An interdependent network of functional enhancers regulates transcription and EZH2 loading at the INK4a/ARF locus

Farooq, Umer; Saravanan, Bharath; Islam, Zubairul; Walavalkar, Kaivalya; Singh, Anurag Kumar; Jayani, Ranveer Singh; Meel, Sweety; Swaminathan, Sudha; Notani, Dimple

doi:10.1016/j.celrep.2021.108898

Cited by 21 publications

(29 citation statements)

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“…Epigenetic regulation of chromatin structure has a key role in the control of cell differentiation and cell identity in embryogenesis. The INK4-ARF locus is epigenetically silenced thanks to the function of the Polycomb group of proteins [19,21] Importantly, repression of the Ink4a/ARF locus represents a roadblock during iPS (induced Pluripotent Stem Cells) generation [20,29], in line with the role of epigenetic regulation of this locus in ES cells homeostasis. While p16Ink4a and p19Arf induction in cultured primary cells cause senescence [30], Bmi-1 overexpression can prevent senescence and extend their replicative lifespan by reducing p16Ink4a and p19Arf expression [31].…”

Section: Discussionmentioning

confidence: 99%

“…The CDKN2A locus has been shown to affect cell metabolism by influencing glucose homeostasis, β-cell functions and mass, hepatic gluconeogenesis, and lipid storage [35]. Genome-wide association studies (GWASs) have unequivocally linked the CDKN2A locus with human diabetes risk, although the mechanisms remain uncertain [21,[36][37][38][39]. Moreover, it is known that CDKN2A mutation occurs in early PDAC (pancreatic ductal adenocarcinoma) [40,41] and, CDKN2A promoter hypermethylation is related to malignant tumor development [42].…”

Section: Discussionmentioning

confidence: 99%

“…It is known that the Cdkn2a locus is not expressed in ES and in iPS (induced Pluripotent Stem) cells but acquires the epigenetic marks of a bivalent chromatin domain, thus retaining the ability to be reactivated if required after differentiation onset [19,20]. Epigenetic sup-pression of the INK4A-ARF locus has been widely shown, and greatly promotes survival and cloning efficiency in individualized human ESCs via deposition of the H3K27me3mark to INK4A-ARF locus [21,22]. In order to verify if epigenetic modifications, specifically DNA methylation and chromatin deacetylation, were responsible for the Ink4a and Arf regulation in ESCs, we performed treatments of cells with widely used epidrugs.…”

Section: Dna Methylation and Chromatin Acetylation Affect Ink4a And Arf Gene Expression In Escsmentioning

confidence: 99%

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Pancreatic Progenitor Commitment Is Marked by an Increase in Ink4a/Arf Expression

et al. 2021

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The identification of the molecular mechanisms controlling early cell fate decisions in mammals is of paramount importance as the ability to determine specific lineage differentiation represents a significant opportunity for new therapies. Pancreatic Progenitor Cells (PPCs) constitute a regenerative reserve essential for the maintenance and regeneration of the pancreas. Besides, PPCs represent an excellent model for understanding pathological pancreatic cellular remodeling. Given the lack of valid markers of early endoderm, the identification of new ones is of fundamental importance. Both products of the Ink4a/Arf locus, in addition to being critical cell-cycle regulators, appear to be involved in several disease pathologies. Moreover, the locus’ expression is epigenetically regulated in ES reprogramming processes, thus constituting the ideal candidates to modulate PPCs homeostasis. In this study, starting from mouse embryonic stem cells (mESCs), we analyzed the early stages of pancreatic commitment. By inducing mESCs commitment to the pancreatic lineage, we observed that both products of the Cdkn2a locus, Ink4a and Arf, mark a naïve pancreatic cellular state that resembled PPC-like specification. Treatment with epi-drugs suggests a role for chromatin remodeling in the CDKN2a (Cycline Dependent Kinase Inhibitor 2A) locus regulation in line with previous observations in other cellular systems. Our data considerably improve the comprehension of pancreatic cellular ontogeny, which could be critical for implementing pluripotent stem cells programming and reprogramming toward pancreatic lineage commitment.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Dna Methylation and Chromatin Acetylation Affect Ink4a And Arf Gene Expression In Escsmentioning

confidence: 99%

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Pancreatic Progenitor Commitment Is Marked by an Increase in Ink4a/Arf Expression

et al. 2021

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“…However, it may easily be adapted to other adherent cell lines with minor variations. For complete details on the use and execution of this protocol, please refer to Farooq et al. (2021) .…”

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confidence: 99%

“…For complete details on the use and execution of this protocol, please refer to Farooq et al. (2021) .…”

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confidence: 99%

Optimized protocol to create deletion in adherent cell lines using CRISPR/Cas9 system

Farooq

Notani

2021

STAR Protocols

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Summary The CRISPR/Cas9 system is a powerful tool for genome editing and is adaptable for a wide range of applications. Here, we have put together a step-by-step protocol for generating knockout cell lines (coding or non-coding region) using CRISPR/Cas9 tool. The protocol below has been tested on adherent cell lines such as HeLa and MCF7. However, it may easily be adapted to other adherent cell lines with minor variations. For complete details on the use and execution of this protocol, please refer to Farooq et al. (2021) .

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Cis‐regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers

Singh,

Walavalkar,

Tavernari

et al. 2023

Molecular Oncology

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Human papillomavirus (HPV) infections are the primary drivers of cervical cancers, and often HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes is relatively well known, the cis‐regulatory effect of integrated HPV DNA on host chromatin structure and gene regulation remains less understood. We investigated genome‐wide patterns of HPV integrations and associated host gene expression changes in the context of host chromatin states and topologically associating domains (TADs). HPV integrations were significantly enriched in active chromatin regions and depleted in inactive ones. Interestingly, regardless of chromatin state, genomic regions flanking HPV integrations showed transcriptional upregulation. Nevertheless, upregulation (both local and long‐range) was mostly confined to TADs with integration, but not affecting adjacent TADs. Few TADs showed recurrent integrations associated with overexpression of oncogenes within them (e.g. MYC, PVT1, TP63 and ERBB2) regardless of proximity. Hi‐C and 4C‐seq analyses in cervical cancer cell line (HeLa) demonstrated chromatin looping interactions between integrated HPV and MYC/PVT1 regions (~ 500 kb apart), leading to allele‐specific overexpression. Based on these, we propose HPV integrations can trigger multimodal oncogenic activation to promote cancer progression.

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An interdependent network of functional enhancers regulates transcription and EZH2 loading at the INK4a/ARF locus

Cited by 21 publications

References 69 publications

Pancreatic Progenitor Commitment Is Marked by an Increase in Ink4a/Arf Expression

Pancreatic Progenitor Commitment Is Marked by an Increase in Ink4a/Arf Expression

Optimized protocol to create deletion in adherent cell lines using CRISPR/Cas9 system

Cis‐regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers

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