The Functional Map of Ultraconserved Regions in Humans, Mice and Rats DOI Creative Commons
Bruno Thiago de Lima Nichio,

Liliane Santana Oliveira,

Ana Carolina Rodrigues

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 28, 2024

Abstract BACKGROUND: Ultraconserved regions (UCRs) encompass 481 DNA segments exceeding 200 base pairs (bp), displaying 100% sequence identity across humans, mice, and rats, indicating profound conservation taxa pivotal functional roles in human health disease. Despite two decades since their discovery, many UCRs remain to be explored owing incomplete annotation, particularly of newly identified long non-coding RNAs (lncRNAs), limited data aggregation large-scale databases. This study offers a comprehensive map UCRs, investigating genomic transcriptomic implications: (i) enriching UCR annotation data, including ancestral genomes; (ii) exploring lncRNAs containing T-UCRs pan-cancers; (iii) elucidating involvement regulatory elements; (iv) analyzing population single-nucleotide variations linked motifs, expression patterns, diseases. RESULTS: Our results indicate that, although high number protein-coding transcripts with (1,945 from 2,303), 1,775 contained outside CDS regions. Focusing on transcripts, 355 are mapped 85 lncRNA genes, 35 them differentially expressed at least one TCGA cancer type, seven strongly associated survival time, 23 according single-cell analysis. Additionally, we elements 373 (77.5%), found 353 SNP-UCRs (with 1% frequency) potential effects, such as motif changes, eQTL potential, associations disease/traits. Finally, 4 novel that had not been previously described. CONCLUSION: report compiles organizes all the above information, providing new insights into mechanisms diagnostic applications.

Language: Английский

LncRNA NR2F1-AS1 as a potential biomarker for prognosis in cancer patients: meta and bioinformatics analysis DOI

Lu Tang,

Qingmei Liu, Shuang Zhang

et al.

Expert Review of Molecular Diagnostics, Journal Year: 2023, Volume and Issue: 23(12), P. 1263 - 1272

Published: Oct. 30, 2023

Background Previous studies have shown that the differential expression of lncRNA NR2F1-AS1 is closely related to prognosis cancer, but conclusion still controversial. Therefore, we conducted a meta-analysis and bioinformatics analysis explore correlation between LncRNA cancer prognosis.

Language: Английский

Citations

1
Transcriptomic Meta-analysis Identifies Long Non-Coding RNAs Mediating Zika’s Oncolytic Impact in Glioblastoma Multiforme DOI Open Access
Youssef A. Kousa, Shriya Singh,

Allison Horvath

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 4, 2024

ABSTRACT Glioblastoma multiforme (GBM) is an aggressive and lethal form of brain cancer with few effective treatments. In this context, Zika virus has emerged as a promising therapeutic agent due to its ability selectively infect kill GBM cells. To elucidate these mechanisms expand the landscape oncolytic virotherapy, we pursued transcriptomic meta-analysis comparing molecular signatures infection in neuroblastoma (NBM). Over-representation analysis dysregulated coding genes showed significant enrichment tumor necrosis factor (TNF), NF-κB, p53 signaling pathways. A refined list long non-coding RNAs consistently Zika-infected GBMs was also developed. Functional review candidates revealed their potential regulatory role Zika-mediated oncolysis. We performed validation less-researched targets adult pediatric cell lines found differential regulation, predicted. Altogether, our results provide novel insights into underlying effect on GBM. highlight that could be further interrogated improve efficacy death utility adjuvant virotherapy for other related cancers.

Language: Английский

Citations

0
The Functional Map of Ultraconserved Regions in Humans, Mice and Rats DOI Creative Commons
Bruno Thiago de Lima Nichio,

Liliane Santana Oliveira,

Ana Carolina Rodrigues

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 28, 2024

Abstract BACKGROUND: Ultraconserved regions (UCRs) encompass 481 DNA segments exceeding 200 base pairs (bp), displaying 100% sequence identity across humans, mice, and rats, indicating profound conservation taxa pivotal functional roles in human health disease. Despite two decades since their discovery, many UCRs remain to be explored owing incomplete annotation, particularly of newly identified long non-coding RNAs (lncRNAs), limited data aggregation large-scale databases. This study offers a comprehensive map UCRs, investigating genomic transcriptomic implications: (i) enriching UCR annotation data, including ancestral genomes; (ii) exploring lncRNAs containing T-UCRs pan-cancers; (iii) elucidating involvement regulatory elements; (iv) analyzing population single-nucleotide variations linked motifs, expression patterns, diseases. RESULTS: Our results indicate that, although high number protein-coding transcripts with (1,945 from 2,303), 1,775 contained outside CDS regions. Focusing on transcripts, 355 are mapped 85 lncRNA genes, 35 them differentially expressed at least one TCGA cancer type, seven strongly associated survival time, 23 according single-cell analysis. Additionally, we elements 373 (77.5%), found 353 SNP-UCRs (with 1% frequency) potential effects, such as motif changes, eQTL potential, associations disease/traits. Finally, 4 novel that had not been previously described. CONCLUSION: report compiles organizes all the above information, providing new insights into mechanisms diagnostic applications.

Language: Английский

Citations

0