The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome
Name:
S1_Table.xlsx
Size:
29.17Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S2_Fig.tif
Size:
14.02Mb
Format:
TIFF image
Description:
Supplemental files
Name:
S2_Table.xlsx
Size:
27.92Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S3_Fig.tif
Size:
19.71Mb
Format:
TIFF image
Description:
Supplemental files
Name:
S3_Table.xlsx
Size:
68.35Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S4_Table.xlsx
Size:
46.51Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S5_Fig.jpeg
Size:
3.284Mb
Format:
JPEG image
Description:
Supplemental files
Name:
S5_Table.xlsx
Size:
61.28Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S6_Fig.jpeg
Size:
12.39Mb
Format:
JPEG image
Description:
Supplemental files
Name:
S6_Table.xlsx
Size:
53.11Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S7_Fig.jpeg
Size:
10.73Mb
Format:
JPEG image
Description:
Supplemental files
Name:
S7_Table.xlsx
Size:
63.06Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S8_Table.xlsx
Size:
93.88Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S9_Fig.png
Size:
93.50Kb
Format:
PNG image
Description:
Supplemental files
Name:
S9_Table.xlsx
Size:
148.3Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S10_Table.xlsx
Size:
44.61Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S11_Table.xlsx
Size:
58.87Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S12_Table.xlsx
Size:
50.79Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S13_Table.xlsx
Size:
39.28Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S14_Table.xlsx
Size:
36.21Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S15_Table.xlsx
Size:
37.95Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S16_Table.xlsx
Size:
35.97Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S17_Table.xlsx
Size:
34.49Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S18_Table.xlsx
Size:
35.98Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S19_Table.xlsx
Size:
37.97Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Name:
S20_Table.xlsx
Size:
39.88Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Type
ArticleAuthors
Hurst, Laurence D.Ghanbarian, Avazeh T.
Forrest, Alistair R.R.
Huminiecki, Lukasz
Rehli, Michael
Kenneth Baillie, J.
de Hoon, Michiel J.L.
Haberle, Vanja
Lassmann, Timo
Kulakovskiy, Ivan V.
Lizio, Marina
Itoh, Masayoshi
Andersson, Robin
Mungall, Christopher J.
Meehan, Terrence F.
Schmeier, Sebastian
Bertin, Nicolas
Jørgensen, Mette
Dimont, Emmanuel
Arner, Erik
Schmidl, Christian
Schaefer, Ulf
Medvedeva, Yulia
Plessy, Charles
Vitezic, Morana
Severin, Jessica
Semple, Colin A.
Ishizu, Yuri
Young, Robert S.
Francescatto, Margherita
Alam, Intikhab
Albanese, Davide
Altschuler, Gabriel M.
Arakawa, Takahiro
Archer, John A.C.
Arner, Peter
Babina, Magda
Baker, Sarah
Balwierz, Piotr J.
Beckhouse, Anthony G.
Pradhan, Swati Bhatt
Blake, Judith A.
Blumenthal, Antje
Bodega, Beatrice
Bonetti, Alessandro
Briggs, James
Brombacher, Frank
Maxwell Burroughs, A.
Califano, Andrea
Cannistraci, Carlo
Carbajo, Daniel
Chen, Yun
Chierici, Marco
Ciani, Yari
Clevers, Hans C.
Dalla, Emiliano
Davis, Carrie A.
Detmar, Michael
Diehl, Alexander D.
Dohi, Taeko
Drabløs, Finn
Edge, Albert S.B.
Edinger, Matthias
Ekwall, Karl
Endoh, Mitsuhiro
Enomoto, Hideki
Fagiolini, Michela
Fairbairn, Lynsey
Fang, Hai
Farach-Carson, Mary C.
Faulkner, Geoffrey J.
Favorov, Alexander V.
Fisher, Malcolm E.
Frith, Martin C.
Fujita, Rie
Fukuda, Shiro
Furlanello, Cesare
Furuno, Masaaki
Furusawa, Jun ichi
Geijtenbeek, Teunis B.
