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      Transvection between nonallelic genomic positions in Drosophila

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          Abstract

          In Drosophila, pairing of maternal and paternal homologous chromosomes can permit trans-interactions between enhancers on one homolog and promoters on another, an example of transvection. Although trans-interactions have been observed at many loci in the Drosophila genome and in other organisms, the parameters that govern enhancer action in trans remain poorly understood. Using a transgenic reporter system, we asked whether enhancers and promoters at nonallelic, but nearby, genomic positions can communication in trans. Using one transgenic insertion carrying the synthetic enhancer GMR and another nearby insertion carrying the hsp70 promoter driving a fluorescent reporter, we show that transgenes separated by 2.6 kb of linear distance can support enhancer action in trans at the 53F8 locus. Furthermore, transvection between the nonallelic insertions can be augmented by a small deletion flanking one insert, likely via changes to the paired configuration of the homologs. Subsequent analyses of other insertions in 53F8 that carry different transgenic sequences demonstrate that the capacity to support transvection between nonallelic sites varies greatly, suggesting that factors beyond the linear distance between insertion sites play an important role. Finally, analysis of transvection between nearby nonallelic sites at other genomic locations shows evidence of position effects, where one locus supported GMR action in trans over a linear distance of over 10 kb, whereas another locus showed no evidence of transvection over a span <200 bp. Overall, our data demonstrate that transvection between nonallelic sites represents a complex interplay between genomic context, interallelic distance, and promoter identity.

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          Most cited references49

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          Fiji: an open-source platform for biological-image analysis.

          Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
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            A complementary transposon tool kit for Drosophila melanogaster using P and piggyBac.

            With the availability of complete genome sequence for Drosophila melanogaster, one of the next strategic goals for fly researchers is a complete gene knockout collection. The P-element transposon, the workhorse of D. melanogaster molecular genetics, has a pronounced nonrandom insertion spectrum. It has been estimated that 87% saturation of the approximately 13,500-gene complement of D. melanogaster might require generating and analyzing up to 150,000 insertions. We describe specific improvements to the lepidopteran transposon piggyBac and the P element that enabled us to tag and disrupt genes in D. melanogaster more efficiently. We generated over 29,000 inserts resulting in 53% gene saturation and a more diverse collection of phenotypically stronger insertional alleles. We found that piggyBac has distinct global and local gene-tagging behavior from that of P elements. Notably, piggyBac excisions from the germ line are nearly always precise, piggyBac does not share chromosomal hotspots associated with P and piggyBac is more effective at gene disruption because it lacks the P bias for insertion in 5' regulatory sequences.
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              The Drosophila gene disruption project: progress using transposons with distinctive site specificities.

              The Drosophila Gene Disruption Project (GDP) has created a public collection of mutant strains containing single transposon insertions associated with different genes. These strains often disrupt gene function directly, allow production of new alleles, and have many other applications for analyzing gene function. Here we describe the addition of ∼7600 new strains, which were selected from >140,000 additional P or piggyBac element integrations and 12,500 newly generated insertions of the Minos transposon. These additions nearly double the size of the collection and increase the number of tagged genes to at least 9440, approximately two-thirds of all annotated protein-coding genes. We also compare the site specificity of the three major transposons used in the project. All three elements insert only rarely within many Polycomb-regulated regions, a property that may contribute to the origin of "transposon-free regions" (TFRs) in metazoan genomes. Within other genomic regions, Minos transposes essentially at random, whereas P or piggyBac elements display distinctive hotspots and coldspots. P elements, as previously shown, have a strong preference for promoters. In contrast, piggyBac site selectivity suggests that it has evolved to reduce deleterious and increase adaptive changes in host gene expression. The propensity of Minos to integrate broadly makes possible a hybrid finishing strategy for the project that will bring >95% of Drosophila genes under experimental control within their native genomic contexts.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                G3 (Bethesda)
                Genetics
                g3journal
                G3: Genes|Genomes|Genetics
                Oxford University Press (US )
                2160-1836
                February 2024
                09 November 2023
                09 November 2023
                : 14
                : 2
                : jkad255
                Affiliations
                Biology Department, 2 Polar Loop, Bowdoin College , Brunswick, ME 04011, USA
                Biology Department, 2 Polar Loop, Bowdoin College , Brunswick, ME 04011, USA
                Biology Department, 2 Polar Loop, Bowdoin College , Brunswick, ME 04011, USA
                Biology Department, 2 Polar Loop, Bowdoin College , Brunswick, ME 04011, USA
                Biology Department, 2 Polar Loop, Bowdoin College , Brunswick, ME 04011, USA
                Author notes
                Corresponding author: Email: jbateman@ 123456bowdoin.edu

                Conflicts of interest The author(s) declare no conflicts of interest.

                Author information
                https://orcid.org/0000-0002-8782-5958
                Article
                jkad255
                10.1093/g3journal/jkad255
                10849331
                37949840
                c4116242-9c3c-4de3-8ff7-9ff5c70fec59
                © The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 26 July 2023
                : 03 November 2023
                : 13 December 2023
                Page count
                Pages: 10
                Funding
                Funded by: National Institute of General Medical Sciences, DOI 10.13039/100000057;
                Award ID: P20 GM0103423
                Funded by: National Institutes of Health, DOI 10.13039/100000002;
                Funded by: National Science Foundation, DOI 10.13039/100000001;
                Award ID: 1349779
                Funded by: Bowdoin College, DOI 10.13039/100015587;
                Categories
                Investigation
                AcademicSubjects/SCI01180
                AcademicSubjects/SCI01140

                Genetics
                transvection,long-range enhancer,somatic homolog pairing,promoter,chromatin,position effects
                Genetics
                transvection, long-range enhancer, somatic homolog pairing, promoter, chromatin, position effects

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