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Genome-wide maps of nucleolus interactions in human cells using 4xAP3 DamID

ABSTRACT: We used DamID to map nucleolus interactions in human cells using a 4x tandem repeat of the nucleolar targeting sequence of AP3D1 (Scott, 2010) ("4xAP3"). These interactions are mapped in various human cell lines, including human K562 cells

ORGANISM(S): Homo sapiens

PROVIDER: GSE148609 | GEO | 2020/12/18

REPOSITORIES: GEO

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Genome-wide maps of nucleolus interactions in human cells using 4xAP3 DamID

Project description:Genome-wide maps of nucleolus interactions in human cells using 4xAP3 DamID

| PRJNA625198 | ENA

Mapping of nucleolus-associated chromosomal domains during replicative senescence.

Project description:Nucleolus-associated DNA was isolated from cross-linked proliferating and senescent IMR90 human fibroblasts and hybridized against genomic (1) or non-nucleolar (2) DNA to map nucleolus-associated chromosomal domains.

2017-06-18 | GSE78043 | GEO

Mapping nucleolus-associated chromatin interactions by nucleolus-Hi-C reveals repression network

Project description:Nucleolus plays a key role in organizing global nuclear structure and facilitating gene regulation, but the three dimensional information within the nucleolus associated chromatins are still unknown, so here we development the Nucleolus Hi-C (NHi-C) experimental technique, which combines the nucleolus isolation with Hi-C experiment, and study the interactions within and surrounding nucleolus in human cells with a high resolution. With NHi-C experiment, we report how the nucleolus-associated chromatin regions interact at genome scale, and how these interactions organize the repressive nucleus architecture.

2021-02-01 | GSE90003 | GEO

FuHsi initiates the nucleolus biogenesis and regulates mouse development.

Project description:The nucleolus is a membraneless condensate in eukaryotic cell nucleus, which is composed of three layers of fibrillar center (FC), dense fibrillar component (DFC), as well as granular component (GC) and regulates ribosome biogenesis1,2. The first step in nucleolar biogenesis is transcription of ribosomal DNA (rDNA) genes, termed as nucleolar organizer regions (NORs), which is binding by upstream binding factor (UBF) and other transcription-associated proteins3-6. However, whether any molecule early onset of rDNA is involved in nucleolar biogenesis remains unknown. Here, we analyze the candidate long noncoding RNAs (lncRNAs) encoded microproteins, preferentially as proteins, based on the nucleoli mass spectrometry (MS) data and identify 7 potential proteins that may be enriched in the nucleolus. Among these proteins, FuHsi solely builds a site that subsequently recruits rDNA, UBF and other transcription-associated proteins to initiate the nucleolus biogenesis. Functionally, FuHsi depletion leads to a dissolved nucleolus, as indicated by the disappearance of rDNA, FC, DFC and GC. Deficient FuHsi impairs rDNA transcription and subsequent ribosome biogenesis. Furthermore, Fuhsi is an evolutionarily conserved protein in mouse, and homolog protein can functionally replace each other in vitro. The heterozygous Fuhsi knockout (KO) mice die within four weeks, and exhibit small size as well as decreased weight, in concordance with the decreased ribosome biogenesis, who are rescued by transgenic human FuHsi. This study reveals that FuHsi is a core protein that initiates nucleolar biogenesis and regulates mouse development.

2024-08-02 | GSE253977 | 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

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

BMAL1 associates with NOP58 in the nucleolus and contributes to pre-rRNA processing

Project description:The transcription factor BMAL1 is a core element of the circadian clock that contributes to cyclic control of genes transcribed by RNA polymerase II. By using biochemical cellular fractionation and immunofluorescence analyses we reveal a previously uncharacterized nucleolar localization for BMAL1. We used an unbiased approach to determine the BMAL1 interactome by mass spectrometry and identified NOP58 as a prominent nucleolar interactor. NOP58, a core component of the box C/D small nucleolar ribonucleoprotein complex, associates with Snord118 to control specific pre-ribosomal RNA (rRNA) processing steps. These results suggest a non-canonical role of BMAL1 in rRNA regulation. Indeed, we show that BMAL1 controls NOP58-associated Snord118 nucleolar levels and cleavage of unique pre-rRNA intermediates. Our findings identify an unsuspected function of BMAL1 in the nucleolus that appears distinct from its canonical role in the circadian clock system

2020-08-25 | PXD018946 | Pride

A Novel Role of Wnt/β Catenin Signaling in Regulating the Nucleolus in Triple Negative Breast CancerA Novel Role of Wnt/β Catenin Signaling in Regulating the Nucleolus in Triple Negative Breast Cancer

Project description:Breast cancer is one of the most common types of cancer in women. One key signaling pathway known to regulate tumor growth, metabolic adaptation, and cellular stress response in breast cancer is Wnt signaling. Breast cancer patients, specifically triple negative breast cancer (TNBC), with upregulated Wnt signaling often have a poor clinical prognosis. However, the effects of Wnt/β-catenin signaling on the nucleolus and the resultant impact on cancer development and progression remain unclear. A notable reduction was observed in the number of nucleoli per nucleus in response to Wnt/β-catenin signaling inhibition in multiple TNBC cell lines. Our comparative proteomic analysis revealed several changes in the composition of the nucleolar proteome of TNBC cells upon inhibition of Wnt signaling. Overall, we demonstrate that Wnt/β-catenin signaling will affects nucleolar functionality and thus influences breast cancer progression. Understanding the role of Wnt signaling in the nucleolus and breast cancer is a critical step towards developing novel therapeutic options for the treatment of breast cancer.

2021-03-05 | PXD021181 | Pride

DamID (LmnB1/Dam) Log2 ratios of C57Bl/6 fibroblasts and RAG2-/- pro-B cells.

Project description:Comparison of DamID profiles and LAD patterning across cell types reveals regions of variable LADs LmnB1 interactions at the nuclear periphery of C57Bl/6 pro-B cells and fibroblasts were identified by DamID in duplicate for both pro-B and fibroblasts (4 samples total). For each sample, Dam-LmnB1/Dam-only Log2 ratios of chromosomes 11 and 12 were calculated, lifted over to mm9, duplicates were normalized and averaged together.

2014-12-16 | E-GEOD-56990 | biostudies-arrayexpress

Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila [DamID-seq]

Project description:Dam identification (DamID) is a powerful technique to generate genome-wide maps of chromatin protein binding. Due to its high sensitivity it is particularly suited to study the genome interactions of chromatin proteins in small tissue samples in model organisms such as Drosophila. Here we report an intein-based approach to tune the expression level of Dam and Dam-fusion proteins in Drosophila by addition of a ligand to fly food. This helps to suppress toxic effects of Dam. In addition we describe a strategy for genetically controlled expression of Dam in a specific cell type in complex tissues. We demonstrate the utility of the latter by generating a glia-specific map of Polycomb in small samples of brain tissue. We determined DamID scores for Polycomb, normalized by Dam only control, for Drosophila larval central brain, larval fat bodies and repo+ glial cells of larval central brain. All samples were performed with 2 biological replicates. In case of Dam only control for larval central brain, each biological replicate was performed with 3 technical replicates.

2016-03-17 | E-GEOD-75831 | biostudies-arrayexpress

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