1
|
Hu H, Tan D, Luo T, Tong X, Han M, Shen J, Dai F. Cyclin B3 plays pleiotropic roles in female reproductive organogenesis and early embryogenesis in the silkworm, Bombyx mori. PEST MANAGEMENT SCIENCE 2024; 80:376-387. [PMID: 37698372 DOI: 10.1002/ps.7767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/22/2023] [Accepted: 09/12/2023] [Indexed: 09/13/2023]
Abstract
BACKGROUND The reproductive system plays a crucial role in insect survival, reproduction and species specificity. Understanding the molecular mechanisms underlying reproductive organogenesis contributes to improving the efficiency of sterile insect technique marked by an eco-friendly pest management strategy. Lepidoptera is one of the largest orders of insects, most of which are major pests in agriculture and forestry. Our study aimed to screen the genes responsible for reproductive organogenesis and unravel the mechanism underlying female reproductive organ defects. RESULTS Morphological investigation of female reproductive organs showed a defective connection between oviductus geminus and oviductus communis on the second day of pupa (P2) in Speckled mutant silkworm. RNA_Seq identified a total of 18 049 transcripts that were expressed in the P2 female internal reproductive organs without ovary in Spc/+ compared to +Spc /+Spc . Differential expression analysis identified 312 up-regulated genes and 221 down-regulated genes in Spc/+. KEGG analysis identified 44 significantly enriched pathways. The results of qRT-PCR performed on 33 genes significantly matched the outcomes of the RNA_Seq. Dysfunction of Cyclin B3 resulted in a defective connection of the oviductus communis with the ovariole, dysfunction of oogenesis, and a petite body. Moreover, homozygous recessive lethality of Cyclin B3/Cyclin B3 occurred during early embryogenesis. CONCLUSION Our results suggest that Cyclin B3 is a pleiotropic functional gene that regulates early embryogenesis, oogenesis, development, and female reproductive organogenesis. These results showed that Cyclin B3 has significant effects on lepidopteran mortality, growth, and reproductive physiology, which might be considered a novel and potentially eco-friendly target for lepidopteran pest management. © 2023 Society of Chemical Industry.
Collapse
Affiliation(s)
- Hai Hu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, China
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Duan Tan
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, China
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Tianfu Luo
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, China
| | - Xiaoling Tong
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, China
| | - Minjin Han
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, China
| | - Jianghong Shen
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, China
| | - Fangyin Dai
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, China
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| |
Collapse
|
2
|
Galouzis CC, Prud’homme B. Relevance and mechanisms of transvection. C R Biol 2021; 344:373-387. [DOI: 10.5802/crbiol.69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 11/15/2021] [Indexed: 11/24/2022]
|
3
|
Verma S, Pathak RU, Mishra RK. Genomic organization of the autonomous regulatory domain of eyeless locus in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2021; 11:6375946. [PMID: 34570231 PMCID: PMC8664461 DOI: 10.1093/g3journal/jkab338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 09/09/2021] [Indexed: 11/29/2022]
Abstract
In Drosophila, expression of eyeless (ey) gene is restricted to the developing eyes and central nervous system. However, the flanking genes, myoglianin (myo), and bent (bt) have different temporal and spatial expression patterns as compared to the ey. How distinct regulation of ey is maintained is mostly unknown. Earlier, we have identified a boundary element intervening myo and ey genes (ME boundary) that prevents the crosstalk between the cis-regulatory elements of myo and ey genes. In the present study, we further searched for the cis-elements that define the domain of ey and maintain its expression pattern. We identify another boundary element between ey and bt, the EB boundary. The EB boundary separates the regulatory landscapes of ey and bt genes. The two boundaries, ME and EB, show a long-range interaction as well as interact with the nuclear architecture. This suggests functional autonomy of the ey locus and its insulation from differentially regulated flanking regions. We also identify a new Polycomb Response Element, the ey-PRE, within the ey domain. The expression state of the ey gene, once established during early development is likely to be maintained with the help of ey-PRE. Our study proposes a general regulatory mechanism by which a gene can be maintained in a functionally independent chromatin domain in gene-rich euchromatin.
Collapse
Affiliation(s)
- Shreekant Verma
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India
| | - Rashmi U Pathak
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India
| | - Rakesh K Mishra
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India
| |
Collapse
|
4
|
Peterson SC, Samuelson KB, Hanlon SL. Multi-Scale Organization of the Drosophila melanogaster Genome. Genes (Basel) 2021; 12:817. [PMID: 34071789 PMCID: PMC8228293 DOI: 10.3390/genes12060817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 12/16/2022] Open
Abstract
Interphase chromatin, despite its appearance, is a highly organized framework of loops and bends. Chromosomes are folded into topologically associating domains, or TADs, and each chromosome and its homolog occupy a distinct territory within the nucleus. In Drosophila, genome organization is exceptional because homologous chromosome pairing is in both germline and somatic tissues, which promote interhomolog interactions such as transvection that can affect gene expression in trans. In this review, we focus on what is known about genome organization in Drosophila and discuss it from TADs to territory. We start by examining intrachromosomal organization at the sub-chromosome level into TADs, followed by a comprehensive analysis of the known proteins that play a key role in TAD formation and boundary establishment. We then zoom out to examine interhomolog interactions such as pairing and transvection that are abundant in Drosophila but rare in other model systems. Finally, we discuss chromosome territories that form within the nucleus, resulting in a complete picture of the multi-scale organization of the Drosophila genome.
Collapse
Affiliation(s)
| | | | - Stacey L. Hanlon
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; (S.C.P.); (K.B.S.)
| |
Collapse
|
5
|
Wang Y, Li J, Wan QX, Zhao Q, Wang KX, Zha XF. Spliceosomal Protein Gene BmSPX Regulates Reproductive Organ Development in Bombyx mori. Int J Mol Sci 2020; 21:ijms21072579. [PMID: 32276369 PMCID: PMC7177926 DOI: 10.3390/ijms21072579] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 02/06/2023] Open
Abstract
Sex determination and differentiation are nearly universal to all eukaryotic organisms, encompassing diverse systems and mechanisms. Here, we identified a spliceosomal protein gene BmSPX involved in sex determination of the lepidopeteran insect, Bombyx mori. In a transgenic silkworm line that overexpressed the BmSPX gene, transgenic silkworm males exhibited differences in their external genitalia compared to wild-type males, but normal internal genitalia. Additionally, transgenic silkworm females exhibited a developmental disorder of the reproductive organs. Upregulation of BmSPX significantly increased the expression levels of sex-determining genes (BmMasc and BmIMP) and reduced the female-type splice isoform of Bmdsx, which is a key switch gene downstream of the sex-determination pathway. Additionally, co-immunoprecipitation assays confirmed an interaction between the BmSPX protein and BmPSI, an upstream regulatory factor of Bmdsx. Quantitative real-time PCR showed that BmSPX over-expression upregulated the expression of the Hox gene abdominal-B (Adb-B), which is required for specification of the posterior abdomen, external genitalia, and gonads of insects, as well as the genes in the Receptor Tyrosine Kinase (RTK) signaling pathway. In conclusion, our study suggested the involvement of BmSPX, identified as a novel regulatory factor, in the sex-determination pathway and regulation of reproductive organ development in silkworms.
Collapse
Affiliation(s)
- Yao Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China; (Y.W.); (J.L.); (Q.-X.W.); (Q.Z.); (K.-X.W.)
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
- Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
- The State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Science, Fudan University, Shanghai 200438, China
| | - Juan Li
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China; (Y.W.); (J.L.); (Q.-X.W.); (Q.Z.); (K.-X.W.)
| | - Qiu-Xing Wan
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China; (Y.W.); (J.L.); (Q.-X.W.); (Q.Z.); (K.-X.W.)
| | - Qin Zhao
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China; (Y.W.); (J.L.); (Q.-X.W.); (Q.Z.); (K.-X.W.)
| | - Kai-Xuan Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China; (Y.W.); (J.L.); (Q.-X.W.); (Q.Z.); (K.-X.W.)
| | - Xing-Fu Zha
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China; (Y.W.); (J.L.); (Q.-X.W.); (Q.Z.); (K.-X.W.)
