCIPAL FINDINGS Using a test of loss-of-heterozygosity, we show that Drosophila strains lacking a functional Mnn1 gene or expressing a Mnn1 dsRNA display increased genome instability in response to non-lethal heat shock or hypoxia treatments. This is also true for strains lacking all Hsp70 genes, implying that a precise control of the stress response is required for genome stability. While menin is required for Hsp70 expression, the results of epistatic studies indicate that the increase in genome instability observed in Mnn1 lack-of-function mutants cannot be accounted for by mis-expression of Hsp70. Therefore, menin may promote genome stability by controlling the expression of other stress-responsive genes. In agreement with this notion, gene profiling reveals that Mnn1 is required for sustained expression of all heat shock protein genes but is dispensable for early induction of the heat shock response. CONCLUSIONS/SIGNIFICANCE Mutants of the Mnn1 gene are hypersensitive to several stresses and display increased genome instability when subjected to conditions, such as heat shock, generally regarded as non-genotoxic. In this report, we describe a role for menin as a global regulator of heat shock gene expression and critical factor in the maintenance of genome integrity. Therefore, menin links the stress response to the control of genome stability in Drosophila melanogaster.
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Affiliation(s)
| | - Alicia N. Pepper
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Ying Wu
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Dahlia Kasimer
- Department of Cell and Systems Biology and Canadian Drosophila Microarray Centre, University of Toronto, Mississauga, Ontario, Canada
| | - Tim Westwood
- Department of Cell and Systems Biology and Canadian Drosophila Microarray Centre, University of Toronto, Mississauga, Ontario, Canada
| | - Ana Regina Campos
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Pierre-André Bédard
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
- * E-mail:
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9
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Gene expression profiling implicates OXPHOS complexes in lifespan extension of flies over-expressing a small mitochondrial chaperone, Hsp22. Exp Gerontol 2009; 45:611-20. [PMID: 20036725 DOI: 10.1016/j.exger.2009.12.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 12/16/2009] [Accepted: 12/17/2009] [Indexed: 11/23/2022]
Abstract
Aging is a complex process accompanied by a decreased capacity to tolerate and respond to various stresses. Heat shock proteins as part of cell defense mechanisms are up-regulated following stress. In Drosophila, the mitochondrial Hsp22 is preferentially up-regulated in aged flies. Its over-expression results in an extension of lifespan and an increased resistance to stress. Hsp22 has chaperone-like activity in vitro, but the mechanism(s) by which it increases lifespan in flies are unknown. Genome-wide analysis was performed on long-lived Hsp22+ and control flies to unveil transcriptional changes brought by Hsp22. Transcriptomes obtained at 45days, 90% and 50% survival were then compared between them to focus more on genes up- or down-regulated in presence of higher levels of hsp22 mRNA. Hsp22+ flies display an up-regulation of genes mainly related to mitochondrial energy production and protein biosynthesis, two functions normally down-regulated during aging. Interestingly, among the 26 genes up-regulated in Hsp22+ flies, 7 genes encode for mitochondrial proteins, 5 of which being involved in OXPHOS complexes. Other genes that could influence aging such as CG5002, dGCC185 and GstS1 also displayed a regulation linked to Hsp22 expression. The up-regulation of genes of the OXPHOS system in Hsp22+ flies suggest that mitochondrial homeostasis is at the center of Hsp22 beneficial effects on lifespan.
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McAnally AA, Yampolsky LY. Widespread transcriptional autosomal dosage compensation in Drosophila correlates with gene expression level. Genome Biol Evol 2009; 2:44-52. [PMID: 20333221 PMCID: PMC2839349 DOI: 10.1093/gbe/evp054] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2009] [Indexed: 11/12/2022] Open
Abstract
Little is known about dosage compensation in autosomal genes. Transcription-level compensation of deletions and other loss-of-function mutations may be a mechanism of dominance of wild-type alleles, a ubiquitous phenomenon whose nature has been a subject of a long debate. We measured gene expression in two isogenic Drosophila lines heterozygous for long deletions and compared our results with previously published gene expression data in a line heterozygous for a long duplication. We find that a majority of genes are at least partially compensated at transcription, both for (1/2)-fold dosage (in heterozygotes for deletions) and for 1.5-fold dosage (in heterozygotes for a duplication). The degree of compensation does not vary among functional classes of genes. Compensation for deletions is stronger for highly expressed genes. In contrast, the degree of compensation for duplications is stronger for weakly expressed genes. Thus, partial transcriptional compensation appears to be based on regulatory mechanisms that insure high transcription levels of some genes and low transcription levels of other genes, instead of precise maintenance of a particular homeostatic expression level. Given the ubiquity of transcriptional compensation, dominance of wild-type alleles may be at least partially caused by of the regulation at transcription level.
