Literature DB >> 21611959

Genome-scale techniques highlight the epigenome and redefine fundamental principles of gene regulation.

J Wesley Pike1.   

Abstract

The regulation of gene expression represents one of the most fundamental of biologic processes that controls cellular proliferation, differentiation, and function. Recent technological advances in genome-wide annotation together with bioinformatic/computational analyses have contributed significantly to our understanding of transcriptional regulation at the epigenomic and regulomic levels. This perspective outlines the techniques that are being utilized and summarizes a few of the outcomes.
Copyright © 2011 American Society for Bone and Mineral Research.

Mesh:

Year:  2011        PMID: 21611959      PMCID: PMC3312753          DOI: 10.1002/jbmr.317

Source DB:  PubMed          Journal:  J Bone Miner Res        ISSN: 0884-0431            Impact factor:   6.741


  57 in total

1.  Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays.

Authors:  Peter J Sabo; Michael S Kuehn; Robert Thurman; Brett E Johnson; Ericka M Johnson; Hua Cao; Man Yu; Elizabeth Rosenzweig; Jeff Goldy; Andrew Haydock; Molly Weaver; Anthony Shafer; Kristin Lee; Fidencio Neri; Richard Humbert; Michael A Singer; Todd A Richmond; Michael O Dorschner; Michael McArthur; Michael Hawrylycz; Roland D Green; Patrick A Navas; William S Noble; John A Stamatoyannopoulos
Journal:  Nat Methods       Date:  2006-07       Impact factor: 28.547

2.  Genome-wide analysis of estrogen receptor binding sites.

Authors:  Jason S Carroll; Clifford A Meyer; Jun Song; Wei Li; Timothy R Geistlinger; Jérôme Eeckhoute; Alexander S Brodsky; Erika Krasnickas Keeton; Kirsten C Fertuck; Giles F Hall; Qianben Wang; Stefan Bekiranov; Victor Sementchenko; Edward A Fox; Pamela A Silver; Thomas R Gingeras; X Shirley Liu; Myles Brown
Journal:  Nat Genet       Date:  2006-10-01       Impact factor: 38.330

3.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.

Authors:  Nathaniel D Heintzman; Rhona K Stuart; Gary Hon; Yutao Fu; Christina W Ching; R David Hawkins; Leah O Barrera; Sara Van Calcar; Chunxu Qu; Keith A Ching; Wei Wang; Zhiping Weng; Roland D Green; Gregory E Crawford; Bing Ren
Journal:  Nat Genet       Date:  2007-02-04       Impact factor: 38.330

4.  Parathyroid hormone controls receptor activator of NF-kappaB ligand gene expression via a distant transcriptional enhancer.

Authors:  Qiang Fu; Stavros C Manolagas; Charles A O'Brien
Journal:  Mol Cell Biol       Date:  2006-09       Impact factor: 4.272

5.  Activation of receptor activator of NF-kappaB ligand gene expression by 1,25-dihydroxyvitamin D3 is mediated through multiple long-range enhancers.

Authors:  Sungtae Kim; Miwa Yamazaki; Lee A Zella; Nirupama K Shevde; J Wesley Pike
Journal:  Mol Cell Biol       Date:  2006-09       Impact factor: 4.272

6.  Transcriptional control of receptor activator of nuclear factor-kappaB ligand by the protein kinase A activator forskolin and the transmembrane glycoprotein 130-activating cytokine, oncostatin M, is exerted through multiple distal enhancers.

Authors:  Sungtae Kim; Miwa Yamazaki; Nirupama K Shevde; J Wesley Pike
Journal:  Mol Endocrinol       Date:  2006-10-19

7.  1,25-Dihydroxyvitamin D3 regulates the expression of low-density lipoprotein receptor-related protein 5 via deoxyribonucleic acid sequence elements located downstream of the start site of transcription.

Authors:  Jackie A Fretz; Lee A Zella; Sungtae Kim; Nirupama K Shevde; J Wesley Pike
Journal:  Mol Endocrinol       Date:  2006-04-13

8.  Bmp2 transcription in osteoblast progenitors is regulated by a distant 3' enhancer located 156.3 kilobases from the promoter.

Authors:  Ronald L Chandler; Kelly J Chandler; Karen A McFarland; Douglas P Mortlock
Journal:  Mol Cell Biol       Date:  2007-02-05       Impact factor: 4.272

9.  Genome-wide mapping of in vivo protein-DNA interactions.

Authors:  David S Johnson; Ali Mortazavi; Richard M Myers; Barbara Wold
Journal:  Science       Date:  2007-05-31       Impact factor: 47.728

10.  Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription.

