| 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. |
- 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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| 4. |
- Girelli, G, et al.
(författare)
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Sequencing Genome Organization
- 2022
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Ingår i: EUROPEAN JOURNAL OF HUMAN GENETICS. - 1018-4813. ; 30:SUPPL 1, s. 16-16
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 5. |
- Mota, A, et al.
(författare)
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Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH
- 2022
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Ingår i: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 9:1, s. 47-
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Tidskriftsartikel (refereegranskat)abstract
- Single-molecule DNA fluorescence in situ hybridization (FISH) techniques enable studying the three-dimensional (3D) organization of the genome at the single cell level. However, there is a major unmet need for open access, high quality, curated and reproducible DNA FISH datasets. Here, we describe a dataset obtained by applying our recently developed iFISH method to simultaneously visualize 16 small (size range: 62–73 kilobases, kb) DNA loci evenly spaced on chromosome 2 in human cells, in a single round of hybridization. We show how combinatorial color coding can be used to precisely localize multiple loci in 3D within single cells, and how inter-locus distances scale inversely with chromosome contact frequencies determined by high-throughput chromosome conformation capture (Hi-C). We provide raw images and 3D coordinates for nearly 10,000 FISH dots. Our dataset provides a free resource that can facilitate studies of 3D genome organization in single cells and can be used to develop automatic FISH analysis algorithms.
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| 6. |
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