Publications by authors named "Jorja G Henikoff"

31Publications

Efficient chromatin accessibility mapping by nucleosome-tethered tagmentation.

Authors:
Steven Henikoff Jorja G Henikoff Hatice S Kaya-Okur Kami Ahmad

Elife 2020 Nov 16;9. Epub 2020 Nov 16.

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.

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November 2020

Efficient low-cost chromatin profiling with CUT&Tag.

Authors:
Hatice S Kaya-Okur Derek H Janssens Jorja G Henikoff Kami Ahmad Steven Henikoff

Nat Protoc 2020 10 10;15(10):3264-3283. Epub 2020 Sep 10.

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

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October 2020

Histone deposition pathways determine the chromatin landscapes of H3.1 and H3.3 K27M oncohistones.

Authors:
Jay F Sarthy Michael P Meers Derek H Janssens Jorja G Henikoff Heather Feldman Patrick J Paddison Christina M Lockwood Nicholas A Vitanza James M Olson Kami Ahmad Steven Henikoff

Elife 2020 09 9;9. Epub 2020 Sep 9.

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.

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September 2020

Improved CUT&RUN chromatin profiling tools.

Authors:
Michael P Meers Terri D Bryson Jorja G Henikoff Steven Henikoff

Elife 2019 06 24;8. Epub 2019 Jun 24.

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.

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June 2019

CUT&Tag for efficient epigenomic profiling of small samples and single cells.

Authors:
Hatice S Kaya-Okur Steven J Wu Christine A Codomo Erica S Pledger Terri D Bryson Jorja G Henikoff Kami Ahmad Steven Henikoff

Nat Commun 2019 04 29;10(1):1930. Epub 2019 Apr 29.

Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100N. FairviewAve, Seattle, WA, 98109, USA.

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April 2019

Targeted in situ genome-wide profiling with high efficiency for low cell numbers.

Authors:
Peter J Skene Jorja G Henikoff Steven Henikoff

Nat Protoc 2018 05 12;13(5):1006-1019. Epub 2018 Apr 12.

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

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May 2018

A unique chromatin complex occupies young α-satellite arrays of human centromeres.

Authors:
Jorja G Henikoff Jitendra Thakur Sivakanthan Kasinathan Steven Henikoff

Sci Adv 2015 Feb;1(1)

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA ; Howard Hughes Medical Institute, Seattle, WA 98109, USA.

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February 2015

The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo.

Authors:
Steven Henikoff Srinivas Ramachandran Kristina Krassovsky Terri D Bryson Christine A Codomo Kristin Brogaard Jonathan Widom Ji-Ping Wang Jorja G Henikoff

Elife 2014 Apr 15;3:e01861. Epub 2014 Apr 15.

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.

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April 2014

The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres.

Authors:
Tao Zhang Paul B Talbert Wenli Zhang Yufeng Wu Zujun Yang Jorja G Henikoff Steven Henikoff Jiming Jiang

Proc Natl Acad Sci U S A 2013 Dec 4;110(50):E4875-83. Epub 2013 Nov 4.

Department of Horticulture, University of Wisconsin, Madison, WI 53706.

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December 2013

"Point" centromeres of Saccharomyces harbor single centromere-specific nucleosomes.

Authors:
Steven Henikoff Jorja G Henikoff

Genetics 2012 Apr 10;190(4):1575-7. Epub 2012 Jan 10.

Basic Sciences Division, Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA.

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April 2012

Tripartite organization of centromeric chromatin in budding yeast.

Authors:
Kristina Krassovsky Jorja G Henikoff Steven Henikoff

Proc Natl Acad Sci U S A 2012 Jan 19;109(1):243-8. Epub 2011 Dec 19.

Basic Sciences Division, Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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January 2012

Epigenome characterization at single base-pair resolution.

Authors:
Jorja G Henikoff Jason A Belsky Kristina Krassovsky David M MacAlpine Steven Henikoff

Proc Natl Acad Sci U S A 2011 Nov 24;108(45):18318-23. Epub 2011 Oct 24.

