Literature DB >> 22930692

Minireview: applications of next-generation sequencing on studies of nuclear receptor regulation and function.

Clifford A Meyer1, Qianzi Tang, X Shirley Liu.   

Abstract

Next-generation sequencing technologies have expanded the experimental possibilities for studying the genome-wide regulation of transcription by nuclear receptors, their collaborating transcription factors, and coregulators. These technologies allow investigators to obtain abundance and DNA sequence information in a single experiment. In this review, we highlight proven and potential uses of next-generation sequencing in the study of gene regulation by nuclear receptors. We also provide suggestions on how to effectively leverage this technology in a collaborative environment.

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Year:  2012        PMID: 22930692      PMCID: PMC3458226          DOI: 10.1210/me.2012-1150

Source DB:  PubMed          Journal:  Mol Endocrinol        ISSN: 0888-8809


  85 in total

1.  Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters.

Authors:  Leighton J Core; Joshua J Waterfall; John T Lis
Journal:  Science       Date:  2008-12-04       Impact factor: 47.728

2.  High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay.

Authors:  Lars Dölken; Zsolt Ruzsics; Bernd Rädle; Caroline C Friedel; Ralf Zimmer; Jörg Mages; Reinhard Hoffmann; Paul Dickinson; Thorsten Forster; Peter Ghazal; Ulrich H Koszinowski
Journal:  RNA       Date:  2008-07-24       Impact factor: 4.942

3.  Unique ERalpha cistromes control cell type-specific gene regulation.

Authors:  Susan A Krum; Gustavo A Miranda-Carboni; Mathieu Lupien; Jerome Eeckhoute; Jason S Carroll; Myles Brown
Journal:  Mol Endocrinol       Date:  2008-09-25

4.  A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations.

Authors:  Vijay K Tiwari; Leslie Cope; Kelly M McGarvey; Joyce E Ohm; Stephen B Baylin
Journal:  Genome Res       Date:  2008-05-23       Impact factor: 9.043

5.  Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Authors:  Ali Mortazavi; Brian A Williams; Kenneth McCue; Lorian Schaeffer; Barbara Wold
Journal:  Nat Methods       Date:  2008-05-30       Impact factor: 28.547

6.  PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale.

Authors:  Martina I Lefterova; Yong Zhang; David J Steger; Michael Schupp; Jonathan Schug; Ana Cristancho; Dan Feng; David Zhuo; Christian J Stoeckert; X Shirley Liu; Mitchell A Lazar
Journal:  Genes Dev       Date:  2008-11-01       Impact factor: 11.361

7.  Genome-scale DNA methylation maps of pluripotent and differentiated cells.

Authors:  Alexander Meissner; Tarjei S Mikkelsen; Hongcang Gu; Marius Wernig; Jacob Hanna; Andrey Sivachenko; Xiaolan Zhang; Bradley E Bernstein; Chad Nusbaum; David B Jaffe; Andreas Gnirke; Rudolf Jaenisch; Eric S Lander
Journal:  Nature       Date:  2008-07-06       Impact factor: 49.962

8.  Stimulation of MAPK-phosphatase 1 gene expression by glucocorticoids occurs through a tethering mechanism involving C/EBP.

Authors:  Krishan Johansson-Haque; Elanchelian Palanichamy; Sam Okret
Journal:  J Mol Endocrinol       Date:  2008-08-05       Impact factor: 5.098

9.  Transcriptome sequencing to detect gene fusions in cancer.

Authors:  Christopher A Maher; Chandan Kumar-Sinha; Xuhong Cao; Shanker Kalyana-Sundaram; Bo Han; Xiaojun Jing; Lee Sam; Terrence Barrette; Nallasivam Palanisamy; Arul M Chinnaiyan
Journal:  Nature       Date:  2009-01-11       Impact factor: 49.962

10.  Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells.

Authors:  Madeleine P Ball; Jin Billy Li; Yuan Gao; Je-Hyuk Lee; Emily M LeProust; In-Hyun Park; Bin Xie; George Q Daley; George M Church
Journal:  Nat Biotechnol       Date:  2009-03-29       Impact factor: 54.908

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  4 in total

Review 1.  What's new in estrogen receptor action in the female reproductive tract.

Authors:  Sylvia C Hewitt; Wipawee Winuthayanon; Kenneth S Korach
Journal:  J Mol Endocrinol       Date:  2016-02       Impact factor: 5.098

Review 2.  The analytical landscape of static and temporal dynamics in transcriptome data.

Authors:  Sunghee Oh; Seongho Song; Nupur Dasgupta; Gregory Grabowski
Journal:  Front Genet       Date:  2014-02-20       Impact factor: 4.599

3.  Binding sites analyser (BiSA): software for genomic binding sites archiving and overlap analysis.

Authors:  Matloob Khushi; Christopher Liddle; Christine L Clarke; J Dinny Graham
Journal:  PLoS One       Date:  2014-02-12       Impact factor: 3.240

4.  Deep sequencing reveals new aspects of progesterone receptor signaling in breast cancer cells.

Authors:  Anastasia Kougioumtzi; Panayiotis Tsaparas; Angeliki Magklara
Journal:  PLoS One       Date:  2014-06-04       Impact factor: 3.240

  4 in total

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