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SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells

Chromatin boundary elements contribute to the partitioning of mammalian genomes into topological domains to regulate gene expression. Certain boundary elements are adopted as DNA insulators for safe and stable transgene expression in mammalian cells. These elements, however, are ill-defined and less...

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Autores principales: Zhang, Meng, Ehmann, Mary Elisabeth, Matukumalli, Srija, Boob, Aashutosh Girish, Gilbert, David M., Zhao, Huimin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10497619/
https://www.ncbi.nlm.nih.gov/pubmed/37699958
http://dx.doi.org/10.1038/s41467-023-41468-3
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author Zhang, Meng
Ehmann, Mary Elisabeth
Matukumalli, Srija
Boob, Aashutosh Girish
Gilbert, David M.
Zhao, Huimin
author_facet Zhang, Meng
Ehmann, Mary Elisabeth
Matukumalli, Srija
Boob, Aashutosh Girish
Gilbert, David M.
Zhao, Huimin
author_sort Zhang, Meng
collection PubMed
description Chromatin boundary elements contribute to the partitioning of mammalian genomes into topological domains to regulate gene expression. Certain boundary elements are adopted as DNA insulators for safe and stable transgene expression in mammalian cells. These elements, however, are ill-defined and less characterized in the non-coding genome, partially due to the lack of a platform to readily evaluate boundary-associated activities of putative DNA sequences. Here we report SHIELD (Site-specific Heterochromatin Insertion of Elements at Lamina-associated Domains), a platform tailored for the high-throughput screening of barrier-type DNA elements in human cells. SHIELD takes advantage of the high specificity of serine integrase at heterochromatin, and exploits the natural heterochromatin spreading inside lamina-associated domains (LADs) for the discovery of potent barrier elements. We adopt SHIELD to evaluate the barrier activity of 1000 DNA elements in a high-throughput manner and identify 8 candidates with barrier activities comparable to the core region of cHS4 element in human HCT116 cells. We anticipate SHIELD could facilitate the discovery of novel barrier DNA elements from the non-coding genome in human cells.
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spelling pubmed-104976192023-09-14 SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells Zhang, Meng Ehmann, Mary Elisabeth Matukumalli, Srija Boob, Aashutosh Girish Gilbert, David M. Zhao, Huimin Nat Commun Article Chromatin boundary elements contribute to the partitioning of mammalian genomes into topological domains to regulate gene expression. Certain boundary elements are adopted as DNA insulators for safe and stable transgene expression in mammalian cells. These elements, however, are ill-defined and less characterized in the non-coding genome, partially due to the lack of a platform to readily evaluate boundary-associated activities of putative DNA sequences. Here we report SHIELD (Site-specific Heterochromatin Insertion of Elements at Lamina-associated Domains), a platform tailored for the high-throughput screening of barrier-type DNA elements in human cells. SHIELD takes advantage of the high specificity of serine integrase at heterochromatin, and exploits the natural heterochromatin spreading inside lamina-associated domains (LADs) for the discovery of potent barrier elements. We adopt SHIELD to evaluate the barrier activity of 1000 DNA elements in a high-throughput manner and identify 8 candidates with barrier activities comparable to the core region of cHS4 element in human HCT116 cells. We anticipate SHIELD could facilitate the discovery of novel barrier DNA elements from the non-coding genome in human cells. Nature Publishing Group UK 2023-09-12 /pmc/articles/PMC10497619/ /pubmed/37699958 http://dx.doi.org/10.1038/s41467-023-41468-3 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Zhang, Meng
Ehmann, Mary Elisabeth
Matukumalli, Srija
Boob, Aashutosh Girish
Gilbert, David M.
Zhao, Huimin
SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells
title SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells
title_full SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells
title_fullStr SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells
title_full_unstemmed SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells
title_short SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells
title_sort shield: a platform for high-throughput screening of barrier-type dna elements in human cells
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10497619/
https://www.ncbi.nlm.nih.gov/pubmed/37699958
http://dx.doi.org/10.1038/s41467-023-41468-3
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