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Dynamics of nuclear matrix attachment regions during 5 th instar posterior silk gland development in Bombyx mori. BMC Genomics 2022; 23:247. [PMID: 35361117 PMCID: PMC8973518 DOI: 10.1186/s12864-022-08446-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/06/2022] [Indexed: 12/02/2022] Open
Abstract
Background Chromatin architecture is critical for gene expression during development. Matrix attachment regions (MARs) control and regulate chromatin dynamics. The position of MARs in the genome determines the expression of genes in the organism. In this study, we set out to elucidate how MARs temporally regulate the expression of the fibroin heavy chain (FIBH) gene during development. We addressed this by identifying MARs and studying their distribution and differentiation, in the posterior silk glands of Bombyx mori during 5th instar development. Results Of the MARs identified on three different days, 7.15% MARs were common to all 3 days, whereas, 1.41, 19.27 and 52.47% MARs were unique to day 1, day 5, and day 7, respectively highlighting the dynamic nature of the matrix associated DNA. The average chromatin loop length based on the chromosome wise distribution of MARs and the distances between these MAR regions decreased from day 1 (253.91 kb) to day 5 (73.54 kb) to day 7 (39.19 kb). Further significant changes in the MARs in the vicinity of the FIBH gene were found during different days of 5th instar development which implied their role in the regulation and expression of the FIBH gene. Conclusions The presence of MARs in the flanking regions of genes found to exhibit differential expression during 5th instar development indicates their possible role in the regulation of their expression. This reiterates the importance of MARs in the genomic functioning as regulators of the molecular mechanisms in the nucleus. This is the first study that takes into account the tissue specific genome-wide MAR association and the potential role of these MARs in developmentally regulated gene expression. The current study lays a foundation to understand the genome wide regulation of chromatin during development. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08446-3.
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Pathak RU, Bihani A, Sureka R, Varma P, Mishra RK. In situ nuclear matrix preparation in Drosophila melanogaster embryos/tissues and its use in studying the components of nuclear architecture. Nucleus 2022; 13:116-128. [PMID: 35239464 PMCID: PMC8896195 DOI: 10.1080/19491034.2022.2043608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The study of nuclear matrix (NuMat) over the last 40 years has been limited to either isolated nuclei from tissues or cells grown in culture. Here, we provide a protocol for NuMat preparation in intact Drosophila melanogaster embryos and its use in dissecting the components of nuclear architecture. The protocol does not require isolation of nuclei and therefore maintains the three-dimensional milieu of an intact embryo, which is biologically more relevant compared to cells in culture. One of the advantages of this protocol is that only a small number of embryos are required. The protocol has been extended to larval tissues like salivary glands with little modification. Taken together, it becomes possible to carry out such studies in parallel to genetic experiments using mutant/transgenic flies. This protocol, therefore, opens the powerful field of fly genetics to cell biology in the study of nuclear architecture. Summary: Nuclear Matrix is a biochemically defined entity and a basic component of the nuclear architecture. Here we present a protocol to isolate and visualize Nuclear Matrix in situ in the Drosophila melanogaster and its potential applications.
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Affiliation(s)
- Rashmi U Pathak
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Ashish Bihani
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | - Parul Varma
- Present Address: Department of Neuroscience, Development and Regenerative Biology, The University of Texas at San Antonio, Texas, USA
| | - Rakesh K Mishra
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India.,Tata Institute for Genetics and Society, Bangalore, India
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Moschetti R, Palazzo A, Lorusso P, Viggiano L, Massimiliano Marsano R. "What You Need, Baby, I Got It": Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila. BIOLOGY 2020; 9:E25. [PMID: 32028630 PMCID: PMC7168160 DOI: 10.3390/biology9020025] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 12/18/2022]
Abstract
Transposable elements (TEs) are constitutive components of both eukaryotic and prokaryotic genomes. The role of TEs in the evolution of genes and genomes has been widely assessed over the past years in a variety of model and non-model organisms. Drosophila is undoubtedly among the most powerful model organisms used for the purpose of studying the role of transposons and their effects on the stability and evolution of genes and genomes. Besides their most intuitive role as insertional mutagens, TEs can modify the transcriptional pattern of host genes by juxtaposing new cis-regulatory sequences. A key element of TE biology is that they carry transcriptional control elements that fine-tune the transcription of their own genes, but that can also perturb the transcriptional activity of neighboring host genes. From this perspective, the transposition-mediated modulation of gene expression is an important issue for the short-term adaptation of physiological functions to the environmental changes, and for long-term evolutionary changes. Here, we review the current literature concerning the regulatory and structural elements operating in cis provided by TEs in Drosophila. Furthermore, we highlight that, besides their influence on both TEs and host genes expression, they can affect the chromatin structure and epigenetic status as well as both the chromosome's structure and stability. It emerges that Drosophila is a good model organism to study the effect of TE-linked regulatory sequences, and it could help future studies on TE-host interactions in any complex eukaryotic genome.