Basic Sciences Division, The Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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November 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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December 2010

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Authors:
Sushmita Roy Jason Ernst Peter V Kharchenko Pouya Kheradpour Nicolas Negre Matthew L Eaton Jane M Landolin Christopher A Bristow Lijia Ma Michael F Lin Stefan Washietl Bradley I Arshinoff Ferhat Ay Patrick E Meyer Nicolas Robine Nicole L Washington Luisa Di Stefano Eugene Berezikov Christopher D Brown Rogerio Candeias Joseph W Carlson Adrian Carr Irwin Jungreis Daniel Marbach Rachel Sealfon Michael Y Tolstorukov Sebastian Will Artyom A Alekseyenko Carlo Artieri Benjamin W Booth Angela N Brooks Qi Dai Carrie A Davis Michael O Duff Xin Feng Andrey A Gorchakov Tingting Gu Jorja G Henikoff Philipp Kapranov Renhua Li Heather K MacAlpine John Malone Aki Minoda Jared Nordman Katsutomo Okamura Marc Perry Sara K Powell Nicole C Riddle Akiko Sakai Anastasia Samsonova Jeremy E Sandler Yuri B Schwartz Noa Sher Rebecca Spokony David Sturgill Marijke van Baren Kenneth H Wan Li Yang Charles Yu Elise Feingold Peter Good Mark Guyer Rebecca Lowdon Kami Ahmad Justen Andrews Bonnie Berger Steven E Brenner Michael R Brent Lucy Cherbas Sarah C R Elgin Thomas R Gingeras Robert Grossman Roger A Hoskins Thomas C Kaufman William Kent Mitzi I Kuroda Terry Orr-Weaver Norbert Perrimon Vincenzo Pirrotta James W Posakony Bing Ren Steven Russell Peter Cherbas Brenton R Graveley Suzanna Lewis Gos Micklem Brian Oliver Peter J Park Susan E Celniker Steven Henikoff Gary H Karpen Eric C Lai David M MacAlpine Lincoln D Stein Kevin P White Manolis Kellis

Science 2010 Dec 22;330(6012):1787-97. Epub 2010 Dec 22.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.

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December 2010

H2A.Z nucleosomes enriched over active genes are homotypic.

Authors:
Christopher M Weber Jorja G Henikoff Steven Henikoff

Nat Struct Mol Biol 2010 Dec 7;17(12):1500-7. Epub 2010 Nov 7.

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

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December 2010

Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones.

Authors:
Roger B Deal Jorja G Henikoff Steven Henikoff

Science 2010 May;328(5982):1161-4

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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May 2010

A comprehensive map of insulator elements for the Drosophila genome.

Authors:
Nicolas Nègre Christopher D Brown Parantu K Shah Pouya Kheradpour Carolyn A Morrison Jorja G Henikoff Xin Feng Kami Ahmad Steven Russell Robert A H White Lincoln Stein Steven Henikoff Manolis Kellis Kevin P White

PLoS Genet 2010 Jan 15;6(1):e1000814. Epub 2010 Jan 15.

Institute for Genomics and Systems Biology, Department of Human Genetics, and Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA.

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January 2010

A native chromatin purification system for epigenomic profiling in Caenorhabditis elegans.

Authors:
Siew Loon Ooi Jorja G Henikoff Steven Henikoff

Nucleic Acids Res 2010 Mar 4;38(4):e26. Epub 2009 Dec 4.

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

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March 2010

Genome-wide profiling of salt fractions maps physical properties of chromatin.

Authors:
Steven Henikoff Jorja G Henikoff Akiko Sakai Gabriel B Loeb Kami Ahmad

Genome Res 2009 Mar 16;19(3):460-9. Epub 2008 Dec 16.

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA.

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March 2009

Using the blocks database to recognize functional domains.