Gibson, Andrew
Gingeras, Thomas
Goldowitz, Daniel
Gough, Julian
Guhl, Sven
Guler, Reto
Gustincich, Stefano
Ha, Thomas J.
Hamaguchi, Masahide
Hara, Mitsuko
Harbers, Matthias
Harshbarger, Jayson
Hasegawa, Akira
Hasegawa, Yuki
Hashimoto, Takehiro
Herlyn, Meenhard
Hitchens, Kelly J.
Ho Sui, Shannan J.
Hofmann, Oliver M.
Hoof, Ilka
Hori, Fumi
Huminiecki, Lukasz
Iida, Kei
Ikawa, Tomokatsu
Jankovic, Boris R.
Jia, Hui
Joshi, Anagha
Jurman, Giuseppe
Kaczkowski, Bogumil
Kai, Chieko
Kaida, Kaoru
Kaiho, Ai
Kajiyama, Kazuhiro
Kanamori, Mutsumi Katayama
Kasianov, Artem S.
Kasukawa, Takeya
Katayama, Shintaro
Kato, Sachi
Kawaguchi, Shuji
Kawamoto, Hiroshi
Kawamura, Yuki I.
Kawashima, Tsugumi
Kempfle, Judith S.
Kenna, Tony J.
Kere, Juha
Khachigian, Levon M.
Kitamura, Toshio
Peter Klinken, S.
Knox, Alan J.
Kojima, Miki
Kojima, Soichi
Kondo, Naoto
Koseki, Haruhiko
Koyasu, Shigeo
Krampitz, Sarah
Kubosaki, Atsutaka
Kwon, Andrew T.
Laros, Jeroen F.J.
Lee, Weonju
Lennartsson, Andreas
Li, Kang
Lilje, Berit
Lipovich, Leonard
Mackay, Alan sim
Manabe, Riichiroh
Mar, Jessica C.
Marchand, Benoit
Mathelier, Anthony
Mejhert, Niklas
Meynert, Alison
Mizuno, Yosuke
de Lima Morais, David A.
Morikawa, Hiromasa
Morimoto, Mitsuru
Moro, Kazuyo
Motakis, Efthymios
Motohashi, Hozumi
Mummery, Christine L.
Murata, Mitsuyoshi
Nagao, Sayaka Sato
Nakachi, Yutaka
Nakahara, Fumio
Nakamura, Toshiyuki
Nakamura, Yukio
Nakazato, Kenichi
Van Nimwegen, Erik
Ninomiya, Noriko
Nishiyori, Hiromi
Noma, Shohei
Nozaki, Tadasuke
Ogishima, Soichi
Ohkura, Naganari
Ohmiya, Hiroko
Ohno, Hiroshi
Ohshima, Mitsuhiro
Okada, Mariko Hatakeyama
Okazaki, Yasushi
Orlando, Valerio
Ovchinnikov, Dmitry A.
Pain, Arnab

Passier, Robert
Patrikakis, Margaret
Persson, Helena
Piazza, Silvano
Prendergast, James G.D.
Rackham, Owen J.L.
Ramilowski, Jordan A.
Rashid, Mamoon

Ravasi, Timothy

Rizzu, Patrizia
Roncador, Marco
Roy, Sugata
Rye, Morten B.
Saijyo, Eri
Sajantila, Antti
Saka, Akiko
Sakaguchi, Shimon
Sakai, Mizuho
Sato, Hiroki
Satoh, Hironori
Savvi, Suzana
Saxena, Alka
Schneider, Claudio
Schultes, Erik A.
Schulze-Tanzil, Gundula G.
Schwegmann, Anita
Sengstag, Thierry
Sheng, Guojun
Shimoji, Hisashi
Shimoni, Yishai
Shin, Jay W.
Simon, Christophe
Sugiyama, Daisuke
Sugiyama, Takaaki
Suzuki, Masanori
Suzuki, Naoko
Swoboda, Rolf K.
't Hoen, Peter A.C.