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Affiliation(s)
- Roberta Moschetti
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy; (R.M.); (P.L.); (L.V.)
| | - Antonio Palazzo
- Laboratory of Translational Nanotechnology, “Istituto Tumori Giovanni Paolo II” I.R.C.C.S, Viale Orazio Flacco 65, 70125 Bari, Italy;
| | - Patrizio Lorusso
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy; (R.M.); (P.L.); (L.V.)
| | - Luigi Viggiano
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy; (R.M.); (P.L.); (L.V.)
| | - René Massimiliano Marsano
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy; (R.M.); (P.L.); (L.V.)
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Merenciano M, Iacometti C, González J. A unique cluster of roo insertions in the promoter region of a stress response gene in Drosophila melanogaster. Mob DNA 2019; 10:10. [PMID: 30911338 PMCID: PMC6415491 DOI: 10.1186/s13100-019-0152-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/28/2019] [Indexed: 01/19/2023] Open
Abstract
Transposable elements (TEs) are not randomly distributed in the genome. A genome-wide analysis of the D. melanogaster genome found that differences in TE density across 50 kb genomic regions was due both to transposition and duplication. At smaller genomic scales, promoter regions of hsp genes and the promoter region of CG18446 have been shown to accumulate TE insertions. In this work, we have further analyzed the promoter region of CG18446. We screened 218 strains collected in 15 natural populations, and we found that the CG18446 promoter region contains 20 independent roo insertions. Based on phylogenetic analysis, we suggest that the presence of multiple roo insertions in this region is likely to be the result of several bursts of transposition. Moreover, we found that the roo insertional cluster in the CG18446 promoter region is unique: no other promoter region in the genome contains a similar number of roo insertions. We found that, similar to hsp gene promoters, chromatin accessibility could be one of the factors explaining the recurrent insertions of roo elements in CG18446 promoter region.
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Affiliation(s)
- Miriam Merenciano
- 1Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37,49, 08003 Barcelona, Spain
| | - Camillo Iacometti
- 1Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37,49, 08003 Barcelona, Spain.,2Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Josefa González
- 1Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37,49, 08003 Barcelona, Spain
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Xie YF, Shang F, Ding BY, Wu YB, Niu JZ, Wei D, Dou W, Christiaens O, Smagghe G, Wang JJ. Tudor knockdown disrupts ovary development in Bactrocera dorsalis. INSECT MOLECULAR BIOLOGY 2019; 28:136-144. [PMID: 30182401 DOI: 10.1111/imb.12533] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
One of the main functions of the piwi-interacting RNA pathway is the post-transcriptional silencing of transposable elements in the germline of many species. In insects, proteins belonging to the Tudor superfamily proteins belonging to the Tudor superfamily play an important role in to play an important role in this mechanism. In this study, we identified the tudor gene in the oriental fruit fly, Bactrocera dorsalis, investigated the spatiotemporal expressional profile of the gene, and performed a functional analysis using RNA interference. We identified one transcript for a tudor homologue in the B. dorsalis transcriptome, which encodes a protein containing the typical 10 Tudor domains and an Adenosine triphosphate (ATP) synthase delta subunit signature. Phylogenetic analysis confirmed the identity of this transcript as a tudor homologue in this species. The expression profile indicated a much higher expression in the adult and pupal stages compared to the larval stages (up to a 60-fold increase), and that the gene was mostly expressed in the ovaries, Malpighian tubules and fat body. Finally, gene knockdown of tudor in B. dorsalis led to clearly underdeveloped ovaries in the female adult and reductions in copulation rate and amount of oviposition, indicating its important role in reproduction. The results of this study shed more light on the role of tudor in ovary development and reproduction.