Authors:
Jorja G Henikoff Elizabeth A Greene Nick Taylor Steven Henikoff Shmuel Pietrokovski

Curr Protoc Bioinformatics 2002 Aug;Chapter 2:Unit 2.2

Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

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August 2002

Histone replacement marks the boundaries of cis-regulatory domains.

Authors:
Yoshiko Mito Jorja G Henikoff Steven Henikoff

Science 2007 Mar;315(5817):1408-11

Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.

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March 2007

High-throughput TILLING for Arabidopsis.

Authors:
Bradley J Till Trenton Colbert Christine Codomo Linda Enns Jessica Johnson Steven H Reynolds Jorja G Henikoff Elizabeth A Greene Michael N Steine Luca Comai Steven Henikoff

Methods Mol Biol 2006 ;323:127-35

Basic Sciences Division, Fred Hutchison Cancer Research Center, Department of Biology, University of Washington, Seattle, USA.

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June 2006

Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis.

Authors:
Robert K Tran Daniel Zilberman Cecilia de Bustos Renata F Ditt Jorja G Henikoff Anders M Lindroth Jeffrey Delrow Tom Boyle Samson Kwong Terri D Bryson Steven E Jacobsen Steven Henikoff

Genome Biol 2005 19;6(11):R90. Epub 2005 Oct 19.

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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June 2006

Genome-scale profiling of histone H3.3 replacement patterns.

Authors:
Yoshiko Mito Jorja G Henikoff Steven Henikoff

Nat Genet 2005 Oct 11;37(10):1090-7. Epub 2005 Sep 11.

Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA.

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October 2005

DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes.

Authors:
Robert K Tran Jorja G Henikoff Daniel Zilberman Renata F Ditt Steven E Jacobsen Steven Henikoff

Curr Biol 2005 Jan;15(2):154-9

Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.

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January 2005

Suboptimal pharmacotherapeutic management of chronic stable angina in the primary care setting.

Authors:
Francine C Wiest Chris L Bryson Marcia Burman Mary B McDonell Jorja G Henikoff Stephan D Fihn

Am J Med 2004 Aug;117(4):234-41

Health Services Research and Development Center of Excellence, Veterans Affairs Puget Sound Health Care System, Seattle, WA 98108, USA.

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August 2004

High-throughput TILLING for functional genomics.

Authors:
Bradley J Till Trenton Colbert Rachel Tompa Linda C Enns Christine A Codomo Jessica E Johnson Steven H Reynolds Jorja G Henikoff Elizabeth A Greene Michael N Steine Luca Comai Steven Henikoff

Methods Mol Biol 2003 ;236:205-20

BasicSciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

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February 2004

CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design.

Authors:
Timothy M Rose Jorja G Henikoff Steven Henikoff

Nucleic Acids Res 2003 Jul;31(13):3763-6

Department of Pathobiology, School of Public Health and Community Medicine, University of Washington, Seattle, WA 98195, USA.

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July 2003

Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis.

Authors:
Elizabeth A Greene Christine A Codomo Nicholas E Taylor Jorja G Henikoff Bradley J Till Steven H Reynolds Linda C Enns Chris Burtner Jessica E Johnson Anthony R Odden Luca Comai Steven Henikoff

Genetics 2003 Jun;164(2):731-40

Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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June 2003

Large-scale discovery of induced point mutations with high-throughput TILLING.

Authors:
Bradley J Till Steven H Reynolds Elizabeth A Greene Christine A Codomo Linda C Enns Jessica E Johnson Chris Burtner Anthony R Odden Kim Young Nicholas E Taylor Jorja G Henikoff Luca Comai Steven Henikoff

Genome Res 2003 Mar;13(3):524-30

Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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March 2003

Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3.

Authors:
Rachel Tompa Claire M McCallum Jeffrey Delrow Jorja G Henikoff Bas van Steensel Steven Henikoff

Curr Biol 2002 Jan;12(1):65-8

Howard Hughes Medical Institute and Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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January 2002