| 1. |
- Ballarino, R, et al.
(författare)
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An atlas of endogenous DNA double-strand breaks arising during human neural cell fate determination
- 2022
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Ingår i: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 9:1, s. 400-
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Tidskriftsartikel (refereegranskat)abstract
- Endogenous DNA double-strand breaks (DSBs) occurring in neural cells have been implicated in the pathogenesis of neurodevelopmental disorders (NDDs). Currently, a genomic map of endogenous DSBs arising during human neurogenesis is missing. Here, we applied in-suspension Breaks Labeling In Situ and Sequencing (sBLISS), RNA-Seq, and Hi-C to chart the genomic landscape of DSBs and relate it to gene expression and genome architecture in 2D cultures of human neuroepithelial stem cells (NES), neural progenitor cells (NPC), and post-mitotic neural cells (NEU). Endogenous DSBs were enriched at the promoter and along the gene body of transcriptionally active genes, at the borders of topologically associating domains (TADs), and around chromatin loop anchors. NDD risk genes harbored significantly more DSBs in comparison to other protein-coding genes, especially in NEU cells. We provide sBLISS, RNA-Seq, and Hi-C datasets for each differentiation stage, and all the scripts needed to reproduce our analyses. Our datasets and tools represent a unique resource that can be harnessed to investigate the role of genome fragility in the pathogenesis of NDDs.
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| 2. |
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| 3. |
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| 4. |
- Bouwman, BAM, et al.
(författare)
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A GC-centered view of 3D genome organization
- 2023
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Ingår i: Current opinion in genetics & development. - : Elsevier BV. - 1879-0380 .- 0959-437X. ; 78, s. 102020-
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Tidskriftsartikel (refereegranskat)
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| 5. |
- Bouwman, BAM, et al.
(författare)
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Endogenous DNA Double-Strand Breaks during DNA Transactions: Emerging Insights and Methods for Genome-Wide Profiling
- 2018
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Ingår i: Genes. - : MDPI AG. - 2073-4425. ; 9:12
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Tidskriftsartikel (refereegranskat)abstract
- DNA double-strand breaks (DSBs) jeopardize genome integrity and can—when repaired unfaithfully—give rise to structural rearrangements associated with cancer. Exogenous agents such as ionizing radiation or chemotherapy can invoke DSBs, but a vast amount of breakage arises during vital endogenous DNA transactions, such as replication and transcription. Additionally, chromatin looping involved in 3D genome organization and gene regulation is increasingly recognized as a possible contributor to DSB events. In this review, we first discuss insights into the mechanisms of endogenous DSB formation, showcasing the trade-off between essential DNA transactions and the intrinsic challenges that these processes impose on genomic integrity. In the second part, we highlight emerging methods for genome-wide profiling of DSBs, and discuss future directions of research that will help advance our understanding of genome-wide DSB formation and repair.
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| 7. |
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| 8. |
- Bouwman, BAM, et al.
(författare)
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The era of 3D and spatial genomics
- 2022
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Ingår i: Trends in genetics : TIG. - : Elsevier BV. - 0168-9525. ; 38:10, s. 1062-1075
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Tidskriftsartikel (refereegranskat)
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| 10. |
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