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Dynamic genome-wide interaction patterns elucidate the roles of Ki67 in chromatin organization

ABSTRACT: Dynamic genome-wide interaction patterns elucidate the roles of Ki67 in chromatin organization

PROVIDER: PRJNA772958 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16497400.fastq.gz	Fastqsanger.gz
	SRR16497500.fastq.gz	Fastqsanger.gz
	SRR16497600.fastq.gz	Fastqsanger.gz
	SRR16497401.fastq.gz	Fastqsanger.gz
	SRR16497501.fastq.gz	Fastqsanger.gz

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Dynamic genome-wide interaction patterns elucidate the roles of Ki67 in chromatin organization

Project description:Ki67 is a widely-used proliferation marker with functions in chromosomal organization. It forms a protective layer around mitotic chromosomes and is involved in genome positioning in interphase. However, a detailed understanding of how Ki67 organizes the genome was still lacking, partially because genome-wide interaction profiles were missing. Here, we generate DNA-Ki67 interaction profiles using our pA-DamID method, and show that Ki67 interacts with the genome in a domain-like pattern that partially overlaps with lamina-associated domains.

2021-10-20 | GSE186206 | GEO

Ki67-mediated chromatin accessibility impedes B-cell antigen-receptor gene rearrangement

Project description:B and T cells can recognise and respond to a vast array of foreign pathogens by virtue of the diverse antigen-receptor repertoire generated by gene rearrangement during development. Here, we show that deficiency in Ki67, a nuclear protein ubiquitously expressed throughout the cell cycle, impairs B-cell development at specific, early stages. We identified that Ki67 maintains global chromatin accessibility in lymphocyte progenitors at stages where antigen-receptor gene rearrangements occur and that gene rearrangement is less efficient in the absence of Ki67. That the defects in B cell development are caused by disrupted antigen-receptor gene rearrangement is shown by pre-rearranged antigen-receptor genes fully compensating for loss of Ki67. Collectively, these results identify a unique contribution from Ki67 to somatic antigen-receptor gene rearrangement.

2024-05-31 | GSE246986 | GEO

Comparison of Her2 and Ki67 as Prognostic Markers in Colorectal Cancer

Project description:Intervention1: Immunohistochemistry: Application of Immunohistochemical markers like Her2 and Ki67 on paraffin blocks of resected specimen of colorectal carcinoma patients for the duration or till the desired sample size is achieved, whichever is earlier. Control Intervention1: NIL: NIL Primary outcome(s): Prognostication of Her2 and Ki67 in colorectal Carcinoma patients.Timepoint: Primary outcome is expected to be achieved by the end of 2 years. Study Design: Other Method of generating randomization sequence: Method of allocation concealment: Blinding and masking:

| 76675 | ecrin-mdr-crc

Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development.

Project description:Lineage-specific gene expression is modulated by a balance between transcriptional activation and repression during animal development. Knowledge about enhancer-centered transcriptional activation has advanced considerably, but silencers and their roles in normal development remain poorly understood. Here, we performed chromatin interaction analyses of Polycomb repressive complex 2 (PRC2), a key inducer of transcriptional gene silencing, to uncover silencers, their molecular identity and associated chromatin connectivity. Systematic analysis of cis-regulatory silencer elements reveals their chromatin features and gene-targeting specificity. Deletion of certain PRC2-bound silencers in mice results in transcriptional derepression of their interacting genes and pleiotropic developmental phenotypes, including embryonic lethality. While some PRC2-bound elements function as silencers in pluripotent cells, they can transition into active tissue-specific enhancers during development, highlighting their regulatory versatility. Our study characterizes the molecular profile of silencers and their associated chromatin architectures, and suggests the possibility of targeted reactivation of epigenetically silenced genes.

| S-EPMC7869692 | biostudies-literature

Ki67-mediated chromatin accessibility impedes B-cell antigen-receptor gene rearrangement

Project description:Ki67-mediated chromatin accessibility impedes B-cell antigen-receptor gene rearrangement

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SRSF3-mediated Ki67 exon 7 alternative splicing regulates Head and Neck Squamous Cell Carcinoma progression via AKR1C2

Project description:The roles of Ki67 exon 7 have rarely been reported.SCC-9 cells were transfected with siE7 and siNC on day 0 and day 2, total RNA was extracted using TRIzol Reagent (Invitrogen, USA) and then used for mRNA sequencing (Wuhan Seqhealth Co., Ltd. China).

2023-02-23 | GSE213022 | GEO

Interaction between TBP and condensing drives the organization and faithful segregation of mitotic chromosomes

Project description:Genome/chromosome organization is highly ordered and controls nuclear events. Here, we show that the TATA box-binding protein (TBP) interacts with the Cnd2 kleisin subunit of condensin to mediate interphase and mitotic chromosome organization in fission yeast. TBP recruits condensin onto RNA polymerase III-transcribed (Pol III) genes and highly transcribed Pol II genes; condensin in turn associates these genes with centromeres. Inhibition of the Cnd2-TBP interaction disrupts condensin localization across the genome and the proper assembly of mitotic chromosomes, leading to severe defects in chromosome segregation and eventually causing cellular lethality. We propose that the Cnd2-TBP interaction coordinates transcription with chromosomal architecture by linking dispersed gene loci with centromeres. This chromosome arrangement can contribute to the efficient transmission of physical force at the kinetochore to chromosomal arms, thereby supporting the fidelity of chromosome segregation. Genome-wide distributions of condensin and Pol III factors in fission yeast.

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2017-04-28 | GSE92961 | GEO

Metaphase-Chromosome-Organization

Project description:Metaphase-Chromosome-Organization

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Analyzing stochastic transcription to elucidate the nucleoid's organization.

Project description:BackgroundThe processes of gene transcription, translation, as well as the reactions taking place between gene products, are subject to stochastic fluctuations. These stochastic events are being increasingly examined as it emerges that they can be crucial in the cell's survival. In a previous study we had examined the transcription patterns of two bacterial species (Escherichia coli and Bacillus subtilis) to elucidate the nucleoid's organization. The basic idea is that genes that share transcription patterns, must share some sort of spatial relationship, even if they are not close to each other on the chromosome. We had found that picking any gene at random, its transcription will be correlated with genes at well-defined short - as well as long-range distances, leaving the explanation of the latter an open question. In this paper we study the transcription correlations when the only transcription taking place is stochastic, in other words, no active or "deterministic" transcription takes place. To this purpose we use transcription data of Sinorhizobium meliloti.ResultsEven when only stochastic transcription takes place, the co-expression of genes varies as a function of the distance between genes: we observe again the short-range as well as the regular, long-range correlation patterns.ConclusionWe explain these latter with a model based on the physical constraints acting on the DNA, forcing it into a conformation of groups of a few successive large and transcribed loops, which are evenly spaced along the chromosome and separated by small, non-transcribed loops. We discuss the question about the link between shared transcription patterns and physiological relationship and come to the conclusion that when genes are distantly placed along the chromosome, the transcription correlation does not imply a physiological relationship.

| S-EPMC2270832 | biostudies-literature

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