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Decoding the determinants of genome-nuclear lamina interactions by a random scrambling approach (pA-DamID)

ABSTRACT: Decoding the determinants of genome-nuclear lamina interactions by a random scrambling approach (pA-DamID)

PROVIDER: PRJNA1053340 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27225400.fastq.gz	Fastqsanger.gz
	SRR27225500.fastq.gz	Fastqsanger.gz
	SRR27225600.fastq.gz	Fastqsanger.gz
	SRR27225401.fastq.gz	Fastqsanger.gz
	SRR27225501.fastq.gz	Fastqsanger.gz

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Similar Datasets

Decoding the determinants of genome-nuclear lamina interactions by a random scrambling approach (pA-DamID)

Project description:Mammalian genomes contain hundreds of lamina-associated domains (LADs), which are large, often megabase-sized heterochromatin domains that are anchored to the nuclear lamina (NL). Even though LADs play a key role in the spatial organization of the genome and potently repress gene activity, it is not yet understood how their interactions with the NL are encoded in their DNA. Here, we investigated the principles that govern LAD-NL interactions by taking a "LAD scrambling" approach. This approach relies on 1) local "hopping" of a Sleeping Beauty transposon to randomly insert loxP sites within and around a LAD of choice; and 2) Cre-mediated recombination between the loxP sites. This approach is highly efficient, enabling us to establish a large collection of clonal cell lines with deletions and inversions up to ~2Mb in size, spanning LAD and their flanking inter-LAD sequences. Mapping of NL interactions in these clones revealed that a single LAD contacts the NL through multiple regions. These regions act cooperatively and redundantly; however, some have more affinity for the NL and can boost NL contacts of neighbouring sequences. We also observed a crosstalk between two neighbouring LADs, when close enough to each other. Finally, changes in the heterochromatin mark H3K9me3 only partially mirrored changes in NL contacts. They also correlated more with gene expression changes than NL contacts did. These principles of LAD - NL interactions provide insight into the overall architecture of the genome and the impact on gene regulation.

2023-12-19 | GSE250306 | GEO

Decoding the determinants of genome-nuclear lamina interactions by a random scrambling approach

Project description:Decoding the determinants of genome-nuclear lamina interactions by a random scrambling approach

| PRJNA1053335 | ENA

Decoding the determinants of genome-nuclear lamina interactions by a random scrambling approach (RNA-Seq)

Project description:Decoding the determinants of genome-nuclear lamina interactions by a random scrambling approach (RNA-Seq)

| PRJNA1052005 | ENA

Decoding the determinants of genome-nuclear lamina interactions by a random scrambling approach (RNA-Seq)

2023-12-19 | GSE250085 | GEO

Decoding the determinants of genome-nuclear lamina interactions by a random scrambling approach

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-12-19 | GSE250307 | 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)

| PRJNA1089230 | ENA

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

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

Acidiphilium sp. PA strain:PA

Project description:Acidiphilium sp. PA strain:PA Genome sequencing and assembly

| PRJNA756838 | ENA

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

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