Cancer-related molecular mechanisms research

Transcriptional stress induces the generation of DoGs in cancer cells.

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

Long-read Transcriptome Landscapes of Primary and Metastatic Liver Cancers at Transcript Resolution

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.

Regulation potential of transcribed simple repeated sequences in developing neurons

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

Mapping Chromatin Occupancy of Ppp1r1b-lncRNA Genome-Wide Using Chromatin Isolation by RNA Purification (ChIRP)-seq

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.

Oligodendrocyte-specific expression of PSG8-AS1 suggests a role in myelination with prognostic value in oligodendroglioma.

The paper identifies PSG8-AS1 as an oligodendrocyte-specific long non-coding RNA with potential diagnostic and prognostic value in oligodendroglioma.

Comparative Genomics Exploration of Shared lncRNA-coding genes in Human and All Annotated Plant Genomes: Potential Implications for Cancer Research

This study identifies 20 human lncRNA-encoding genes with potential orthologs in plant genomes, including 3 linked to cancer-related lncRNAs in databases.

Pan-cancer characterization of ncRNA synergistic competition uncovers potential carcinogenic biomarkers

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

In silico approaches to identify the role of lncRNAs in Prostate cancer and Androgen receptor-targeted proteins

The paper identifies three lncRNAs that interact with prostate cancer and androgen receptor-targeted proteins and suggests SCARNA10 as a prognostic signature for prostate cancer.

Prognostic implications and biological roles of EMT-related lncRNAs in lung squamous cell carcinoma: an in-depth analysis utilizing a novel prognostic signature and classification system

The paper develops an EMT-related lncRNA prognostic signature and classification system for lung squamous cell carcinoma, identifying key genes and subtypes with distinct prognostic and immunotherapy profiles.

Identification of SYT10 as a potential prognostic biomarker in esophageal cancer by comprehensive analysis of a mRNA-pseudogene/lncRNA-miRNA ceRNA network

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.

linc2function: A deep learning model to identify and assign function to long noncoding RNA (lncRNA)

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

Effect of Single Nucleotide Polymorphisms on the structure of long noncoding RNAs and their interaction with RNA Binding Proteins

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

Functional evolutionary convergence of long noncoding RNAs involved in embryonic development.

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.

Discovery of a Well-Folded Protein Interaction Hub Within the Human Long Non-Coding RNA NORAD

The paper identifies a structured protein interaction hub in the long non-coding RNA NORAD using biochemical and sequencing methods.

The long non-coding RNA LINC00941 modulates MTA2/NuRD occupancy to suppress premature human epidermal differentiation

This study shows that LINC00941 interacts with the NuRD complex to regulate epigenetic occupancy and suppress premature human epidermal differentiation.

The lncRNA TRG-AS1 promotes the growth of colorectal cancer cells through the regulation of P2RY10/GNA13

This study shows that TRG-AS1 promotes colorectal cancer growth by regulating P2RY10 and GNA13 expression, as demonstrated through in vitro and in vivo experiments.

HOXDeRNA activates a cancerous transcription program and super-enhancers genome-wide

This study identifies HOXDeRNA as a long non-coding RNA that derepresses glioma-specific transcription factors by interacting with PRC2 and RNA quadruplex structures, driving astrocyte transformation into glioma-like cells.

LINC01117 inhibits invasion and migration of lung adenocarcinoma through influencing EMT process

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.

GRAS1 non-coding RNA protects against DNA damage and cell death by binding and stabilizing NKAP

This study identifies GRAS1 lncRNA as a protector against DNA damage and cell death by stabilizing NKAP protein.

Tumour mutations in long noncoding RNAs enhance cell fitness

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

BCLncRDB: A comprehensive database of LncRNAs associated with breast cancer

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

Fendrr synergizes with Wnt signalling to regulate fibrosis related genes during lung development via its RNA:dsDNA Triplex Element

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.

Ectopically expressed Airn lncRNA deposits Polycomb with a potency that rivals Xist

The paper shows that Airn lncRNA can deposit Polycomb with potency comparable to Xist when expressed at similar levels, but Xist is more potent when promoter activation is equal.

Targeting long non-coding RNA NUDT6 enhances smooth muscle cell survival and limits vascular disease progression

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: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape

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

linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells

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

Dysregulation of murine long non-coding single cell transcriptome in non-alcoholic steatohepatitis and liver fibrosis

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

EphrinA5 regulates cell motility by modulating the targeting of DNMT1 to the Ncam1 promoter via lncRNA/DNA triplex formation

The paper shows ephrinA5 reduces cell motility by decreasing Snhg15 expression, which lowers DNMT1 binding to the Ncam1 promoter, reducing methylation and increasing Ncam1 expression.

Discovery of long non-coding RNAs in the liver fluke, Fasciola hepatica

The paper identifies 6,436 putative long non-coding RNAs in Fasciola hepatica, showing distinct features from mRNAs and potential regulatory roles.

Human skin specific long noncoding RNA HOXC13-AS regulates epidermal differentiation by interfering with Golgi-ER retrograde transport

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