Cancer-related molecular mechanisms research

Antisense ncRNAs during early vertebrate development are divided in groups with distinct features

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

Expression of the miR-302/367 microRNA cluster is regulated by a conserved long non-coding host gene

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: a comprehensive database of rice long non-coding RNAs

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: A computational tool to infer genome-wide competing endogenous RNA (ceRNA) 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.

HASTER is a transcriptional stabilizer of HNF1A

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

Global analysis of expression, maturation and subcellular localization of mouse liver transcriptome identifies novel sex-biased and TCPOBOP-responsive long non-coding RNAs

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

Sequence and phylogenetic analysis revealed structurally conserved domains and motifs in lincRNA-p21

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

Network based multifactorial modelling of miRNA-target interactions

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.

A long intergenic non-coding RNA regulates nuclear localisation of DNA methyl transferase-1

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

The dynamic interactive network of long non-coding RNAs and chromatin accessibility facilitates erythroid differentiation

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.

The G2-phase enriched lncRNA SNHG26 is necessary for proper cell cycle progression and proliferation

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.

LncRNA Mrhl orchestrates differentiation programs in mouse embryonic stem cells through chromatin mediated regulation

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

Sox2-RNA mechanisms of chromosome topological control in developing forebrain

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

Direct RNA-RNA interaction between Neat1 and RNA targets, as a mechanism for RNAs paraspeckle retention

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.

LETR1 is a lymphatic endothelial-specific lncRNA that governs cell proliferation and migration through KLF4 and SEMA3C

The lncRNA EPB41L4A-AS1 regulates gene expression in the nucleus and exerts cell type-dependent effects on cell cycle progression

Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency

The paper uses CRISPR interference to identify lncRNA loci critical for differentiation and pluripotency in human embryonic stem cells.

Systematic identification of cis-interacting lncRNAs and their targets

The paper identifies cis-interacting lncRNAs and their targets using RNA-chromatin and Hi-C data across 18 human cell types.

Structural characterization of NORAD reveals a stabilizing role of spacers and two new repeat units.

The paper experimentally determines the secondary structure of NORAD, identifies spacers that stabilize its repeat units, and discovers two new repeat units.

Predictive modeling of long non-coding RNA chromatin (dis-)association

The paper models lncRNA chromatin (dis-)association using nascent RNA sequencing and identifies factors influencing dissociation and its functional impact.

Genome-wide identification of novel long non-coding RNAs and their possible roles in hypoxic zebrafish brain

The paper identifies novel lncRNAs in hypoxic zebrafish brain regions and links some to AD-related pathways and conserved functions.

Epigenomic reprogramming of repetitive noncoding RNAs and IFN-stimulated genes by mutant KRAS

This study identifies how mutant KRAS reprograms the noncoding transcriptome, upregulating repetitive noncoding RNAs and inducing IFN-stimulated genes through epigenetic and RNA-based mechanisms.

Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation

The paper identifies and functionally validates Wnt-regulated lncRNAs using in vivo models and CRISPRi screens, finding more functional lncRNAs in vivo than in vitro.

Assessing the role of long-noncoding RNA in nucleus accumbens in subjects with alcohol dependence

The paper profiles lncRNA and protein coding gene expression in nucleus accumbens from alcohol-dependent and control subjects, identifying differentially expressed genes and their functional roles in alcohol dependence.

Genome-wide identification of long non-coding RNAs in the gravid ectoparasite Varroa destructor

The paper identifies 6,645 novel lncRNA transcripts in Varroa destructor using high-throughput sequencing, revealing their characteristics and potential roles in biological processes.

piRPheno: a manually curated database to prioritize and analyze human disease related piRNAs

piRPheno is a manually curated database that provides experimentally supported piRNA-disease associations with confidence scores and clinical correlations.

lncRNAKB: A comprehensive knowledgebase of long non-coding RNAs

The paper introduces lncRNAKB, a comprehensive knowledgebase of 77,199 human lncRNAs with expression, conservation, and cis-eQTL data from GTEx.

LncRNAs interacting with the translation machinery contribute to human neuronal differentiation.

The paper identifies lncRNAs that interact with the translation machinery during neuronal differentiation and shows some produce peptides that affect neurite length.

Functional Enrichment Analysis of Deregulated Long Non-Coding RNAs in Cancer Based on their Genomic Neighbors

The paper analyzes deregulated long non-coding RNAs in cancer by examining their genomic neighbors and functional enrichment, finding cancer-specific and shared lncRNAs and functional similarities across cancer types.

Elements at the 5' end of Xist harbor SPEN-independent transcriptional antiterminator activity

The paper identifies SPEN-independent transcriptional antiterminator activity in the 5' end of Xist that promotes full-length RNA production and resists silencing.