Literature DB >> 27286290

Methods to Discover Alternative Promoter Usage and Transcriptional Regulation of Murine Bcrp1.

Karthika Natarajan1, Yi Xie2, Takeo Nakanishi3, Rebecca S Moreci4, Pancharatnam Jeyasuria5, Arif Hussain6, Douglas D Ross7.   

Abstract

Gene expression in different tissues is often controlled by alternative promoters that result in the synthesis of mRNA with unique - usually untranslated - first exons. Bcrp1 (Abcg2), the murine orthologue of the ABC transporter Breast Cancer Resistance Protein (BCRP, ABCG2), has at least four alternative promoters that are designated by the corresponding four alternative first exons produced: E1U, E1A, E1B, and E1C. Herein, in-silico protocols are presented to predict alternative promoter usage for Bcrp1. Furthermore, reporter assay methods are described to produce reporter constructs for alternative promoters and to determine the functionality of putative promoters upstream of the alternative first exons that are identified.

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Year:  2016        PMID： 27286290      PMCID： PMC6620892          DOI： 10.3791/53827

Source DB:  PubMed          Journal:  J Vis Exp        ISSN： 1940-087X            Impact factor:   1.355


  23 in total

1.  Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Authors:  Y Okazaki; M Furuno; T Kasukawa; J Adachi; H Bono; S Kondo; I Nikaido; N Osato; R Saito; H Suzuki; I Yamanaka; H Kiyosawa; K Yagi; Y Tomaru; Y Hasegawa; A Nogami; C Schönbach; T Gojobori; R Baldarelli; D P Hill; C Bult; D A Hume; J Quackenbush; L M Schriml; A Kanapin; H Matsuda; S Batalov; K W Beisel; J A Blake; D Bradt; V Brusic; C Chothia; L E Corbani; S Cousins; E Dalla; T A Dragani; C F Fletcher; A Forrest; K S Frazer; T Gaasterland; M Gariboldi; C Gissi; A Godzik; J Gough; S Grimmond; S Gustincich; N Hirokawa; I J Jackson; E D Jarvis; A Kanai; H Kawaji; Y Kawasawa; R M Kedzierski; B L King; A Konagaya; I V Kurochkin; Y Lee; B Lenhard; P A Lyons; D R Maglott; L Maltais; L Marchionni; L McKenzie; H Miki; T Nagashima; K Numata; T Okido; W J Pavan; G Pertea; G Pesole; N Petrovsky; R Pillai; J U Pontius; D Qi; S Ramachandran; T Ravasi; J C Reed; D J Reed; J Reid; B Z Ring; M Ringwald; A Sandelin; C Schneider; C A M Semple; M Setou; K Shimada; R Sultana; Y Takenaka; M S Taylor; R D Teasdale; M Tomita; R Verardo; L Wagner; C Wahlestedt; Y Wang; Y Watanabe; C Wells; L G Wilming; A Wynshaw-Boris; M Yanagisawa; I Yang; L Yang; Z Yuan; M Zavolan; Y Zhu; A Zimmer; P Carninci; N Hayatsu; T Hirozane-Kishikawa; H Konno; M Nakamura; N Sakazume; K Sato; T Shiraki; K Waki; J Kawai; K Aizawa; T Arakawa; S Fukuda; A Hara; W Hashizume; K Imotani; Y Ishii; M Itoh; I Kagawa; A Miyazaki; K Sakai; D Sasaki; K Shibata; A Shinagawa; A Yasunishi; M Yoshino; R Waterston; E S Lander; J Rogers; E Birney; Y Hayashizaki
Journal:  Nature       Date:  2002-12-05       Impact factor: 49.962

2.  Assembly, verification, and initial annotation of the NIA mouse 7.4K cDNA clone set.

Authors:  Vincent VanBuren; Yulan Piao; Dawood B Dudekula; Yong Qian; Mark G Carter; Patrick R Martin; Carole A Stagg; Uwem C Bassey; Kazuhiro Aiba; Toshio Hamatani; George J Kargul; Amber G Luo; Janet Kelso; Winston Hide; Minoru S H Ko
Journal:  Genome Res       Date:  2002-12       Impact factor: 9.043

Review 3.  Complex controls: the role of alternative promoters in mammalian genomes.

Authors:  Josette-Renée Landry; Dixie L Mager; Brian T Wilhelm
Journal:  Trends Genet       Date:  2003-11       Impact factor: 11.639

4.  Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes.

Authors:  Kouichi Kimura; Ai Wakamatsu; Yutaka Suzuki; Toshio Ota; Tetsuo Nishikawa; Riu Yamashita; Jun-ichi Yamamoto; Mitsuo Sekine; Katsuki Tsuritani; Hiroyuki Wakaguri; Shizuko Ishii; Tomoyasu Sugiyama; Kaoru Saito; Yuko Isono; Ryotaro Irie; Norihiro Kushida; Takahiro Yoneyama; Rie Otsuka; Katsuhiro Kanda; Takahide Yokoi; Hiroshi Kondo; Masako Wagatsuma; Katsuji Murakawa; Shinichi Ishida; Tadashi Ishibashi; Asako Takahashi-Fujii; Tomoo Tanase; Keiichi Nagai; Hisashi Kikuchi; Kenta Nakai; Takao Isogai; Sumio Sugano
Journal:  Genome Res       Date:  2005-12-12       Impact factor: 9.043

5.  Localization of the ABCG2 mitoxantrone resistance-associated protein in normal tissues.

Authors:  Patricia A Fetsch; Andrea Abati; Thomas Litman; Kuniaki Morisaki; Yasumasa Honjo; Khush Mittal; Susan E Bates
Journal:  Cancer Lett       Date:  2005-06-28       Impact factor: 8.679

6.  Subcellular localization and distribution of the breast cancer resistance protein transporter in normal human tissues.