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Affiliation(s)
- Y-F Xie
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Hunan Academy of Forestry, Changsha, China
| | - F Shang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - B-Y Ding
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Y-B Wu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - J-Z Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - D Wei
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - W Dou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - O Christiaens
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - G Smagghe
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - J-J Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
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Merenciano M, Ullastres A, de Cara MAR, Barrón MG, González J. Multiple Independent Retroelement Insertions in the Promoter of a Stress Response Gene Have Variable Molecular and Functional Effects in Drosophila. PLoS Genet 2016; 12:e1006249. [PMID: 27517860 PMCID: PMC4982627 DOI: 10.1371/journal.pgen.1006249] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 07/18/2016] [Indexed: 12/20/2022] Open
Abstract
Promoters are structurally and functionally diverse gene regulatory regions. The presence or absence of sequence motifs and the spacing between the motifs defines the properties of promoters. Recent alternative promoter usage analyses in Drosophila melanogaster revealed that transposable elements significantly contribute to promote diversity. In this work, we analyzed in detail one of the transposable element insertions, named FBti0019985, that has been co-opted to drive expression of CG18446, a candidate stress response gene. We analyzed strains from different natural populations and we found that besides FBti0019985, there are another eight independent transposable elements inserted in the proximal promoter region of CG18446. All nine insertions are solo-LTRs that belong to the roo family. We analyzed the sequence of the nine roo insertions and we investigated whether the different insertions were functionally equivalent by performing 5'-RACE, gene expression, and cold-stress survival experiments. We found that different insertions have different molecular and functional consequences. The exact position where the transposable elements are inserted matters, as they all showed highly conserved sequences but only two of the analyzed insertions provided alternative transcription start sites, and only the FBti0019985 insertion consistently affects CG18446 expression. The phenotypic consequences of the different insertions also vary: only FBti0019985 was associated with cold-stress tolerance. Interestingly, the only previous report of transposable elements inserting repeatedly and independently in a promoter region in D. melanogaster, were also located upstream of a stress response gene. Our results suggest that functional validation of individual structural variants is needed to resolve the complexity of insertion clusters.
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Affiliation(s)
- Miriam Merenciano
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona. Spain
| | - Anna Ullastres
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona. Spain
| | - M. A. R. de Cara
- Laboratoire d’Eco-anthropologie et Ethnobiologie, UMR 7206, CNRS/MNHN/Universite Paris 7, Museum National d’Histoire Naturelle, F-75116 Paris, France
| | - Maite G. Barrón
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona. Spain
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona. Spain
- * E-mail:
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Mita P, Boeke JD. How retrotransposons shape genome regulation. Curr Opin Genet Dev 2016; 37:90-100. [PMID: 26855260 DOI: 10.1016/j.gde.2016.01.001] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/30/2015] [Accepted: 01/17/2016] [Indexed: 12/30/2022]
Abstract
Retrotransposons are mutagenic units able to move within the genome. Despite many defenses deployed by the host to suppress potentially harmful activities of retrotransposons, these genetic units have found ways to meld with normal cellular functions through processes of exaptation and domestication. The same host mechanisms targeting transposon mobility allow for expansion and rewiring of gene regulatory networks on an evolutionary time scale. Recent works demonstrating retrotransposon activity during development, cell differentiation and neurogenesis shed new light on unexpected activities of transposable elements. Moreover, new technological advances illuminated subtler nuances of the complex relationship between retrotransposons and the host genome, clarifying the role of retroelements in evolution, development and impact on human disease.
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Affiliation(s)
- Paolo Mita
- Institute for Systems Genetics, Department of Biochemistry & Molecular Pharmacology, NYU Langone Medical Center, 430 East 29 Street, NY, NY 10016, USA.
| | - Jef D Boeke
- Institute for Systems Genetics, Department of Biochemistry & Molecular Pharmacology, NYU Langone Medical Center, 430 East 29 Street, NY, NY 10016, USA
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Turan S, Qiao J, Madden S, Benham C, Kotz M, Schambach A, Bode J. Expanding Flp-RMCE options: the potential of Recombinase Mediated Twin-Site Targeting (RMTT). Gene 2014; 546:135-44. [DOI: 10.1016/j.gene.2014.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 06/02/2014] [Indexed: 01/02/2023]
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