Authors:  Xiangting Wang; Shigeki Arai; Xiaoyuan Song; Donna Reichart; Kun Du; Gabriel Pascual; Paul Tempst; Michael G Rosenfeld; Christopher K Glass; Riki Kurokawa
Journal:  Nature       Date:  2008-05-28       Impact factor: 49.962

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  10 in total

Review 1.  Genome-wide principles of gene regulation by the vitamin D receptor and its activating ligand.

Authors:  J Wesley Pike
Journal:  Mol Cell Endocrinol       Date:  2011-06-01       Impact factor: 4.102

2.  The need for mouse models in osteoporosis genetics research.

Authors:  Cheryl L Ackert-Bicknell; Matthew A Hibbs
Journal:  Bonekey Rep       Date:  2012-06-13

3.  Epigenetic Control of Skeletal Development by the Histone Methyltransferase Ezh2.

Authors:  Amel Dudakovic; Emily T Camilleri; Fuhua Xu; Scott M Riester; Meghan E McGee-Lawrence; Elizabeth W Bradley; Christopher R Paradise; Eric A Lewallen; Roman Thaler; David R Deyle; A Noelle Larson; David G Lewallen; Allan B Dietz; Gary S Stein; Martin A Montecino; Jennifer J Westendorf; Andre J van Wijnen
Journal:  J Biol Chem       Date:  2015-09-30       Impact factor: 5.157

4.  PI3Kγ deletion reduces variability in the in vivo osteolytic response induced by orthopaedic wear particles.

Authors:  Edward M Greenfield; Joscelyn M Tatro; Matthew V Smith; Erik A Schnaser; Dianqing Wu
Journal:  J Orthop Res       Date:  2011-04-27       Impact factor: 3.494

Review 5.  Regulation of target gene expression by the vitamin D receptor - an update on mechanisms.

Authors:  J Wesley Pike; Mark B Meyer; Kathleen A Bishop
Journal:  Rev Endocr Metab Disord       Date:  2012-03       Impact factor: 6.514

6.  Regulation of mouse Cyp24a1 expression via promoter-proximal and downstream-distal enhancers highlights new concepts of 1,25-dihydroxyvitamin D(3) action.

Authors:  J Wesley Pike; Mark B Meyer
Journal:  Arch Biochem Biophys       Date:  2011-12-09       Impact factor: 4.013

7.  Enhancer of Zeste Homolog 2 Inhibition Stimulates Bone Formation and Mitigates Bone Loss Caused by Ovariectomy in Skeletally Mature Mice.

Authors:  Amel Dudakovic; Emily T Camilleri; Scott M Riester; Christopher R Paradise; Martina Gluscevic; Thomas M O'Toole; Roman Thaler; Jared M Evans; Huihuang Yan; Malayannan Subramaniam; John R Hawse; Gary S Stein; Martin A Montecino; Meghan E McGee-Lawrence; Jennifer J Westendorf; Andre J van Wijnen
Journal:  J Biol Chem       Date:  2016-10-10       Impact factor: 5.157

Review 8.  Fundamentals of vitamin D hormone-regulated gene expression.

Authors:  J Wesley Pike; Mark B Meyer
Journal:  J Steroid Biochem Mol Biol       Date:  2013-11-12       Impact factor: 4.292

9.  Osteocytes, not Osteoblasts or Lining Cells, are the Main Source of the RANKL Required for Osteoclast Formation in Remodeling Bone.

Authors:  Jinhu Xiong; Marilina Piemontese; Melda Onal; Josh Campbell; Joseph J Goellner; Vladimir Dusevich; Lynda Bonewald; Stavros C Manolagas; Charles A O'Brien
Journal:  PLoS One       Date:  2015-09-22       Impact factor: 3.240

10.  Identification of an enhancer that increases miR-200b~200a~429 gene expression in breast cancer cells.

Authors:  Joanne L Attema; Andrew G Bert; Yat-Yuen Lim; Natasha Kolesnikoff; David M Lawrence; Katherine A Pillman; Eric Smith; Paul A Drew; Yeesim Khew-Goodall; Frances Shannon; Gregory J Goodall
Journal:  PLoS One       Date:  2013-09-25       Impact factor: 3.240

  10 in total

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