Tagami, Michihira
Takahashi, Naoko
Takai, Jun
Tanaka, Hiroshi
Tatsukawa, Hideki
Tatum, Zuotian
Thompson, Mark
Toyoda, Hiroo
Toyoda, Tetsuro
Valen, Eivind
van de Wetering, Marc
Van Den Berg, Linda M.
Verardo, Roberto
Vijayan, Dipti
Vorontsov, Ilya E.
Wasserman, Wyeth W.
Watanabe, Shoko
Wells, Christine A.
Winteringham, Louise N.
Wolvetang, Ernst
Wood, Emily J.
Yamaguchi, Yoko
Yamamoto, Masayuki
Yoneda, Misako
Yonekura, Yohei
Yoshida, Shigehiro
Zabierowski, Suzan E.
Zhang, Peter G.
Zhao, Xiaobei
Zucchelli, Silvia
Summers, Kim M.
Suzuki, Harukazu
Daub, Carsten O.
Kawai, Jun
Heutink, Peter
Hide, Winston
Freeman, Tom C.
Lenhard, Boris
Bajic, Vladimir B.

Taylor, Martin S.
Makeev, Vsevolod J.
Sandelin, Albin
Hume, David A.
Carninci, Piero
Hayashizaki, Yoshihide
KAUST Department
Academic AffairsApplied Mathematics and Computational Science Program
Biological and Environmental Sciences and Engineering (BESE) Division
Bioscience Program
Computational Bioscience Research Center (CBRC)
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Integrative Systems Biology Lab
Office of the VP
Pathogen Genomics Laboratory
Red Sea Research Center (RSRC)
Research Applications
Research Computing
Date
2015-12-18Permanent link to this record
http://hdl.handle.net/10754/614423
Metadata
Show full item recordAbstract
X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X’s gene content, gene expression, and evolution.Citation
Hurst, L. D., Ghanbarian, A. T., Forrest, A. R. R., & Huminiecki, L. (2015). The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome. PLOS Biology, 13(12), e1002315. doi:10.1371/journal.pbio.1002315Sponsors
FANTOM5 was made possible by a Research Grant for RIKEN Omics Science Center from MEXT to YH and a Grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan to YH. Vetenskapsrådet's project grant 2011-5893 funded LH. European Research Council's grant (ERC-2014-ADG 669207) supports LDH. LDH would also like to acknowledge a Medical Research Council's award MR/L007215/1. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Publisher
Public Library of Science (PLoS)Journal
PLoS BiologyAdditional Links
https://dx.plos.org/10.1371/journal.pbio.1002315ae974a485f413a2113503eed53cd6c53
10.1371/journal.pbio.1002315
Scopus Count
Collections
Articles; Biological and Environmental Science and Engineering (BESE) Division; Red Sea Research Center (RSRC); Bioscience Program; Applied Mathematics and Computational Science Program; Integrative Systems Biology Lab; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division
Except where otherwise noted, this item's license is described as This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. http://creativecommons.org/licenses/by/4.0/
Related items
Showing items related by title, author, creator and subject.
