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ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

In chromatin endogenous cleavage (ChEC), micrococcal nuclease (MNase) is fused to a protein of interest and its cleavage is thus targeted to specific genomic loci in vivo. Here, the authors show that time-resolved ChEC-seq (high-throughput sequencing after ChEC) can detect DNA shape patterns regardless of motif strength.

Gabriel E. Zentner
Sivakanthan Kasinathan
Steven Henikoff
ResearchOpen Access22 Oct 2015
Nature Communications

Volume: 6, P: 1-13
Correction: Corrigendum: ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

Gabriel E. Zentner
Sivakanthan Kasinathan
Steven Henikoff
Amendments and CorrectionsOpen Access16 Dec 2015
Nature Communications

Volume: 6, P: 1
Correction: Corrigendum: ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

Gabriel E. Zentner
Sivakanthan Kasinathan
Steven Henikoff
Amendments and CorrectionsOpen Access05 Jun 2017
Nature Communications

Volume: 8, P: 1
Design and testing of a humanized porcine donor for xenotransplantation

Using kidneys from a genetically engineered porcine donor transplanted into a cynomolgus monkey model, the design, creation and long-term function of kidney grafts supporting life are explored.

Ranjith P. Anand
Jacob V. Layer
Wenning Qin
ResearchOpen Access11 Oct 2023
Nature

Volume: 622, P: 393-401
Epigenome editing made easy

Fusions of Cas9 to histone-modifying enzymes enable functional interrogation of the epigenome.

Gabriel E Zentner
Steven Henikoff
News & Views09 Jun 2015
Nature Biotechnology

Volume: 33, P: 606-607
High-resolution mapping of transcription factor binding sites on native chromatin

A method to map transcription factor binding across the genome, at high resolution and without cross-linking.

Sivakanthan Kasinathan
Guillermo A Orsi
Steven Henikoff
Research15 Dec 2013
Nature Methods

Volume: 11, P: 203-209
Correspondence: Reply to ‘DNA shape is insufficient to explain binding’

Sivakanthan Kasinathan
Gabriel E. Zentner
Steven Henikoff
CorrespondenceOpen Access05 Jun 2017
Nature Communications

Volume: 8, P: 1-3
High-resolution digital profiling of the epigenome

The resolution of epigenomic profiling has been vastly augmented with the adoption of new approaches to interrogate varied features of the epigenome. This Review describes these techniques and outlines the ways in which these genome-wide tools can be used to examine the epigenome.

Gabriel E. Zentner
Steven Henikoff
Reviews09 Oct 2014
Nature Reviews Genetics

Volume: 15, P: 814-827
Testis-specific transcriptional regulators selectively occupy BORIS-bound CTCF target regions in mouse male germ cells

Samuel Rivero-Hinojosa
Sungyun Kang
Gabriel E. Zentner
ResearchOpen Access01 Feb 2017
Scientific Reports

Volume: 7, P: 1-13
Regulation of nucleosome dynamics by histone modifications

The properties of nucleosomes can be altered in various ways, including by covalent modification of histones. In this Review, the known properties of key histone modifications and the biological processes to which they are linked are examined to place the modifications in the context of nucleosome dynamics—that is, processes in which nucleosomes are translocated, unwrapped, evicted or replaced.

Gabriel E Zentner
Steven Henikoff
Reviews05 Mar 2013
Nature Structural & Molecular Biology

Volume: 20, P: 259-266
Correction: Corrigendum: Testis-specific transcriptional regulators selectively occupy BORIS-bound CTCF target regions in mouse male germ cells

Samuel Rivero-Hinojosa
Sungyun Kang
Gabriel E. Zentner
Amendments and CorrectionsOpen Access04 Aug 2017
Scientific Reports

Volume: 7, P: 1

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ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

Correction: Corrigendum: ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

Correction: Corrigendum: ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

Design and testing of a humanized porcine donor for xenotransplantation

Epigenome editing made easy

High-resolution mapping of transcription factor binding sites on native chromatin

Correspondence: Reply to ‘DNA shape is insufficient to explain binding’

High-resolution digital profiling of the epigenome

Testis-specific transcriptional regulators selectively occupy BORIS-bound CTCF target regions in mouse male germ cells

Regulation of nucleosome dynamics by histone modifications

Correction: Corrigendum: Testis-specific transcriptional regulators selectively occupy BORIS-bound CTCF target regions in mouse male germ cells

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