Numerous lncRNAs Research Articles

Long Non-coding RNAs Expression in Renal Cell Carcinoma

Renal cell carcinoma (RCC) is among common cancers of the urogenital system. Several cancer-related pathways have been shown to be implicated in its pathogenesis. More recently, dysregulation of a group of non-coding RNAs named long non-coding RNAs (lncRNAs) have been demonstrated in many cancer types such as RCC. LncRNAs have been classified to oncogenic and tumor suppressor lncRNAs based on the pattern of expression in RCC samples as well as functional in vitro studies. Expression of several oncogenic lncRNAs such as CCAT2, HOTAIR, UCA1, TUG1 and FTX in RCC samples has been shown to be associated with tumor size and tumor stage. In addition, expression levels of numerous lncRNAs have been demonstrated to be independent prognostic factors in RCC patients. Consequently, lncRNA signature would be applied as diagnostic or prognostic biomarker as well as target for treatment modalities.

Long non-coding RNA TUG1 promotes cell proliferation and metastasis in human breast cancer.

Long non-coding RNAs (LncRNAs) utilize a wide variety of mechanisms to regulate RNAs or proteins on the transcriptional or post-transcriptional levels. Accumulating studies have identified numerous LncRNAs to exert critical effects on different physiological processes, genetic disorders, and human diseases. Both clinical tissues from breast cancer patients and cultured cells were used for the qRT-PCR analysis. Specific siRNAs were included to assess the roles of TUG1 with cell viability assay, transwell assay, and cell apoptosis assay, respectively. The expression of TUG1 was enhanced in breast cancerous tissues and in highly invasive breast cancer cell lines and was associated with clinical variables, including tumor size, distant metastasis and TNM staging. Knockdown of TUG1 significantly slowed down cell proliferation, cell migration, and invasion in breast cancer cell lines MDA-MB-231 and MDA-MB-436. In addition, cell apoptotic rate was shown to increase upon siTUG1 treatment as evidenced by increases of the activities of caspase-3 and caspase-9. The identification of TUG1 as a critical mediator of breast cancer progression implied that it might serve as a biomarker for the diagnosis and treatment of breast cancer in clinic.

Analysis of Senescence-Related Differentiation Potentials and Gene Expression Profiles in Human Dental Pulp Stem Cells

Introduction: Dental pulp stem cell (DPSC)-mediated dental pulp regeneration is considered a promising method for the treatment of deep caries with pulpitis. However, mesenchymal stem cell (MSC) senescence is an adverse factor from the perspective of cell-based therapies. In this study, we investigated the characteristics and expression profiles of DPSCs from young and old donors. Methods: DPSCs from young and old donors were cultured in differentiation medium, and their differentiation potentials were assessed. Long noncoding RNA (LncRNA) microarray assays and a bioinformatic analysis were performed to investigate differences in LncRNA and mRNA expression profiles between DPSCs from young and old donors. Results: We found that DPSCs from young donors exhibited more powerful proliferation ability and greater osteogenic and adipogenic differentiation potentials than DPSCs from old donors. In DPSCs from young donors, numerous LncRNAs were significantly up- (n = 389) or down-regulated (n = 172) compared to DPSCs from old donors. Furthermore, 304 mRNAs were differentially expressed, including 247 up-regulated genes and 57 down-regulated genes in DPSCs from young donors. The bioinformatic analysis identified that several pathways may be associated with DPSC characteristics, such as those involved in the cell cycle and RNA transport, and revealed nuclear transcription factor Y subunit β, general transcription factor IIB, and nuclear receptor subfamily 3 group C member 1 as core regulatory factors and FR249114, FR299091, and ENST00000450004 as core LncRNAs. Conclusions: Our results indicated that senescence impaired the proliferation and differentiation potentials of DPSCs and that donor age is an important factor that affects their use for tooth regeneration. We also provide insight into the mechanisms responsible for senescence in DPSCs.