Authors:  M Maliepaard; G L Scheffer; I F Faneyte; M A van Gastelen; A C Pijnenborg; A H Schinkel; M J van De Vijver; R J Scheper; J H Schellens
Journal:  Cancer Res       Date:  2001-04-15       Impact factor: 12.701

7.  Localisation of breast cancer resistance protein in microvessel endothelium of human brain.

Authors:  Hiran C Cooray; Colin G Blackmore; Lynn Maskell; Margery A Barrand
Journal:  Neuroreport       Date:  2002-11-15       Impact factor: 1.837

8.  Novel 5' untranslated region variants of BCRP mRNA are differentially expressed in drug-selected cancer cells and in normal human tissues: implications for drug resistance, tissue-specific expression, and alternative promoter usage.

Authors:  Takeo Nakanishi; Kimberly J Bailey-Dell; Bret A Hassel; Ken Shiozawa; Daniel M Sullivan; Joel Turner; Douglas D Ross
Journal:  Cancer Res       Date:  2006-05-15       Impact factor: 12.701

9.  Expression and function of ABCB1 and ABCG2 in human placental tissue.

Authors:  Dhanashri Kolwankar; Douglas D Glover; Joseph A Ware; Timothy S Tracy
Journal:  Drug Metab Dispos       Date:  2005-01-07       Impact factor: 3.922

10.  The transcriptional landscape of the mammalian genome.

Authors:  P Carninci; T Kasukawa; S Katayama; J Gough; M C Frith; N Maeda; R Oyama; T Ravasi; B Lenhard; C Wells; R Kodzius; K Shimokawa; V B Bajic; S E Brenner; S Batalov; A R R Forrest; M Zavolan; M J Davis; L G Wilming; V Aidinis; J E Allen; A Ambesi-Impiombato; R Apweiler; R N Aturaliya; T L Bailey; M Bansal; L Baxter; K W Beisel; T Bersano; H Bono; A M Chalk; K P Chiu; V Choudhary; A Christoffels; D R Clutterbuck; M L Crowe; E Dalla; B P Dalrymple; B de Bono; G Della Gatta; D di Bernardo; T Down; P Engstrom; M Fagiolini; G Faulkner; C F Fletcher; T Fukushima; M Furuno; S Futaki; M Gariboldi; P Georgii-Hemming; T R Gingeras; T Gojobori; R E Green; S Gustincich; M Harbers; Y Hayashi; T K Hensch; N Hirokawa; D Hill; L Huminiecki; M Iacono; K Ikeo; A Iwama; T Ishikawa; M Jakt; A Kanapin; M Katoh; Y Kawasawa; J Kelso; H Kitamura; H Kitano; G Kollias; S P T Krishnan; A Kruger; S K Kummerfeld; I V Kurochkin; L F Lareau; D Lazarevic; L Lipovich; J Liu; S Liuni; S McWilliam; M Madan Babu; M Madera; L Marchionni; H Matsuda; S Matsuzawa; H Miki; F Mignone; S Miyake; K Morris; S Mottagui-Tabar; N Mulder; N Nakano; H Nakauchi; P Ng; R Nilsson; S Nishiguchi; S Nishikawa; F Nori; O Ohara; Y Okazaki; V Orlando; K C Pang; W J Pavan; G Pavesi; G Pesole; N Petrovsky; S Piazza; J Reed; J F Reid; B Z Ring; M Ringwald; B Rost; Y Ruan; S L Salzberg; A Sandelin; C Schneider; C Schönbach; K Sekiguchi; C A M Semple; S Seno; L Sessa; Y Sheng; Y Shibata; H Shimada; K Shimada; D Silva; B Sinclair; S Sperling; E Stupka; K Sugiura; R Sultana; Y Takenaka; K Taki; K Tammoja; S L Tan; S Tang; M S Taylor; J Tegner; S A Teichmann; H R Ueda; E van Nimwegen; R Verardo; C L Wei; K Yagi; H Yamanishi; E Zabarovsky; S Zhu; A Zimmer; W Hide; C Bult; S M Grimmond; R D Teasdale; E T Liu; V Brusic; J Quackenbush; C Wahlestedt; J S Mattick; D A Hume; C Kai; D Sasaki; Y Tomaru; S Fukuda; M Kanamori-Katayama; M Suzuki; J Aoki; T Arakawa; J Iida; K Imamura; M Itoh; T Kato; H Kawaji; N Kawagashira; T Kawashima; M Kojima; S Kondo; H Konno; K Nakano; N Ninomiya; T Nishio; M Okada; C Plessy; K Shibata; T Shiraki; S Suzuki; M Tagami; K Waki; A Watahiki; Y Okamura-Oho; H Suzuki; J Kawai; Y Hayashizaki
Journal:  Science       Date:  2005-09-02       Impact factor: 47.728
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  1 in total

1.  Identification of Functional Transcriptional Binding Sites within Chicken Abcg2 Gene Promoter and Screening Its Regulators.

Authors:  Yujuan Zhang; Jinhu Huang; Xiangxiu Li; Ci Fang; Liping Wang
Journal:  Genes (Basel)       Date:  2020-02-10       Impact factor: 4.096
  1 in total

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