Jason D Lieb

Jason D Lieb

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Jason D Lieb

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Phosphorylated Lamin A/C in the Nuclear Interior Binds Active Enhancers Associated with Abnormal Transcription in Progeria.

Dev Cell 2020 Mar;52(6):699-713.e11

Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA; Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA; Department of Pathology, The University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1016/j.devcel.2020.02.011DOI Listing
March 2020

Tissue- and strain-specific effects of a genotoxic carcinogen 1,3-butadiene on chromatin and transcription.

Mamm Genome 2018 02 10;29(1-2):153-167. Epub 2018 Feb 10.

Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.

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http://dx.doi.org/10.1007/s00335-018-9739-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6095468PMC
February 2018

Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans.

Genome Res 2017 01 14;27(1):75-86. Epub 2016 Nov 14.

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA.

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http://dx.doi.org/10.1101/gr.208173.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5204346PMC
January 2017

Cisplatin DNA damage and repair maps of the human genome at single-nucleotide resolution.

Proc Natl Acad Sci U S A 2016 10 29;113(41):11507-11512. Epub 2016 Sep 29.

Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7260;

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http://dx.doi.org/10.1073/pnas.1614430113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5068337PMC
October 2016

Chromatin profiling of Drosophila CNS subpopulations identifies active transcriptional enhancers.

Development 2016 10;143(20):3723-3732

Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA

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http://dx.doi.org/10.1242/dev.136895DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5087646PMC
October 2016

Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis.

Proc Natl Acad Sci U S A 2016 Apr 28;113(15):E2124-33. Epub 2016 Mar 28.

Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599;

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http://dx.doi.org/10.1073/pnas.1603388113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4839430PMC
April 2016

The function and regulation of the GATA factor ELT-2 in the C. elegans endoderm.

Development 2016 Feb 23;143(3):483-91. Epub 2015 Dec 23.

Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1

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http://dx.doi.org/10.1242/dev.130914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4760314PMC
February 2016

Single-cell ATAC-seq: strength in numbers.

Genome Biol 2015 Aug 21;16:172. Epub 2015 Aug 21.

Department of Human Genetics, The University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA.

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http://dx.doi.org/10.1186/s13059-015-0737-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4546161PMC
August 2015

Histone modifications predispose genome regions to breakage and translocation.

Genes Dev 2015 Jul 23;29(13):1393-402. Epub 2015 Jun 23.

National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;

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http://dx.doi.org/10.1101/gad.262170.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4511214PMC
July 2015

Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution.

Genes Dev 2015 May;29(9):948-60

Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA;

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http://dx.doi.org/10.1101/gad.261271.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4421983PMC
May 2015

Asymmetric transcript discovery by RNA-seq in C. elegans blastomeres identifies neg-1, a gene important for anterior morphogenesis.

PLoS Genet 2015 Apr 13;11(4):e1005117. Epub 2015 Apr 13.

Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America; Department of Biology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America; Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4395330PMC
April 2015

STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer.

Epigenetics Chromatin 2015 14;8. Epub 2015 Feb 14.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA.

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http://dx.doi.org/10.1186/1756-8935-8-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362815PMC
March 2015

Interrogating the function of metazoan histones using engineered gene clusters.

Dev Cell 2015 Feb;32(3):373-86

Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2014.12.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4385256PMC
February 2015

What are super-enhancers?

Nat Genet 2015 Jan;47(1):8-12

Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.

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http://dx.doi.org/10.1038/ng.3167DOI Listing
January 2015

A split personality for nucleosomes.

Cell 2014 Dec;159(6):1249-51

Department of Human Genetics, The University of Chicago, 920 East 58(th) Street, Chicago, IL, 60637, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.11.030DOI Listing
December 2014

Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.

PLoS Genet 2014 Nov 20;10(11):e1004798. Epub 2014 Nov 20.

The European Molecular Biology Laboratory, The European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1004798DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4238955PMC
November 2014

Comparative analysis of metazoan chromatin organization.

Nature 2014 Aug;512(7515):449-52

1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Informatics Program, Children's Hospital, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1038/nature13415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227084PMC
August 2014

Regulation of the X chromosomes in Caenorhabditis elegans.