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
- Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
- Correspondence: ; Tel.: +86-23-68251573; Fax: +86-23-68251128
| |
Collapse
|
6
|
King TD, Johnson JE, Bateman JR. Position Effects Influence Transvection in Drosophila melanogaster. Genetics 2019; 213:1289-1299. [PMID: 31611231 PMCID: PMC6893391 DOI: 10.1534/genetics.119.302583] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 10/03/2019] [Indexed: 01/14/2023] Open
Abstract
Transvection is an epigenetic phenomenon wherein regulatory elements communicate between different chromosomes in trans, and is thereby dependent upon the three-dimensional organization of the genome. Transvection is best understood in Drosophila, where homologous chromosomes are closely paired in most somatic nuclei, although similar phenomena have been observed in other species. Previous data have supported that the Drosophila genome is generally permissive to enhancer action in trans, a form of transvection where an enhancer on one homolog activates gene expression from a promoter on a paired homolog. However, the capacity of different genomic positions to influence the quantitative output of transvection has yet to be addressed. To investigate this question, we employed a transgenic system that assesses and compares enhancer action in cis and in trans at defined chromosomal locations. Using the strong synthetic eye-specific enhancer GMR, we show that loci supporting strong cis-expression tend to support robust enhancer action in trans, whereas locations with weaker cis-expression show reduced transvection in a fluorescent reporter assay. Our subsequent analysis is consistent with a model wherein the chromatin state of the transgenic insertion site is a primary determinant of the degree to which enhancer action in trans will be supported, whereas other factors such as locus-specific variation in somatic homolog pairing are of less importance in influencing position effects on transvection.
Collapse
Affiliation(s)
- Thomas D King
- Biology Department, Bowdoin College, Brunswick, Maine 04011
| | | | - Jack R Bateman
- Biology Department, Bowdoin College, Brunswick, Maine 04011
| |
Collapse
|
7
|
Viets K, Sauria MEG, Chernoff C, Rodriguez Viales R, Echterling M, Anderson C, Tran S, Dove A, Goyal R, Voortman L, Gordus A, Furlong EEM, Taylor J, Johnston RJ. Characterization of Button Loci that Promote Homologous Chromosome Pairing and Cell-Type-Specific Interchromosomal Gene Regulation. Dev Cell 2019; 51:341-356.e7. [PMID: 31607649 DOI: 10.1016/j.devcel.2019.09.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 06/07/2019] [Accepted: 09/09/2019] [Indexed: 01/05/2023]
Abstract
Homologous chromosomes colocalize to regulate gene expression in processes including genomic imprinting, X-inactivation, and transvection. In Drosophila, homologous chromosomes pair throughout development, promoting transvection. The "button" model of pairing proposes that specific regions along chromosomes pair with high affinity. Here, we identify buttons interspersed across the fly genome that pair with their homologous sequences, even when relocated to multiple positions in the genome. A majority of transgenes that span a full topologically associating domain (TAD) function as buttons, but not all buttons contain TADs. Additionally, buttons are enriched for insulator protein clusters. Fragments of buttons do not pair, suggesting that combinations of elements within a button are required for pairing. Pairing is necessary but not sufficient for transvection. Additionally, pairing and transvection are stronger in some cell types than in others, suggesting that pairing strength regulates transvection efficiency between cell types. Thus, buttons pair homologous chromosomes to facilitate cell-type-specific interchromosomal gene regulation.
Collapse
Affiliation(s)
- Kayla Viets
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Michael E G Sauria
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Chaim Chernoff
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | | | - Max Echterling
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Caitlin Anderson
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sang Tran
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Abigail Dove
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Raghav Goyal
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Lukas Voortman
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew Gordus
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Eileen E M Furlong
- European Molecular Biology Laboratory, Department of Genome Biology, Heidelberg 69117, Germany
| | - James Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Robert J Johnston
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
| |
Collapse
|
8
|
Abstract
Fukaya and Levine explain the basic features of the genetic phenomenon of transvection, a special class of genetic complementation of mutant alleles on homologous chromosomes.
Collapse
Affiliation(s)
- Takashi Fukaya
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - Michael Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| |
Collapse
|
9
|
Epigenetic inheritance mediated by coupling of RNAi and histone H3K9 methylation. Nature 2018; 558:615-619. [PMID: 29925950 PMCID: PMC6312107 DOI: 10.1038/s41586-018-0239-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 04/30/2018] [Indexed: 02/06/2023]
Abstract
Histone posttranslational modifications (PTMs) are associated with epigenetic states that form the basis for cell type specific gene expression1,2. Once established, histone PTMs can be maintained by positive feedback involving enzymes that recognize and catalyze the same modification on newly deposited histones. Recent studies suggest that in wild-type cells, histone PTM-based positive feedback is too weak to mediate epigenetic inheritance in the absence of other inputs3–7. RNAi-mediated histone H3 lysine 9 methylation (H3K9me) and heterochromatin formation define a potential epigenetic inheritance mechanism in which positive feedback involving small interfering RNA (siRNA) amplification can be directly coupled to histone PTM positive feedback8–14. However, it remains unknown whether such a coupling of two feedback loops can maintain epigenetic silencing independently of DNA sequence and in the absence of enabling mutations that disrupt genome-wide chromatin structure or transcription15–17. Here using fission yeast S. pombe, we show that siRNA-induced H3K9me and silencing of a euchromatic gene can be epigenetically inherited in cis during multiple mitotic and meiotic cell divisions in wild-type cells. This inheritance involves the spreading of secondary siRNAs and H3K9me3 to the targeted gene and surrounding areas and requires both RNAi and H3K9me, suggesting that siRNA and H3K9me positive feedback loops act synergistically to maintain silencing. In contrast, when maintained solely by histone PTM positive feedback, silencing is erased by H3K9 demethylation promoted by Epe1, or by interallelic interactions following mating to cells containing an expressed epiallele even in the absence of Epe1. These findings demonstrate that the RNAi machinery can mediate transgenerational epigenetic inheritance independently of DNA sequence or enabling mutations and reveal a role for the coupling of siRNA and H3K9me positive feedback loops in protection of epigenetic alleles from erasure.
Collapse
|
10
|
Three-Dimensional Genome Organization and Function in Drosophila. Genetics 2017; 205:5-24. [PMID: 28049701 PMCID: PMC5223523 DOI: 10.1534/genetics.115.185132] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/15/2016] [Indexed: 12/18/2022] Open
Abstract
Understanding how the metazoan genome is used during development and cell differentiation is one of the major challenges in the postgenomic era. Early studies in Drosophila suggested that three-dimensional (3D) chromosome organization plays important regulatory roles in this process and recent technological advances started to reveal connections at the molecular level. Here we will consider general features of the architectural organization of the Drosophila genome, providing historical perspective and insights from recent work. We will compare the linear and spatial segmentation of the fly genome and focus on the two key regulators of genome architecture: insulator components and Polycomb group proteins. With its unique set of genetic tools and a compact, well annotated genome, Drosophila is poised to remain a model system of choice for rapid progress in understanding principles of genome organization and to serve as a proving ground for development of 3D genome-engineering techniques.
