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Chromatin associated α-satellite RNA maintains chromosome stability by re-establishing SAF-A in the mitotic cell cycle [ChIRP-seq]

ABSTRACT: Chromatin associated α-satellite RNA maintains chromosome stability by re-establishing SAF-A in the mitotic cell cycle [ChIRP-seq]

PROVIDER: PRJNA1126165 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29478730_1.fastq.gz	Fastqsanger.gz
	SRR29478730_2.fastq.gz	Fastqsanger.gz
	SRR29478731_1.fastq.gz	Fastqsanger.gz
	SRR29478731_2.fastq.gz	Fastqsanger.gz
	SRR29478732_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Chromatin associated α-satellite RNA maintains chromosome stability by re-establishing SAF-A in the mitotic cell cycle [ChIRP-seq]

Project description:RNA components seem to be required for the localization of SAF-A on chromatin. A SAF-A/RNA mesh model has been proposed and supported by super-resolved images, in which SAF-A forms a homogeneous mesh together with nuclear scaffolding RNA species to regulate chromatin structure. As an evolutionarily conserved RNA-binding protein, SAF-A has been reported to interact with a wide variety of RNAs in different cell types. Particularly, a recent study points out that repetitive non-coding sequences of pre-mRNAs and lncRNAs can serve as scaffold RNAs to counter chromatin compaction and maintain chromosome territory architecture together with SAF-A. At this moment, most studies have demonstrated the role of SAF-A/RNA in regulating interphase chromatin structure, and very few works have covered the role of SAF-A/RNA in mitosis. A recent study showed that SAF-A, together with most of its interacting RNAs, needs to be evicted from the condensing chromosomes during mitosis. This brings out an open question of how the SAF-A/RNA scaffold is disassembled and rebuilt when the cell enters and exits mitosis. Here, we showed that α-satellite RNA is dynamically expressed and stays associated with the centromeric chromatin throughout the mitotic cell cycle. Specific interactions between α-satellite RNA and SAF-A were observed both in vitro and in vivo. Depletion of either α-satellite RNA or SAF-A would lead to chromosome missegregation phenotypes during mitosis. More importantly, interfering with α-satellite RNA showed an evident effect on the chromatin relocalization of SAF-A, and further LAP2 upon mitosis exit. Therefore, we proposed that α-satellite RNA may act as a foundation stone for recruiting SAF-A scaffold upon mitosis exit.

2025-03-25 | GSE270307 | GEO

Chromatin associated α-satellite RNA maintains chromosome stability by re-establishing SAF-A in the mitotic cell cycle [CUT&TAG]

Project description:α-satellite RNA has been shown to interact with specific sets of RNA-binding proteins. By forming complexes with centromere proteins CENPA, CENPB, and CENPC, α-satellite RNA demonstrated its essential role in maintaining functional human centromeres. Also, α-satellite RNA has been reported to interact with SUV39H1, which is the histone methyltransferase that is responsible for H3K9me3. Together with the findings in mice and some other eukaryotes that RNA components are required for the recruitment of heterochromatin proteins and the maintenance of pericentric heterochromatin, it has long been suspected that α-satellite RNA might also be involved in the heterochromatin formation and recruitment of HP1 in human cells. In this study, we identified Scaffold Attachment Factor-A (SAF-A) as a novel α-satellite RNA binding protein. SAF-A, also known as hnRNPU, the most abundant member in the hnRNP complex, was initially identified as the major component of the nuclear scaffold. It binds to the nuclear scaffold in AT-rich regions through its DNA-binding domain. In recent years, several studies have suggested that SAF-A may play a more fundamental and general role in nuclear organization in interphase. Depletion of SAF-A will lead to pronounced chromatin condensation of gene-rich regions and global changes in 3D genome architecture.

2025-03-31 | GSE286152 | GEO

Chromatin associated α-satellite RNA maintains chromosome stability by re-establishing SAF-A in the mitotic cell cycle [RNA-seq]

2025-03-25 | GSE286151 | GEO

Chromatin associated α-satellite RNA maintains chromosome stability by re-establishing SAF-A in the mitotic cell cycle [CUT&TAG]

Project description:Chromatin associated α-satellite RNA maintains chromosome stability by re-establishing SAF-A in the mitotic cell cycle [CUT&TAG]

| PRJNA1208008 | ENA

Chromatin associated α-satellite RNA maintains chromosome stability by re-establishing SAF-A in the mitotic cell cycle [RNA-seq]

Project description:Chromatin associated α-satellite RNA maintains chromosome stability by re-establishing SAF-A in the mitotic cell cycle [RNA-seq]

| PRJNA1208003 | ENA

Long noncoding RNA CCTT recruits CENP-C to centromeres by directly binding to centromeric DNA [ChIRP-Seq]

Project description:To investigate the exact locations of CCTT-chromatin interaction on a genome-wide scale, we modified previously reported ChIRP-seq (chromatin isolation by RNA purification followed by deep-sequencing) with a crosslinker 4’- aminomethyltrioxalen (AMT, a psoralen derivative), which allows fixation of nucleic acid interaction by ultraviolet light without crosslinking proteins. We designed 8 complementary DNA oligonucleotides that tiled the Alu-depleted part of CCTT. Affinity-purified CCTT-binding DNAs were sequenced and mapped to the HuRef genome hg38, which contains human α-satellite sequence models in each centromeric region. In contrast with 5.38% of input reads mapping to α-satellite sequence, 16.89% of CCTT-binding reads were enriched at α-satellites. Peaks bound by lnc-CCTT were identified by MACS2 algorithm, which compared the reads in CCTT-captured samples with that in input ones. CCTT-binding peaks mapped across the centromeric regions of all 23 reference centromeres. Next, we validated the enrichment of centromeric peaks located at all chromosomes via ChIRP-qPCR. To validate our ChIRP-seq results, we selected representatives of three major subpopulations: multimapping peaks in one specific chromosome and several chromosomes, as well as single-copy peaks. We performed ChIRP-qPCR and found abundant CCTT-binding centromeric peaks throughout all 23 chromosomes. Importantly, CCTT ChIRP-seq profile was highly correlated with the previously reported ChIP-seq profiles of CENP-C (Pearson correlation R = 0.82), both of which showed very strong, extensive signals across entire centromeric regions in HeLa cells.

2022-04-20 | GSE149532 | GEO

SAF PP Metagenome

Project description:SAF PP Metagenome Raw sequence reads

| PRJNA668809 | ENA

JPL SAF Metagenome

Project description:JPL SAF Metagenome Raw sequence reads

| PRJNA641034 | ENA

Identification of alpha-satellite RNA interacting proteins

Project description:We set out to identify proteins that bind alpha-satellite ncRNAs in HCT-116 and SW-480 colorectal cancer human cell lines. We performed RNA pulldown followed by mass spectrometry identification of the associated proteins. Among the identified proteins, we observed a statistical overrepresenttion of some ontology ssociated to mitotic progression in HCT-116 cells, but not in SW-480 cells.

2022-08-12 | PXD024582 | Pride

RNA-seq analysis of scaffold attachment factor A (SAF-A) knockdown in RPE1 cells

Project description:Analysis of gene expression by RNA-seq upon siRNA mediated knockdown of scaffold attachment factor A (SAF-A) versus control siRNA in RPE1 cells at 24 hour and 48 hour time points post transfection reveals SAF-A loss does not impact on gene transcription

2017-06-01 | GSE98541 | GEO

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