Cold Spring Harb Perspect Biol 2014 Mar 1;6(3). Epub 2014 Mar 1.

Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California 95064.

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http://dx.doi.org/10.1101/cshperspect.a018366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3942922PMC
March 2014

Genome-wide measurement of protein-DNA binding dynamics using competition ChIP.

Nat Protoc 2013 13;8(7):1337-53. Epub 2013 Jun 13.

Department of Biology, Carolina Center for the Genome Sciences, Curriculum in Genetics and Molecular Biology and Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA.

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http://www.nature.com/articles/nprot.2013.077
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http://dx.doi.org/10.1038/nprot.2013.077DOI Listing
January 2014

The open chromatin landscape of Kaposi's sarcoma-associated herpesvirus.

J Virol 2013 Nov 28;87(21):11831-42. Epub 2013 Aug 28.

Lineberger Comprehensive Cancer Center.

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http://dx.doi.org/10.1128/JVI.01685-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3807352PMC
November 2013

A common set of DNA regulatory elements shapes Drosophila appendages.

Dev Cell 2013 Nov;27(3):306-18

Department of Biology, Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2013.10.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866527PMC
November 2013

TRA-1 ChIP-seq reveals regulators of sexual differentiation and multilevel feedback in nematode sex determination.

Proc Natl Acad Sci U S A 2013 Oct 17;110(40):16033-8. Epub 2013 Sep 17.

Department of Genetics, Cell Biology, and Development and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455.

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http://dx.doi.org/10.1073/pnas.1312087110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791753PMC
October 2013

Integral nuclear pore proteins bind to Pol III-transcribed genes and are required for Pol III transcript processing in C. elegans.

Mol Cell 2013 Sep 5;51(6):840-9. Epub 2013 Sep 5.

Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1016/j.molcel.2013.08.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3788088PMC
September 2013

A detailed protocol for formaldehyde-assisted isolation of regulatory elements (FAIRE).

Curr Protoc Mol Biol 2013 ;Chapter 21:Unit21.26

Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

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http://dx.doi.org/10.1002/0471142727.mb2126s102DOI Listing
June 2013

A guanosine-centric mechanism for RNA chaperone function.

Science 2013 Apr 7;340(6129):190-5. Epub 2013 Mar 7.

Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA.

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http://dx.doi.org/10.1126/science.1230715DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338410PMC
April 2013

In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae.

PLoS Genet 2012 21;8(6):e1002771. Epub 2012 Jun 21.

Department of Biology, Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1002771DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3380831PMC
September 2012

An inverse relationship to germline transcription defines centromeric chromatin in C. elegans.

Nature 2012 Apr 8;484(7395):534-7. Epub 2012 Apr 8.

Ludwig Institute for Cancer Research and Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1038/nature10973DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3538161PMC
April 2012

Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function.

Nature 2012 Apr 11;484(7393):251-5. Epub 2012 Apr 11.

Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA.

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http://www.nature.com/doifinder/10.1038/nature10985
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http://dx.doi.org/10.1038/nature10985DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3341663PMC
April 2012

Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription.

Genome Res 2012 Feb 15;22(2):259-70. Epub 2011 Nov 15.

Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.

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http://dx.doi.org/10.1101/gr.125666.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266033PMC
February 2012

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells.

Genome Res 2012 Jan 16;22(1):9-24. Epub 2011 Nov 16.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712, USA.

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http://dx.doi.org/10.1101/gr.127597.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246210PMC
January 2012

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA.

Nat Protoc 2012 Jan 19;7(2):256-67. Epub 2012 Jan 19.

Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

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http://dx.doi.org/10.1038/nprot.2011.444DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784247PMC
January 2012

A conserved PHD finger protein and endogenous RNAi modulate insulin signaling in Caenorhabditis elegans.

PLoS Genet 2011 Sep 29;7(9):e1002299. Epub 2011 Sep 29.

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1002299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183084PMC
September 2011

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions.

Genome Biol 2011 Jul 25;12(7):R67. Epub 2011 Jul 25.

Department of Biostatistics, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1186/gb-2011-12-7-r67DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218829PMC
July 2011

Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology.

