Resurrection of DNA Function In Vivo from an Extinct Genome
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{"title"=>"Resurrection of DNA function in vivo from an extinct genome", "type"=>"journal", "authors"=>[{"first_name"=>"Andrew J.", "last_name"=>"Pask", "scopus_author_id"=>"6603831918"}, {"first_name"=>"Richard R.", "last_name"=>"Behringer", "scopus_author_id"=>"7102050240"}, {"first_name"=>"Marilyn B.", "last_name"=>"Renfree", "scopus_author_id"=>"7005587252"}], "year"=>2008, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-48249090058", "pmid"=>"18493600", "sgr"=>"48249090058", "doi"=>"10.1371/journal.pone.0002240", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "issn"=>"19326203", "pui"=>"352069104"}, "id"=>"ca5f8d55-f40b-3b40-a8f3-4c7e6dc67c0c", "abstract"=>"There is a burgeoning repository of information available from ancient DNA that can be used to understand how genomes have evolved and to determine the genetic features that defined a particular species. To assess the functional consequences of changes to a genome, a variety of methods are needed to examine extinct DNA function. We isolated a transcriptional enhancer element from the genome of an extinct marsupial, the Tasmanian tiger (Thylacinus cynocephalus or thylacine), obtained from 100 year-old ethanol-fixed tissues from museum collections. We then examined the function of the enhancer in vivo. Using a transgenic approach, it was possible to resurrect DNA function in transgenic mice. The results demonstrate that the thylacine Col2A1 enhancer directed chondrocyte-specific expression in this extinct mammalian species in the same way as its orthologue does in mice. While other studies have examined extinct coding DNA function in vitro, this is the first example of the restoration of extinct non-coding DNA and examination of its function in vivo. Our method using transgenesis can be used to explore the function of regulatory and protein-coding sequences obtained from any extinct species in an in vivo model system, providing important insights into gene evolution and diversity.", "link"=>"http://www.mendeley.com/research/resurrection-dna-function-vivo-extinct-genome", "reader_count"=>94, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Librarian"=>1, "Researcher"=>15, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>3, "Student > Master"=>11, "Other"=>5, "Student > Bachelor"=>21, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>2, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Librarian"=>1, "Researcher"=>15, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>3, "Student > Master"=>11, "Other"=>5, "Student > Bachelor"=>21, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>2, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Agricultural and Biological Sciences"=>68, "Philosophy"=>2, "Veterinary Science and Veterinary Medicine"=>1, "Chemistry"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>2, "Environmental Science"=>5, "Biochemistry, Genetics and Molecular Biology"=>6, "Mathematics"=>1, "Medicine and Dentistry"=>1, "Physics and Astronomy"=>1, "Social Sciences"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>5}, "Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>68}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Philosophy"=>{"Philosophy"=>2}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Greece"=>1, "Canada"=>1, "Austria"=>1, "United States"=>2, "Uruguay"=>2, "Japan"=>1, "Brazil"=>2, "United Kingdom"=>1, "Chile"=>1, "Germany"=>3}, "group_count"=>5}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/931250"], "description"=>"<p>Functional analysis of the thylacine non-coding DNA fragment. (a) Diagram of transgene construct. 4 copies of a 264-bp fragment containing the Thylacine <i>Col2a1</i> enhancer (<i>TcyCol2a1</i>) region was ligated to the human b-globin minimal promoter (black box) and ligated to <i>lacZpA</i>. (b–e) X-gal stained 14.5 dpc <i>TcyCol2a1-lacZpA</i> transgenic mouse embryo showing varying levels of reporter gene expression within the developing cartilage (blue). (f) Non-transgenic littermate, negative control fetus. (g) Top panel; Magnified image of forelimb from fetus in (b) black line indicates the plane of section shown in (g) bottom panel. Bottom panel; Histological section of transgenic forelimb digit, showing <i>lacZ</i>-expressing chondrogenic tissue (blue) counterstained with eosin (pink).</p>", "links"=>[], "tags"=>["extinction"], "article_id"=>601703, "categories"=>["Developmental Biology", "Molecular Biology", "Evolutionary Biology"], "users"=>["Andrew J. Pask", "Richard R. Behringer", "Marilyn B. Renfree"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002240.g003", "stats"=>{"downloads"=>3, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_From_extinction_to_gene_expression_/601703", "title"=>"From extinction to gene expression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 10:26:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/931045"], "description"=>"<p>(a) Young male thylacine in Hobart Zoo in 1928, photograph (Q4437). (b) One of the preserved pouch young specimens (head length 34 mm) from which DNA was extracted, from the Museum Victoria collection. (c-f) The skull of the thylacine (c,e) compared with that of the domestic dog <i>Canis canis</i> (d,f). The morphology of the head shows remarkable convergent evolution. However, there are some differences: in marsupials, the lacrymal extends outside the orbit and the angle of the dentary is medially inflected (c). The thylacine palatine has the vacuities characteristic of marsupial skulls (e). The teeth also show striking convergent evolution but the muzzle of the thylacine is quite narrow compared to that of the dog (e,f). Scale bar = 5cm.</p>", "links"=>[], "tags"=>["Evolutionary biology", "developmental biology/developmental evolution", "developmental biology/developmental molecular mechanisms", "evolutionary biology/developmental evolution", "molecular biology/molecular evolution"], "article_id"=>601485, "categories"=>["Developmental Biology", "Molecular Biology", "Evolutionary Biology"], "users"=>["Andrew J. Pask", "Richard R. Behringer", "Marilyn B. Renfree"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002240.g001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_thylacine_Thylacinus_cynocephalus_/601485", "title"=>"The thylacine, <i>Thylacinus cynocephalus.</i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 10:25:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/931157"], "description"=>"<p>(a) Sequence alignment of the thylacine PCR cloned <i>Col2a1</i> enhancer. Identical alignment between species is shown by black boxes. The thylacine sequence was most similar to, but distinct from that of another marsupial, the tammar wallaby, <i>Macropus eugenii</i>. The black box outlines the minimal 18-bp element. Inverted repeats (arrows) surrounding the minimal element are shown with complementary nucleotides in red. The outer repeat is highly conserved between all mammals, but the inner repeat differs by 2 nucleotides in the thylacine. (b) Phylogenetic analysis of the thylacine <i>Col2a1</i> enhancer. The thylacine sequence groups with the tammar wallaby, both of which are more similar to the human sequence than to mouse or rat. Numbers indicate bootstrap values based on 100 replicates.</p>", "links"=>[], "tags"=>["thylacine", "enhancer"], "article_id"=>601607, "categories"=>["Developmental Biology", "Molecular Biology", "Evolutionary Biology"], "users"=>["Andrew J. Pask", "Richard R. Behringer", "Marilyn B. Renfree"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002240.g002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analyses_of_the_thylacine_Col2a1_enhancer_element_/601607", "title"=>"Analyses of the thylacine <i>Col2a1</i> enhancer element.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 10:26:10"}

