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  1. Article ; Online: Lamina-associated domains: Tethers and looseners.

    Manzo, Stefano Giustino / Dauban, Lise / van Steensel, Bas

    Current opinion in cell biology

    2022  Volume 74, Page(s) 80–87

    Abstract: Lamina-associated domains (LADs) are large heterochromatic regions that are positioned at the nuclear lamina (NL). A major question is how LAD-NL interactions are mediated and controlled. Here, we review recent progress in the search for molecular ... ...

    Abstract Lamina-associated domains (LADs) are large heterochromatic regions that are positioned at the nuclear lamina (NL). A major question is how LAD-NL interactions are mediated and controlled. Here, we review recent progress in the search for molecular tethers and looseners of LADs and we discuss the link between LAD-NL tethering, transcription regulation, and genome replication. We also provide a brief summary of technological advances that may uncover new aspects of LAD biology.
    MeSH term(s) Chromatin ; Gene Expression Regulation ; Genome ; Nuclear Lamina
    Chemical Substances Chromatin
    Language English
    Publishing date 2022-02-18
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 1026381-0
    ISSN 1879-0410 ; 0955-0674
    ISSN (online) 1879-0410
    ISSN 0955-0674
    DOI 10.1016/j.ceb.2022.01.004
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    Zs.A 2963: Show issues Location:
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  2. Article ; Online: Genome-Wide Mapping and Microscopy Visualization of Protein-DNA Interactions by pA-DamID.

    van Schaik, Tom / Manzo, Stefano G / van Steensel, Bas

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2458, Page(s) 215–229

    Abstract: Several methods have been developed to map protein-DNA interactions genome-wide in the last decades. Protein A-DamID (pA-DamID) is a recent addition to this list with distinct advantages. pA-DamID relies on antibody-based targeting of the bacterial Dam ... ...

    Abstract Several methods have been developed to map protein-DNA interactions genome-wide in the last decades. Protein A-DamID (pA-DamID) is a recent addition to this list with distinct advantages. pA-DamID relies on antibody-based targeting of the bacterial Dam enzyme, resulting in adenine methylation of DNA in contact with the protein of interest. This
    MeSH term(s) Chromatin/genetics ; DNA/chemistry ; DNA Methylation ; Microscopy ; Staphylococcal Protein A/genetics
    Chemical Substances Chromatin ; Staphylococcal Protein A ; DNA (9007-49-2)
    Language English
    Publishing date 2022-02-01
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2140-0_12
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  3. Article ; Online: Scientific honesty and publicly shared lab notebooks: Sharing lab notebooks along with publication would increase transparency and help to improve honesty when reporting results.

    van Steensel, Bas

    EMBO reports

    2018  Volume 19, Issue 10

    MeSH term(s) Ethics, Research ; Humans ; Publications/ethics ; Publications/standards ; Publishing/ethics ; Publishing/standards ; Scientific Misconduct/ethics
    Language English
    Publishing date 2018-08-29
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020896-0
    ISSN 1469-3178 ; 1469-221X
    ISSN (online) 1469-3178
    ISSN 1469-221X
    DOI 10.15252/embr.201846866
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    Zs.A 5433: Show issues Location:
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  4. Article ; Online: From fluorescent foci to sequence: Illuminating DNA double strand break repair by high-throughput sequencing technologies.

    Vergara, Xabier / Schep, Ruben / Medema, René H / van Steensel, Bas

    DNA repair

    2022  Volume 118, Page(s) 103388

    Abstract: Technologies to study DNA double-strand break (DSB) repair have traditionally mostly relied on fluorescence read-outs, either by microscopy or flow cytometry. The advent of high throughput sequencing (HTS) has created fundamentally new opportunities to ... ...

    Abstract Technologies to study DNA double-strand break (DSB) repair have traditionally mostly relied on fluorescence read-outs, either by microscopy or flow cytometry. The advent of high throughput sequencing (HTS) has created fundamentally new opportunities to study the mechanisms underlying DSB repair. Here, we review the suite of HTS-based assays that are used to study three different aspects of DNA repair: detection of broken ends, protein recruitment and pathway usage. We highlight new opportunities that HTS technology offers towards a better understanding of the DSB repair process.
    MeSH term(s) DNA/metabolism ; DNA Breaks, Double-Stranded ; DNA Repair ; High-Throughput Nucleotide Sequencing ; Technology
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2022-08-19
    Publishing country Netherlands
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2071608-4
    ISSN 1568-7856 ; 1568-7864
    ISSN (online) 1568-7856
    ISSN 1568-7864
    DOI 10.1016/j.dnarep.2022.103388
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    Zs.A 5555: Show issues Location:
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  5. Article ; Online: Optimisation of TP53 reporters by systematic dissection of synthetic TP53 response elements.