-
A promoter-level mammalian expression atlasForest, Alistair R R; Kawaji, Hideya; Rehli, Michael; Baillie, John Kenneth; De Hoon, Michiel Jl L; Haberle, Vanja; Lassmann, Timo; Kulakovskiy, Ivan V.; Lizio, Marina; Itoh, Masayoshi; Andersson, Robin; Iida, Kei; Ikawa, Tomokatsu; Jankovic, Boris R.; Jia, Hui; Joshi, Anagha Madhusudan; Jurman, Giuseppe; Kaczkowski, Bogumił; Kai, Chieko; Kaida, Kaoru; Kaiho, Ai; Mungall, Christopher J.; Kajiyama, Kazuhiro; Kanamori-Katayama, Mutsumi; Kasianov, Artem S.; Kasukawa, Takeya; Katayama, Shintaro; Kato, Sachi; Kawaguchi, Shuji; Kawamoto, Hiroshi; Kawamura, Yuki I.; Kawashima, Tsugumi; Meehan, Terrence F.; Kempfle, Judith S.; Kenna, Tony J.; Kere, Juha; Khachigian, Levon M.; Kitamura, Toshio; Klinken, Svend Peter; Knox, Alan; Kojima, Miki; Kojima, Soichi; Kondo, Naoto; Schmeier, Sebastian; Koseki, Haruhiko; Koyasu, Shigeo; Krampitz, Sarah; Kubosaki, Atsutaka; Kwon, Andrew T.; Laros, Jeroen F J; Lee, Weonju; Lennartsson, Andreas; Li, Kang; Lilje, Berit; Bertin, Nicolas; Lipovich, Leonard; MacKay-Sim, Alan; Manabe, Riichiroh; Mar, Jessica; Marchand, Benoit; Mathelier, Anthony; Mejhert, Niklas; Meynert, Alison M.; Mizuno, Yosuke; De Morais, David A Lima; Jørgensen, Mette Christine; Morikawa, Hiromasa; Morimoto, Mitsuru; Moro, Kazuyo; Motakis, Efthymios; Motohashi, Hozumi; Mummery, Christine L.; Murata, Mitsuyoshi; Nagao-Sato, Sayaka; Nakachi, Yutaka; Nakahara, Fumio; Dimont, Emmanuel; Nakamura, Toshiyuki; Nakamura, Yukio; Nakazato, Kenichi; Van Nimwegen, Erik; Ninomiya, Noriko; Nishiyori, Hiromi; Noma, Shohei; Nozaki, Tadasuke; Ogishima, Soichi; Ohkura, Naganari; Arner, Erik; Ohmiya, Hiroko; Ohno, Hiroshi; Ohshima, Mitsuhiro; Okada-Hatakeyama, Mariko; Okazaki, Yasushi; Orlando, Valerio; Ovchinnikov, Dmitry A.; Pain, Arnab; Passier, Robert C J J; Patrikakis, Margaret; Schmidl, Christian; Persson, Helena A.; Piazza, Silvano; Prendergast, James G D; Rackham, Owen J L; Ramilowski, Jordan A.; Rashid, Mamoon; Ravasi, Timothy; Rizzu, Patrizia; Roncador, Marco; Roy, Sugata; Schaefer, Ulf; Rye, Morten Beck; Saijyo, Eri; Sajantila, Antti; Saka, Akiko; Sakaguchi, Shimon; Sakai, Mizuho; Sato, Hiroki; Satoh, Hironori; Savvi, Suzana; Saxena, Alka; Medvedeva, Yulia; Schneider, Claudio H.; Schultes, Erik A.; Schulze-Tanzil, Gundula G.; Schwegmann, Anita; Sengstag, Thierry; Sheng, Guojun; Shimoji, Hisashi; Shimoni, Yishai; Shin, Jay W.; Simon, Chris M.; Plessy, Charles; Sugiyama, Daisuke; Sugiyama, Takaaki; Suzuki, Masanori; Suzuki, Naoko; Swoboda, Rolf K.; 't Hoen, Peter Ac Chr; Tagami, Michihira; Tagami, Naokotakahashi; Takai, Jun; Tanaka, Hiroshi; Vitezic, Morana; Tatsukawa, Hideki; Tatum, Zuotian; Thompson, Mark; Toyoda, Hiroo; Toyoda, Tetsuro; Valen, Eivind; Van De Wetering, Marc L.; Van Den Berg, Linda M.; Verardo, Roberto; Vijayan, Dipti; Severin, Jessica M.; Vorontsov, Ilya E.; Wasserman, Wyeth W.; Watanabe, Shoko; Wells, Christine A.; Winteringham, Louise Natalie; Wolvetang, Ernst