Genome-wide and sister chromatid-resolved profiling of protein occupancy in replicated chromatin with ChOR-seq and SCAR-seq

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Genome-wide and sister chromatid-resolved profiling of protein occupancy in replicated chromatin with ChOR-seq and SCAR-seq. / Petryk, Nataliya; Reverón-Gómez, Nazaret; González-Aguilera, Cristina; Dalby, Maria; Andersson, Robin; Groth, Anja.

In: Nature Protocols, Vol. 16, 2021, p. 4446-4493.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Petryk, N, Reverón-Gómez, N, González-Aguilera, C, Dalby, M, Andersson, R & Groth, A 2021, 'Genome-wide and sister chromatid-resolved profiling of protein occupancy in replicated chromatin with ChOR-seq and SCAR-seq', Nature Protocols, vol. 16, pp. 4446-4493. https://doi.org/10.1038/s41596-021-00585-3

APA

Petryk, N., Reverón-Gómez, N., González-Aguilera, C., Dalby, M., Andersson, R., & Groth, A. (2021). Genome-wide and sister chromatid-resolved profiling of protein occupancy in replicated chromatin with ChOR-seq and SCAR-seq. Nature Protocols, 16, 4446-4493. https://doi.org/10.1038/s41596-021-00585-3

Vancouver

Petryk N, Reverón-Gómez N, González-Aguilera C, Dalby M, Andersson R, Groth A. Genome-wide and sister chromatid-resolved profiling of protein occupancy in replicated chromatin with ChOR-seq and SCAR-seq. Nature Protocols. 2021;16:4446-4493. https://doi.org/10.1038/s41596-021-00585-3

Author

Petryk, Nataliya ; Reverón-Gómez, Nazaret ; González-Aguilera, Cristina ; Dalby, Maria ; Andersson, Robin ; Groth, Anja. / Genome-wide and sister chromatid-resolved profiling of protein occupancy in replicated chromatin with ChOR-seq and SCAR-seq. In: Nature Protocols. 2021 ; Vol. 16. pp. 4446-4493.

Bibtex

@article{4679cab9204b42bab097fe9247fc1e3c,
title = "Genome-wide and sister chromatid-resolved profiling of protein occupancy in replicated chromatin with ChOR-seq and SCAR-seq",
abstract = "Elucidating the mechanisms underlying chromatin maintenance upon genome replication is critical for the understanding of how gene expression programs and cell identity are preserved across cell divisions. Here, we describe two recently developed techniques, chromatin occupancy after replication (ChOR)-seq and sister chromatids after replication (SCAR)-seq, that profile chromatin occupancy on newly replicated DNA in mammalian cells in 5 d of bench work. Both techniques share a common strategy that includes pulse labeling of newly synthesized DNA and chromatin immunoprecipitation (ChIP), followed by purification and high-throughput sequencing. Whereas ChOR-seq quantitatively profiles the post-replicative abundance of histone modifications and chromatin-associated proteins, SCAR-seq distinguishes chromatin occupancy between nascent sister chromatids. Together, these two complementary techniques have unraveled key mechanisms controlling the inheritance of modified histones during replication and revealed locus-specific dynamics of histone modifications across the cell cycle. Here, we provide the experimental protocols and bioinformatic pipelines for these methods.",
author = "Nataliya Petryk and Nazaret Rever{\'o}n-G{\'o}mez and Cristina Gonz{\'a}lez-Aguilera and Maria Dalby and Robin Andersson and Anja Groth",
note = "{\textcopyright} 2021. The Author(s), under exclusive licence to Springer Nature Limited.",
year = "2021",
doi = "10.1038/s41596-021-00585-3",
language = "English",
volume = "16",
pages = "4446--4493",
journal = "Nature Protocols",
issn = "1754-2189",
publisher = "nature publishing group",

}

RIS

TY - JOUR

T1 - Genome-wide and sister chromatid-resolved profiling of protein occupancy in replicated chromatin with ChOR-seq and SCAR-seq

AU - Petryk, Nataliya

AU - Reverón-Gómez, Nazaret

AU - González-Aguilera, Cristina

AU - Dalby, Maria

AU - Andersson, Robin

AU - Groth, Anja

N1 - © 2021. The Author(s), under exclusive licence to Springer Nature Limited.

PY - 2021

Y1 - 2021

N2 - Elucidating the mechanisms underlying chromatin maintenance upon genome replication is critical for the understanding of how gene expression programs and cell identity are preserved across cell divisions. Here, we describe two recently developed techniques, chromatin occupancy after replication (ChOR)-seq and sister chromatids after replication (SCAR)-seq, that profile chromatin occupancy on newly replicated DNA in mammalian cells in 5 d of bench work. Both techniques share a common strategy that includes pulse labeling of newly synthesized DNA and chromatin immunoprecipitation (ChIP), followed by purification and high-throughput sequencing. Whereas ChOR-seq quantitatively profiles the post-replicative abundance of histone modifications and chromatin-associated proteins, SCAR-seq distinguishes chromatin occupancy between nascent sister chromatids. Together, these two complementary techniques have unraveled key mechanisms controlling the inheritance of modified histones during replication and revealed locus-specific dynamics of histone modifications across the cell cycle. Here, we provide the experimental protocols and bioinformatic pipelines for these methods.

AB - Elucidating the mechanisms underlying chromatin maintenance upon genome replication is critical for the understanding of how gene expression programs and cell identity are preserved across cell divisions. Here, we describe two recently developed techniques, chromatin occupancy after replication (ChOR)-seq and sister chromatids after replication (SCAR)-seq, that profile chromatin occupancy on newly replicated DNA in mammalian cells in 5 d of bench work. Both techniques share a common strategy that includes pulse labeling of newly synthesized DNA and chromatin immunoprecipitation (ChIP), followed by purification and high-throughput sequencing. Whereas ChOR-seq quantitatively profiles the post-replicative abundance of histone modifications and chromatin-associated proteins, SCAR-seq distinguishes chromatin occupancy between nascent sister chromatids. Together, these two complementary techniques have unraveled key mechanisms controlling the inheritance of modified histones during replication and revealed locus-specific dynamics of histone modifications across the cell cycle. Here, we provide the experimental protocols and bioinformatic pipelines for these methods.

U2 - 10.1038/s41596-021-00585-3

DO - 10.1038/s41596-021-00585-3

M3 - Journal article

C2 - 34363071

VL - 16

SP - 4446

EP - 4493

JO - Nature Protocols

JF - Nature Protocols

SN - 1754-2189

ER -

ID: 275935943