    Trauernicht, Max / Rastogi, Chaitanya / Manzo, Stefano G / Bussemaker, Harmen J / van Steensel, Bas

    Nucleic acids research

    2023  Volume 51, Issue 18, Page(s) 9690–9702

    Abstract: TP53 is a transcription factor that controls multiple cellular processes, including cell cycle arrest, DNA repair and apoptosis. The relation between TP53 binding site architecture and transcriptional output is still not fully understood. Here, we ... ...

    Abstract TP53 is a transcription factor that controls multiple cellular processes, including cell cycle arrest, DNA repair and apoptosis. The relation between TP53 binding site architecture and transcriptional output is still not fully understood. Here, we systematically examined in three different cell lines the effects of binding site affinity and copy number on TP53-dependent transcriptional output, and also probed the impact of spacer length and sequence between adjacent binding sites, and of core promoter identity. Paradoxically, we found that high-affinity TP53 binding sites are less potent than medium-affinity sites. TP53 achieves supra-additive transcriptional activation through optimally spaced adjacent binding sites, suggesting a cooperative mechanism. Optimally spaced adjacent binding sites have a ∼10-bp periodicity, suggesting a role for spatial orientation along the DNA double helix. We leveraged these insights to construct a log-linear model that explains activity from sequence features, and to identify new highly active and sensitive TP53 reporters.
    Language English
    Publishing date 2023-08-31
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad718
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    Zs.A 1067: Show issues Location:
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  6. Article ; Online: Defining the fine structure of promoter activity on a genome-wide scale with CISSECTOR.

    FitzPatrick, Vincent D / Leemans, Christ / van Arensbergen, Joris / van Steensel, Bas / Bussemaker, Harmen J

    Nucleic acids research

    2023  Volume 51, Issue 11, Page(s) 5499–5511

    Abstract: Classic promoter mutagenesis strategies can be used to study how proximal promoter regions regulate the expression of particular genes of interest. This is a laborious process, in which the smallest sub-region of the promoter still capable of ... ...

    Abstract Classic promoter mutagenesis strategies can be used to study how proximal promoter regions regulate the expression of particular genes of interest. This is a laborious process, in which the smallest sub-region of the promoter still capable of recapitulating expression in an ectopic setting is first identified, followed by targeted mutation of putative transcription factor binding sites. Massively parallel reporter assays such as survey of regulatory elements (SuRE) provide an alternative way to study millions of promoter fragments in parallel. Here we show how a generalized linear model (GLM) can be used to transform genome-scale SuRE data into a high-resolution genomic track that quantifies the contribution of local sequence to promoter activity. This coefficient track helps identify regulatory elements and can be used to predict promoter activity of any sub-region in the genome. It thus allows in silico dissection of any promoter in the human genome to be performed. We developed a web application, available at cissector.nki.nl, that lets researchers easily perform this analysis as a starting point for their research into any promoter of interest.
    MeSH term(s) Humans ; Binding Sites ; Genome, Human/genetics ; Promoter Regions, Genetic ; Protein Binding ; Regulatory Sequences, Nucleic Acid ; Software
    Language English
    Publishing date 2023-04-03
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad232
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  7. Article ; Online: Phosphorylated Lamins in Euchromatin: New Clues to Progeria.

    Manzo, Stefano Giustino / van Steensel, Bas

    Developmental cell

    2020  Volume 52, Issue 6, Page(s) 676–678

    Abstract: Lamin proteins not only form the nuclear lamina, but some are also found in the nuclear interior. In this issue of Developmental Cell, Ikegami et al. describe that phosphorylated Lamin C in the nuclear interior interacts with enhancer-like elements and ... ...

    Abstract Lamin proteins not only form the nuclear lamina, but some are also found in the nuclear interior. In this issue of Developmental Cell, Ikegami et al. describe that phosphorylated Lamin C in the nuclear interior interacts with enhancer-like elements and link this to deregulated transcription in progeria.
    MeSH term(s) Cell Nucleus ; Euchromatin ; Humans ; Lamin Type A/genetics ; Nuclear Lamina ; Progeria
    Chemical Substances Euchromatin ; Lamin Type A
    Language English
    Publishing date 2020-03-30
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2054967-2
    ISSN 1878-1551 ; 1534-5807
    ISSN (online) 1878-1551
    ISSN 1534-5807
    DOI 10.1016/j.devcel.2020.03.003
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    Zs.A 5742: Show issues Location:
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  8. Article: Protocol: A Multiplexed Reporter Assay to Study Effects of Chromatin Context on DNA Double-Strand Break Repair.

    Schep, Ruben / Leemans, Christ / Brinkman, Eva K / van Schaik, Tom / van Steensel, Bas

    Frontiers in genetics

    2022  Volume 12, Page(s) 785947

    Abstract: DNA double-strand breaks (DSBs) can be repaired through various pathways. Understanding how these pathways are regulated is of great interest for cancer research and optimization of gene editing. The local chromatin environment can affect the balance ... ...