Long noncoding RNAs in the progression, metastasis, and prognosis of osteosarcoma

Long noncoding RNAs (lncRNAs) are a class of non-protein-coding molecules longer than 200 nucleotides that are involved in the development and progression of many types of tumors. Numerous lncRNAs regulate cell proliferation, metastasis, and chemotherapeutic drug resistance. Osteosarcoma is one of the main bone tumor subtypes that poses a serious threat to adolescent health. We summarized how lncRNAs regulate osteosarcoma progression, invasion, and drug resistance, as well as how lncRNAs can function as biomarkers or independent prognostic indicators with respect to osteosarcoma therapy.

Long non-coding RNAs: An emerging powerhouse in the battle between life and death of tumor cells.

Long non-coding RNAs (lncRNAs) represent a class of non-protein coding transcripts longer than 200 nucleotides that have aptitude for regulating gene expression at the transcriptional, post-transcriptional or epigenetic levels. In recent years, lncRNAs, which are believed to be the largest transcript class in the transcriptomes, have emerged as important players in a variety of biological processes. Notably, the identification and characterization of numerous lncRNAs in the past decade has revealed a role for these molecules in the regulation of cancer cell survival and death. It is likely that this class of non-coding RNA constitutes a critical contributor to the assorted known or/and unknown mechanisms of intrinsic or acquired drug resistance. Moreover, the expression of lncRNAs is altered in various patho-physiological conditions, including cancer. Therefore, lncRNAs represent potentially important targets in predicting or altering the sensitivity or resistance of cancer cells to various therapies. Here, we provide an overview on the molecular functions of lncRNAs, and discuss their impact and importance in cancer development, progression, and therapeutic outcome. We also provide a perspective on how lncRNAs may alter the efficacy of cancer therapy and the promise of lncRNAs as novel therapeutic targets for overcoming chemoresistance. A better understanding of the functional roles of lncRNA in cancer can ultimately translate to the development of novel, lncRNA-based intervention strategies for the treatment or prevention of drug-resistant cancer.

Abstract A43: Long noncoding RNAs as targets of mammary tumor cell proliferation and migration

Abstract Objective: Recent genome-wide studies revealed that as much as 80% of the human genome can be transcribed whereas only 2% of this RNA is translated into proteins. Non-coding transcripts can be subdivided into several groups, with long non-coding RNAs (lncRNAs) representing the largest and most diverse class. With breast cancer being the most frequent malignancy in women worldwide, we set out to investigate the potential of lncRNAs as novel therapeutic targets. Methods: We focused on the luminal B and the HER2/neu-positive subtypes of breast cancer, as both are associated with high prevalence and bad prognosis. By performing RNA-Seq on tumor sections and mammary organoids from MMTV-PyMT and MMTV-Neu-NDL mice, modeling the luminal B and HER2/neu-amplified subtypes of human breast cancer respectively, we generated a comprehensive catalog of differentially expressed lncRNAs. We functionally validated the role of a subset of these lncRNAs by antisense oligonucleotide (ASO) mediated knockdown in primary mammary tumor cells and 3D ex vivo organoids. Results: We identified several hundred potentially oncogenic lncRNAs that were over-expressed in a subtype-specific manner as well as numerous lncRNAs up-regulated in both MMTV-PyMT and MMTV-Neu-NDL tumors. To narrow down the candidate list of lncRNAs with the highest therapeutic potential, we sorted the data computationally and defined a subset of previously uncharacterized lncRNAs as Mammary Tumor Associated RNAs (MaTARs). Upon independent knockdown of several MaTARs, we observed significantly reduced cell proliferation, invasion and/or collective cell migration in a cancer-specific context. Conclusion: MaTARs are likely important drivers of mammary tumor progression and/or metastasis and represent promising new therapeutic targets. Future studies will focus on the molecular characterization of these lncRNAs and elucidation of their potential role(s) in mammary tumor progression and metastasis. Citation Format: Sarah D. Diermeier, Kung-Chi Chang, Susan M. Freier, Frank Rigo, C. Frank Bennett, David L. Spector. Long noncoding RNAs as targets of mammary tumor cell proliferation and migration. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A43.

