Mice and Men: Their Promoter Properties
Publication Date
April 28, 2006
Journal
PLOS Genetics
Authors
Vladimir B Bajic, Sin Lam Tan, Alan Christoffels, Christian Schönbach, et al
Volume
2
Issue
4
Pages
e54
DOI
https://dx.plos.org/10.1371/journal.pgen.0020054
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.0020054
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/16683032
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449896
Europe PMC
http://europepmc.org/abstract/MED/16683032
Web of Science
000239494500024
Scopus
33646472425
Mendeley
http://www.mendeley.com/research/mice-men-promoter-properties
Events
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Mendeley | Further Information

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We classified TSSs into four types based on compositional properties of regions immediately surrounding them. These properties highlighted distinctive features in the extended core promoters that helped us delineate boundaries of the transcription initiation domain space for both species. The TSS types were analyzed for associations with initiating dinucleotides, CpG islands, TATA boxes, and an extensive collection of statistically significant cis-elements in mouse and human. We found that different TSS types show preferences for different sets of initiating dinucleotides and cis-elements. Through Gene Ontology and eVOC categories and tissue expression libraries we linked TSS characteristics to expression. Moreover, we show a link of TSS characteristics to very specific genomic organization in an example of immune-response-related genes (GO:0006955). Our results shed light on the global properties of the two transcriptomes not revealed before and therefore provide the framework for better understanding of the transcriptional mechanisms in the two species, as well as a framework for development of new and more efficient promoter- and gene-finding tools.", "link"=>"http://www.mendeley.com/research/mice-men-promoter-properties", "reader_count"=>91, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>6, "Student > Doctoral Student"=>2, "Researcher"=>39, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>4, "Student > Master"=>7, "Other"=>4, "Student > Bachelor"=>4, "Lecturer"=>2, "Professor"=>7}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>6, "Student > Doctoral Student"=>2, "Researcher"=>39, "Student > Ph. D. 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CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/959263"], "description"=>"<p>The upstream region considered covers [−100, −1], while the downstream\n\t\t\t\t\t\t\tregion covers [+1, +100] relative to the TSS. In all TSS types, the\n\t\t\t\t\t\t\tupstream region contains significantly more enriched PEs than the\n\t\t\t\t\t\t\tdownstream region.</p>", "links"=>[], "tags"=>["groups", "pes", "enriched", "upstream", "downstream"], "article_id"=>629282, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Vladimir B Bajic", "Sin Lam Tan", "Alan Christoffels", "Christian Schönbach", "Leonard Lipovich", "Liang Yang", "Oliver Hofmann", "Adele Kruger", "Winston Hide", "Chikatoshi Kai", "Jun Kawai", "David A Hume", "Piero Carninci", "Yoshihide Hayashizaki"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020054.g004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_Selected_Groups_of_PEs_That_Are_Highly_Enriched_at_Least_3_Fold_Upstream_or_Downstream_of_the_TSS_/629282", "title"=>"Distribution of Selected Groups of PEs That Are Highly Enriched (at\n\t\t\t\t\t\t\tLeast 3-Fold) Upstream or Downstream of the TSS", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:41:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/959166"], "description"=>"<div><p>The density of PEs is calculated from the region covering [−100, +100]\n\t\t\t\t\t\t\trelative to the TSS. Density is determined for bins of length 50 bp and\n\t\t\t\t\t\t\tshifted by 10 bp. In total, there are 17 bins. The vertical axis shows\n\t\t\t\t\t\t\tthe percentage of TSSs of the considered type that contain the PE.</p>\n\t\t\t\t\t\t<p>(A) Distribution of selected PEs that prefer GC-rich (left) and AT-rich\n\t\t\t\t\t\t\t(right) domains in type B (above) and type C (below) TSS groups. Bin\n\t\t\t\t\t\t\tnumber 9 is centered around the TSS. It can be seen that groups of PEs\n\t\t\t\t\t\t\tchange significantly in their concentrations in transition from upstream\n\t\t\t\t\t\t\tto downstream regions and characterize two distinct TSS types (B and\n\t\t\t\t\t\t\tC).</p>\n\t\t\t\t\t\t<p>(B) Distribution of selected PEs across all four TSS types. Blue, green,\n\t\t\t\t\t\t\tred, and light blue correspond to distributions characterized by type A,\n\t\t\t\t\t\t\tB, C, and D TSSs. The first five PEs are those that prefer GC-rich\n\t\t\t\t\t\t\tregions, and the last seven PEs prefer AT-rich regions (the plus or\n\t\t\t\t\t\t\tminus sign in front of the TFBS symbol denotes the strand where the TFBS\n\t\t\t\t\t\t\tis found).