Cancer-related molecular mechanisms research

Inhibition of TFIIH translocase reveals a novel lncRNA regulatory network at the BRCA1 locus

The paper identifies a novel lncRNA regulatory network at the BRCA1 locus that is activated during transcriptional stress induced by XPB inhibition.

The PVT1, HULC, and HOTTIP expression changes due to treatment in Diffuse Large B-cell lymphoma

The paper evaluates expression changes of PVT1, HULC, and HOTTIP in DLBCL patients before and after treatment, finding significant upregulation pre-treatment and normalization post-treatment.

Synergistic RAS-MAPK and AKT Activation in MYC-Driven Tumors via Adjacent PVT1 Rearrangements

This paper identifies how PVT1 rearrangements in MYC+ cancers generate oncogenic peptides that synergistically activate MYC, AKT, and RAS-MAPK pathways, enhancing tumor aggressiveness.

Decoding DNA methylation and non-coding RNAs mediated regulatory landscape of breast tumor and adjacent normal tissues

The paper integrates DNA methylation and non-coding RNA data from breast tumor and adjacent normal tissues to identify key regulatory hubs and bottlenecks involved in transcriptional misregulation in cancer.

LCLNCRdb: A Comprehensive Resource for Investigating long non-coding RNAs in Lung Cancer

LCLNCRdb is a manually curated database of 1102 lung cancer-associated lncRNAs with expression, network, and survival data, providing a resource for research and data sharing.

AGO1 interacts with NEAT1 lncRNA and impacts nuclear compartments

This study identifies a novel interaction between AGO1 and NEAT1 lncRNA, showing their roles in nuclear compartmentalization and chromatin organization.

In Silico Analysis of Non-Coding RNA Regulation in Human Gene Expression: A Systematic Computational Approach to Understanding Regulatory Networks

This study uses computational methods to analyze non-coding RNA regulation in human gene expression, identifying novel regulators and their targets in disease-related processes.

Elucidating role of long non-coding RNAs of Tamarindus indica Linn. in post-transcriptional gene regulation.

This study predicts and validates 320 lncRNAs in tamarind, analyzing their roles in gene regulation and biological pathways.

Cell Type-Specific and Diabetic Kidney Disease-Associated Expression of Long Non-Coding RNAs in Human Kidneys

The paper identifies cell type-specific lncRNAs in human kidneys and finds TARID, a podocyte-specific lncRNA, is upregulated in diabetic kidney disease and critical for actin cytoskeleton reorganization.

A Novel XACT lncRNA Transcript with Functions Transcending X-Chromosome Inactivation.

The paper identifies a novel XACT lncRNA transcript expressed in both active and inactive X chromosomes, with roles in erythroid differentiation and AML subtypes beyond its role in XCI.

Genome biology of long non-coding RNAs in humans: a virtual karyotype

The paper creates a statistical genomics portrait of lncRNA genes for comparison with protein-coding genes to explore the non-coding genome.

A comprehensive analysis of the inherited lncRNA and circRNA repertoire of zebrafish

The paper identifies inherited lncRNAs and circRNAs in zebrafish, finding that 20% of lncRNAs and 7% of circRNAs are inherited, with many conserved in mammals and expressed in adult tissues.

Enhancer lncRNA LOC730338 modulates BCR signaling and immune evasion in lymphoma by regulating RNA homeostasis.

This paper identifies ADARreg, an elncRNA that modulates BCR signaling and immune evasion in lymphoma by altering RNA stability, localization, and editing, providing a potential therapeutic target.

RNA splicing variants of the novel long non-coding RNA, CyKILR, possess divergent biological functions in non-small cell lung cancer

The paper identifies a long non-coding RNA, CyKILR, with two splice variants that have opposing effects on tumor growth and cell survival in NSCLC.

Identification of transcriptome-wide cobalt chloride-induced hypoxia-responsive long noncoding RNAs regulated by cytoplasmic mRNA capping enzyme

The paper identifies hypoxia-responsive lncRNAs regulated by cytoplasmic mRNA capping enzyme in osteosarcoma cells under cobalt chloride-induced hypoxia.

Mechano-sensing role of oncogenic lncRNA NEAT1 on soft vs. stiff substrates and its implications for glioblastoma progression

This study investigates how NEAT1 expression changes with substrate stiffness in glioblastoma cells and shows its role in cancer progression through mechano-sensitivity.

A new cancer-testis long noncoding RNA, the OTP-AS1 RNA

The paper identifies a new cancer-testis long noncoding RNA, OTP-AS1, which is antisense to the OTP gene and may regulate its expression in tumors.

Long noncoding RNA HSCHARME is altered in human cardiomyopathies and promotes stem cell-derived cardiomyocyte differentiation by splicing regulation.

This study identifies HSCHARME, a lncRNA altered in cardiomyopathies, which promotes cardiomyocyte differentiation through splicing regulation.

The GENCODE CLS project: massively expanding the lncRNA catalog through capture long-read RNA sequencing

The paper expands the lncRNA catalog using capture long-read RNA sequencing, significantly increasing the number of annotated transcripts in human and mouse genomes.

Integrated Spatial and Single-Nuclei Transcriptomic Analysis of Long Non-Coding RNAs in Alzheimer's Disease

The paper identifies AD-associated lncRNAs with spatial and cell-type-specific expression patterns and shows OIP5-AS1 contributes to microglial activation in AD.

Differential expression of oncogenic lncRNAs NEAT1 and MALAT1 in 2D monolayer vs. 3D tumoroid culture and its implications in cancer progression

This study compares the expression of oncogenic lncRNAs NEAT1 and MALAT1 in 2D and 3D cancer cultures, showing significant differences and functional impacts in 3D tumoroids.

Identification and Functional Characterization of lncRNAs involved in Human Monocyte-to-Macrophage Differentiation

The paper identifies and functionally characterizes lncRNAs involved in human monocyte-to-macrophage differentiation using RNA-seq and high-throughput screening.

CytoLNCpred - A computational method for predicting cytoplasm associated long-coding RNAs in 15 cell-lines

This paper introduces CytoLNCpred, a method to predict cytoplasm-associated lncRNAs in 15 human cell lines using machine learning and DNABERT-2 embeddings, showing correlation-based models outperform LLM-based ones.

Alternative polyadenylation of a polycistronic locus regulates the tumor-suppressive miR-317 and the lncRNA Peony in Drosophila

The paper identifies a polycistronic locus in Drosophila testes producing miR-317 and Peony, showing alternative polyadenylation regulates their expression and function in tumor suppression and tissue integrity.

Syntenic lncRNAs exhibit DNA regulatory functions with sequence evolution

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

Cross-species orthology detection of long non-coding RNAs (lncRNA) through 13 species using genomic and functional annotations.

The paper develops a workflow to detect cross-species orthology of lncRNAs across 13 vertebrate species using syntenic methods and motif analysis, revealing conserved lncRNAs and functional motifs.

SCAR-6 elncRNA locus epigenetically regulates PROZ and modulates coagulation and vascular function

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.

Transcriptome-based identification of long noncoding RNAs (lncRNAs) across the genome of Anopheles gambiae

The paper identifies 2684 lncRNA genes in Anopheles gambiae using RNA-seq data and analyzes their expression and regulatory roles across different biological contexts.

Modelling cell type-specific lncRNA regulatory network in autism with Cycle

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

Detection of statistically robust interactions from diverse RNA-DNA ligation data

The paper introduces RADIAnT, a computational pipeline for detecting RNA-DNA interactions from ligation data, showing improved accuracy in identifying Malat1-DNA interactions and dynamic chromatin-associated RNAs.