Approaches for Modes of Action Study of Long Non-Coding RNAs: From Single Verification to Genome-Wide Determination

Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides (nt) that are not translated into known functional proteins. This broad definition covers a large collection of transcripts with diverse genomic origins, biogenesis, and modes of action. Thus, it is very important to choose appropriate research methodologies when investigating lncRNAs with biological significance. Multiple reviews to date have summarized the mechanisms of lncRNA biogenesis, their localization, their functions in gene regulation at multiple levels, and also their potential applications. However, little has been reviewed on the leading strategies for lncRNA research. Here, we generalize a basic and systemic mind map for lncRNA research and discuss the mechanisms and the application scenarios of ‘up-to-date’ techniques as applied to molecular function studies of lncRNAs. Taking advantage of documented lncRNA research paradigms as examples, we aim to provide an overview of the developing techniques for elucidating lncRNA interactions with genomic DNA, proteins, and other RNAs. In the end, we propose the future direction and potential technological challenges of lncRNA studies, focusing on techniques and applications.

• Publication year

  2023

• Venue

  International Journal of Molecular Sciences

• Publication date

  2023-03-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.3390/ijms24065562PMID 36982636PMCID 10054671
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Protocol to detect nucleotide-protein interaction in vitro using a non-radioactive competitive electrophoretic mobility shift assay

  2022cited by this paper
• Towards higher-resolution and in vivo understanding of lncRNA biogenesis and function

  2022cited by this paper
• SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding

  2022cited by this paper
• Real-time dynamic single-molecule protein sequencing on an integrated semiconductor device

  2022cited by this paper
• The landscape of promoter-centred RNA–DNA interactions in rice

  2022cited by this paper
• In vivo single-molecule analysis reveals COOLAIR RNA structural diversity

  2022cited by this paper
• Global profiling of RNA–chromatin interactions reveals co-regulatory gene expression networks in Arabidopsis

  2021influential reference
• Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro

  2021cited by this paper
• Programmable RNA targeting with the single-protein CRISPR effector Cas7-11

  2021cited by this paper
• Hi‐C 3.0: Improved Protocol for Genome‐Wide Chromosome Conformation Capture

  2021cited by this paper
• Optimized protocol for single-molecule RNA FISH to visualize gene expression in S. cerevisiae

  2021cited by this paper
• Nanopore sequencing of single-cell transcriptomes with scCOLOR-seq

  2021cited by this paper
• RNA structure probing uncovers RNA structure-dependent biological functions

  2021cited by this paper
• Neofunctionalization of a polyploidization-activated cotton long intergenic non-coding RNA DAN1 during drought stress regulation

  2021cited by this paper
• Global in situ profiling of RNA-RNA spatial interactions with RIC-seq

  2021cited by this paper
• Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease.

  2021cited by this paper
• N6-methyladenosine modification of MALAT1 promotes metastasis via reshaping nuclear speckles.

  2021cited by this paper
• Identifying high-confidence capture Hi-C interactions using CHiCANE

  2021cited by this paper
• RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins

  2021cited by this paper
• Understanding lncRNA-protein assemblies with imaging and single-molecule approaches.

  2021cited by this paper
• Integrative analysis of reference epigenomes in 20 rice varieties

  2020cited by this paper
• RADICL-seq identifies general and cell type specific principles of genome-wide RNA-chromatin interactions

  2020cited by this paper
• Long non-coding RNAs in plants: emerging modulators of gene activity in development and stress responses

  2020cited by this paper
• Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation

  2020cited by this paper
• An Optimized Protocol for ChIP-Seq from Human Embryonic Stem Cell Cultures

  2020cited by this paper
• Efficient low-cost chromatin profiling with CUT&Tag

  2020cited by this paper
• Efficient chromatin profiling of H3K4me3 modification in cotton using CUT&Tag

  2020cited by this paper
• RNA promotes the formation of spatial compartments in the nucleus

  2020cited by this paper
• Immunoprecipitation of DNA:RNA Hybrids Using the S9.6 Antibody.

  2020cited by this paper
• Xist Repeats A and B Account for Two Distinct Phases of X Inactivation Establishment.

  2020cited by this paper
• Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics

  2020cited by this paper
• RIC-seq for global in situ profiling of RNA–RNA spatial interactions

  2020cited by this paper
• Distinct Processing of lncRNAs Contributes to Non-conserved Functions in Stem Cells.

  2020cited by this paper
• Methods for ChIP-seq analysis: A practical workflow and advanced applications.

  2020cited by this paper
• Quantitative Proteomics to Identify Nuclear RNA-Binding Proteins of Malat1

  2020cited by this paper
• From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis

  2020cited by this paper
• Regulatory R-loops as facilitators of gene expression and genome stability

  2020cited by this paper
• R-Loop Mediated trans Action of the APOLO Long Noncoding RNA.

  2020cited by this paper
• Gene regulation by long non-coding RNAs and its biological functions

  2020cited by this paper
• Deep learning based DNA:RNA triplex forming potential prediction

  2020cited by this paper
• fCLIP-seq for transcriptomic footprinting of dsRNA-binding proteins: Lessons from DROSHA.

  2019cited by this paper
• The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest.

  2019cited by this paper
• Neutralization of the Positive Charges on Histone Tails by RNA Promotes an Open Chromatin Structure.

