Cancer-related molecular mechanisms research

This study investigates syntenic lncRNAs across humans and zebrafish, finding they exhibit regulatory functions through DNA elements despite limited sequence conservation.

This paper identifies and functionally validates the scar-6 lncRNA locus, showing it regulates prozb expression and modulates coagulation and vascular function in zebrafish through epigenetic mechanisms.

Cycle identifies cell type-specific lncRNA regulatory networks in ASD, revealing rewired and conserved modules and hubs associated with ASD-related functions.

The paper identifies prognostically relevant co-expression patterns between coding and noncoding RNAs in HPV16-positive cervical cancers and links them to patient survival.

This study shows that the lncRNA Pnky has sex-specific effects on mouse behavior, with male and female knockout mice displaying distinct behavioral deficits that can be reversed by a transgenic Pnky expression.

The paper identifies functionally conserved lncRNA metabolic regulators in human and mouse livers that regulate triglyceride levels through a shared mechanism involving PABPC1 binding.

eRNA-IDO identifies enhancer RNAs, discovers their interactomes, and annotates their functions using a computational platform.

The paper shows that neutrally evolving lncRNAs from SNHGs influence cell fate and are involved in epidermal homeostasis through microRNA binding.

The paper identifies novel lncRNA biomarkers in squamous cell carcinoma through RNA co-expression network clustering and validates their association with poor prognosis.

The paper identifies DoG RNAs as noncoding transcripts that are differentially expressed in cancer and linked to poor prognosis and carcinogenesis.

The paper identifies conserved modular exonic regions in human lncRNAs, showing evidence of purifying selection and suggesting functional units similar to protein-coding genes.

The paper identifies evolutionary shifts in lncRNA expression in the developing human cerebral cortex, showing increased de novo expression in excitatory neurons and associations with autism spectrum disorder.

The paper expands the LncRNA gene-disease landscape by introducing the GeneCaRNA database, which includes 280,000 non-coding RNA genes and links 1,547 LncRNAs to diseases.

The paper uses CRISPRi screens to identify the lncRNA LOUP as a regulator of macrophage differentiation and inflammatory signaling through epigenetic and peptide-mediated mechanisms.

The paper identifies KILR, a breast cancer risk-associated lncRNA, and shows it regulates DNA replication and repair by sequestering RPA1.

The paper identifies cell type-specific lncRNAs in CRC using single-cell and bulk transcriptomes, showing their enrichment in epithelial cells and validating their role in CRC proliferation.

This paper develops an 11-gene signature for metastatic clear cell renal cell carcinoma using a ceRNA network, showing good generalization and associations with survival and metastasis.

This paper identifies JUNI, a stress-induced lncRNA critical for cancer cell survival, and shows its interactome predicts prognosis in clear cell renal cell carcinoma.

SCancerRNA is a database that compiles single-cell expression data and interaction networks of non-coding RNA biomarkers for cancer diagnosis and therapy.

The paper identifies ASAR lncRNAs as regulators of DNA replication timing through interactions with hnRNP proteins, showing their role in chromosome stability and replication synchronization.

The paper develops a machine learning model to identify functional lncRNAs and validates SNHG6's role in hematopoietic differentiation and leukemia.

The paper introduces TransCistor, a framework to identify cis-regulatory lncRNAs with controlled false discovery rates, finding that only a minority of lncRNAs are cis-acting, primarily as activators.

The paper shows that transcription inhibition in cancer cells leads to the generation of DoGs, suggesting they are part of a cellular stress response.

The paper defines the full-length transcriptome of primary and metastatic liver cancers and identifies isoform-level diversity and metastasis-specific transcripts with clinical implications.

The paper identifies SRS-lncRNAs expressed during neuronal differentiation and shows their potential to interact with RNA-binding proteins.

The paper maps Ppp1r1b-lncRNA chromatin occupancy genome-wide in mouse muscle myoblasts using ChIRP-seq, identifying binding sites enriched for myogenic regulators and enhancers.

This paper introduces SCOM, a framework to identify ncRNA synergistic competition across cancers, revealing hub ncRNAs and potential biomarkers for diagnosis and prognosis.

The paper constructs a ceRNA network in esophageal cancer and identifies SYT10 as a potential prognostic biomarker based on survival analysis of differentially expressed RNAs.

The paper introduces linc2function, a deep learning model that identifies and functionally annotates long noncoding RNAs using sequence, structure, and interactome features across species.

This study examines how SNPs in lncRNAs affect their secondary structure and RNA binding protein interactions, potentially contributing to disease.