</p></div>", "links"=>[], "tags"=>["densities", "pes", "promoters", "types"], "article_id"=>629188, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Vladimir B Bajic", "Sin Lam Tan", "Alan Christoffels", "Christian Schönbach", "Leonard Lipovich", "Liang Yang", "Oliver Hofmann", "Adele Kruger", "Winston Hide", "Chikatoshi Kai", "Jun Kawai", "David A Hume", "Piero Carninci", "Yoshihide Hayashizaki"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020054.g003", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_Densities_of_Selected_PEs_in_Promoters_of_the_Four_TSS_Types_in_Mouse_/629188", "title"=>"Distribution of Densities of Selected PEs in Promoters of the Four\n\t\t\t\t\t\t\tTSS Types in Mouse", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:40:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/471574", "https://ndownloader.figshare.com/files/471593", "https://ndownloader.figshare.com/files/471605", "https://ndownloader.figshare.com/files/471615", "https://ndownloader.figshare.com/files/471628", "https://ndownloader.figshare.com/files/471644", "https://ndownloader.figshare.com/files/471654", "https://ndownloader.figshare.com/files/471669"], "description"=>"<div><p>Using the two largest collections of Mus musculus and Homo sapiens transcription start sites (TSSs) determined based on CAGE tags, ditags, full-length cDNAs, and other transcript data, we describe the compositional landscape surrounding TSSs with the aim of gaining better insight into the properties of mammalian promoters. We classified TSSs into four types based on compositional properties of regions immediately surrounding them. These properties highlighted distinctive features in the extended core promoters that helped us delineate boundaries of the transcription initiation domain space for both species. The TSS types were analyzed for associations with initiating dinucleotides, CpG islands, TATA boxes, and an extensive collection of statistically significant <em>cis</em>-elements in mouse and human. We found that different TSS types show preferences for different sets of initiating dinucleotides and <em>cis</em>-elements. Through Gene Ontology and eVOC categories and tissue expression libraries we linked TSS characteristics to expression. Moreover, we show a link of TSS characteristics to very specific genomic organization in an example of immune-response-related genes (GO:0006955). Our results shed light on the global properties of the two transcriptomes not revealed before and therefore provide the framework for better understanding of the transcriptional mechanisms in the two species, as well as a framework for development of new and more efficient promoter- and gene-finding tools.</p> </div>", "links"=>[], "tags"=>["mice", "promoter", "properties"], "article_id"=>152981, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Vladimir B Bajic", "Sin Lam Tan", "Alan Christoffels", "Christian Schönbach", "Leonard Lipovich", "Liang Yang", "Oliver Hofmann", "Adele Kruger", "Winston Hide", "Chikatoshi Kai", "Jun Kawai", "David A Hume", "Piero Carninci", "Yoshihide Hayashizaki"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.0020054.sd001", "https://dx.doi.org/10.1371/journal.pgen.0020054.sg001", "https://dx.doi.org/10.1371/journal.pgen.0020054.sg002", "https://dx.doi.org/10.1371/journal.pgen.0020054.st001", "https://dx.doi.org/10.1371/journal.pgen.0020054.st002", "https://dx.doi.org/10.1371/journal.pgen.0020054.st003", "https://dx.doi.org/10.1371/journal.pgen.0020054.st004", "https://dx.doi.org/10.1371/journal.pgen.0020054.st005"], "stats"=>{"downloads"=>87, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Mice_and_Men_Their_Promoter_Properties/152981", "title"=>"Mice and Men: Their Promoter Properties", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2006-04-28 00:49:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/959046"], "description"=>"<p>The nucleotides adenine, cytosine, guanine, and thymine are represented\n\t\t\t\t\t\t\tby blue, green, red, and light blue, respectively. The TSS types that\n\t\t\t\t\t\t\tare GC-poor upstream (C and D) show very characteristic enrichment in\n\t\t\t\t\t\t\tadenine and thymine nucleotides around [−35, −20], suggesting a\n\t\t\t\t\t\t\tpotential dominant influence of TATA box and similar AT-rich elements in\n\t\t\t\t\t\t\ttranscription initiation in these types. In type B and A TSSs, this\n\t\t\t\t\t\t\tinfluence does not seem to be dominant, but the presence of such\n\t\t\t\t\t\t\telements is suggested by a significant reduction of the GC content in\n\t\t\t\t\t\t\tthe [−35, −20] region. In principle, one could attempt to link the types\n\t\t\t\t\t\t\tof AT-rich upstream elements with initiating dinucleotides\n\t\t\t\t\t\t\tcharacteristic of different TSS types.