Transcriptome profiling of esophageal squamous cell carcinoma reveals a long noncoding RNA acting as a tumor suppressor.

Esophageal Squamous Cell Carcinoma (ESCC) is among the most common malignant cancers worldwide. In the past, extensive efforts have been made to characterize the involvement of protein-coding genes in ESCC tumorigenesis but few for long noncoding RNAs (lncRNAs). To investigate the transcriptome profile and functional relevance of lncRNAs, we performed an integrative analysis of a customized combined lncRNA-mRNA microarray and RNA-seq data on ESCCs and matched normal tissues. We identified numerous lncRNAs that were differentially expressed between the normal and tumor tissues, termed "ESCC-associated lncRNAs (ESCALs)", of which, the majority displayed restricted expression pattern. Also, a subset of ESCALs appeared to be associated with ESCC patient survival. Gene set enrichment analysis (GSEA) further suggested that over half of the ESCALs were positively-or negatively-associated with metastasis. Among these, we identified a novel nuclear-retained lncRNA, named Epist, which is generally highly expressed in esophagus, and which is down-regulated during ESCC progression. Epist over-expression and knockdown studies further suggest that Epist inhibits the metastasis, acting as a tumor suppressor in ESCC. Collectively, our analysis of the ESCC transcriptome identified the potential tumor suppressing lncRNA Epist, and provided a foundation for future efforts to identify functional lncRNAs for cancerous therapeutic targeting.

Study strategies for long non-coding RNAs and their roles in regulating gene expression.

Long non-coding RNAs (lncRNAs) have attracted considerable attention recently due to their involvement in numerous key cellular processes and in the development of various disorders. New high-throughput methods enable their study on a genome-wide scale. Numerous lncRNAs have been identified and characterized as important members of the biological regulatory network, with significant roles in regulating gene expression at the epigenetic, transcriptional and post-transcriptional levels. This paper summarizes the diverse mechanisms of action of these lncRNAs and looks at the study strategies in this field. A major challenge in future study is to establish more effective bioinformatics and experimental methods to explore the functions, detailed mechanisms of action and structures deciding the functional diversity of lncRNAs, since the vast majority remain unresolved.

Microarray expression profile analysis of long non-coding RNAs in human breast cancer: A study of Chinese women

Breast cancer (BC) is the most commonly diagnosed cancer and the second leading cause of cancer death among women. Long non-coding RNAs (lncRNAs) are key regulators of gene expression. Numerous lncRNAs have performed critical roles in cancer biology including breast cancer (BC). The expression levels of certain lncRNAs are associated with tumor development, recurrence, metastasis, and prognosis. However, the potential roles that lncRNAs regulate breast cancer tumorigenesis and tumor progression are still poorly understood. To investigate the potential roles of lncRNAs in the breast cancer, we constructed BC related lncRNA libraries by using microarray. Microarray expression profiling suggests 790 up-regulated and 637 down-regulated (log fold-change>2.3) lncRNAs were differently expressed between BC tissues and its paired adjacent tissues. Furthermore, we found differently expressed lncRNAs associated with immune regulation. RP4-583P15.10, an up-regulated lncRNA, was found to be located downstream of the natural antisense of the ZBTB46 gene, which may regulated breast cancer through influence immune system. In conclusion, our results for the first time indicate that distinct lncRNAs expression profiles of BC, which related to the immune network, may provide information for further research on immune regulation during the BC process.

Detection of long-chain non-encoding RNA differential expression in non-small cell lung cancer by microarray analysis and preliminary verification.