Genome Biol 2010 30;11(11):140. Epub 2010 Nov 30.

Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel.

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http://dx.doi.org/10.1186/gb-2010-11-11-140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156944PMC
June 2011

Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2.

Genome Biol 2010 23;11(12):R120. Epub 2010 Dec 23.

Department of Biology, Carolina Center for Genome Sciences and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, 407 Fordham Hall, Chapel Hill, North Carolina 27599, USA.

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http://dx.doi.org/10.1186/gb-2010-11-12-r120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3046480PMC
June 2011

The stress response factors Yap6, Cin5, Phd1, and Skn7 direct targeting of the conserved co-repressor Tup1-Ssn6 in S. cerevisiae.

PLoS One 2011 Apr 28;6(4):e19060. Epub 2011 Apr 28.

Department of Biology, Carolina Center for Genome Sciences and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019060PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3084262PMC
April 2011

High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans.

Genome Res 2011 Feb 22;21(2):237-44. Epub 2010 Dec 22.

Department of Biology, Carolina Center for the Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599-3280, USA.

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http://dx.doi.org/10.1101/gr.115931.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3032927PMC
February 2011

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Authors:
Mark B Gerstein Zhi John Lu Eric L Van Nostrand Chao Cheng Bradley I Arshinoff Tao Liu Kevin Y Yip Rebecca Robilotto Andreas Rechtsteiner Kohta Ikegami Pedro Alves Aurelien Chateigner Marc Perry Mitzi Morris Raymond K Auerbach Xin Feng Jing Leng Anne Vielle Wei Niu Kahn Rhrissorrakrai Ashish Agarwal Roger P Alexander Galt Barber Cathleen M Brdlik Jennifer Brennan Jeremy Jean Brouillet Adrian Carr Ming-Sin Cheung Hiram Clawson Sergio Contrino Luke O Dannenberg Abby F Dernburg Arshad Desai Lindsay Dick Andréa C Dosé Jiang Du Thea Egelhofer Sevinc Ercan Ghia Euskirchen Brent Ewing Elise A Feingold Reto Gassmann Peter J Good Phil Green Francois Gullier Michelle Gutwein Mark S Guyer Lukas Habegger Ting Han Jorja G Henikoff Stefan R Henz Angie Hinrichs Heather Holster Tony Hyman A Leo Iniguez Judith Janette Morten Jensen Masaomi Kato W James Kent Ellen Kephart Vishal Khivansara Ekta Khurana John K Kim Paulina Kolasinska-Zwierz Eric C Lai Isabel Latorre Amber Leahey Suzanna Lewis Paul Lloyd Lucas Lochovsky Rebecca F Lowdon Yaniv Lubling Rachel Lyne Michael MacCoss Sebastian D Mackowiak Marco Mangone Sheldon McKay Desirea Mecenas Gennifer Merrihew David M Miller Andrew Muroyama John I Murray Siew-Loon Ooi Hoang Pham Taryn Phippen Elicia A Preston Nikolaus Rajewsky Gunnar Rätsch Heidi Rosenbaum Joel Rozowsky Kim Rutherford Peter Ruzanov Mihail Sarov Rajkumar Sasidharan Andrea Sboner Paul Scheid Eran Segal Hyunjin Shin Chong Shou Frank J Slack Cindie Slightam Richard Smith William C Spencer E O Stinson Scott Taing Teruaki Takasaki Dionne Vafeados Ksenia Voronina Guilin Wang Nicole L Washington Christina M Whittle Beijing Wu Koon-Kiu Yan Georg Zeller Zheng Zha Mei Zhong Xingliang Zhou Julie Ahringer Susan Strome Kristin C Gunsalus Gos Micklem X Shirley Liu Valerie Reinke Stuart K Kim LaDeana W Hillier Steven Henikoff Fabio Piano Michael Snyder Lincoln Stein Jason D Lieb Robert H Waterston

Science 2010 Dec 22;330(6012):1775-87. Epub 2010 Dec 22.

Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1126/science.1196914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142569PMC
December 2010

Allele-specific and heritable chromatin signatures in humans.