  2019cited by this paper
• Comprehensive identification of RNA–protein interactions in any organism using orthogonal organic phase separation (OOPS)

  2019cited by this paper
• Examining global RNA-binding proteomes

  2019cited by this paper
• Methods to study RNA–protein interactions

  2019influential reference
• Structural modularity of the XIST ribonucleoprotein complex

  2019cited by this paper
• RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions

  2019cited by this paper
• GRID-seq for comprehensive analysis of global RNA–chromatin interactions

  2019cited by this paper
• High-resolution, strand-specific R-loop mapping via S9.6-based DNA–RNA immunoprecipitation and high-throughput sequencing

  2019cited by this paper
• lncRNA KHPS1 Activates a Poised Enhancer by Triplex-Dependent Recruitment of Epigenomic Regulators.

  2019cited by this paper
• Single-cell RNA counting at allele and isoform resolution using Smart-seq3

  2019cited by this paper
• Regulation of gene expression by cis-acting long non-coding RNAs

  2019cited by this paper
• Nucleosomes Stabilize ssRNA-dsDNA Triple Helices in Human Cells.

  2019cited by this paper
• R-Loops Promote Antisense Transcription across the Mammalian Genome

  2019cited by this paper
• Mapping RNA–chromatin interactions by sequencing with iMARGI

  2019cited by this paper
• Towards a complete map of the human long non-coding RNA transcriptome

  2018cited by this paper
• RNA–protein interaction detection in living cells

  2018cited by this paper
• An HDAC9-MALAT1-BRG1 complex mediates smooth muscle dysfunction in thoracic aortic aneurysm

  2018cited by this paper
• RAP-MS: A Method to Identify Proteins that Interact Directly with a Specific RNA Molecule in Cells.

  2018cited by this paper
• GoldCLIP: Gel-omitted Ligation-dependent CLIP

  2018cited by this paper
• RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA

  2018cited by this paper
• Feedback regulation of COOLAIR expression controls seed dormancy and flowering time

  2018cited by this paper
• Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus.

  2018cited by this paper
• Overexpressing lncRNA LAIR increases grain yield and regulates neighbouring gene cluster expression in rice

  2018cited by this paper
• Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

  2018cited by this paper
• Long non-coding RNA MALAT1 suppresses breast cancer metastasis

  2018cited by this paper
• Regulation of Neuroregeneration by Long Noncoding RNAs.

  2018cited by this paper
• Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments

  2018cited by this paper
• Hi-C analysis: from data generation to integration

  2018cited by this paper
• GADD45A binds R-loops and recruits TET1 to CpG island promoters

  2018cited by this paper
• Xist RNA antagonizes the SWI/SNF chromatin remodeler BRG1 on the inactive X chromosome

  2018cited by this paper
• An HDAC 9-MALAT 1-BRG 1 complex mediates smooth muscle dysfunction in thoracic aortic aneurysm

  2018cited by this paper
• A Nucleus-Localized Long Non-Coding RNA Enhances Drought and Salt Stress Tolerance[OPEN]

  2017cited by this paper
• GRID-seq reveals the global RNA-chromatin interactome

  2017cited by this paper
• A regulated PNUTS mRNA to lncRNA splice switch mediates EMT and tumor progression

  2017cited by this paper
• Systematic Mapping of RNA-Chromatin Interactions In Vivo.

  2017cited by this paper
• A fast, efficient chromatin immunoprecipitation method for studying protein-DNA binding in Arabidopsis mesophyll protoplasts

  2017cited by this paper
• Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions

  2017cited by this paper
• Gene regulation in the immune system by long noncoding RNAs

  2017cited by this paper
• Modular function of long noncoding RNA, COLDAIR, in the vernalization response

  2017cited by this paper
• The human lncRNA LINC-PINT inhibits tumor cell invasion through a highly conserved sequence element

  2017cited by this paper
• Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts

  2017cited by this paper
• High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing

  2017cited by this paper
• Single Molecule RNA FISH in Arabidopsis Root Cells.

  2017cited by this paper
• RNA editing with CRISPR-Cas13

  2017cited by this paper
• Vernalization-Triggered Intragenic Chromatin Loop Formation by Long Noncoding RNAs.

  2017cited by this paper
• NONCODEV5: a comprehensive annotation database for long non-coding RNAs

  2017cited by this paper
• Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution

  2017cited by this paper
• Computational analysis of CLIP-seq data.

  2017cited by this paper
• A versatile tandem RNA isolation procedure to capture in vivo formed mRNA-protein complexes.

  2017cited by this paper
• Immunobiology of Long Noncoding RNAs.

  2017cited by this paper
• Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins.

  2016cited by this paper
• Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells.

  2016cited by this paper
• Robust transcriptome-wide discovery of RNA binding protein binding sites with enhanced CLIP (eCLIP)

  2016cited by this paper
• Post-Transcriptional Gene Regulation

  2016cited by this paper
• Massively multiplex single-cell Hi-C

  2016cited by this paper
• RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure.

  2016cited by this paper
• The lncRNA HOTAIR impacts on mesenchymal stem cells via triple helix formation

  2016cited by this paper
• PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites.

  2016cited by this paper

• Structural Characterization of Protein–Nucleic Acid Complexes: An Overview of the Recent Innovation in the Analytic Methods

  2025cites this paper
• The long non-coding RNA VIVIpary promotes seed dormancy release and pre-harvest sprouting through chromatin remodeling in rice.

  2025cites this paper
• Cellular and molecular functions of long noncoding RNAs in testis, aging and diseases

  2025cites this paper
• Long non-coding RNA NEAT1 modulates microglial NLRP3 inflammasome activation.

  2025cites this paper
• From diagnosis to therapy: The transformative role of lncRNAs in eye cancer management.

  2024cites this paper
• Underground communication: Long non-coding RNA signaling in the plant rhizosphere

  2024cites this paper
• Epigenetic control of dental stem cells: progress and prospects in multidirectional differentiation

  2024cites this paper
• Localization is the key to action: regulatory peculiarities of lncRNAs

  2024cites this paper