دورية أكاديمية
أعرض في EDS

Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells.

التفاصيل البيبلوغرافية
العنوان: Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells.
المؤلفون: Khan AH; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-1735, USA., Lin A; Office of Information Technology, UCLA, Los Angeles, California 90095-1557, USA., Wang RT; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-7088, USA., Bloom JS; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-7088, USA.; Howard Hughes Medical Institute, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-7088, USA., Lange K; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-7088, USA., Smith DJ; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, California 90095-1735, USA.
المصدر: Genome research [Genome Res] 2020 Oct; Vol. 30 (10), pp. 1458-1467. Date of Electronic Publication: 2020 Sep 02.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9518021 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-5469 (Electronic) Linking ISSN: 10889051 NLM ISO Abbreviation: Genome Res Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Cold Spring Harbor, N.Y. : Cold Spring Harbor Laboratory Press, c1995-
مواضيع طبية MeSH: Cell Growth Processes/*genetics , Radiation Hybrid Mapping/*methods, Animals ; Centromere ; Cricetinae ; DNA ; Disease/genetics ; Genetic Loci ; HEK293 Cells ; Humans ; Mitochondria ; Mycoplasma/isolation & purification ; Paclitaxel/pharmacology
مستخلص: Genetic screens in mammalian cells commonly focus on loss-of-function approaches. To evaluate the phenotypic consequences of extra gene copies, we used bulk segregant analysis (BSA) of radiation hybrid (RH) cells. We constructed six pools of RH cells, each consisting of ∼2500 independent clones, and placed the pools under selection in media with or without paclitaxel. Low pass sequencing identified 859 growth loci, 38 paclitaxel loci, 62 interaction loci, and three loci for mitochondrial abundance at genome-wide significance. Resolution was measured as ∼30 kb, close to single-gene. Divergent properties were displayed by the RH-BSA growth genes compared to those from loss-of-function screens, refuting the balance hypothesis. In addition, enhanced retention of human centromeres in the RH pools suggests a new approach to functional dissection of these chromosomal elements. Pooled analysis of RH cells showed high power and resolution and should be a useful addition to the mammalian genetic toolkit.
(© 2020 Khan et al.; Published by Cold Spring Harbor Laboratory Press.)
References: Bioinformatics. 2009 Jul 15;25(14):1754-60. (PMID: 19451168)
Genome Res. 2016 Oct;26(10):1301-1311. (PMID: 27510565)
BMC Genomics. 2015;16 Suppl 8:S2. (PMID: 26110515)
Mol Cell. 2006 Feb 3;21(3):319-30. (PMID: 16455487)
Cell. 2015 Dec 3;163(6):1515-26. (PMID: 26627737)
PLoS One. 2013 Sep 11;8(9):e74623. (PMID: 24040298)
BMC Genomics. 2014 Feb 27;15:165. (PMID: 24571093)
Cell. 2014 Oct 23;159(3):647-61. (PMID: 25307932)
Bioinformatics. 2009 Aug 15;25(16):2078-9. (PMID: 19505943)
BMC Genomics. 2011 Nov 16;12:562. (PMID: 22085887)
Nature. 2010 Apr 15;464(7291):1039-42. (PMID: 20393561)
Genome Med. 2014 Apr 29;6(4):32. (PMID: 24944581)
PLoS Genet. 2008 Jun 13;4(6):e1000097. (PMID: 18551174)
PLoS Genet. 2014 Dec 18;10(12):e1004894. (PMID: 25521586)
Nat Genet. 1994 May;7(1):22-8. (PMID: 8075634)
Nat Genet. 2007 Apr;39(4):534-9. (PMID: 17384640)
Science. 2001 Feb 16;291(5507):1298-302. (PMID: 11181994)
BMC Bioinformatics. 2013 Apr 15;14:128. (PMID: 23586463)
J Cell Sci. 1995 Apr;108 ( Pt 4):1659-67. (PMID: 7542257)
Nucleic Acids Res. 2014 Jan;42(Database issue):D68-73. (PMID: 24275495)
Trends Genet. 2014 Aug;30(8):340-7. (PMID: 24951248)
FEBS J. 2016 Sep;283(17):3232-8. (PMID: 27276584)
Science. 2014 Jan 3;343(6166):84-87. (PMID: 24336571)
Nat Protoc. 2009;4(1):44-57. (PMID: 19131956)
FEBS Open Bio. 2018 Jun 19;8(7):1064-1082. (PMID: 29988566)
Nat Genet. 2001 Oct;29(2):194-200. (PMID: 11586301)