Hum Mol Genet 2010 Oct 16;19(R2):R204-9. Epub 2010 Sep 16.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1093/hmg/ddq404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953746PMC
October 2010

The histone H3K36 methyltransferase MES-4 acts epigenetically to transmit the memory of germline gene expression to progeny.

PLoS Genet 2010 Sep 2;6(9):e1001091. Epub 2010 Sep 2.

Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1001091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2932692PMC
September 2010

Nucleosome dynamics define transcriptional enhancers.

Nat Genet 2010 Apr 7;42(4):343-7. Epub 2010 Mar 7.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/ng.545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2932437PMC
April 2010

Heritable individual-specific and allele-specific chromatin signatures in humans.

Science 2010 Apr 18;328(5975):235-9. Epub 2010 Mar 18.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712, USA.

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http://dx.doi.org/10.1126/science.1184655DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929018PMC
April 2010

Nucleoporins and transcription: new connections, new questions.

PLoS Genet 2010 Feb 26;6(2):e1000861. Epub 2010 Feb 26.

Department of Biology, Carolina Center for Genome Sciences and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000861DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829065PMC
February 2010

A positive but complex association between meiotic double-strand break hotspots and open chromatin in Saccharomyces cerevisiae.

Genome Res 2009 Dec 2;19(12):2245-57. Epub 2009 Oct 2.

Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA.

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http://dx.doi.org/10.1101/gr.096297.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2792181PMC
December 2009

The C. elegans dosage compensation complex propagates dynamically and independently of X chromosome sequence.

Curr Biol 2009 Nov 22;19(21):1777-87. Epub 2009 Oct 22.

Department of Biology, Carolina Center for Genome Sciences and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1016/j.cub.2009.09.047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783177PMC
November 2009

Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements).

Methods 2009 Jul 18;48(3):233-9. Epub 2009 Mar 18.

Department of Biology and Carolina Center for the Genome Sciences, University of North Carolina at Chapel Hill, CB #3280, 408 Fordham Hall, Chapel Hill, NC 27599-3280, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S104620230900050
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http://dx.doi.org/10.1016/j.ymeth.2009.03.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2710428PMC
July 2009

DNA-binding specificity and in vivo targets of Caenorhabditis elegans nuclear factor I.

Proc Natl Acad Sci U S A 2009 Jul 7;106(29):12049-54. Epub 2009 Jul 7.

Department of Biology, Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-3280, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0812894106
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http://dx.doi.org/10.1073/pnas.0812894106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715542PMC
July 2009

C. elegans dosage compensation: a window into mechanisms of domain-scale gene regulation.

Chromosome Res 2009 ;17(2):215-27

Department of Biology and Carolina Center for the Genome Sciences, CB #3280, 406 Fordham Hall, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.

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http://dx.doi.org/10.1007/s10577-008-9011-0DOI Listing
June 2009

The Set2/Rpd3S pathway suppresses cryptic transcription without regard to gene length or transcription frequency.

PLoS One 2009 19;4(3):e4886. Epub 2009 Mar 19.

Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0004886PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2654109PMC
May 2009

Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization.

Nat Genet 2009 Apr 1;41(4):438-45. Epub 2009 Mar 1.

Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.

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http://dx.doi.org/10.1038/ng.324DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2744203PMC
April 2009

The DNA-encoded nucleosome organization of a eukaryotic genome.

Nature 2009 Mar 17;458(7236):362-6. Epub 2008 Dec 17.

Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel.

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http://dx.doi.org/10.1038/nature07667DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2658732PMC
March 2009

The genomic distribution and function of histone variant HTZ-1 during C. elegans embryogenesis.

PLoS Genet 2008 Sep 12;4(9):e1000187. Epub 2008 Sep 12.

Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000187DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2522285PMC
September 2008

Chromatin proteins do double duty.

Cell 2008 May;133(5):763-5

Department of Biology and Carolina Center for the Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.

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http://dx.doi.org/10.1016/j.cell.2008.05.011DOI Listing
May 2008

DNA Immunoprecipitation (DIP) for the Determination of DNA-Binding Specificity.

CSH Protoc 2008 Mar 1;2008:pdb.prot4972. Epub 2008 Mar 1.

Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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March 2008

Forkhead proteins control the outcome of transcription factor binding by antiactivation.