Jurgen; Wood, Emily J.; Yamaguchi, Yoko; Yamamoto, Masayuki; Yoneda, Misako; Semple, Colin Am M; Yonekura, Yohei; Yoshida, Shigehiro; Zabierowski, Susan E.; Zhang, Peter; Zhao, Xiaobei; Zucchelli, Silvia; Summers, Kim M.; Suzuki, Harukazu; Daub, Carsten Olivier; Kawai, Jun; Ishizu, Yuri; Heutink, Peter; Hide, Winston; Freeman, Tom C.; Lenhard, Boris; Bajic, Vladimir B.; Taylor, Martin S.; Makeev, Vsevolod J.; Sandelin, Albin; Hume, David A.; Carninci, Piero; Young, Robert S.; Hayashizaki, Yoshihide Yoshihide; Francescatto, Margherita; Alam, Intikhab; Albanese, Davide; Altschule, Gabriel M.; Arakawa, Takahiro; Archer, John A.C.; Arner, Peter; Babina, Magda; Rennie, Sarah; Balwierz, Piotr J.; Beckhouse, Anthony G.; Pradhan-Bhatt, Swati; Blake, Judith A.; Blumenthal, Antje; Bodega, Beatrice; Bonetti, Alessandro; Briggs, James A.; Brombacher, Frank; Burroughs, Alexander Maxwell; Califano, Andrea C.; Cannistraci, Carlo; Carbajo, Daniel; Chen, Yun; Chierici, Marco; Ciani, Yari; Clevers, Hans C.; Dalla, Emiliano; Davis, Carrie Anne; Detmar, Michael J.; Diehl, Alexander D.; Dohi, Taeko; Drabløs, Finn; Edge, Albert SB B; Edinger, Matthias G.; Ekwall, Karl; Endoh, Mitsuhiro; Enomoto, Hideki; Fagiolini, Michela; Fairbairn, Lynsey R.; Fang, Hai; Farach-Carson, Mary Cindy; Faulkner, Geoffrey J.; Favorov, Alexander V.; Fisher, Malcolm E.; Frith, Martin C.; Fujita, Rie; Fukuda, Shiro; Furlanello, Cesare; Furuno, Masaaki; Furusawa, Junichi; Geijtenbeek, Teunis Bh H; Gibson, Andrew P.; Gingeras, Thomas R.; Goldowitz, Dan; Gough, Julian; Guhl, Sven; Guler, Reto; Gustincich, Stefano; Ha, Thomas; Hamaguchi, Masahide; Hara, Mitsuko; Harbers, Matthias; Harshbarger, Jayson; Hasegawa, Akira; Hasegawa, Yuki; Hashimoto, Takehiro; Herlyn, Meenhard F.; Hitchens, Kelly J.; Sui, Shannan J Ho; Hofmann, Oliver M.; Hoof, Ilka; Hori, Fumi; Huminiecki, Łukasz B. (Nature, Springer Nature, 2014-03-27) [Article]Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly ‘housekeeping’, whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.
-
FANTOM5 CAGE profiles of human and mouse samplesNoguchi, Shuhei; Arakawa, Takahiro; Fukuda, Shiro; Furuno, Masaaki; Hasegawa, Akira; Hori, Fumi; Ishikawa-Kato, Sachi; Kaida, Kaoru; Kaiho, Ai; Kanamori-Katayama, Mutsumi; Kawashima, Tsugumi; Kojima, Miki; Kubosaki, Atsutaka; Manabe, Ri-ichiroh; Murata, Mitsuyoshi; Nagao-Sato, Sayaka; Nakazato, Kenichi; Ninomiya, Noriko; Nishiyori-Sueki, Hiromi; Noma, Shohei; Saijyo, Eri; Saka, Akiko; Sakai, Mizuho; Simon, Christophe; Suzuki, Naoko; Tagami, Michihira; Watanabe, Shoko; Yoshida, Shigehiro; Arner, Peter; Axton, Richard A.; Babina, Magda; Baillie, J. Kenneth; Barnett, Timothy C.; Beckhouse, Anthony G.; Blumenthal, Antje; Bodega, Beatrice; Bonetti, Alessandro; Briggs, James; Brombacher, Frank; Carlisle, Ailsa J.; Clevers, Hans C.; Davis, Carrie A.; Detmar, Michael; Dohi, Taeko; Edge, Albert