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DNA Adenine Methyltransferase Identification (DamID) Coupled to Next Generation Sequencing For Profiling Lamina Associated Domains

ABSTRACT: DNA Adenine Methyltransferase Identification (DamID) Coupled to Next Generation Sequencing For Profiling Lamina Associated Domains

PROVIDER: PRJNA526868 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8719735.fastq.gz	Fastqsanger.gz
	SRR8719736.fastq.gz	Fastqsanger.gz
	SRR8719737.fastq.gz	Fastqsanger.gz

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DNA Adenine Methyltransferase Identification (DamID) Coupled to Next Generation Sequencing For Profiling Lamina Associated Domains

Project description:Purpose: To compare the interaction of various proteins (in particular Lap2b and Lamin A) at the nuclear periphery with the Lamina Associated Domains (LADs) Results: Using an optimized data analysis workflow (LADetector, available at https://github.com/thereddylab/LADetector), We found near identical sequences within the genome-wide maps indicating that LAP2β and Lamin A, and hence LaminB1, are in close proximity to all LADs, suggesting that these proteins are not involved in discriminating subsets of LADs.

2019-11-01 | GSE128239 | GEO

Genome-wide maps of nuclear lamina interactions in AML12 cells upon MATR3 KD [DamID-Seq]

Project description:We performed DamID-seq assay in WT and MATR3-depleted AML12 cells to investigate the Lamina-associated-domains (LADs) affected by loss of MATR3.

2025-03-14 | GSE200242 | GEO

DamID LaminB1 data in mouse MEFs, wild-type and POU2F1-/-. DamID LaminA data in mouse Neural Precursor Cells and Astrocytes.

2012-10-10 | E-GEOD-36132 | biostudies-arrayexpress

Effects of transcription on genome - nuclear lamina interactions: DamID-seq data

Project description:In mammalian nuclei, transcriptionally active genomic regions tend to localize to the interior of the nucleus while inactive regions are often located at at the nuclear lamina. In this study we activated specific genes in lamina-associated domains by TALE-VP64 or CRISPRa-mediated activation. We also reduced transcription of individual genes by knockout of promoter/enhancer regions, or by insertion of a transcription termination sequence. In each case we generated genome-wide DamID maps to determine changes in nuclear lamina interactions, and in selected cases we also generated Repli-seq maps and/or RNAseq data.

2019-06-28 | GSE133272 | GEO

Identification of Chromatin proteins involved in gene repression in lamina-associated domains (pA-DamID)

Project description:Identification of Chromatin proteins involved in gene repression in lamina-associated domains (pA-DamID)

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LaminB1 DamID analysis in RIF1 depleted preimplantation mouse embryos

Project description:We investigated how RIF1 depletion affects the nuclear organization in mouse preimplantation embryos by performing DamID-seq to map lamina-associated domains (LADs).

2025-03-18 | GSE262788 | GEO

DamID LaminB1 data in mouse MEFs, wild-type and POU2F1-/-. DamID LaminA data in mouse Neural Precursor Cells and Astrocytes.

Project description:DamID LaminB1 data were generated in POU2F1-/- MEFs to study the potential role of POU2F1/Oct1 in genome - nuclear lamina interactions. DamID LaminA data were generated in NPCs and Astrocytes to study similarities/differences between LaminA and LaminB1 binding. The procedure to arrive at the provided Hidden Markov Model (HMM) state calls is as follows: We fitted a two-state HMM whereby emissions are distributed as Student's t variables. Mean and variance of DamID signals differ between states, but the degree of freedom (nu) is the same. Gaps in the probe coverage were filled by evenly spaced null probe-values. The parameters were estimated by an adaptation of the ECME algorithm to the HMM framework, showing faster convergence than regular EM when nu is unknown (Filion et al., Cell, 2010). State calls were derived through the Viterbi algorithm. This process was repeated separately for each cell type, yielding per-probe calls. Probes in the ‘bound’ (1) state are indicated as LAD-probes, probes in the ‘unbound’ (0) state as inter-LAD-probes.

2012-10-10 | GSE36132 | GEO

The insulator protein SU(HW) modulates nuclear lamina interactions of the Drosophila genome: DamID

Project description:Specific interactions of the genome with the nuclear lamina (NL) are thought to assist chromosome folding inside the nucleus and to contribute to the regulation of gene expression. High-resolution mapping has recently identified hundreds of large, sharply defined lamina-associated domains (LADs) in the human genome, and suggested that the insulator protein CTCF may help to demarcate these domains. Here, we report the detailed structure of LADs in Drosophila cells, and investigate the putative roles of five insulator proteins in LAD organization. We found that of these five proteins, only SU(HW) binds preferentially at LAD borders and at specific positions inside LADs, while GAF, CTCF, BEAF-32 and DWG are mostly absent from these regions. By knockdown and overexpression studies we demonstrate that SU(HW) weakens LAD – NL interactions by a local antagonistic effect. Our results provide insights into the evolution of LAD organization and reveal a role for SU(HW) in the regulation of genome – NL interactions. DamID experiments for Lamin, CTCF, SU(HW), GAF, DWG, and BEAF-32, and for Lamin after overexpression and after knockdown of SU(HW), were performed in Drosophila cell cultures. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing. Every experiment was done in duplicate in the reverse dye orientation. The supplementary file 'GSE20311_DamID_norm_mean.txt' contains the mean log2(Dam-fusion/Dam-only) values of two replicates.

2011-01-24 | E-GEOD-20311 | biostudies-arrayexpress

Identification of Chromatin proteins involved in gene repression in lamina-associated domains (pA-DamID)

Project description:Lamina-associated domains (LADs) are large chromatin regions that are associated with the nuclear lamina and form a repressive environment for transcription. The molecular players that mediate gene repression in LADs are currently unknown. Here we performed a full-genome genetic screen in human cells using LAD-integrated fluorescent reporters to identify such regulators. Surprisingly, the screen identified very few lamina proteins, but revealed roles for dozens of known chromatin regulators. Among these are the negative elongation factor (NELF) complex and interacting factors, suggesting that regulation of RNA polymerase pausing can be a mechanism to repress transcription in LADs. Furthermore, the chromatin remodeler complex BAF and the activation complex Mediator can work both as activators and repressors in LADs, depending on the local context and possibly rewiring of heterochromatin. Our data suggest that fundamental regulatory steps of the transcription process and chromatin remodeling, rather than interaction with NL proteins, have a major role in the regulation of transcription in LADs.

2024-07-10 | GSE261868 | GEO

Gene regulatory loops at lamina-associated domains

Project description:Gene regulatory loops at lamina-associated domains

| PRJNA913836 | ENA