Cancer-related molecular mechanisms research

The paper identifies functionally conserved non-homologous lncRNAs across species using k-mer content and structural analysis, validated through CRISPR Display in human and chicken cells.

This study identifies LINC01117 as a regulator of EMT in lung adenocarcinoma, showing its role in promoting cell migration and invasion through modulation of EMT markers.

The paper identifies mutated long noncoding RNAs (lncRNAs) as contributors to tumour cell fitness through experimental validation of their oncogenic effects.

BCLncRDB is a database of breast cancer-associated lncRNAs containing 5,279 associations with features like expression, methylation, and drug information.

The paper shows that Fendrr's triplex forming sequence is important for regulating fibrosis-related genes during lung development, and that Fendrr works with Wnt signaling to control these genes.

This study identifies NUDT6 as an antisense transcript of FGF2, showing that its silencing enhances smooth muscle cell survival and limits vascular disease progression.

spongEffects identifies patient-specific ceRNA modules to provide insights into miRNA regulatory activity using gene expression data alone.

The paper identifies two micropeptides encoded by lincRNAs that regulate chromatin accessibility in vertebrate-specific neural cells and show their role in brain development.

The paper identifies dysregulated lncRNAs in mouse liver disease using single-cell RNA-seq and links them to biological pathways and potential therapeutic targets.

The paper identifies HOXC13-AS, a lncRNA that regulates epidermal differentiation by interfering with Golgi-ER transport during wound healing.

This paper introduces lncDLSM, a deep learning framework for identifying long non-coding RNAs without prior biological knowledge, showing effectiveness across species.

This study identifies LINC00607 as an endothelial-specific lncRNA that supports angiogenic function by interacting with BRG1 to regulate chromatin accessibility and ERG target gene transcription.

The paper identifies and characterizes LNCSOX17, a lncRNA essential for human endoderm formation, showing its role in regulating transcriptome and differentiation.

The paper identifies lncRNAs in human germ cells and shows LNC1845 regulates LHX8 through histone modifications during gonadal development.

The paper curates a database of RNA-DNA binding sites and introduces a tool to predict RNA:DNA:DNA triple helices, showing most lncRNAs can bind the genome via this mechanism.

The paper performs knockdown of 200 lncRNAs in human iPS cells, identifies 36 with growth inhibition, and finds molecular phenotypes in 29.3% of cases, with higher agreement in molecular than cell growth phenotypes across cell types.

This study investigates the pleiotropic effects of the lncRNA Uhg4 in Drosophila melanogaster by generating deletions and analyzing fitness traits and gene expression.

The paper identifies HIF1α-AS1 as a DNA:DNA:RNA triplex-forming lncRNA that interacts with the HUSH complex to repress gene expression and modulates angiogenesis in pulmonary hypertension.

This paper identifies a cuproptosis-related lncRNA signature that predicts prognosis in hepatocellular carcinoma and shows its association with survival and immune responses.

The paper uses long-read RNA capture-seq to annotate HOTAIR transcripts in human adipose stem cells, revealing a differentiation-driven isoform switch.

The paper identifies 60 high-confidence oncogenic lncRNAs in NSCLC using CRISPR deletion screens and ASO validation, revealing therapeutic vulnerabilities.

The paper analyzes high-resolution RNA-seq time course data to show lncRNAs are expressed synchronously with adjacent protein-coding genes, suggesting they may be by-products rather than regulators.

The paper maps lncRNA subcellular localization in human RPE under normal and oxidative stress conditions, finding increased compartmentalization under stress.

The paper analyzes THAP9 and THAP9-AS1 across multiple cancers to show their expression correlates with poor patient survival and identifies coexpressed genes involved in DNA binding and viral infection.

The paper identifies Wnt-responsive cis-regulatory elements that coordinate Paupar-Pax6 expression in neuronal cells through chromatin interactions.

This study identifies RUS, a lncRNA that promotes neurogenesis by regulating gene expression and epigenetic interactions during neuronal differentiation.

The paper identifies 30 high-confidence lncRNAs critical for cancer proliferation by integrating CRISPR data with multi-omics, showing their role in cell cycle regulation and patient survival.

This study investigates the role of Hotair and Malat1 lncRNAs in regulating Bdnf expression and oligodendrocyte precursor cells differentiation.

The paper identifies LEVER RNA as a regulator of ε-globin expression by inhibiting PRC2-mediated H3K27 methylation and disrupting promoter-LCR interactions.

This study investigates the transcriptional dynamics and functions of long non-coding RNAs using single-cell RNA-seq, revealing distinct burst kinetics and cell-state specific roles.