S.B.; Edinger, Matthias; Ehrlund, Anna; Ekwall, Karl; Endoh, Mitsuhiro; Enomoto, Hideki; Eslami, Afsaneh; Fagiolini, Michela; Fairbairn, Lynsey; Farach-Carson, Mary C.; Faulkner, Geoffrey J.; Ferrai, Carmelo; Fisher, Malcolm E.; Forrester, Lesley M.; Fujita, Rie; Furusawa, Jun-ichi; Geijtenbeek, Teunis B.; Gingeras, Thomas; Goldowitz, Daniel; Guhl, Sven; Guler, Reto; Gustincich, Stefano; Ha, Thomas J.; Hamaguchi, Masahide; Hara, Mitsuko; Hasegawa, Yuki; Herlyn, Meenhard; Heutink, Peter; Hitchens, Kelly J.; Hume, David A.; Ikawa, Tomokatsu; Ishizu, Yuri; Kai, Chieko; Kawamoto, Hiroshi; Kawamura, Yuki I.; Kempfle, Judith S.; Kenna, Tony J.; Kere, Juha; Khachigian, Levon M.; Kitamura, Toshio; Klein, Sarah; Klinken, S. Peter; Knox, Alan J.; Kojima, Soichi; Koseki, Haruhiko; Koyasu, Shigeo; Lee, Weonju; Lennartsson, Andreas; Mackay-sim, Alan; Mejhert, Niklas; Mizuno, Yosuke; Morikawa, Hiromasa; Morimoto, Mitsuru; Moro, Kazuyo; Morris, Kelly J.; Motohashi, Hozumi; Mummery, Christine L.; Nakachi, Yutaka; Nakahara, Fumio; Nakamura, Toshiyuki; Nakamura, Yukio; Nozaki, Tadasuke; Ogishima, Soichi; Ohkura, Naganari; Ohno, Hiroshi; Ohshima, Mitsuhiro; Okada-Hatakeyama, Mariko; Okazaki, Yasushi; Orlando, Valerio; Ovchinnikov, Dmitry A.; Passier, Robert; Patrikakis, Margaret; Pombo, Ana; Pradhan-Bhatt, Swati; Qin, Xian-Yang; Rehli, Michael; Rizzu, Patrizia; Roy, Sugata; Sajantila, Antti; Sakaguchi, Shimon; Sato, Hiroki; Satoh, Hironori; Savvi, Suzana; Saxena, Alka; Schmidl, Christian; Schneider, Claudio; Schulze-Tanzil, Gundula G.; Schwegmann, Anita; Sheng, Guojun; Shin, Jay W.; Sugiyama, Daisuke; Sugiyama, Takaaki; Summers, Kim M.; Takahashi, Naoko; Takai, Jun; Tanaka, Hiroshi; Tatsukawa, Hideki; Tomoiu, Andru; Toyoda, Hiroo; van de Wetering, Marc; van den Berg, Linda M.; Verardo, Roberto; Vijayan, Dipti; Wells, Christine A.; Winteringham, Louise N.; Wolvetang, Ernst; Yamaguchi, Yoko; Yamamoto, Masayuki; Yanagi-Mizuochi, Chiyo; Yoneda, Misako; Yonekura, Yohei; Zhang, Peter G.; Zucchelli, Silvia; Abugessaisa, Imad; Arner, Erik; Harshbarger, Jayson; Kondo, Atsushi; Lassmann, Timo; Lizio, Marina; Sahin, Serkan; Sengstag, Thierry; Severin, Jessica; Shimoji, Hisashi; Suzuki, Masanori; Suzuki, Harukazu; Kawai, Jun; Kondo, Naoto; Itoh, Masayoshi; Daub, Carsten O.; Kasukawa, Takeya; Kawaji, Hideya; Carninci, Piero; Forrest, Alistair R.R.; Hayashizaki, Yoshihide (figshare, 2017) [Dataset]In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
-
A Multilaboratory Comparison of Calibration Accuracy and the Performance of External References in Analytical UltracentrifugationZhao, Huaying; Ghirlando, Rodolfo; Alfonso, Carlos; Arisaka, Fumio; Attali, Ilan; Bain, David L.; Bakhtina, Marina M.; Becker, Donald F.; Bedwell, Gregory J.; Bekdemir, Ahmet; Besong, Tabot M.D.; Birck, Catherine; Brautigam, Chad A.; Brennerman, William; Byron, Olwyn; Bzowska, Agnieszka; Chaires, Jonathan B.; Chaton, Catherine T.; Cölfen, Helmut; Connaghan, Keith D.; Crowley, Kimberly A.; Curth, Ute; Daviter, Tina; Dean, William