    Abstract DNA double-strand breaks (DSBs) can be repaired through various pathways. Understanding how these pathways are regulated is of great interest for cancer research and optimization of gene editing. The local chromatin environment can affect the balance between repair pathways, but this is still poorly understood. Here we provide a detailed protocol for DSB-TRIP, a technique that utilizes the specific DNA scars left by DSB repair pathways to study pathway usage throughout the genome. DSB-TRIP randomly integrates a repair reporter into many genomic locations, followed by the induction of DSBs in the reporter. Multiplexed sequencing of the resulting scars at all integration sites then reveals the balance between several repair pathways, which can be linked to the local chromatin state of the integration sites. Here we present a step-by-step protocol to perform DSB-TRIP in K562 cells and to analyse the data by a dedicated computational pipeline. We discuss strengths and limitations of the technique, as well as potential additional applications to study DNA repair.
    Language English
    Publishing date 2022-01-31
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2021.785947
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  9. Article: Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function.

    Gholamalamdari, Omid / van Schaik, Tom / Wang, Yuchuan / Kumar, Pradeep / Zhang, Liguo / Zhang, Yang / Hernandez Gonzalez, Gabriela A / Vouzas, Athanasios E / Zhao, Peiyao A / Gilbert, David M / Ma, Jian / van Steensel, Bas / Belmont, Andrew S

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Models of nuclear genome organization often propose a binary division into active versus inactive compartments, yet they overlook nuclear bodies. Here we integrated analysis of sequencing and image-based data to compare genome organization in four human ... ...

    Abstract Models of nuclear genome organization often propose a binary division into active versus inactive compartments, yet they overlook nuclear bodies. Here we integrated analysis of sequencing and image-based data to compare genome organization in four human cell types relative to three different nuclear locales: the nuclear lamina, nuclear speckles, and nucleoli. Whereas gene expression correlates mostly with nuclear speckle proximity, DNA replication timing correlates with proximity to multiple nuclear locales. Speckle attachment regions emerge as DNA replication initiation zones whose replication timing and gene composition vary with their attachment frequency. Most facultative LADs retain a partially repressed state as iLADs, despite their positioning in the nuclear interior. Knock out of two lamina proteins, Lamin A and LBR, causes a shift of H3K9me3-enriched LADs from lamina to nucleolus, and a reciprocal relocation of H3K27me3-enriched partially repressed iLADs from nucleolus to lamina. Thus, these partially repressed iLADs appear to compete with LADs for nuclear lamina attachment with consequences for replication timing. The nuclear organization in adherent cells is polarized with nuclear bodies and genomic regions segregating both radially and relative to the equatorial plane. Together, our results underscore the importance of considering genome organization relative to nuclear locales for a more complete understanding of the spatial and functional organization of the human genome.
    Language English
    Publishing date 2024-04-23
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.04.23.590809
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  10. Article ; Online: Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome.

    Martinez-Ara, Miguel / Comoglio, Federico / van Arensbergen, Joris / van Steensel, Bas

    Molecular cell

    2022  Volume 82, Issue 13, Page(s) 2519–2531.e6

    Abstract: Gene expression is in part controlled by cis-regulatory elements (CREs) such as enhancers and repressive elements. Anecdotal evidence has indicated that a CRE and a promoter need to be biochemically compatible for promoter regulation to occur, but this ... ...

    Abstract Gene expression is in part controlled by cis-regulatory elements (CREs) such as enhancers and repressive elements. Anecdotal evidence has indicated that a CRE and a promoter need to be biochemically compatible for promoter regulation to occur, but this compatibility has remained poorly characterized in mammalian cells. We used high-throughput combinatorial reporter assays to test thousands of CRE-promoter pairs from three Mb-sized genomic regions in mouse cells. This revealed that CREs vary substantially in their promoter compatibility, ranging from striking specificity to broad promiscuity. More than half of the tested CREs exhibit significant promoter selectivity. Housekeeping promoters tend to have similar CRE preferences, but other promoters exhibit a wide diversity of compatibilities. Higher-order transcription factors (TF) motif combinations may account for compatibility. CRE-promoter selectivity does not correlate with looping interactions in the native genomic context, suggesting that chromatin folding and compatibility are two orthogonal mechanisms that confer specificity to gene regulation.
    MeSH term(s) Animals ; Enhancer Elements, Genetic/genetics ; Gene Expression Regulation ; Genome/genetics ; Genomics ; Mammals/metabolism ; Mice ; Promoter Regions, Genetic/genetics ; Regulatory Sequences, Nucleic Acid/genetics ; Transcription Factors/genetics ; Transcription Factors/metabolism
    Chemical Substances Transcription Factors
    Language English
    Publishing date 2022-04-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2022.04.009
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