</p>", "links"=>[], "tags"=>["mononucleotides", "promoters"], "article_id"=>629078, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Vladimir B Bajic", "Sin Lam Tan", "Alan Christoffels", "Christian Schönbach", "Leonard Lipovich", "Liang Yang", "Oliver Hofmann", "Adele Kruger", "Winston Hide", "Chikatoshi Kai", "Jun Kawai", "David A Hume", "Piero Carninci", "Yoshihide Hayashizaki"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020054.g002", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_Mononucleotides_in_Mouse_Promoters_in_the_Region_Surrounding_the_TSS_/629078", "title"=>"Distribution of Mononucleotides in Mouse Promoters in the Region\n\t\t\t\t\t\t\tSurrounding the TSS", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:40:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/959533"], "description"=>"<p>There are 1.58-, 4.85-, and 3.35-fold more transcripts having TSS types\n\t\t\t\t\t\t\tB, C, and D than one would expect based on the proportion of transcripts\n\t\t\t\t\t\t\tin these groups in our reference mouse data. Enrichment is statistically\n\t\t\t\t\t\t\tsignificant for types C and D based on Bonferroni corrected\n\t\t\t\t\t\t\t\t<i>p</i>-values obtained by the right-sided Fisher's exact\n\t\t\t\t\t\t\ttest (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020054#pgen-0020054-t005\" target=\"_blank\">Table\n\t\t\t\t\t\t\t5</a>).</p>", "links"=>[], "tags"=>["tsss", "transcripts"], "article_id"=>629548, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Vladimir B Bajic", "Sin Lam Tan", "Alan Christoffels", "Christian Schönbach", "Leonard Lipovich", "Liang Yang", "Oliver Hofmann", "Adele Kruger", "Winston Hide", "Chikatoshi Kai", "Jun Kawai", "David A Hume", "Piero Carninci", "Yoshihide Hayashizaki"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020054.g006", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_TSSs_for_Transcripts_Related_to_Immune_Response_through_GO_0006955_/629548", "title"=>"Distribution of TSSs for Transcripts Related to Immune Response\n\t\t\t\t\t\t\tthrough GO:0006955", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:43:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/959408"], "description"=>"<div><p>(A) Sequence logos for Inr in human (left) and mouse (right) obtained\n\t\t\t\t\t\t\tusing [−5, +5] segments relative to TSS locations. There is an evident\n\t\t\t\t\t\t\tbias in the nucleotide composition surrounding the TSS that effectively\n\t\t\t\t\t\t\tdetermines different Inr elements.</p>\n\t\t\t\t\t\t<p>(B) Sequence logos for segments [−35, +20] relative to TSS locations.\n\t\t\t\t\t\t\tStrong similarity exists between human (left) and mouse (right) in TSS\n\t\t\t\t\t\t\ttype A, while that similarity is considerably reduced for the other TSS\n\t\t\t\t\t\t\ttypes.</p></div>", "links"=>[], "tags"=>["Computational biology", "biotechnology", "Evolutionary biology", "genetics and genomics", "genetics and genomics/gene expression"], "article_id"=>629421, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Vladimir B Bajic", "Sin Lam Tan", "Alan Christoffels", "Christian Schönbach", "Leonard Lipovich", "Liang Yang", "Oliver Hofmann", "Adele Kruger", "Winston Hide", "Chikatoshi Kai", "Jun Kawai", "David A Hume", "Piero Carninci", "Yoshihide Hayashizaki"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020054.g005", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_Logos_/629421", "title"=>"Sequence Logos", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:42:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/958986"], "description"=>"<p>Distribution of mouse (red) TSSs overlapped by human (blue) TSSs based on\n\t\t\t\t\t\t\t(A) C + G content, (B) A + G content, and (C) T + G content. Nucleotide\n\t\t\t\t\t\t\tcontent is determined for upstream [−100, −1] and downstream [+1, +100]\n\t\t\t\t\t\t\tregions relative to the TSS. The distribution of TSS locations is more\n\t\t\t\t\t\t\tor less random when viewed in terms of A + G content (B) or T + G\n\t\t\t\t\t\t\tcontent (C). Strong polarization of distributions is evident only in the\n\t\t\t\t\t\t\tG + C case (A).</p>", "links"=>[], "tags"=>["initiation", "domains"], "article_id"=>629013, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Vladimir B Bajic", "Sin Lam Tan", "Alan Christoffels", "Christian Schönbach", "Leonard Lipovich", "Liang Yang", "Oliver Hofmann", "Adele Kruger", "Winston Hide", "Chikatoshi Kai", "Jun Kawai", "David A Hume", "Piero Carninci", "Yoshihide Hayashizaki"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020054.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Transcription_Initiation_Domains_for_Mouse_and_Human_/629013", "title"=>"Transcription Initiation Domains for Mouse and Human", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:39:33"}

PMC Usage Stats | Further Information

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