Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag.

Developmental Dynamics : an Official Publication of the American Association of Anatomists
Bagdeser Akdogan-OzdilekMary G Goll


Cell fate decisions are governed by interactions between sequence-specific transcription factors and a dynamic chromatin landscape. Zebrafish offer a powerful system for probing the mechanisms that drive these cell fate choices, especially in the context of early embryogenesis. However, technical challenges associated with conventional methods for chromatin profiling have slowed progress toward understanding the exact relationships between chromatin changes, transcription factor binding, and cellular differentiation during zebrafish embryogenesis. To overcome these challenges, we adapted the chromatin profiling methods Cleavage Under Targets and Release Using Nuclease (CUT&RUN) and CUT&Tag for use in zebrafish and applied these methods to generate high-resolution enrichment maps for H3K4me3, H3K27me3, H3K9me3, RNA polymerase II, and the histone variant H2A.Z using tissue isolated from whole, mid-gastrula stage embryos. Using this data, we identify a subset of genes that may be bivalently regulated during both zebrafish and mouse gastrulation, provide evidence for an evolving H2A.Z landscape during embryo development, and demonstrate the effectiveness of CUT&RUN for detecting H3K9me3 enrichment at repetitive sequences. Our resul...Continue Reading


Oct 1, 1985·Proceedings of the National Academy of Sciences of the United States of America·M J Solomon, A Varshavsky
Jun 2, 2007·Science·David S JohnsonBarbara Wold
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Sep 9, 2009·Nature Reviews. Genetics·Peter J Park
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Mar 26, 2010·Nature·Nadine L VastenhouwAlexander F Schier
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Sep 8, 2012·Genome Research·Stephen G LandtMichael Snyder
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Dec 18, 2013·Nature Methods·Sivakanthan KasinathanSteven Henikoff
Jan 22, 2015·Nature Communications·Julie Brind'AmourMatthew C Lorincz
Feb 24, 2015·F1000prime Reports·Vidya SubramanianLaurie A Boyer
Dec 26, 2015·Trends in Genetics : TIG·Moyra LawrenceRobert Schneider
Apr 16, 2016·Nucleic Acids Research·Fidel RamírezThomas Manke
Mar 2, 2017·Nature Reviews. Molecular Cell Biology·Kevin M Harlen, L Stirling Churchman
Nov 17, 2017·ELife·Richard J WhiteElisabeth M Busch-Nentwich
Dec 14, 2017·Nature Reviews. Molecular Cell Biology·Robin C Allshire, Hiten D Madhani
Apr 14, 2018·Nature Protocols·Peter J SkeneSteven Henikoff
May 10, 2018·Nature Reviews. Molecular Cell Biology·Fei Xavier ChenAli Shilatifard
Jul 26, 2018·Annual Review of Cell and Developmental Biology·Aniek JanssenGary H Karpen
Nov 1, 2018·Bioinformatics·Roberto Vera AlvarezDavid Landsman
Nov 26, 2018·Cell Stem Cell·Sun-Mi ParkMichael G Kharas
Dec 24, 2018·Nature Reviews. Genetics·Katharine N Schulz, Melissa M Harrison
Jan 29, 2019·Current Protocols in Molecular Biology·Sarah J Hainer, Thomas G Fazzio
Feb 6, 2019·Plant Reproduction·Xiao-Yu Zheng, Mary Gehring
Mar 20, 2019·Nature Reviews. Genetics·Paul B TalbertSteven Henikoff
Apr 7, 2019·Biochemical Society Transactions·Julia A Horsfield
Apr 26, 2019·Proceedings of the National Academy of Sciences of the United States of America·Christopher M Uyehara, Daniel J McKay
May 1, 2019·Nature Communications·Hatice S Kaya-OkurSteven Henikoff

❮ Previous
Next ❯

Related Concepts

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.


Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.


Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.