L.; Díez, Ana I.; Ebel, Christine; Eckert, Debra M.; Eisele, Leslie E.; Eisenstein, Edward; England, Patrick; Escalante, Carlos; Fagan, Jeffrey A.; Fairman, Robert; Finn, Ron M.; Fischle, Wolfgang; de la Torre, José García; Gor, Jayesh; Gustafsson, Henning; Hall, Damien; Harding, Stephen E.; Cifre, José G. Hernández; Herr, Andrew B.; Howell, Elizabeth E.; Isaac, Richard S.; Jao, Shu-Chuan; Jose, Davis; Kim, Soon-Jong; Kokona, Bashkim; Kornblatt, Jack A.; Kosek, Dalibor; Krayukhina, Elena; Krzizike, Daniel; Kusznir, Eric A.; Kwon, Hyewon; Larson, Adam; Laue, Thomas M.; Le Roy, Aline; Leech, Andrew P.; Lilie, Hauke; Luger, Karolin; Luque-Ortega, Juan R.; Ma, Jia; May, Carrie A.; Maynard, Ernest L.; Modrak-Wojcik, Anna; Mok, Yee-Foong; Mücke, Norbert; Nagel-Steger, Luitgard; Narlikar, Geeta J.; Noda, Masanori; Piszczek, Grzegorz; Nourse, Amanda; Obsil, Tomas; Park, Chad K.; Park, Jin-Ku; Pawelek, Peter D.; Perdue, Erby E.; Perkins, Stephen J.; Perugini, Matthew A.; Peterson, Craig L.; Peverelli, Martin G.; Prag, Gali; Prevelige, Peter E.; Raynal, Bertrand D. E.; Rezabkova, Lenka; Richter, Klaus; Ringel, Alison E.; Rosenberg, Rose; Rowe, Arthur J.; Rufer, Arne C.; Swygert, Sarah G.; Scott, David J.; Seravalli, Javier G.; Solovyova, Alexandra S.; Song, Renjie; Staunton, David; Stoddard, Caitlin; Stott, Katherine; Strauss, Holger M.; Streicher, Werner W.; Sumida, John P.; Szczepanowski, Roman H.; Tessmer, Ingrid; Toth, Ronald T.; Tripathy, Ashutosh; Uchiyama, Susumu; Uebel, Stephan F. W.; Unzai, Satoru; Gruber, Anna Vitlin; von Hippel, Peter H.; ; Wandrey, Christine; Wang, Szu-Huan; Weitzel, Steven E.; Wielgus-Kutrowska, Beata; Wolberger, Cynthia; Wolff, Martin; Wright, Edward; Wu, Yu-Sung; Wubben, Jacinta M.; Schuck, Peter (PLoS ONE, Public Library of Science (PLoS), 2015-05-21) [Article]Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy of the reported scan time after the start of centrifugation, the accuracy of the temperature calibration, and the accuracy of the radial magnification. The range of sedimentation coefficients obtained for BSA monomer in different instruments and using different optical systems was from 3.655 S to 4.949 S, with a mean and standard deviation of (4.304 ± 0.188) S (4.4%). After the combined application of correction factors derived from the external calibration references for elapsed time, scan velocity, temperature, and radial magnification, the range of s-values was reduced 7-fold with a mean of 4.325 S and a 6-fold reduced standard deviation of ± 0.030 S (0.7%). In addition, the large data set provided an opportunity to determine the instrument-to-instrument variation of the absolute radial positions reported in the scan files, the precision of photometric or refractometric signal magnitudes, and the precision of the calculated apparent molar mass of BSA monomer and the fraction of BSA dimers. These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies.