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Effect of deleting ultra-conserved elements PAX6_Tarzan, PBX3_Claudia on gene expression in K562 cells

ABSTRACT: Effect of deleting ultra-conserved elements PAX6_Tarzan, PBX3_Claudia on gene expression in K562 cells

PROVIDER: PRJNA1036670 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26707510_1.fastq.gz	Fastqsanger.gz
	SRR26707510_2.fastq.gz	Fastqsanger.gz
	SRR26707511_1.fastq.gz	Fastqsanger.gz
	SRR26707511_2.fastq.gz	Fastqsanger.gz
	SRR26707512_1.fastq.gz	Fastqsanger.gz

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Effect of deleting ultra-conserved elements PAX6_Tarzan, PBX3_Claudia on gene expression in K562 cells

Project description:Non-coding regulatory elements (NCRE) represent a major fraction of the human genome, play important roles in different biological pathways, and have the potential as genomic medicine targets. We developed a straightforward dual-CRISPR screening system capable of deleting thousands of NCREs genome-wide to study their functions in distinct biological contexts in K562 cells. Here we reported 4 top hits from the genome-wide screen of ultra-conserved elements (UCE), i.e. PAX6_Tarzan(chr11:31810437-31810870, hg19) and PBX3_Claudia(chr9:128457564-128457785, hg19) play essential roles in cell growth and drug response.

2024-03-10 | GSE247234 | GEO

Expressional Alterations in Ultra-Conserved Non-Coding RNA in Response to ATRA-induced Differentiation

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An Evolutionary Cancer Epigenetic approach revealed DNA hypermethylation of Ultra-Conserved Non-coding Elements in squamous cell carcinoma of different mammalian species

Project description:Background: Ultra-Conserved-Non-coding Elements (UCNEs) are genomic sequences that exhibit >95% sequence identity between human, mammals, birds, reptiles and fishes. Recent findings reported their functional role in cancer. Aim of this study was to evaluate their DNA methylation modifications in squamous cell carcinoma (SCC) from different mammal species Methods: Fifty SCC from 26 humans, 17 cats, 3 dogs, 1 horse, 1 bovine, 1 badger and 1 porcupine were investigated. Fourteen feline stomatitis and normal samples from 36 healthy human donors, 7 cats, 5 dogs, 5 horses, 2 bovines and 1 badger were collected as normal controls. Bisulfite Next Generation Sequencing evaluated the DNA methylation level from seven UCNEs (uc.160, uc.283, uc.416, uc.339, uc.270, uc.299, uc.328). Results: 57/59 CpGs were significantly different according to the Kruskal-Wallis test (P<0.05) comparing normal vs SCC. A common DNA hypermethylation pattern was observed in SCC from all the species evaluated in this study, with an increasing trend of hypermethylation starting from normal mucosa, through stomatitis to SCC. Conclusions: Our findings indicate that UCNEs are hypermethylated in human SCC, and this behavior is also conserved among different species of mammals.

2020-09-04 | GSE157436 | GEO

An Evolutionary Cancer Epigenetic approach revealed DNA hypermethylation of Ultra-Conserved Non-coding Elements in squamous cell carcinoma of different mammalian species

Project description:An Evolutionary Cancer Epigenetic approach revealed DNA hypermethylation of Ultra-Conserved Non-coding Elements in squamous cell carcinoma of different mammalian species

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Silencing of ultra-conserved long non-coding RNA Uc.291 causes delay of keratinocyte differentiation

Project description:Development of the skin includes a complicated program of cellular differentiation. Here, we study the role of Uc.291, a long non-coding RNA derived from ultra-conserved region, upregulated in suprabasal layer of the skin and during in vitro differentiation of keratinocytes. Depletion of Uc.291 causes delay of keratinocyte differentiation with decreased levels of the expression of epidermal differentiation complex (EDC) genes.

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Identification of conserved cis-regulatory elements impact Mecp2 level and neurological functions

Project description:Methyl-CpG binding protein 2 (MeCP2) is a nuclear protein that binds to methylated cytosines and regulates gene expression. Normal brain function requires precise control of MeCP2 level. Loss of function mutations in the X-linked gene, MECP2 cause Rett Syndrome (RTT), a progressive neurological disorder. Increase in MeCP2 level leads to the neurological disorder MECP2 duplication syndrome (MDS). Despite the functional importance of MeCP2 in the brain, its transcriptional regulation remains poorly understood. Here, we utilized ATAC-seq in the mouse brain across development to identify five putative adult brain cis-regulatory elements (CREs) of Mecp2. We found that knocking out these CREs using CRISPR-Cas9 altered Mecp2 levels. Furthermore, two of the CREs were conserved in human, and when we delete either of these in mice, the animals show progressive neurological dysfunction. Deletion of one of the conserved CREs led to a decreased MeCP2 level and caused phenotypes similar, albeit milder, to those seen in Mecp2-null mice whereas the deletion of the second CRE led to an increased MeCP2 level and phenotypically resembled, but also milder than, MECP2 duplication mice. Deleting these two conserved CREs levels in human iPSC-derived neurons also similarly altered MECP2 levels. Taken together, our discovery of CREs that modulate Mecp2/MECP2 expression provides insight into regulation of Mecp2/MECP2 in the mouse brain and human neurons, respectively. These CREs could be candidate sites for non-coding mutations that lead to neurodevelopmental disorders characterized by partial features of RTT or MDS.

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Comparison of ultra-conserved elements in drosophilids and vertebrates.

Project description:Metazoan genomes contain many ultra-conserved elements (UCEs), long sequences identical between distant species. In this study we identified UCEs in drosophilid and vertebrate species with a similar level of phylogenetic divergence measured at protein-coding regions, and demonstrated that both the length and number of UCEs are larger in vertebrates. The proportion of non-exonic UCEs declines in distant drosophilids whilst an opposite trend was observed in vertebrates. We generated a set of 2,126 Sophophora UCEs by merging elements identified in several drosophila species and compared these to the eutherian UCEs identified in placental mammals. In contrast to vertebrates, the Sophophora UCEs are depleted around transcription start sites. Analysis of 52,954 P-element, piggyBac and Minos insertions in the D. melanogaster genome revealed depletion of the P-element and piggyBac insertions in and around the Sophophora UCEs. We examined eleven fly strains with transposon insertions into the intergenic UCEs and identified associated phenotypes in five strains. Four insertions behave as recessive lethals, and in one case we observed a suppression of the marker gene within the transgene, presumably by silenced chromatin around the integration site. To confirm the lethality is caused by integration of transposons we performed a phenotype rescue experiment for two stocks and demonstrated that the excision of the transposons from the intergenic UCEs restores viability. Sequencing of DNA after the transposon excision in one fly strain with the restored viability revealed a 47 bp insertion at the original transposon integration site suggesting that the nature of the mutation is important for the appearance of the phenotype. Our results suggest that the UCEs in flies and vertebrates have both common and distinct features, and demonstrate that a significant proportion of intergenic drosophila UCEs are sensitive to disruption.

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A transcribed ultra-conserved noncoding RNA, uc.285+, promotes colorectal cancer proliferation via directly binding mRNA

Project description:To further explore the differential expression profile of Transcribed ultra-conserved region (TUCR) in human colorectal cancer, we have employed TUCR microarray expression profiling as a discovery platform to identify potential differential expression profile of TUCR between human colorectal cancer tissue (CCRT) and human normal mucosal epithelial tissue of the colorectal (NT). Results showed that multiple differentially expressed TUCRs were found between CCRT and NT. In this study, We selected T-UCRs with large differences to verification and found that uc.285+ upregulation was most obvious. Then we further explored the biological function and mechanism of uc.285+ in colorectal cancer.

2021-06-15 | GSE167326 | GEO

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