Collapse
|
11
|
Yao J. Imaging Transcriptional Regulation of Eukaryotic mRNA Genes: Advances and Outlook. J Mol Biol 2017; 429:14-31. [DOI: 10.1016/j.jmb.2016.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/03/2016] [Accepted: 11/10/2016] [Indexed: 01/07/2023]
|
12
|
Kao D, Lai AG, Stamataki E, Rosic S, Konstantinides N, Jarvis E, Di Donfrancesco A, Pouchkina-Stancheva N, Sémon M, Grillo M, Bruce H, Kumar S, Siwanowicz I, Le A, Lemire A, Eisen MB, Extavour C, Browne WE, Wolff C, Averof M, Patel NH, Sarkies P, Pavlopoulos A, Aboobaker A. The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion. eLife 2016; 5:20062. [PMID: 27849518 PMCID: PMC5111886 DOI: 10.7554/elife.20062] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/19/2016] [Indexed: 12/17/2022] Open
Abstract
The amphipod crustacean Parhyale hawaiensis is a blossoming model system for studies of developmental mechanisms and more recently regeneration. We have sequenced the genome allowing annotation of all key signaling pathways, transcription factors, and non-coding RNAs that will enhance ongoing functional studies. Parhyale is a member of the Malacostraca clade, which includes crustacean food crop species. We analysed the immunity related genes of Parhyale as an important comparative system for these species, where immunity related aquaculture problems have increased as farming has intensified. We also find that Parhyale and other species within Multicrustacea contain the enzyme sets necessary to perform lignocellulose digestion ('wood eating'), suggesting this ability may predate the diversification of this lineage. Our data provide an essential resource for further development of Parhyale as an experimental model. The first malacostracan genome will underpin ongoing comparative work in food crop species and research investigating lignocellulose as an energy source. DOI:http://dx.doi.org/10.7554/eLife.20062.001 The marine crustacean known as Parhyale hawaiensis is related to prawns, shrimps and crabs and is found at tropical coastlines around the world. This species has recently attracted scientific interest as a possible new model to study how animal embryos develop before birth and, because Parhyale can rapidly regrow lost limbs, how tissues and organs regenerate. Indeed, Parhyale has many characteristics that make it a good model organism, being small, fast-growing and easy to keep and care for in the laboratory. Several research tools have already been developed to make it easier to study Parhyale. This includes the creation of a system for using the popular gene editing technology, CRISPR, in this animal. However, one critical resource that is available for most model organisms was missing; the complete sequence of all the genetic information of this crustacean, also known as its genome, was not available. Kao, Lai, Stamataki et al. have now compiled the Parhyale genome – which is slightly larger than the human genome – and studied its genetics. Analysis revealed that Parhyale has genes that allow it to fully digest plant material. This is unusual because most animals that do this rely upon the help of bacteria. Kao, Lai, Stamataki et al. also identified genes that provide some of the first insights into the immune system of crustaceans, which protects these creatures from diseases. Kao, Lai, Stamataki et al. have provided a resource and findings that could help to establish Parhyale as a popular model organism for studying several ideas in biology, including organ regeneration and embryonic development. Understanding how Parhyale digests plant matter, for example, could progress the biofuel industry towards efficient production of greener energy. Insights from its immune system could also be adapted to make farmed shrimp and prawns more resistant to infections, boosting seafood production. DOI:http://dx.doi.org/10.7554/eLife.20062.002
Collapse
Affiliation(s)
- Damian Kao
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Alvina G Lai
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Evangelia Stamataki
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Silvana Rosic
- MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom.,Clinical Sciences, Imperial College London, London, United Kingdom
| | - Nikolaos Konstantinides
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Erin Jarvis
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | | | | | - Marie Sémon
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Marco Grillo
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Heather Bruce
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Suyash Kumar
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Igor Siwanowicz
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Andy Le
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Andrew Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
| | - Michael B Eisen
- Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Cassandra Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
| | - William E Browne
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, United States
| | - Carsten Wolff
- Vergleichende Zoologie, Institut fur Biologie,Humboldt-Universitat zu Berlin, Berlin, Germany
| | - Michalis Averof
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
| | - Nipam H Patel
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Peter Sarkies
- MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom.,Clinical Sciences, Imperial College London, London, United Kingdom
| | | | - Aziz Aboobaker
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
13
|
Blick AJ, Mayer-Hirshfeld I, Malibiran BR, Cooper MA, Martino PA, Johnson JE, Bateman JR. The Capacity to Act in Trans Varies Among Drosophila Enhancers. Genetics 2016; 203:203-18. [PMID: 26984057 PMCID: PMC4858774 DOI: 10.1534/genetics.115.185645] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/07/2016] [Indexed: 01/10/2023] Open
Abstract
The interphase nucleus is organized such that genomic segments interact in cis, on the same chromosome, and in trans, between different chromosomes. In Drosophila and other Dipterans, extensive interactions are observed between homologous chromosomes, which can permit enhancers and promoters to communicate in trans Enhancer action in trans has been observed for a handful of genes in Drosophila, but it is as yet unclear whether this is a general property of all enhancers or specific to a few. Here, we test a collection of well-characterized enhancers for the capacity to act in trans Specifically, we tested 18 enhancers that are active in either the eye or wing disc of third instar Drosophila larvae and, using two different assays, found evidence that each enhancer can act in trans However, the degree to which trans-action was supported varied greatly between enhancers. Quantitative analysis of enhancer activity supports a model wherein an enhancer's strength of transcriptional activation is a major determinant of its ability to act in trans, but that additional factors may also contribute to an enhancer's trans-activity. In sum, our data suggest that a capacity to activate a promoter on a paired chromosome is common among Drosophila enhancers.
Collapse
Affiliation(s)
- Amanda J Blick
- Biology Department, Bowdoin College, Brunswick, Maine 04011
| | | | | | | | | | | | - Jack R Bateman
- Biology Department, Bowdoin College, Brunswick, Maine 04011
| |
Collapse
|
14
|
Zhao P, Sun MX. The Maternal-to-Zygotic Transition in Higher Plants: Available Approaches, Critical Limitations, and Technical Requirements. Curr Top Dev Biol 2015; 113:373-98. [PMID: 26358879 DOI: 10.1016/bs.ctdb.2015.06.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Fertilization marks the turnover from the gametophyte to sporophyte generation in higher plants. After fertilization, sporophytic development undergoes genetic turnover from maternal to zygotic control: the maternal-to-zygotic transition (MZT). The MZT is thought to be critical for early embryogenesis; however, little is known about the time course or developmental impact of the MZT in higher plants. Here, we discuss what is known in the field and focus on techniques used in relevant studies and their limitations. Some significant questions and technical requirements for further investigations are also discussed.
Collapse
Affiliation(s)
- Peng Zhao
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, China
| | - Meng-Xiang Sun
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Hybrid Rice, Wuhan University, Wuhan, China.
| |
Collapse
|
15
|
Chromatin-Driven Behavior of Topologically Associating Domains. J Mol Biol 2015; 427:608-25. [DOI: 10.1016/j.jmb.2014.09.013] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/17/2014] [Accepted: 09/23/2014] [Indexed: 12/19/2022]
|
16
|
de Graaff LCG, Clark AJL, Tauber M, Ranke MB, Johnston LB, Caliebe J, Molinas C, Amin N, van Duijn C, Wollmann H, Wallaschofski H, Savage MO, Hokken-Koelega ACS. Association analysis of ten candidate genes in a large multinational cohort of small for gestational age children and children with idiopathic short stature (NESTEGG study). Horm Res Paediatr 2014; 80:466-76. [PMID: 24280783 DOI: 10.1159/000355409] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 07/24/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Fetal growth failure has been associated with an increased risk of hypertension, cardiovascular disease and diabetes in adulthood. Exploring the mechanisms underlying this association should improve our understanding of these common adult diseases. PATIENTS AND METHODS We investigated 225 SNPs in 10 genes involved in growth and glucose metabolism (GH1, GHR, IGF1, IGF1R, STAT5A, STAT5B, MAPK1, MAPK3, PPARγ and INS) in 1,437 children from the multinational NESTEGG consortium: 345 patients born small for gestational age who remained short (SGA-S), 288 who showed catch-up growth (SGA-Cu), 410 idiopathic short stature (ISS) and 394 controls. We related genotype to pre- and/or postnatal growth parameters, response to growth hormone (if applicable) and blood pressure. RESULTS We found several clinical associations for GH1, GHR, IGF1, IGF1R, PPARγ and MAPK1. One SNP remained significant after Bonferroni's correction: IGF1R SNP rs4966035's minor allele A was significantly more prevalent among SGA and associated with smaller birth length (p = 0.000378) and birth weight (weaker association), independent of gestational age. CONCLUSION IGF1R SNP rs4966035 is significantly associated with birth length, independent of gestational age. This and other associations suggest that polymorphisms in these genes might partly explain the phenotype of short children born SGA and children with ISS.
