Literature DB >> 22037706

Enhanced Y1H assays for Arabidopsis.

Allison Gaudinier1, Lifang Zhang, John S Reece-Hoyes, Mallorie Taylor-Teeples, Li Pu, Zhijie Liu, Ghislain Breton, Jose L Pruneda-Paz, Dahae Kim, Steve A Kay, Albertha J M Walhout, Doreen Ware, Siobhan M Brady.   

Abstract

We present an Arabidopsis thaliana full-length transcription factor resource of 92% of root stele-expressed transcription factors and 74.5% of root-expressed transcription factors. We demonstrate its use with enhanced yeast one-hybrid (eY1H) screening for rapid, systematic mapping of plant transcription factor-promoter interactions. We identified 158 interactions with 13 stele-expressed promoters, many of which occur physically or are regulatory in planta.

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Year:  2011        PMID: 22037706      PMCID: PMC3821074          DOI: 10.1038/nmeth.1750

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  9 in total

1.  Exhaustive benchmarking of the yeast two-hybrid system.

Authors:  Yu-Chi Chen; Seesandra Venkatappa Rajagopala; Thorsten Stellberger; Peter Uetz
Journal:  Nat Methods       Date:  2010-09       Impact factor: 28.547

2.  A high-resolution root spatiotemporal map reveals dominant expression patterns.

Authors:  Siobhan M Brady; David A Orlando; Ji-Young Lee; Jean Y Wang; Jeremy Koch; José R Dinneny; Daniel Mace; Uwe Ohler; Philip N Benfey
Journal:  Science       Date:  2007-11-02       Impact factor: 47.728

3.  Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping.

Authors:  Vanessa Vermeirssen; Bart Deplancke; M Inmaculada Barrasa; John S Reece-Hoyes; H Efsun Arda; Christian A Grove; Natalia J Martinez; Reynaldo Sequerra; Lynn Doucette-Stamm; Michael R Brent; Albertha J M Walhout
Journal:  Nat Methods       Date:  2007-06-24       Impact factor: 28.547

Review 4.  Insights from genomic profiling of transcription factors.

Authors:  Peggy J Farnham
Journal:  Nat Rev Genet       Date:  2009-08-11       Impact factor: 53.242

5.  Orchestration of floral initiation by APETALA1.

Authors:  Kerstin Kaufmann; Frank Wellmer; Jose M Muiño; Thilia Ferrier; Samuel E Wuest; Vijaya Kumar; Antonio Serrano-Mislata; Francisco Madueño; Pawel Krajewski; Elliot M Meyerowitz; Gerco C Angenent; José Luis Riechmann
Journal:  Science       Date:  2010-04-02       Impact factor: 47.728

6.  A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies.

Authors:  Yuling Jiao; S Lori Tausta; Neeru Gandotra; Ning Sun; Tie Liu; Nicole K Clay; Teresa Ceserani; Meiqin Chen; Ligeng Ma; Matthew Holford; Hui-yong Zhang; Hongyu Zhao; Xing-Wang Deng; Timothy Nelson
Journal:  Nat Genet       Date:  2009-01-04       Impact factor: 38.330

Review 7.  Omics meet networks - using systems approaches to infer regulatory networks in plants.

Authors:  Miguel A Moreno-Risueno; Wolfgang Busch; Philip N Benfey
Journal:  Curr Opin Plant Biol       Date:  2009-12-28       Impact factor: 7.834

8.  A stele-enriched gene regulatory network in the Arabidopsis root.

Authors:  Siobhan M Brady; Lifang Zhang; Molly Megraw; Natalia J Martinez; Eric Jiang; Charles S Yi; Weilin Liu; Anna Zeng; Mallorie Taylor-Teeples; Dahae Kim; Sebastian Ahnert; Uwe Ohler; Doreen Ware; Albertha J M Walhout; Philip N Benfey
Journal:  Mol Syst Biol       Date:  2011-01-18       Impact factor: 11.429