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  • {"unique-ip"=>"10", "full-text"=>"6", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"8"}
  • {"unique-ip"=>"12", "full-text"=>"11", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"9"}

Relative Metric

{"start_date"=>"2008-01-01T00:00:00Z", "end_date"=>"2008-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[324, 674, 863, 1015, 1146, 1259, 1360, 1452, 1540, 1621, 1704, 1776, 1843, 1905, 1968, 2029, 2097, 2162, 2233, 2289, 2352, 2412, 2476, 2538, 2601, 2655, 2714, 2777, 2841, 2894, 2946, 2998, 3047, 3103, 3151, 3201, 3258, 3317, 3369, 3424, 3471, 3521, 3583, 3625, 3687, 3743, 3788, 3838, 3896, 3953, 4015, 4075, 4148, 4201, 4275, 4347, 4420, 4486, 4535, 4592, 4660, 4731, 4792, 4845, 4901, 4971, 5027, 5089, 5148, 5200, 5261, 5318, 5374]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[329, 686, 873, 1009, 1130, 1239, 1337, 1426, 1509, 1585, 1667, 1746, 1816, 1880, 1937, 1999, 2058, 2120, 2179, 2245, 2311, 2374, 2437, 2511, 2565, 2616, 2671, 2723, 2783, 2844, 2902, 2958, 3017, 3056, 3104, 3169, 3206, 3249, 3298, 3354, 3428, 3479, 3526, 3579, 3628, 3679, 3727, 3771, 3819, 3865, 3927, 4006, 4075, 4116, 4164, 4250, 4323, 4380, 4436, 4492, 4547, 4599, 4652, 4708, 4761, 4811, 4889, 4966, 5025, 5071, 5134, 5186, 5258]}, {"subject_area"=>"/Earth sciences", "average_usage"=>[355, 650, 946, 1060, 1167, 1272, 1389, 1483, 1569, 1646, 1740, 1800, 1882, 1945, 2025, 2102, 2176, 2233, 2307, 2387, 2492, 2577, 2671, 2718, 2801, 2863, 2925, 2994, 3056, 3123, 3195, 3286, 3332, 3372, 3437, 3494, 3579, 3678, 3749, 3806, 3876, 3982, 4050, 4134, 4208, 4284, 4394, 4443, 4497, 4720, 4806, 4868, 4941, 5006, 5080, 5147, 5212, 5267, 5335, 5399, 5492, 5561, 5618, 5680, 5747, 5820, 5886, 5977, 6036, 6071, 6109, 6144, 6188, 6239]}, {"subject_area"=>"/Earth sciences/Paleontology", "average_usage"=>[381, 910, 1140, 1289, 1410, 1538, 1622, 1702, 1810, 1935, 2039, 2164, 2271, 2359, 2494, 2594, 2680, 2773, 2845, 2949, 3021, 3102, 3178, 3272, 3370, 3454, 3549, 3651, 3766, 3835, 3911, 4002, 4079, 4144, 4224, 4297, 4366, 4407, 4435, 4517, 4595, 4663, 4725, 4837, 4930, 5125, 5251, 5351, 5465, 5563, 5655, 5780, 5943, 5990, 6060, 6112, 6187, 6233, 6279, 6335, 6378, 6427, 6477, 6521, 6549, 6593, 6658, 6722, 6755, 6789, 6824, 6973, 7012, 7161]}]}

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