Cancer-related molecular mechanisms research

The paper investigates the structural features of the NORAD lncRNA and their role in modulating Pumilio protein activity through RNA structure and interactions.

This paper introduces a multi-run Concrete Autoencoder (mrCAE) to identify prognostic lncRNAs across 12 cancers, achieving 95% accuracy in cancer classification and identifying 76 prognostic lncRNAs.

The paper uses bulk RNA sequencing data to analyze lncRNA expression specificity across 13 brain regions and shows their utility in deconvolving brain regions and cell-type identification.

This study shows Xist uses spatial amplification of SHARP to achieve chromosome-wide silencing while maintaining specificity to the X chromosome.

The paper identifies lncRNA-miRNA-mRNA networks involved in fetal hemoglobin regulation using machine learning and public datasets.

The study characterizes LINC01016, showing its conserved expression in non-human primates, differential exon usage, and isoform-specific roles in gynecological cancers.

The paper identifies non-coding RNAs involved in cell cycle regulation by analyzing RNA, RNA polymerase II, and promoter activity changes across the cell cycle in human keratinocytes.

The paper constructs a ceRNA network and immune infiltration profiles in KIRC using TCGA data, develops two prognostic nomograms, and identifies key genes and immune cells associated with patient survival.

The paper introduces a custom lncRNA capture sequencing approach to improve detection sensitivity of lncRNAs in various human sample types.

The paper identifies 418 novel lncRNAs in rectal neuroendocrine tumors and analyzes their expression and regulatory roles in cancer-related genes.

This paper analyzes XIST expression and its prognostic roles across multiple cancers using public databases, finding it associated with prognosis, miRNAs, immune infiltration, and mutations.

The paper analyzes public RNAseq data to identify lncRNAs specific to mesenchymal stem cells and proposes them as potential cell markers.

NoRCE performs cis enrichment analysis for non-coding RNAs by examining nearby coding genes' functional annotations and integrates additional biological data to infer functional associations.

The paper provides a comprehensive catalog of lncRNAs in human T cells across three cancer types, identifies 154 signature lncRNAs associated with T cell states, and highlights their potential roles in cancer immunity.

The paper analyzes antisense lncRNAs in zebrafish development, identifying two groups with distinct expression patterns, localization, and regulatory features.

The paper investigates the transcriptional regulation and processing of the miR-302/367 host gene, revealing complex regulatory sequences and conserved elements between mouse and human.

RiceLncPedia compiles and characterizes 6978 rice lncRNAs using 2313 RNA-seq libraries and multi-omics data, providing features like expression profiles, genome browser, SNPs, and miRNA interactions.

Crinet infers genome-wide ceRNA networks by considering mRNAs, lncRNAs, and pseudogenes and using network deconvolution to exclude spurious interactions, showing enrichment in cancer-related genes.

This study identifies HASTER, a lncRNA that stabilizes HNF1A expression through cis-regulatory mechanisms, and shows its disruption leads to diabetes.

The paper characterizes transcript expression, maturation, and localization of lncRNAs in mouse liver, identifying novel sex-biased and TCPOBOP-responsive lncRNAs.

The paper identifies structurally conserved domains and motifs in lincRNA-p21 through sequence and phylogenetic analysis, highlighting their potential functional importance.

The paper introduces a network-based model to analyze miRNA:target interactions in breast cancer, identifying highly perturbing genes that align with cancer-related genes and miRNAs.

The paper shows that CCDC26 RNA regulates DNMT1 nuclear localisation, affecting DNA methylation and cell viability.

The paper investigates the interaction between long non-coding RNAs and chromatin accessibility during erythroid differentiation, identifying stage-specific regulatory networks and key lncRNAs involved in the process.

This study shows that SNHG26, a G2-phase enriched lncRNA, is necessary for cell cycle progression and proliferation, with effects on mitochondrial stress and gene expression.

This study identifies lncRNA Mrhl as a chromatin-bound regulator that influences differentiation programs in mouse embryonic stem cells by modulating chromatin architecture.

The paper shows Evf2 RNA regulates gene expression in mouse forebrain by interacting with Sox2 to control enhancer interactions and chromosome topology.

The paper identifies 1791 RNAs directly interacting with Neat1 in paraspeckles, showing Neat1 binds over 30% of paraspeckle-targeted transcripts and preferentially binds their 5' ends.