9.  An experimentally derived confidence score for binary protein-protein interactions.

Authors:  Pascal Braun; Murat Tasan; Matija Dreze; Miriam Barrios-Rodiles; Irma Lemmens; Haiyuan Yu; Julie M Sahalie; Ryan R Murray; Luba Roncari; Anne-Sophie de Smet; Kavitha Venkatesan; Jean-François Rual; Jean Vandenhaute; Michael E Cusick; Tony Pawson; David E Hill; Jan Tavernier; Jeffrey L Wrana; Frederick P Roth; Marc Vidal
Journal:  Nat Methods       Date:  2008-12-07       Impact factor: 28.547

  9 in total
  45 in total

1.  Exciting times: bountiful data to facilitate studies of cis-regulatory control.

Authors:  Anil Ozdemir; Angelike Stathopoulos
Journal:  Nat Methods       Date:  2011-11-29       Impact factor: 28.547

2.  High-Throughput Yeast One-Hybrid Screens Using a Cell Surface gLUC Reporter.

Authors:  Zheng Li; Katia Bonaldi; S Earl Kang; Jose L Pruneda-Paz
Journal:  Curr Protoc Plant Biol       Date:  2019-02-11

Review 3.  Global approaches for telling time: omics and the Arabidopsis circadian clock.

Authors:  Brenda Y Chow; Steve A Kay
Journal:  Semin Cell Dev Biol       Date:  2013-02-20       Impact factor: 7.727

Review 4.  Molecular and epigenetic regulations and functions of the LAFL transcriptional regulators that control seed development.

Authors:  L Lepiniec; M Devic; T J Roscoe; D Bouyer; D-X Zhou; C Boulard; S Baud; B Dubreucq
Journal:  Plant Reprod       Date:  2018-05-24       Impact factor: 3.767

Review 5.  Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks.

Authors:  George W Bassel; Allison Gaudinier; Siobhan M Brady; Lars Hennig; Seung Y Rhee; Ive De Smet
Journal:  Plant Cell       Date:  2012-10-30       Impact factor: 11.277

6.  Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors.

Authors:  Erin E Sparks; Colleen Drapek; Allison Gaudinier; Song Li; Mitra Ansariola; Ning Shen; Jessica H Hennacy; Jingyuan Zhang; Gina Turco; Jalean J Petricka; Jessica Foret; Alexander J Hartemink; Raluca Gordân; Molly Megraw; Siobhan M Brady; Philip N Benfey
Journal:  Dev Cell       Date:  2016-10-27       Impact factor: 12.270

7.  Zebrafish Transcription Factor ORFeome for Gene Discovery and Regulatory Network Elucidation.

Authors:  Justin King; Justin Foster; James M Davison; John F Rawls; Ghislain Breton
Journal:  Zebrafish       Date:  2017-11-27       Impact factor: 1.985

Review 8.  pENCODE: a plant encyclopedia of DNA elements.

Authors:  Amanda K Lane; Chad E Niederhuth; Lexiang Ji; Robert J Schmitz
Journal:  Annu Rev Genet       Date:  2014-08-15       Impact factor: 16.830

9.  BEL1-LIKE HOMEODOMAIN6 and KNOTTED ARABIDOPSIS THALIANA7 interact and regulate secondary cell wall formation via repression of REVOLUTA.

Authors:  Yuanyuan Liu; Shijun You; Mallorie Taylor-Teeples; Wenhua L Li; Mathias Schuetz; Siobhan M Brady; Carl J Douglas
Journal:  Plant Cell       Date:  2014-12-09       Impact factor: 11.277

10.  The Proteasome Stress Regulon Is Controlled by a Pair of NAC Transcription Factors in Arabidopsis.

Authors:  Nicholas P Gladman; Richard S Marshall; Kwang-Hee Lee; Richard D Vierstra
Journal:  Plant Cell       Date:  2016-05-18       Impact factor: 11.277

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