Cancer-related molecular mechanisms research

Long non-coding RNAs are largely dispensable for zebrafish embryogenesis, viability and fertility

This study shows that most zebrafish lncRNAs are not essential for embryogenesis, viability, or fertility, with only a few exceptions.

Bases of antisense lncRNA-associated regulation of gene expression in fission yeast

This paper investigates how antisense long non-coding RNAs (asXUTs) regulate gene expression in fission yeast by stabilizing Exo2-sensitive asXUTs, leading to transcriptional attenuation of paired-sense genes.

Long non-coding RNA repertoire and regulation by nuclear exosome, cytoplasmic exonuclease and RNAi in fission yeast

The paper identifies 5775 novel lncRNAs in fission yeast and characterizes their regulation by RNA-processing pathways.

A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain

The lncRNA Cyrano drives multiple-turnover degradation of miR-7 in mouse brain, which protects the circRNA Cdr1as from miR-7-dependent, partly miR-671-sliced destruction.

Identification and characterization of moonlighting long non-coding RNAs based on RNA and protein interactome

The paper identifies and characterizes moonlighting long non-coding RNAs using a statistical algorithm integrating protein interactome and functional data, revealing distinct sequence and localization features.

LncRNA OIP5-AS1 is overexpressed in undifferentiated oral tumors and integrated analysis identifies as a downstream effector of stemness-associated transcription factors.

The paper identifies OIP5-AS1 as overexpressed in undifferentiated oral tumors and shows it modulates miRNAs and downstream targets, potentially maintaining cancer stemness through stemness-associated transcription factors.

Assembly and validation of conserved long non-coding RNAs in the ruminant transcriptome

The paper identifies a consensus set of ruminant lncRNAs by combining cross-species RNA-seq data and positional conservation, showing that stochastic sampling can be mitigated through this approach.

Paupar LncRNA Promotes KAP1 Dependent Chromatin Changes And Regulates Subventricular Zone Neurogenesis

The paper identifies Paupar, a lncRNA that interacts with KAP1 to regulate chromatin structure and neurogenesis in the subventricular zone.

MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions

MechRNA predicts lncRNA mechanisms by integrating RNA-RNA and RNA-protein interaction predictions to identify potential targets and mechanisms for cancer-related lncRNAs.

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA, and mRNA data in GDC

GDCRNATools provides an R/Bioconductor package for analyzing lncRNA, miRNA, and mRNA data from the GDC to study ceRNA regulatory networks in cancers.

Transcriptome-Wide Prediction Of lncRNA-RNA Interactions By A Thermodynamics Algorithm

The paper introduces ASSA, a computational pipeline that predicts RNA-RNA interactions by combining sequence alignment and thermodynamics, outperforming existing tools.

High-throughput identification of RNA nuclear enrichment sequences

The paper identifies RNA sequences responsible for nuclear enrichment in lncRNAs using a modified MPRA approach and validates findings with smRNA-FISH.

Transcriptome wide analysis of natural antisense transcripts shows their potential role in breast cancer.

The paper analyzes natural antisense transcripts (NATs) in breast cancer using RNA sequencing to identify their potential role in gene regulation and survival outcomes.

Chromatin-release of the long ncRNA A-ROD is required for transcriptional activation of its target gene DKK1

The paper identifies A-ROD as a long ncRNA that requires chromatin-release to activate DKK1 transcription by recruiting EBP1 to the promoter.

Comparative genomic analyses highlight the contribution of pseudogenized protein-coding genes to human lincRNAs

This study identifies that a significant portion of human lincRNAs may originate from pseudogenized protein-coding genes through comparative genomic analysis.

GIC: A computational method for predicting the essentiality of long noncoding lncRNAs

GIC predicts the essentiality of protein-coding genes and lncRNAs using RNA sequence data, achieving high performance for lncRNAs in a mouse dataset.

Translating ceRNA susceptibilities into correlation functions

The paper translates ceRNA susceptibilities into correlation functions to estimate crosstalk strength and validates this approach using simulations and TCGA data.

lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets

lncRNA-screen is a pipeline for computationally screening lncRNAs in large genomics datasets, generating interactive reports for further experimental validation.

Evolinc: a comparative transcriptomics and genomics pipeline for quickly identifyingsequence conserved lincRNAs for functional analysis.

Evolinc identifies and characterizes sequence-conserved lincRNAs across species to prioritize candidates for functional analysis.

Clusterization in head and neck squamous carcinomas based on lncRNA expression: molecular and clinical correlates

The paper clusters head and neck squamous cell carcinomas based on lncRNA expression and identifies molecular and clinical associations.

LncATLAS database for subcellular localisation of long noncoding RNAs

LncATLAS provides a database of lncRNA subcellular localization in human cells using RNA-seq data, offering tools to query and compare localization across cell types and organelles.

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

The paper identifies differences in chromatin environment, transcriptional regulation, and splicing between lincRNAs and mRNAs in human cell lines.