Collapse
Affiliation(s)
- L C G de Graaff
- Division of Endocrinology, Department of Paediatrics, Erasmus MC-Sophia Children's Hospital, Erasmus MC, Rotterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Gregor T, Garcia HG, Little SC. The embryo as a laboratory: quantifying transcription in Drosophila. Trends Genet 2014; 30:364-75. [PMID: 25005921 DOI: 10.1016/j.tig.2014.06.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 06/08/2014] [Accepted: 06/16/2014] [Indexed: 11/16/2022]
Abstract
Transcriptional regulation of gene expression is fundamental to most cellular processes, including determination of cellular fates. Quantitative studies of transcription in cultured cells have led to significant advances in identifying mechanisms underlying transcriptional control. Recent progress allowed implementation of these same quantitative methods in multicellular organisms to ask how transcriptional regulation unfolds both in vivo and at the single molecule level in the context of embryonic development. Here we review some of these advances in early Drosophila development, which bring the embryo on par with its single celled counterparts. In particular, we discuss progress in methods to measure mRNA and protein distributions in fixed and living embryos, and we highlight some initial applications that lead to fundamental new insights about molecular transcription processes. We end with an outlook on how to further exploit the unique advantages that come with investigating transcriptional control in the multicellular context of development.
Collapse
Affiliation(s)
- Thomas Gregor
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 085444, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - Hernan G Garcia
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 085444, USA
| | - Shawn C Little
- Department of Molecular Biology, Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA
| |
Collapse
|
18
|
Schoborg T, Kuruganti S, Rickels R, Labrador M. The Drosophila gypsy insulator supports transvection in the presence of the vestigial enhancer. PLoS One 2013; 8:e81331. [PMID: 24236213 PMCID: PMC3827471 DOI: 10.1371/journal.pone.0081331] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 10/21/2013] [Indexed: 12/17/2022] Open
Abstract
Though operationally defined as cis-regulatory elements, enhancers can also communicate with promoters on a separate homolog in trans, a mechanism that has been suggested to account for the ability of certain alleles of the same gene to complement one another in a process otherwise known as transvection. This homolog-pairing dependent process is facilitated in Drosophila by chromatin-associated pairing proteins, many of which remain unknown and their mechanism of action uncharacterized. Here we have tested the role of the gypsy chromatin insulator in facilitating pairing and communication between enhancers and promoters in trans using a transgenic eGFP reporter system engineered to allow for targeted deletions in the vestigial Boundary Enhancer (vgBE) and the hsp70 minimal promoter, along with one or two flanking gypsy elements. We found a modest 2.5-3x increase in eGFP reporter levels from homozygotes carrying an intact copy of the reporter on each homolog compared to unpaired hemizygotes, although this behavior was independent of gypsy. However, detectable levels of GFP protein along the DV wing boundary in trans-heterozygotes lacking a single enhancer and promoter was only observed in the presence of two flanking gypsy elements. Our results demonstrate that gypsy can stimulate enhancer-promoter communication in trans throughout the genome in a context-dependent manner, likely through modulation of local chromatin dynamics once pairing has been established by other elements and highlights chromatin structure as the master regulator of this phenomenon.
Collapse
Affiliation(s)
- Todd Schoborg
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Srilalitha Kuruganti
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Ryan Rickels
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Mariano Labrador
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| |
Collapse
|
19
|
Belele CL, Sidorenko L, Stam M, Bader R, Arteaga-Vazquez MA, Chandler VL. Specific tandem repeats are sufficient for paramutation-induced trans-generational silencing. PLoS Genet 2013; 9:e1003773. [PMID: 24146624 PMCID: PMC3798267 DOI: 10.1371/journal.pgen.1003773] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 07/24/2013] [Indexed: 11/19/2022] Open
Abstract
Paramutation is a well-studied epigenetic phenomenon in which trans communication between two different alleles leads to meiotically heritable transcriptional silencing of one of the alleles. Paramutation at the b1 locus involves RNA-mediated transcriptional silencing and requires specific tandem repeats that generate siRNAs. This study addressed three important questions: 1) are the tandem repeats sufficient for paramutation, 2) do they need to be in an allelic position to mediate paramutation, and 3) is there an association between the ability to mediate paramutation and repeat DNA methylation levels? Paramutation was achieved using multiple transgenes containing the b1 tandem repeats, including events with tandem repeats of only one half of the repeat unit (413 bp), demonstrating that these sequences are sufficient for paramutation and an allelic position is not required for the repeats to communicate. Furthermore, the transgenic tandem repeats increased the expression of a reporter gene in maize, demonstrating the repeats contain transcriptional regulatory sequences. Transgene-mediated paramutation required the mediator of paramutation1 gene, which is necessary for endogenous paramutation, suggesting endogenous and transgene-mediated paramutation both require an RNA-mediated transcriptional silencing pathway. While all tested repeat transgenes produced small interfering RNAs (siRNAs), not all transgenes induced paramutation suggesting that, as with endogenous alleles, siRNA production is not sufficient for paramutation. The repeat transgene-induced silencing was less efficiently transmitted than silencing induced by the repeats of endogenous b1 alleles, which is always 100% efficient. The variability in the strength of the repeat transgene-induced silencing enabled testing whether the extent of DNA methylation within the repeats correlated with differences in efficiency of paramutation. Transgene-induced paramutation does not require extensive DNA methylation within the transgene. However, increased DNA methylation within the endogenous b1 repeats after transgene-induced paramutation was associated with stronger silencing of the endogenous allele. Paramutation is a fascinating process in which genes communicate to efficiently establish changes in their expression that are stably transmitted to future generations without any changes in DNA sequences. While paramutation was first described in the 1950s and extensively studied through the 1960s, its underlying mechanism remained mysterious for many years. Over the past ten years paramutation at the b1 locus in maize was shown to require transcribed, non-coding tandem repeats located 100 kb upstream of b1. These repeats generate small RNAs, and mutations in multiple genes mediating small RNA silencing at the transcriptional level prevent paramutation. While underlying mechanisms are shared, current models for RNA-mediated transcriptional silencing that are based on experiments with S. pombe and Arabidopsis do not explain many aspects of paramutation. In this manuscript we used a transgenic approach to demonstrate that the b1 non-coding tandem repeats are sufficient to send and respond to the paramutation signals and that this occurs even when the repeats are not at their normal chromosomal location.
Collapse
Affiliation(s)
- Christiane L. Belele
- Department of Plant Sciences, BIO5, University of Arizona, Tucson, Arizona, United States of America
| | - Lyudmila Sidorenko
- Department of Plant Sciences, BIO5, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
| | - Maike Stam
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Rechien Bader
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Mario A. Arteaga-Vazquez
- Department of Plant Sciences, BIO5, University of Arizona, Tucson, Arizona, United States of America
| | - Vicki L. Chandler
- Department of Plant Sciences, BIO5, University of Arizona, Tucson, Arizona, United States of America
| |
Collapse
|
20
|
Saunders A, Core LJ, Sutcliffe C, Lis JT, Ashe HL. Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription. Genes Dev 2013; 27:1146-58. [PMID: 23699410 DOI: 10.1101/gad.215459.113] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Cascades of zygotic gene expression pattern the anterior-posterior (AP) and dorsal-ventral (DV) axes of the early Drosophila embryo. Here, we used the global run-on sequencing assay (GRO-seq) to map the genome-wide RNA polymerase distribution during early Drosophila embryogenesis, thus providing insights into how genes are regulated. We identify widespread promoter-proximal pausing yet show that the presence of paused polymerase does not necessarily equate to direct regulation through pause release to productive elongation. Our data reveal that a subset of early Zelda-activated genes is regulated at the level of polymerase recruitment, whereas other Zelda target and axis patterning genes are predominantly regulated through pause release. In contrast to other signaling pathways, we found that bone morphogenetic protein (BMP) target genes are collectively more highly paused than BMP pathway components and show that BMP target gene expression requires the pause-inducing negative elongation factor (NELF) complex. Our data also suggest that polymerase pausing allows plasticity in gene activation throughout embryogenesis, as transiently repressed and transcriptionally silenced genes maintain and lose promoter polymerases, respectively. Finally, we provide evidence that the major effect of pausing is on the levels, rather than timing, of transcription. These data are discussed in terms of the efficiency of transcriptional activation required across cell populations during developmental time constraints.