EMBO J 2007 Oct 27;26(20):4324-34. Epub 2007 Sep 27.

Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA.

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http://dx.doi.org/10.1038/sj.emboj.7601859DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2034669PMC
October 2007

The Saccharomyces cerevisiae histone demethylase Jhd1 fine-tunes the distribution of H3K36me2.

Mol Cell Biol 2007 Jul 30;27(13):5055-65. Epub 2007 Apr 30.

Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1128/MCB.00127-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1951470PMC
July 2007

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin.

Genome Res 2007 Jun 19;17(6):877-85. Epub 2006 Dec 19.

Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA.

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http://dx.doi.org/10.1101/gr.5533506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891346PMC
June 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Identification of histone H3 lysine 36 acetylation as a highly conserved histone modification.

J Biol Chem 2007 Mar 21;282(10):7632-40. Epub 2006 Dec 21.

Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA.

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http://dx.doi.org/10.1074/jbc.M607909200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2811852PMC
March 2007

X chromosome repression by localization of the C. elegans dosage compensation machinery to sites of transcription initiation.

Nat Genet 2007 Mar 11;39(3):403-8. Epub 2007 Feb 11.

Department of Biology and Carolina Center for the Genome Sciences, 202 Fordham Hall, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA.

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http://www.nature.com/articles/ng1983
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2753834PMC
March 2007

Loss of a histone deacetylase dramatically alters the genomic distribution of Spo11p-catalyzed DNA breaks in Saccharomyces cerevisiae.

Proc Natl Acad Sci U S A 2007 Mar 28;104(10):3955-60. Epub 2007 Feb 28.

Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0700412104
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http://dx.doi.org/10.1073/pnas.0700412104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1805699PMC
March 2007

The RNA polymerase II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes.

Mol Cell Biol 2007 Jan 6;27(2):721-31. Epub 2006 Nov 6.

Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, 405 Mary Ellen Jones, Chapel Hill, NC 27599-7260, USA.

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http://dx.doi.org/10.1128/MCB.01628-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1800795PMC
January 2007

Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection.

Genome Res 2006 Dec 19;16(12):1517-28. Epub 2006 Oct 19.

Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1101/gr.5655606DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665635PMC
December 2006

A chromatin-mediated mechanism for specification of conditional transcription factor targets.

Nat Genet 2006 Dec 12;38(12):1446-51. Epub 2006 Nov 12.

Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.

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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756100/
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December 2006

New evidence that DNA encodes its packaging.

Nat Genet 2006 Oct;38(10):1104-5

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October 2006

Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters.

PLoS Genet 2006 Sep 8;2(9):e158. Epub 2006 Aug 8.

Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.0020158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1570381PMC
September 2006

How to find an opening (or lots of them).

Nat Methods 2006 Jul;3(7):501-2

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http://dx.doi.org/10.1038/nmeth0706-501DOI Listing
July 2006

ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data.

Genome Biol 2005 19;6(11):R97. Epub 2005 Oct 19.

Department of Biology, Carolina Center for Genome Sciences, CB 3280, University of North Carolina, Chapel Hill, NC 27599-3280, USA.

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http://dx.doi.org/10.1186/gb-2005-6-11-r97DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1297653PMC
June 2006

Regulation of nucleosome stability as a mediator of chromatin function.

Curr Opin Genet Dev 2006 Apr 28;16(2):171-6. Epub 2006 Feb 28.

Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S0959437X0600025
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http://dx.doi.org/10.1016/j.gde.2006.02.003DOI Listing
April 2006

Global analysis of the relationship between the binding of the Bas1p transcription factor and meiosis-specific double-strand DNA breaks in Saccharomyces cerevisiae.

Mol Cell Biol 2006 Feb;26(3):1014-27

Department of Biology and Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA.

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http://dx.doi.org/10.1128/MCB.26.3.1014-1027.2006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347019PMC
February 2006

Control of transcription through intragenic patterns of nucleosome composition.

Cell 2005 Dec;123(7):1187-90

Department of Biology and the Carolina Center for Genome Sciences, 202 Fordham Hall, CB 3280, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1016/j.cell.2005.12.010DOI Listing
December 2005