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Affiliation(s)
- Ashley A McAnally
- Department of Biological Sciences, East Tennessee State University, USA
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11
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Benoit B, He CH, Zhang F, Votruba SM, Tadros W, Westwood JT, Smibert CA, Lipshitz HD, Theurkauf WE. An essential role for the RNA-binding protein Smaug during the Drosophila maternal-to-zygotic transition. Development 2009; 136:923-32. [PMID: 19234062 DOI: 10.1242/dev.031815] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Genetic control of embryogenesis switches from the maternal to the zygotic genome during the maternal-to-zygotic transition (MZT), when maternal mRNAs are destroyed, high-level zygotic transcription is initiated, the replication checkpoint is activated and the cell cycle slows. The midblastula transition (MBT) is the first morphological event that requires zygotic gene expression. The Drosophila MBT is marked by blastoderm cellularization and follows 13 cleavage-stage divisions. The RNA-binding protein Smaug is required for cleavage-independent maternal transcript destruction during the Drosophila MZT. Here, we show that smaug mutants also disrupt syncytial blastoderm stage cell-cycle delays, DNA replication checkpoint activation, cellularization, and high-level zygotic expression of protein coding and micro RNA genes. We also show that Smaug protein levels increase through the cleavage divisions and peak when the checkpoint is activated and zygotic transcription initiates, and that transgenic expression of Smaug in an anterior-to-posterior gradient produces a concomitant gradient in the timing of maternal transcript destruction, cleavage cell cycle delays, zygotic gene transcription, cellularization and gastrulation. Smaug accumulation thus coordinates progression through the MZT.
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Affiliation(s)
- Beatrice Benoit
- Program in Molecular Medicine, University of Massachusetts Medical School, 377 Plantation Street, Worcester, MA 01605, USA
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12
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de Wit E, Greil F, van Steensel B. High-resolution mapping reveals links of HP1 with active and inactive chromatin components. PLoS Genet 2007; 3:e38. [PMID: 17335352 PMCID: PMC1808074 DOI: 10.1371/journal.pgen.0030038] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Accepted: 01/19/2007] [Indexed: 12/22/2022] Open
Abstract
Heterochromatin protein 1 (HP1) is commonly seen as a key factor of repressive heterochromatin, even though a few genes are known to require HP1-chromatin for their expression. To obtain insight into the targeting of HP1 and its interplay with other chromatin components, we have mapped HP1-binding sites on Chromosomes 2 and 4 in Drosophila Kc cells using high-density oligonucleotide arrays and the DNA adenine methyltransferase identification (DamID) technique. The resulting high-resolution maps show that HP1 forms large domains in pericentric regions, but is targeted to single genes on chromosome arms. Intriguingly, HP1 shows a striking preference for exon-dense genes on chromosome arms. Furthermore, HP1 binds along entire transcription units, except for 5′ regions. Comparison with expression data shows that most of these genes are actively transcribed. HP1 target genes are also marked by the histone variant H3.3 and dimethylated histone 3 lysine 4 (H3K4me2), which are both typical of active chromatin. Interestingly, H3.3 deposition, which is usually observed along entire transcription units, is limited to the 5′ ends of HP1-bound genes. Thus, H3.3 and HP1 are mutually exclusive marks on active chromatin. Additionally, we observed that HP1-chromatin and Polycomb-chromatin are nonoverlapping, but often closely juxtaposed, suggesting an interplay between both types of chromatin. These results demonstrate that HP1-chromatin is transcriptionally active and has extensive links with several other chromatin components. In each of our cells, a variety of proteins helps to organize the very long DNA fibers into a more compacted structure termed chromatin. Several different types of chromatin exist. Some types of chromatin package DNA rather loosely and thereby allow the genes to be active. Other types, often referred to as heterochromatin, are thought to package the DNA into a condensed structure that prevents the genes from being active. Thus, the different types of chromatin together determine the “gene expression programs” of cells. To understand how this works, it is necessary to identify the genes that are packaged by a particular type of chromatin and to reveal how various chromatin proteins work together to achieve this. Here we present highly detailed maps of the DNA sequences that are packaged by a heterochromatin protein named HP1. The results show that HP1 preferentially binds along the genes themselves and much less to intergenic regions. Contrary to what was previously thought, most genes packaged by HP1 are active. Finally, the data suggest that HP1 may compete with other types of chromatin proteins. These results contribute to our fundamental understanding of the roles of chromatin packaging in gene regulation.
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Affiliation(s)
- Elzo de Wit
- Department of Molecular Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Frauke Greil
- Department of Molecular Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bas van Steensel
- Department of Molecular Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- * To whom correspondence should be addressed. E-mail:
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13
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Maisonhaute C, Ogereau D, Hua-Van A, Capy P. Amplification of the 1731 LTR retrotransposon in Drosophila melanogaster cultured cells: Origin of neocopies and impact on the genome. Gene 2007; 393:116-26. [PMID: 17382490 DOI: 10.1016/j.gene.2007.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Revised: 01/31/2007] [Accepted: 02/01/2007] [Indexed: 10/23/2022]
Abstract
Transposable elements (TEs), represent a large fraction of the eukaryotic genome. In Drosophila melanogaster, about 20% of the genome corresponds to such middle repetitive DNA dispersed sequences. A fraction of TEs is composed of elements showing a retrovirus-like structure, the LTR-retrotransposons, the first TEs to be described in the Drosophila genome. Interestingly, in D. melanogaster embryonic immortal cell culture genomes the copy number of these LTR-retrotransposons was revealed to be higher than the copy number in the Drosophila genome, presumably as the result of transposition of some copies to new genomic locations [Potter, S.S., Brorein Jr., W.J., Dunsmuir, P., Rubin, G.M., 1979. Transposition of elements of the 412, copia and 297 dispersed repeated gene families in Drosophila. Cell 17, 415-427; Junakovic, N., Di Franco, C., Best-Belpomme, M., Echalier, G., 1988. On the transposition of copia-like nomadic elements in cultured Drosophila cells. Chromosoma 97, 212-218]. This suggests that so many transpositions modified the genome organisation and consequently the expression of targeted genes. To understand what has directed the transposition of TEs in Drosophila cell culture genomes, a search to identify the newly transposed copies was undertaken using 1731, a LTR-retrotransposon. A comparison between 1731 full-length elements found in the fly sequenced genome (y(1); cn(1)bw(1), sp(1) stock) and 1731 full-length elements amplified by PCR in the two cell line was done. The resulting data provide evidence that all 1731 neocopies were derived from a single copy slightly active in the Drosophila genome and subsequently strongly activated in cultured cells; and that this active copy is related to a newly evolved genomic variant (Kalmykova, A.I., et al., 2004. Selective expansion of the newly evolved genomic variants of retrotransposon 1731 in the Drosophila genomes. Mol. Biol. Evol. 21, 2281-2289). Moreover, neocopies are shown to be inserted in different sets of genes in the two cell lines suggesting they might be involved in the biological and physiological differences observed between Kc and S2 cell lines.
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Affiliation(s)
- Claude Maisonhaute
- Laboratoire Evolution Génomes et Spéciation, CNRS Bat.13, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
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14
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Tadros W, Goldman AL, Babak T, Menzies F, Vardy L, Orr-Weaver T, Hughes TR, Westwood JT, Smibert CA, Lipshitz HD. SMAUG is a major regulator of maternal mRNA destabilization in Drosophila and its translation is activated by the PAN GU kinase. Dev Cell 2007; 12:143-55. [PMID: 17199047 DOI: 10.1016/j.devcel.2006.10.005] [Citation(s) in RCA: 239] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Revised: 07/10/2006] [Accepted: 10/06/2006] [Indexed: 11/23/2022]
Abstract
In animals, egg activation triggers a cascade of posttranscriptional events that act on maternally synthesized RNAs. We show that, in Drosophila, the PAN GU (PNG) kinase sits near the top of this cascade, triggering translation of SMAUG (SMG), a multifunctional posttranscriptional regulator conserved from yeast to humans. Although PNG is required for cytoplasmic polyadenylation of smg mRNA, it regulates translation via mechanisms that are independent of its effects on the poly(A) tail. Analyses of mutants suggest that PNG relieves translational repression by PUMILIO (PUM) and one or more additional factors, which act in parallel through the smg mRNA's 3' untranslated region (UTR). Microarray-based gene expression profiling shows that SMG is a major regulator of maternal transcript destabilization. SMG-dependent mRNAs are enriched for gene ontology annotations for function in the cell cycle, suggesting a possible causal relationship between failure to eliminate these transcripts and the cell cycle defects in smg mutants.
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Affiliation(s)
- Wael Tadros
- Graduate Department of Molecular and Medical Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
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15
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Levitin A, Marcil A, Tettweiler G, Laforest MJ, Oberholzer U, Alarco AM, Thomas DY, Lasko P, Whiteway M. Drosophila melanogaster Thor and response to Candida albicans infection. EUKARYOTIC CELL 2007; 6:658-63. [PMID: 17277170 PMCID: PMC1865646 DOI: 10.1128/ec.00346-06] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We used Drosophila melanogaster macrophage-like Schneider 2 (S2) cells as a model to study cell-mediated innate immunity against infection by the opportunistic fungal pathogen Candida albicans. Transcriptional profiling of S2 cells coincubated with C. albicans cells revealed up-regulation of several genes. One of the most highly up-regulated genes during this interaction is the D. melanogaster translational regulator 4E-BP encoded by the Thor gene. Analysis of Drosophila 4E-BP(null) mutant survival upon infection with C. albicans showed that 4E-BP plays an important role in host defense, suggesting a role for translational control in the D. melanogaster response to C. albicans infection.
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Affiliation(s)
- A Levitin
- Genetics Group, Biotechnology Research Institute, National Research Council, Montreal, Quebec H4P 2R2, Canada.
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16
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Abstract
This chapter outlines considerations and methods of experimental design for spotted microarray studies that contribute to the robustness of the acquired data. The chapter is divided into two principal sections: (1) a summary of factors that affect the quality of individual array results; and (2) a discussion of experimental design features and replication criteria that enable researchers to gain confidence in their findings. The goal of section (2) is to promote the careful design of microarray studies, with downstream statistical analysis in mind, such that a minimal amount of biological and/or technical replication is required to achieve reproducible results. Topics addressed include choosing appropriate samples to be compared, determining the optimal amount of sample to use, flagging uninformative data, establishing confidence limits in normalized data and the application of statistical tests to identify differentially expressed genes.
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Affiliation(s)
- Scott J Neal
- Department of Zoology, University of Toronto, Canadian Drosophila Microarray Centre, Mississauga, Ontario, Canada
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17
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Haerty W, Singh RS. Gene regulation divergence is a major contributor to the evolution of Dobzhansky-Muller incompatibilities between species of Drosophila. Mol Biol Evol 2006; 23:1707-14. [PMID: 16757655 DOI: 10.1093/molbev/msl033] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The Dobzhansky-Muller model denotes incompatible gene interactions between diverging populations/species and is recognized as the basis of postzygotic reproductive isolation. Little is known about the molecular nature of such gene interactions. We have carried out comparative gene expression analyses in the testes of 3 closely related species of the Drosophila melanogaster subgroup and their hybrids (all of which are sterile). We show that in hybrids 1) a higher proportion of male-biased genes (i.e., genes with a higher level of expression in males) are underexpressed (or not expressed) compared with non-sex-biased genes, 2) the majority of the underexpressed genes appear to be under stabilizing selection by virtue of showing similar levels of expression in the parental species, and only a small proportion of genes show signs of directional selection, 3) very few of the misexpressed genes are shared between species pairs, suggesting that there may not be a "common" set of "speciation genes," and 4) expression of non-testes-specific genes is observed in the testes of interspecific hybrids, and the number of such genes is positively correlated with divergence time. These results suggest that gene regulation divergence of sex- and reproduction-related genes is a major contributor to the evolution of Dobzhansky-Muller incompatibilities between species of Drosophila.
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Affiliation(s)
- Wilfried Haerty
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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18
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Jensen HR, Scott IM, Sims SR, Trudeau VL, Arnason JT. The effect of a synergistic concentration of a Piper nigrum extract used in conjunction with pyrethrum upon gene expression in Drosophila melanogaster. INSECT MOLECULAR BIOLOGY 2006; 15:329-39. [PMID: 16756552 DOI: 10.1111/j.1365-2583.2006.00648.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
An ethyl acetate extract of Piper nigrum L. (Piperaceae) peppercorns was tested as a synergist for the botanical insecticide pyrethrum. A high synergist ratio of 11.6 against Drosophila melanogaster was obtained for the combination of pyrethrum supplemented with P. nigrum. The effect of this combination was investigated using cDNA microarray analysis of gene expression profiles in D. melanogaster. Treatment of D. melanogaster with pyrethrum alone resulted in a large number of differentially expressed genes, principally associated with stress responses. Seven genes were identified as being commonly expressed in D. melanogaster treated with at least two of the following treatments: P. nigrum, pyrethrum or P. nigrum plus pyrethrum. These are likely implicated in Drosophila defence responses to toxins.
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Affiliation(s)
- H R Jensen
- Department of Biology, University of Ottawa, Center for Advanced Research in Environmental Genomics, Ottawa, Ontario, Canada
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19
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Neal SJ, Karunanithi S, Best A, So AKC, Tanguay RM, Atwood HL, Westwood JT. Thermoprotection of synaptic transmission in aDrosophilaheat shock factor mutant is accompanied by increased expression of Hsp83 and DnaJ-1. Physiol Genomics 2006; 25:493-501. [PMID: 16595740 DOI: 10.1152/physiolgenomics.00195.2005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In Drosophila larvae, acquired synaptic thermotolerance after heat shock has previously been shown to correlate with the induction of heat shock proteins (Hsps) including HSP70. We tested the hypothesis that synaptic thermotolerance would be significantly diminished in a temperature-sensitive strain ( Drosophila heat shock factor mutant hsf4), which has been reported not to be able to produce inducible Hsps in response to heat shock. Contrary to our hypothesis, considerable thermoprotection was still observed at hsf4larval synapses after heat shock. To investigate the cause of this thermoprotection, we conducted DNA microarray experiments to identify heat-induced transcript changes in these organisms. Transcripts of the hsp83, dnaJ-1 ( hsp40), and glutathione- S-transferase gstE1 genes were significantly upregulated in hsf4larvae after heat shock. In addition, increases in the levels of Hsp83 and DnaJ-1 proteins but not in the inducible form of Hsp70 were detected by Western blot analysis. The mode of heat shock administration differentially affected the relative transcript and translational changes for these chaperones. These results indicate that the compensatory upregulation of constitutively expressed Hsps, in the absence of the synthesis of the major inducible Hsp, Hsp70, could still provide substantial thermoprotection to both synapses and the whole organism.
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Affiliation(s)
- Scott J Neal
- Department of Biology, University of Toronto, Mississauga, Ontario, Canada
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20
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Qin W, Neal SJ, Robertson RM, Westwood JT, Walker VK. Cold hardening and transcriptional change in Drosophila melanogaster. INSECT MOLECULAR BIOLOGY 2005; 14:607-13. [PMID: 16313561 DOI: 10.1111/j.1365-2583.2005.00589.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cold hardening treatment - a brief exposure to low temperatures - can protect certain insects against subsequent exposure to temperatures sufficiently low to cause damage or lethality. Microarray analysis to examine the changes in transcript abundance associated with cold hardening treatment (0 degrees C for 2 h followed by 30 min recovery at 25 degrees C) was undertaken in Drosophila melanogaster in order to gain insight into this phenomenon. Transcripts associated with 36 genes were identified, a subset of which appeared to be also differentially expressed after heat shock treatment. Quantitative RT-PCR was used to independently determine transcript abundance of a subset of these sequences. Taken together, these assays suggest that stress proteins, including Hsp23, Hsp26, Hsp83 and Frost as well as membrane-associated proteins may contribute to the cold hardening response.
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Affiliation(s)
- W Qin
- Department of Biology, Queen's University, Ontario, Canada
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21
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Riedl CAL, Neal SJ, Robichon A, Westwood JT, Sokolowski MB. Drosophila soluble guanylyl cyclase mutants exhibit increased foraging locomotion: behavioral and genomic investigations. Behav Genet 2005; 35:231-44. [PMID: 15864439 DOI: 10.1007/s10519-005-3216-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Accepted: 02/01/2005] [Indexed: 10/25/2022]
Abstract
Genetic variation in the gene foraging (for) is associated with a natural behavioral dimorphism in the fruit fly, Drosophila melanogaster. Some larvae, called 'rovers', have increased foraging locomotion compared to others, called 'sitters', and this difference is directly related to for-encoded cGMP-dependent protein kinase (PKG) activity. Here we report that larvae with mutations in the gene dgcalpha1, which encodes a soluble guanylyl cyclase (sGC) subunit, have increases in both PKG activity and foraging locomotion. This is contrary to our original prediction that, based on the role of sGC in the synthesis of cGMP, dgcalpha1 mutant larvae would have deficient cGMP production leading to decreased PKG activation and thus reduced larval foraging locomotion. We performed DNA microarray analyses to compare transcriptional changes induced by a dgcalpha1 mutation in both rover and sitter wildtype genetic backgrounds. In either background, we identified many genes that are differentially transcribed, and interestingly, relatively few are affected in both backgrounds. Furthermore, several of these commonly affected genes are enhanced or suppressed in a background-dependent manner. Thus, genetic background has a critical influence on the molecular effects of this mutation. These findings will support future investigations of Drosophila foraging behavior.
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Affiliation(s)
- Craig A L Riedl
- Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
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22
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Sarropoulou E, Kotoulas G, Power DM, Geisler R. Gene expression profiling of gilthead sea bream during early development and detection of stress-related genes by the application of cDNA microarray technology. Physiol Genomics 2005; 23:182-91. [PMID: 16046618 DOI: 10.1152/physiolgenomics.00139.2005] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Large-scale gene expression studies were performed for one of the main European aquaculture species, the gilthead sea bream Sparus auratus L. For this purpose, a cDNA microarray containing 10,176 clones from a cDNA library of mixed embryonic and larval stages was constructed. In addition to its importance for aquaculture, the taxonomic position and the relatively small genome size of sea bream makes it a prospective model for evolutionary biology and comparative genomics. However, so far, no large-scale analysis of gene expression exists for this species. In the present study, gene expression was analyzed in gilthead sea bream during early development, a significant period in the determination of quantitative traits and therefore of considerable interest for aquaculture. Synexpression groups expressed primarily early and late in development were determined and were composed of both known and novel genes. Furthermore, it was possible to identify stress response genes induced by cortisol injections using the cDNA microarray generated. The creation of gene expression profiles for sea bream by microarray hybridization will accelerate identification of candidate genes involved in multifactorial traits and certain regulatory pathways and will also contribute to a better understanding of the genetic background of fish physiology, which may help to improve aquaculture practices.
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Affiliation(s)
- Elena Sarropoulou
- Hellenic Center for Marine Research, Institute for Marine Biology and Genetics, Iraklio, Crete, Greece.
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23
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Zahiri AR, Babu MR, Saville BJ. Differential gene expression during teliospore germination in Ustilago maydis. Mol Genet Genomics 2005; 273:394-403. [PMID: 15887033 DOI: 10.1007/s00438-005-1142-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2004] [Accepted: 03/04/2005] [Indexed: 10/25/2022]
Abstract
Ustilago maydis is a model fungal pathogen that induces the formation of tumors in maize. The tumor provides an environment for hyphal differentiation, leading to the formation of thick-walled, diploid teliospores. Such spores serve as a dispersal agent for smut and rust fungi, and their germination leads to new rounds of infection. The morphological changes that occur during teliospore germination in U. maydis have been described in detail. However, the specific molecular events that facilitate this process have not been identified. Through the construction and hybridization of microarrays containing a set of 3918 non-redundant cDNAs, we have identified genes that are differentially regulated during teliospore germination. Teliospores induced to germinate for 4 and 11 h were selected for comparison with dormant teliospores. Genes identified as differentially expressed included many that are presumably involved in as yet undescribed molecular events during teliospore germination, as well as characterized genes previously shown to be required for the process. This study represents the first large-scale investigation of changes in gene expression during teliospore germination.
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Affiliation(s)
- Ali R Zahiri
- Department of Botany, University of Toronto at Mississauga, 3359 Mississauga Road, Mississauga, ON, Canada, L5L 1C6
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24
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Babu MR, Choffe K, Saville BJ. Differential gene expression in filamentous cells of Ustilago maydis. Curr Genet 2005; 47:316-33. [PMID: 15809875 DOI: 10.1007/s00294-005-0574-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2004] [Revised: 02/15/2005] [Accepted: 02/21/2005] [Indexed: 10/25/2022]
Abstract
When fungi interact with plants as pathogens or as symbionts, there are often changes in fungal cell morphology and nuclear state. This study establishes the use of cDNA microarrays to detect gene expression changes in Ustilago maydis cells that differ in structure and nuclear content. Categorizing differentially expressed genes on the basis of function indicated that U. maydis cell types vary most in the expression of genes related to metabolism. We also observed that more genes are up-regulated in the filamentous dikaryon than in the filamentous diploid, relative to non-pathogenic budding cells. Our comparison of pathogenic development indicated that the dikaryon is more virulent than the diploid. Other identified expression patterns suggest a cell-specific difference in nutrient acquisition, cell metabolism and signal transduction. The relevance of gene expression change to cell type biology is discussed.
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Affiliation(s)
- Mohan R Babu
- Department of Botany, University of Toronto at Mississauga, 3359 Mississauga Rd. N., Mississauga, Ontario, L5L 1C6, Canada
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