Collapse
Affiliation(s)
- Abbie Saunders
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | | | | | | | | |
Collapse
|
21
|
Hövel I, Louwers M, Stam M. 3C Technologies in plants. Methods 2012; 58:204-11. [PMID: 22728034 DOI: 10.1016/j.ymeth.2012.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 06/11/2012] [Accepted: 06/11/2012] [Indexed: 10/28/2022] Open
Abstract
Chromosome conformation capture (3C) and 3C-based technology have revolutionized studies on chromosomal interactions and their role in gene regulation and chromosome organization. 3C allows the in vivo identification of physical interactions between chromosomal regions. Such interactions are shown to play a role in various aspects of gene regulation, for example transcriptional activation of genes by remote enhancer sequences, or the silencing by Polycomb-group complexes. The last few years the number of publications involving chromosomal interactions increased significantly. Until now, however, the vast majority of the studies reported are performed in yeast or animal systems. So far, studies on plant systems are extremely limited, possibly due to the plant-specific characteristics that hamper the implementation of the 3C technique. In this paper we provide a plant-specific 3C protocol, optimized for maize tissue, and an extensive discussion on (i) plant-specific adjustments to the protocol, and (ii) solutions to problems that may arise when optimizing the protocol for the tissue or plant of interest. Together, this paper should facilitate the application of 3C technology to plant tissue and stimulate studies on the 3D conformation of chromosomal regions and chromosomes in plants.
Collapse
Affiliation(s)
- Iris Hövel
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands
| | | | | |
Collapse
|
22
|
Abstract
Studies from diverse systems have shown that distinct interchromosomal interactions are a central component of nuclear organization. In some cases, these interactions allow an enhancer to act in trans, modulating the expression of a gene encoded on a separate chromosome held in close proximity. Despite recent advances in uncovering such phenomena, our understanding of how a regulatory element acts on another chromosome remains incomplete. Here, we describe a transgenic approach to better understand enhancer action in trans in Drosophila melanogaster. Using phiC31-based recombinase-mediated cassette exchange (RMCE), we placed transgenes carrying combinations of the simple enhancer GMR, a minimal promoter, and different fluorescent reporters at equivalent positions on homologous chromosomes so that they would pair via the endogenous somatic pairing machinery of Drosophila. Our data demonstrate that the enhancer GMR is capable of activating a promoter in trans and does so in a variegated pattern, suggesting stochastic interactions between the enhancer and the promoter when they are carried on separate chromosomes. Furthermore, we quantitatively assessed the impact of two concurrent promoter targets in cis and in trans to GMR, demonstrating that each promoter is capable of competing for the enhancer's activity, with the presence of one negatively affecting expression from the other. Finally, the single-cell resolution afforded by our approach allowed us to show that promoters in cis and in trans to GMR can both be activated in the same nucleus, implying that a single enhancer can share its activity between multiple promoter targets carried on separate chromosomes.
Collapse
|
23
|
He F, Ren J, Wang W, Ma J. A multiscale investigation of bicoid-dependent transcriptional events in Drosophila embryos. PLoS One 2011; 6:e19122. [PMID: 21544208 PMCID: PMC3081338 DOI: 10.1371/journal.pone.0019122] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 03/16/2011] [Indexed: 01/11/2023] Open
Abstract
Background Morphogen molecules form concentration gradients to provide spatial information to cells in a developing embryo. Precisely how cells decode such information to form patterns with sharp boundaries remains an open question. For example, it remains controversial whether the Drosophila morphogenetic protein Bicoid (Bcd) plays a transient or sustained role in activating its target genes to establish sharp expression boundaries during development. Methodology/Principal Findings In this study, we describe a method to simultaneously detect Bcd and the nascent transcripts of its target genes in developing embryos. This method allows us to investigate the relationship between Bcd and the transcriptional status of individual copies of its target genes on distinct scales. We show that, on three scales analyzed concurrently—embryonic, nuclear and local, the actively-transcribing gene copies are associated with high Bcd concentrations. These results underscore the importance of Bcd as a sustained input for transcriptional decisions of individual copies of its target genes during development. We also show that the Bcd-dependent transcriptional decisions have a significantly higher noise than Bcd-dependent gene products, suggesting that, consistent with theoretical studies, time and/or space averaging reduces the noise of Bcd-activated transcriptional output. Finally, our analysis of an X-linked Bcd target gene reveals that Bcd-dependent transcription bursts at twice the frequency in males as in females, providing a mechanism for dosage compensation in early Drosophila embryos. Conclusion/Significance Our study represents a first experimental uncovering of the actions of Bcd in controlling the actual transcriptional events while its positional information is decoded during development. It establishes a sustained role of Bcd in transcriptional decisions of individual copies of its target genes to generate sharp expression boundaries. It also provides an experimental evaluation of the effect of time and/or space averaging on Bcd-dependent transcriptional output, and establishes a dosage compensation mechanism in early Drosophila embryos.
Collapse
Affiliation(s)
- Feng He
- Division of Biomedical Informatics, Cincinnati Children's Research Foundation, Cincinnati, Ohio, United States of America
| | - Jie Ren
- Division of Biomedical Informatics, Cincinnati Children's Research Foundation, Cincinnati, Ohio, United States of America
- Key Laboratory of Cell Proliferation and Differentiation, Center of Developmental Biology and Genetics, College of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Wei Wang
- Division of Biomedical Informatics, Cincinnati Children's Research Foundation, Cincinnati, Ohio, United States of America
| | - Jun Ma
- Division of Biomedical Informatics, Cincinnati Children's Research Foundation, Cincinnati, Ohio, United States of America
- Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, Ohio, United States of America
- * E-mail:
| |
Collapse
|
24
|
Ho MCW, Schiller BJ, Akbari OS, Bae E, Drewell RA. Disruption of the abdominal-B promoter tethering element results in a loss of long-range enhancer-directed Hox gene expression in Drosophila. PLoS One 2011; 6:e16283. [PMID: 21283702 PMCID: PMC3025016 DOI: 10.1371/journal.pone.0016283] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 12/21/2010] [Indexed: 11/29/2022] Open
Abstract
There are many examples within gene complexes of transcriptional enhancers interacting with only a subset of target promoters. A number of molecular mechanisms including promoter competition, insulators and chromatin looping are thought to play a role in regulating these interactions. At the Drosophila bithorax complex (BX-C), the IAB5 enhancer specifically drives gene expression only from the Abdominal-B (Abd-B) promoter, even though the enhancer and promoter are 55 kb apart and are separated by at least three insulators. In previous studies, we discovered that a 255 bp cis-regulatory module, the promoter tethering element (PTE), located 5′ of the Abd-B transcriptional start site is able to tether IAB5 to the Abd-B promoter in transgenic embryo assays. In this study we examine the functional role of the PTE at the endogenous BX-C using transposon-mediated mutagenesis. Disruption of the PTE by P element insertion results in a loss of enhancer-directed Abd-B expression during embryonic development and a homeotic transformation of abdominal segments. A partial deletion of the PTE and neighboring upstream genomic sequences by imprecise excision of the P element also results in a similar loss of Abd-B expression in embryos. These results demonstrate that the PTE is an essential component of the regulatory network at the BX-C and is required in vivo to mediate specific long-range enhancer-promoter interactions.
Collapse
Affiliation(s)
- Margaret C. W. Ho
- Biology Department, Harvey Mudd College, Claremont, California, United States of America
| | - Benjamin J. Schiller
- Biology Department, Harvey Mudd College, Claremont, California, United States of America
| | - Omar S. Akbari
- Biology Department, Harvey Mudd College, Claremont, California, United States of America
| | - Esther Bae
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, California, United States of America
| | - Robert A. Drewell
- Biology Department, Harvey Mudd College, Claremont, California, United States of America
- * E-mail:
| |
Collapse
|
25
|
When needles look like hay: how to find tissue-specific enhancers in model organism genomes. Dev Biol 2010; 350:239-54. [PMID: 21130761 DOI: 10.1016/j.ydbio.2010.11.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 11/11/2010] [Accepted: 11/22/2010] [Indexed: 01/22/2023]
Abstract
A major prerequisite for the investigation of tissue-specific processes is the identification of cis-regulatory elements. No generally applicable technique is available to distinguish them from any other type of genomic non-coding sequence. Therefore, researchers often have to identify these elements by elaborate in vivo screens, testing individual regions until the right one is found. Here, based on many examples from the literature, we summarize how functional enhancers have been isolated from other elements in the genome and how they have been characterized in transgenic animals. Covering computational and experimental studies, we provide an overview of the global properties of cis-regulatory elements, like their specific interactions with promoters and target gene distances. We describe conserved non-coding elements (CNEs) and their internal structure, nucleotide composition, binding site clustering and overlap, with a special focus on developmental enhancers. Conflicting data and unresolved questions on the nature of these elements are highlighted. Our comprehensive overview of the experimental shortcuts that have been found in the different model organism communities and the new field of high-throughput assays should help during the preparation phase of a screen for enhancers. The review is accompanied by a list of general guidelines for such a project.