Mol Cell. 2015 May 21;58(4):575-85. (PMID: 26000843)
Genome Res. 2004 Apr;14(4):750-7. (PMID: 15060019)
FASEB J. 1993 Jul;7(10):978-9. (PMID: 8344496)
Proc Natl Acad Sci U S A. 2017 Dec 12;114(50):E10687-E10696. (PMID: 29162697)
Nat Biotechnol. 2014 Mar;32(3):267-73. (PMID: 24535568)
Nat Genet. 2001 Oct;29(2):201-5. (PMID: 11586302)
Cancer Res. 2004 Mar 1;64(5):1744-50. (PMID: 14996735)
PLoS One. 2011;6(5):e20057. (PMID: 21629697)
J Cell Biol. 2017 Oct 2;216(10):3179-3198. (PMID: 28814570)
Nat Biotechnol. 2018 Apr;36(4):321-323. (PMID: 29553574)
Science. 2013 Mar 29;339(6127):1546-58. (PMID: 23539594)
Nat Methods. 2006 Sep;3(9):715-9. (PMID: 16929317)
PLoS One. 2016 Jun 07;11(6):e0157187. (PMID: 27271046)
Science. 2015 Nov 27;350(6264):1096-101. (PMID: 26472758)
PLoS One. 2014 Sep 08;9(9):e105912. (PMID: 25198505)
Bioinformatics. 2010 Aug 15;26(16):2004-11. (PMID: 20554690)
PLoS One. 2015 Jun 26;10(6):e0129593. (PMID: 26115510)
Methods. 2016 Jul 1;103:157-66. (PMID: 27083402)
Pharmacogenomics J. 2016 Apr;16(2):164-72. (PMID: 26149735)
Genome Res. 2012 Sep;22(9):1775-89. (PMID: 22955988)
Mutat Res Rev Mutat Res. 2015 Apr-Jun;764:16-30. (PMID: 26041263)
J Biomed Biotechnol. 2012;2012:267678. (PMID: 23091342)
BMC Biotechnol. 2015 Jun 19;15:58. (PMID: 26088202)
Nature. 2020 Sep;585(7823):79-84. (PMID: 32663838)
ACS Chem Biol. 2018 Feb 16;13(2):406-416. (PMID: 29035510)
Nat Genet. 2008 Apr;40(4):421-9. (PMID: 18362883)
Methods Mol Biol. 2011;781:161-82. (PMID: 21877282)
Cell. 2018 Aug 23;174(5):1039-1041. (PMID: 30142340)
Mol Ther Methods Clin Dev. 2016 Jun 22;3:16043. (PMID: 27382603)
Nat Methods. 2011 Jun 26;8(8):659-61. (PMID: 21706014)
Nat Rev Mol Cell Biol. 2014 Sep;15(9):591-600. (PMID: 25145850)
J Virol. 2019 Jun 14;93(13):. (PMID: 30996094)
Am J Hum Genet. 2018 May 3;102(5):717-730. (PMID: 29727686)
Nat Commun. 2018 Mar 26;9(1):1224. (PMID: 29581457)
Drugs. 2017 Mar;77(4):459-472. (PMID: 28213862)
Mol Cell. 2016 Aug 4;63(3):355-70. (PMID: 27494557)
Proc Natl Acad Sci U S A. 2018 Dec 18;115(51):13075-13080. (PMID: 30509973)
Wiley Interdiscip Rev RNA. 2016 May;7(3):316-29. (PMID: 26840434)
Int J Mol Sci. 2018 Nov 20;19(11):. (PMID: 30463289)
Sci Rep. 2014 Jan 27;4:3887. (PMID: 24463429)
Nature. 1975 Jun 26;255(5511):680-4. (PMID: 1169690)
Am J Hum Genet. 2013 Nov 7;93(5):779-97. (PMID: 24210251)
Nat Commun. 2014 Sep 03;5:4767. (PMID: 25182477)
Traffic. 2018 Jul;19(7):522-535. (PMID: 29655266)
Genome Res. 2002 Jun;12(6):996-1006. (PMID: 12045153)
Curr Protoc Hum Genet. 2001 May;Chapter 3:Unit 3.1. (PMID: 18428274)
Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613. (PMID: 30476243)
PLoS Comput Biol. 2009 Jun;5(6):e1000407. (PMID: 19521529)
Nature. 2003 Jul 10;424(6945):194-7. (PMID: 12853957)
Ann Intern Med. 1975 Oct;83(4):553-60. (PMID: 1101764)
Biotechnol Bioeng. 2018 Aug;115(8):2087-2100. (PMID: 29704459)
Mamm Genome. 2000 Sep;11(9):791-5. (PMID: 10967141)
PLoS Comput Biol. 2013;9(11):e1003314. (PMID: 24244129)
Genetics. 2012 Mar;190(3):841-54. (PMID: 22419077)
Science. 2015 May 8;348(6235):648-60. (PMID: 25954001)
Bioinformatics. 2010 Mar 15;26(6):841-2. (PMID: 20110278)
Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9828-32. (PMID: 1682921)
Elife. 2016 Feb 22;5:. (PMID: 26901439)
Genome Res. 2010 Aug;20(8):1122-32. (PMID: 20508145)
Science. 1990 Oct 12;250(4978):245-50. (PMID: 2218528)
Science. 2017 Jan 6;355(6320):. (PMID: 27980086)
Nucleic Acids Res. 2014 Jan;42(Database issue):D975-9. (PMID: 24297256)
PLoS Genet. 2016 Mar 15;12(3):e1005939. (PMID: 26978189)
معلومات مُعتمدة: R21 HG007405 United States HG NHGRI NIH HHS
المشرفين على المادة: 9007-49-2 (DNA)
P88XT4IS4D (Paclitaxel)
تواريخ الأحداث: Date Created: 20200904 Date Completed: 20211116 Latest Revision: 20240922
رمز التحديث: 20240922
مُعرف محوري في PubMed: PMC7605260
DOI: 10.1101/gr.262204.120
PMID: 32878976
قاعدة البيانات: MEDLINE
الوصف
تدمد:1549-5469
DOI:10.1101/gr.262204.120