Collapse
|
26
|
Chromosomal organization at the level of gene complexes. Cell Mol Life Sci 2010; 68:977-90. [PMID: 21080026 PMCID: PMC3043239 DOI: 10.1007/s00018-010-0585-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 10/17/2010] [Accepted: 10/26/2010] [Indexed: 01/10/2023]
Abstract
Metazoan genomes primarily consist of non-coding DNA in comparison to coding regions. Non-coding fraction of the genome contains cis-regulatory elements, which ensure that the genetic code is read properly at the right time and space during development. Regulatory elements and their target genes define functional landscapes within the genome, and some developmentally important genes evolve by keeping the genes involved in specification of common organs/tissues in clusters and are termed gene complex. The clustering of genes involved in a common function may help in robust spatio-temporal gene expression. Gene complexes are often found to be evolutionarily conserved, and the classic example is the hox complex. The evolutionary constraints seen among gene complexes provide an ideal model system to understand cis and trans-regulation of gene function. This review will discuss the various characteristics of gene regulatory modules found within gene complexes and how they can be characterized.
Collapse
|
27
|
Ou SA, Chang E, Lee S, So K, Wu CT, Morris JR. Effects of chromosomal rearrangements on transvection at the yellow gene of Drosophila melanogaster. Genetics 2009; 183:483-96. [PMID: 19667134 PMCID: PMC2766311 DOI: 10.1534/genetics.109.106559] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 08/05/2009] [Indexed: 11/18/2022] Open
Abstract
Homologous chromosomes are paired in somatic cells of Drosophila melanogaster. This pairing can lead to transvection, which is a process by which the proximity of homologous genes can lead to a change in gene expression. At the yellow gene, transvection is the basis for several examples of intragenic complementation involving the enhancers of one allele acting in trans on the promoter of a paired second allele. Using complementation as our assay, we explored the chromosomal requirements for pairing and transvection at yellow. Following a protocol established by Ed Lewis, we generated and characterized chromosomal rearrangements to define a region in cis to yellow that must remain intact for complementation to occur. Our data indicate that homolog pairing at yellow is efficient, as complementation was disrupted only in the presence of chromosomal rearrangements that break
Collapse
Affiliation(s)
- Sharon A Ou
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | | |
Collapse
|
28
|
Sexton T, Bantignies F, Cavalli G. Genomic interactions: Chromatin loops and gene meeting points in transcriptional regulation. Semin Cell Dev Biol 2009; 20:849-55. [DOI: 10.1016/j.semcdb.2009.06.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 06/17/2009] [Indexed: 12/17/2022]
|
29
|
Jeziorska DM, Jordan KW, Vance KW. A systems biology approach to understanding cis-regulatory module function. Semin Cell Dev Biol 2009; 20:856-62. [PMID: 19660565 DOI: 10.1016/j.semcdb.2009.07.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 07/29/2009] [Indexed: 12/27/2022]
Abstract
The genomic instructions used to regulate development are encoded within a set of functional DNA elements called cis-regulatory modules (CRMs). These elements determine the precise patterns of temporal and spatial gene expression. Here we summarize recent progress made towards cataloguing and characterizing the complete repertoire of CRMs. We describe CRMs as genomic information processing devices containing clusters of transcription factor binding sites and we position CRMs as nodes within large gene regulatory networks. We define CRM architecture and describe how these genomic elements process the information they encode to their target genes. Furthermore, we present an overview describing high-throughput techniques to identify CRMs genome wide and experimental methodologies to validate their function on a large scale. This review emphasizes the advantages and power of a systems biology approach which integrates computational and experimental technologies to further our understanding of CRM function.
Collapse
Affiliation(s)
- Danuta M Jeziorska
- Departments of Systems Biology and Biological Sciences, University of Warwick, Biomedical Research Institute, Gibbet Hill, Coventry CV4 7AL, UK
| | | | | |
Collapse
|
30
|
Miele A, Dekker J. Long-range chromosomal interactions and gene regulation. MOLECULAR BIOSYSTEMS 2008; 4:1046-57. [PMID: 18931780 PMCID: PMC2653627 DOI: 10.1039/b803580f] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over the last few years important new insights into the process of long-range gene regulation have been obtained. Gene regulatory elements are found to engage in direct physical interactions with distant target genes and with loci on other chromosomes to modulate transcription. An overview of recently discovered long-range chromosomal interactions is presented, and a network approach is proposed to unravel gene-element relationships. Gene expression is controlled by regulatory elements that can be located far away along the chromosome or in some cases even on other chromosomes. Genes and regulatory elements physically associate with each other resulting in complex genome-wide networks of chromosomal interactions. Here we describe several well-characterized cases of long-range interactions involved in the activation and repression of transcription. We speculate on how these interactions may affect gene expression and outline possible mechanisms that may facilitate encounters between distant elements. Finally, we propose that a genome-wide network analysis may provide new insights into the logic of long-range gene regulation.
Collapse
Affiliation(s)
- Adriana Miele
- Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester MA 01605-0103
| | - Job Dekker
- Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester MA 01605-0103
| |
Collapse
|
31
|
Chromatin loops in gene regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1789:17-25. [PMID: 18675948 DOI: 10.1016/j.bbagrm.2008.07.002] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Revised: 07/02/2008] [Accepted: 07/06/2008] [Indexed: 12/26/2022]
Abstract
The control of gene expression involves regulatory elements that can be very far from the genes they control. Several recent technological advances have allowed the direct detection of chromatin loops that juxtapose distant genomic sites in the nucleus. Here we review recent studies from various model organisms that have provided new insights into the functions of chromatin loops and the mechanisms that form them. We discuss the widespread impact of chromatin loops on gene activation, repression, genomic imprinting and the function of enhancers and insulators.
Collapse
|
32
|
Abstract
Intra- and interchromosomal interactions have been implicated in a number of genetic phenomena in diverse organisms, suggesting that the higher-order structural organization of chromosomes in the nucleus can have a profound impact on gene regulation. In Drosophila, homologous chromosomes remain paired in somatic tissues, allowing for trans interactions between genes and regulatory elements on the two homologs. One consequence of homolog pairing is the phenomenon of transvection, in which regulatory elements on one homolog can affect the expression of a gene in trans. We report a new instance of transvection at the Drosophila apterous (ap) locus. Two different insertions of boundary elements in the ap regulatory region were identified. The boundaries are inserted between the ap wing enhancer and the ap promoter and have highly penetrant wing defects typical of mutants in ap. When crossed to an ap promoter deletion, both boundary inserts exhibit the interallelic complementation characteristic of transvection. To confirm that transvection occurs at ap, we generated a deletion of the ap wing enhancer by FRT-mediated recombination. When the wing-enhancer deletion is crossed to the ap promoter deletion, strong transvection is observed. Interestingly, the two boundary elements, which are inserted approximately 10 kb apart, fail to block enhancer action when they are present in trans to one another. We demonstrate that this is unlikely to be due to insulator bypass. The transvection effects described here may provide insight into the role that boundary element pairing plays in enhancer blocking both in cis and in trans.
Collapse
|
33
|
Barzel A, Kupiec M. Finding a match: how do homologous sequences get together for recombination? Nat Rev Genet 2008; 9:27-37. [PMID: 18040271 DOI: 10.1038/nrg2224] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Decades of research into homologous recombination have unravelled many of the details concerning the transfer of information between two homologous sequences. By contrast, the processes by which the interacting molecules initially colocalize are largely unknown. How can two homologous needles find each other in the genomic haystack? Is homologous pairing the result of a damage-induced homology search, or is it an enduring and general feature of the genomic architecture that facilitates homologous recombination whenever and wherever damage occurs? This Review presents the homologous-pairing enigma, delineates our current understanding of the process and offers guidelines for future research.
Collapse
Affiliation(s)
- Adi Barzel
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
| | | |
Collapse
|
34
|
Schneider R, Grosschedl R. Dynamics and interplay of nuclear architecture, genome organization, and gene expression. Genes Dev 2008; 21:3027-43. [PMID: 18056419 DOI: 10.1101/gad.1604607] [Citation(s) in RCA: 316] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The organization of the genome in the nucleus of a eukaryotic cell is fairly complex and dynamic. Various features of the nuclear architecture, including compartmentalization of molecular machines and the spatial arrangement of genomic sequences, help to carry out and regulate nuclear processes, such as DNA replication, DNA repair, gene transcription, RNA processing, and mRNA transport. Compartmentalized multiprotein complexes undergo extensive modifications or exchange of protein subunits, allowing for an exquisite dynamics of structural components and functional processes of the nucleus. The architecture of the interphase nucleus is linked to the spatial arrangement of genes and gene clusters, the structure of chromatin, and the accessibility of regulatory DNA elements. In this review, we discuss recent studies that have provided exciting insight into the interplay between nuclear architecture, genome organization, and gene expression.
Collapse
|
35
|
Abstract
DNA transposons are efficient tools in transgenesis and have therefore become popular in the analysis of the regulatory genome in vertebrates via enhancer trap screens. Here, I discuss recent progress in this field of research, with a focus on the application of one of these transposons, namely the medaka fish derived Tol2, to enhancer trapping in zebrafish, and how this approach compares with others that have a similar objective.
Collapse
Affiliation(s)
- Vladimir Korzh
- Institute of Molecular and Cell Biology, Biopolis Dr, Proteos, 138673, Singapore.
| |
Collapse
|
36
|
Lanzuolo C, Roure V, Dekker J, Bantignies F, Orlando V. Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nat Cell Biol 2007; 9:1167-74. [PMID: 17828248 DOI: 10.1038/ncb1637] [Citation(s) in RCA: 230] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Accepted: 07/26/2007] [Indexed: 12/12/2022]
Abstract
In Drosophila, the function of the Polycomb group genes (PcGs) and their target sequences (Polycomb response elements (PREs)) is to convey mitotic heritability of transcription programmes--in particular, gene silencing. As part of the mechanisms involved, PREs are thought to mediate this transcriptional memory function by building up higher-order structures in the nucleus. To address this question, we analysed in vivo the three-dimensional structure of the homeotic locus bithorax complex (BX-C) by combining chromosome conformation capture (3C) with fluorescent in situ hybridization (FISH) and FISH immunostaining (FISH-I) analysis. We found that, in the repressed state, all major elements that have been shown to bind PcG proteins, including PREs and core promoters, interact at a distance, giving rise to a topologically complex structure. We show that this structure is important for epigenetic silencing of the BX-C, as we find that major changes in higher-order structures must occur to stably maintain alternative transcription states, whereas histone modification and reduced levels of PcG proteins determine an epigenetic switch that is only partially heritable.
Collapse
Affiliation(s)
- Chiara Lanzuolo
- Dulbecco Telethon Institute at IGB CNR, Epigenetics and Genome Reprogramming, Via Pietro Castellino 111, 80131 Naples, Italy
| | | | | | | | | |
Collapse
|
37
|
Williams BR, Bateman JR, Novikov ND, Wu CT. Disruption of topoisomerase II perturbs pairing in drosophila cell culture. Genetics 2007; 177:31-46. [PMID: 17890361 PMCID: PMC2013714 DOI: 10.1534/genetics.107.076356] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Accepted: 06/22/2007] [Indexed: 12/16/2022] Open
Abstract
Homolog pairing refers to the alignment and physical apposition of homologous chromosomal segments. Although commonly observed during meiosis, homolog pairing also occurs in nonmeiotic cells of several organisms, including humans and Drosophila. The mechanism underlying nonmeiotic pairing, however, remains largely unknown. Here, we explore the use of established Drosophila cell lines for the analysis of pairing in somatic cells. Using fluorescent in situ hybridization (FISH), we assayed pairing at nine regions scattered throughout the genome of Kc167 cells, observing high levels of homolog pairing at all six euchromatic regions assayed and variably lower levels in regions in or near centromeric heterochromatin. We have also observed extensive pairing in six additional cell lines representing different tissues of origin, different ploidies, and two different species, demonstrating homolog pairing in cell culture to be impervious to cell type or culture history. Furthermore, by sorting Kc167 cells into G1, S, and G2 subpopulations, we show that even progression through these stages of the cell cycle does not significantly change pairing levels. Finally, our data indicate that disrupting Drosophila topoisomerase II (Top2) gene function with RNAi and chemical inhibitors perturbs homolog pairing, suggesting Top2 to be a gene important for pairing.
Collapse
Affiliation(s)
- Benjamin R Williams
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | | | |
Collapse
|
38
|
Abstract
SUMMARY
It is usually thought that the development of complex organisms is controlled by protein regulatory factors and morphogenetic signals exchanged between cells and differentiating tissues during ontogeny. However, it is now evident that the majority of all animal genomes is transcribed, apparently in a developmentally regulated manner, suggesting that these genomes largely encode RNA machines and that there may be a vast hidden layer of RNA regulatory transactions in the background. I propose that the epigenetic trajectories of differentiation and development are primarily programmed by feed-forward RNA regulatory networks and that most of the information required for multicellular development is embedded in these networks, with cell–cell signalling required to provide important positional information and to correct stochastic errors in the endogenous RNA-directed program.
Collapse
Affiliation(s)
- John S Mattick
- ARC Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia.
| |
Collapse
|
39
|
Samanta MP, Tongprasit W, Istrail S, Cameron RA, Tu Q, Davidson EH, Stolc V. The Transcriptome of the Sea Urchin Embryo. Science 2006; 314:960-2. [PMID: 17095694 DOI: 10.1126/science.1131898] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The sea urchin Strongylocentrotus purpuratus is a model organism for study of the genomic control circuitry underlying embryonic development. We examined the complete repertoire of genes expressed in the S. purpuratus embryo, up to late gastrula stage, by means of high-resolution custom tiling arrays covering the whole genome. We detected complete spliced structures even for genes known to be expressed at low levels in only a few cells. At least 11,000 to 12,000 genes are used in embryogenesis. These include most of the genes encoding transcription factors and signaling proteins, as well as some classes of general cytoskeletal and metabolic proteins, but only a minor fraction of genes encoding immune functions and sensory receptors. Thousands of small asymmetric transcripts of unknown function were also detected in intergenic regions throughout the genome. The tiling array data were used to correct and authenticate several thousand gene models during the genome annotation process.
Collapse
|
40
|
Lee AM, Wu CT. Enhancer-promoter communication at the yellow gene of Drosophila melanogaster: diverse promoters participate in and regulate trans interactions. Genetics 2006; 174:1867-80. [PMID: 17057235 PMCID: PMC1698615 DOI: 10.1534/genetics.106.064121] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The many reports of trans interactions between homologous as well as nonhomologous loci in a wide variety of organisms argue that such interactions play an important role in gene regulation. The yellow locus of Drosophila is especially useful for investigating the mechanisms of trans interactions due to its ability to support transvection and the relative ease with which it can be altered by targeted gene replacement. In this study, we exploit these aspects of yellow to further our understanding of cis as well as trans forms of enhancer-promoter communication. Through the analysis of yellow alleles whose promoters have been replaced with wild-type or altered promoters from other genes, we show that mutation of single core promoter elements of two of the three heterologous promoters tested can influence whether yellow enhancers act in cis or in trans. This finding parallels observations of the yellow promoter, suggesting that the manner in which trans interactions are controlled by core promoter elements describes a general mechanism. We further demonstrate that heterologous promoters themselves can be activated in trans as well as participate in pairing-mediated insulator bypass. These results highlight the potential of diverse promoters to partake in many forms of trans interactions.
Collapse
Affiliation(s)
- Anne M Lee
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | |
Collapse
|
41
|
Abstract
The family of Hox genes, which number 4 to 48 per genome depending on the animal, control morphologies on the main body axis of nearly all metazoans. The conventional wisdom is that Hox genes are arranged in chromosomal clusters in colinear order with their expression patterns on the body axis. However, recent evidence has shown that Hox gene clusters are fragmented, reduced, or expanded in many animals-findings that correlate with interesting morphological changes in evolution. Hox gene clusters also contain many noncoding RNAs, such as intergenic regulatory transcripts and evolutionarily conserved microRNAs, some of whose developmental functions have recently been explored.
Collapse
Affiliation(s)
- Derek Lemons
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | | |
Collapse
|
42
|
Nakamura S, Kobayashi D, Aoki Y, Yokoi H, Ebe Y, Wittbrodt J, Tanaka M. Identification and lineage tracing of two populations of somatic gonadal precursors in medaka embryos. Dev Biol 2006; 295:678-88. [PMID: 16682019 DOI: 10.1016/j.ydbio.2006.03.052] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2005] [Revised: 03/30/2006] [Accepted: 03/31/2006] [Indexed: 11/18/2022]
Abstract
The gonad contains two major cell lineages, germline and somatic cells. Little is known, however, about the somatic gonadal cell lineage in vertebrates. Using fate mapping studies and ablation experiments in medaka fish (Oryzias latipes), we determined that somatic gonadal precursors arise from the most posterior part of the sdf-1a expression domain in the lateral plate mesoderm at the early segmentation stage; this region has the properties of a gonadal field. Somatic gonadal precursors in this field, which continuously express sdf-1a, move anteriorly and medially to the prospective gonadal area by convergent movement. By the stage at which these somatic gonadal precursors have become located adjacent to the embryonic body, the precursors no longer replace the surrounding lateral plate mesoderm, becoming spatially organized into two distinct populations. We further show that, prior to reaching the prospective gonadal area, these populations can be distinguished by expression of either ftz-f1 or sox9b. These results clearly indicate that different populations of gonadal precursors are present before the formation of a single gonadal primordium, shedding new light on the developmental processes of somatic gonadal cell and subsequent sex differentiation.
Collapse
Affiliation(s)
- Shuhei Nakamura
- Laboratory of Molecular Genetics for Reproduction, National Institute for Basic Biology, Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | | | | | | | | | | | | |
Collapse
|
43
|
Brown JM, Leach J, Reittie JE, Atzberger A, Lee-Prudhoe J, Wood WG, Higgs DR, Iborra FJ, Buckle VJ. Coregulated human globin genes are frequently in spatial proximity when active. ACTA ACUST UNITED AC 2006; 172:177-87. [PMID: 16418531 PMCID: PMC2063548 DOI: 10.1083/jcb.200507073] [Citation(s) in RCA: 177] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The organization of genes within the nucleus may influence transcription. We have analyzed the nuclear positioning of the coordinately regulated α- and β-globin genes and show that the gene-dense chromatin surrounding the human α-globin genes is frequently decondensed, independent of transcription. Against this background, we show the frequent juxtaposition of active α- and β-globin genes and of homologous α-globin loci that occurs at nuclear speckles and correlates with transcription. However, we did not see increased colocalization of signals, which would be expected with direct physical interaction. The same degree of proximity does not occur between human β-globin genes or between murine globin genes, which are more constrained to their chromosome territories. Our findings suggest that the distribution of globin genes within erythroblast nuclei is the result of a self-organizing process, involving transcriptional status, diffusional ability of chromatin, and physical interactions with nuclear proteins, rather than a directed form of higher-order control.
Collapse
Affiliation(s)
- Jill M Brown
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, England, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Aboobaker AA, Tomancak P, Patel N, Rubin GM, Lai EC. Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development. Proc Natl Acad Sci U S A 2005; 102:18017-22. [PMID: 16330759 PMCID: PMC1306796 DOI: 10.1073/pnas.0508823102] [Citation(s) in RCA: 212] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are an extensive class of regulatory RNA whose specific functions in animals are generally unknown. Although computational methods have identified many potential targets of miRNAs, elucidating the spatial expression patterns of miRNAs is necessary to identify the sites of miRNA action. Here, we report the spatial patterns of miRNA transcription during Drosophila embryonic development, as revealed by in situ hybridization to nascent miRNA transcripts. We detect expression of 15 "stand-alone" miRNA loci and 9 intronic miRNA loci, which collectively represent 38 miRNA genes. We observe great variety in the spatial patterns of miRNA transcription, including preblastoderm stripes, in aspects of the central and peripheral nervous systems, and in cellular subsets of the mesoderm and endoderm. We also describe an intronic miRNA (miR-7) whose expression pattern is distinct from that of its host mRNA (bancal), which demonstrates that intronic miRNAs can be subject to independent cis-regulatory control. Intriguingly, the expression patterns of several fly miRNAs are analogous to those of their vertebrate counterparts, suggesting that these miRNAs may have ancient roles in animal patterning.
Collapse
Affiliation(s)
- A Aziz Aboobaker
- Department of Molecular and Cell Biology, University of California, Berkeley, 94720-3200, USA
| | | | | | | | | |
Collapse
|
45
|
Abstract
Enhancers can activate their target genes over large linear distances. Insulators can delimit the influence of an enhancer to an appropriate target. There are a number of intertwined mechanisms by which the regulatory functions of enhancers and insulators might be carried out at the level of the chromatin fiber. Recent evidence suggests that both enhancers and insulators participate in higher-order organization of chromatin in the nucleus and in localization of their regulated sequences to both subnuclear structures and compartments. Novel experimental approaches are helping to reveal the mechanisms underlying nuclear organization of developmentally regulated genes.
Collapse
Affiliation(s)
- Hui Zhao
- Laboratory of Cellular and Developmental Biology, NIDDK, NIH, Bethesda, MD 20892, USA
| | | |
Collapse
|
46
|
Abstract
A recent paper demonstrates that coregulated genes on different chromosomes show surprisingly high frequencies of colocalization within the nucleus. A recent paper demonstrates that coregulated genes on different chromosomes show surprisingly high frequencies of colocalization within the nucleus; this complements similar results found previously for genes localized tens of megabases apart on a single chromosome. Colocalization could be related to the earlier observation of active genes associating with foci where RNA polymerase II is concentrated.
Collapse
Affiliation(s)
- Chien-Hui Chuang
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 South Goodwin Avenue, Urbana, IL 61801, USA
| | - Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 South Goodwin Avenue, Urbana, IL 61801, USA
| |
Collapse
|
47
|
Dorsett D, Eissenberg JC, Misulovin Z, Martens A, Redding B, McKim K. Effects of sister chromatid cohesion proteins on cut gene expression during wing development in Drosophila. Development 2005; 132:4743-53. [PMID: 16207752 PMCID: PMC1635493 DOI: 10.1242/dev.02064] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The cohesin protein complex is a conserved structural component of chromosomes. Cohesin binds numerous sites along interphase chromosomes and is essential for sister chromatid cohesion and DNA repair. Here, we test the idea that cohesin also regulates gene expression. This idea arose from the finding that the Drosophila Nipped-B protein, a functional homolog of the yeast Scc2 factor that loads cohesin onto chromosomes, facilitates the transcriptional activation of certain genes by enhancers located many kilobases away from their promoters. We find that cohesin binds between a remote wing margin enhancer and the promoter at the cut locus in cultured cells, and that reducing the dosage of the Smc1 cohesin subunit increases cut expression in the developing wing margin. We also find that cut expression is increased by a unique pds5 gene mutation that reduces the binding of cohesin to chromosomes. On the basis of these results, we posit that cohesin inhibits long-range activation of the Drosophila cut gene, and that Nipped-B facilitates activation by regulating cohesin-chromosome binding. Such effects of cohesin on gene expression could be responsible for many of the developmental deficits that occur in Cornelia de Lange syndrome, which is caused by mutations in the human homolog of Nipped-B.
Collapse
Affiliation(s)
- Dale Dorsett
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA.
| | | | | | | | | | | |
Collapse
|
48
|
Skipper M. Loop the loop with your partner. Nat Rev Genet 2005. [DOI: 10.1038/nrg1541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|