Long‑chain non‑coding RNAs (lncRNAs) have been shown to be involved in the development and progression of non‑small cell lung cancer (NSCLC). However, the roles of lncRNAs in NSCLC are not well understood. In this study, a high‑throughput microarray was used to compare the lncRNA and mRNA expression profiles in NSCLC and normal tissue (NT) samples. Several candidate adenocarcinoma‑associated lncRNAs were verified by reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR). Using abundant and varied probes, we were able to assess 30,586 lncRNAs and 26,109 coding transcripts in our microarray. It was observed that 1,242 lncRNAs and 1,102 mRNAs were differentially expressed (≥2‑fold change) in NSCLC compared with NT samples, indicating that numerous lncRNAs were significantly upregulated or downregulated in NSCLC. We also observed via RT‑qPCR that 10 lncRNAs were aberrantly expressed in NSCLC compared with histologically matched normal lung tissues. Among these, RP11‑385J1.2 and TUBA4B were the most aberrantly expressed lncRNAs, as estimated by RT‑qPCR in 90 pairs of NSCLC and NT samples. In conclusion, the present study detected the lncRNA expression patterns in NSCLC by microarray. The results revealed that a number of lncRNAs were differentially expressed in NSCLC tissues, suggesting that they may play a key role in tumor development.

TE composition of human long noncoding RNAs and their expression patterns in human tissues

High-throughput sequencing analyses have revealed that transposable elements (TEs) comprise approximately half of the human genome and frequently involved in genomic rearrangements and instability by various mechanisms. Interestingly, many noncoding RNAs (ncRNAs) contain TEs and the TE-containing ncRNAs that have been implicated in cellular processes and various diseases in mammals. In this study, we retrieved 94 human long noncoding RNAs (lncRNAs; >200 nucleotides in length) from lncRNAdb and analyzed TEs which are embedded within the lncRNAs, focusing on their chromosomal distribution. The result showed that TEs occupy ~27 % of the lncRNA transcripts in mass and lncRNA containing TEs are enriched in human chromosome 11. We further analyzed subfamily of the TEs and found that most of the TEs belong to AluSx and L1 which are the most successful TE subfamilies in the human genome. Numerous lncRNAs have been reported to be expressed in a cell-type specific manner. Thus, using reverse transcription PCR with specific primers for the lncRNAs, we examined their expression pattern in human normal tissues and cancer cells. Most of the lncRNAs were universally amplified from 20 different types of normal human tissues but some of them displayed tissue-specific expression. Especially, 11 lncRNAs were expressed only in human cancer cells, implying the possibility of their involvement in carcinogenesis.

The parasite Trichomonasvaginalis expresses thousands of pseudogenes and long non-coding RNAs independently from functional neighbouring genes.

BackgroundThe human pathogen Trichomonas vaginalis is a parabasalian flagellate that is estimated to infect 3% of the world’s population annually. With a 160 megabase genome and up to 60,000 genes residing in six chromosomes, the parasite has the largest genome among sequenced protists. Although it is thought that the genome size and unusual large coding capacity is owed to genome duplication events, the exact reason and its consequences are less well studied.ResultsAmong transcriptome data we found thousands of instances, in which reads mapped onto genomic loci not annotated as genes, some reaching up to several kilobases in length. At first sight these appear to represent long non-coding RNAs (lncRNAs), however, about half of these lncRNAs have significant sequence similarities to genomic loci annotated as protein-coding genes. This provides evidence for the transcription of hundreds of pseudogenes in the parasite. Conventional lncRNAs and pseudogenes are expressed in Trichomonas through their own transcription start sites and independently from flanking genes in Trichomonas. Expression of several representative lncRNAs was verified through reverse-transcriptase PCR in different T. vaginalis strains and case studies exclude the use of alternative start codons or stop codon suppression for the genes analysed.ConclusionOur results demonstrate that T. vaginalis expresses thousands of intergenic loci, including numerous transcribed pseudogenes. In contrast to yeast these are expressed independently from neighbouring genes. Our results furthermore illustrate the effect genome duplication events can have on the transcriptome of a protist. The parasite’s genome is in a steady state of changing and we hypothesize that the numerous lncRNAs could offer a large pool for potential innovation from which novel proteins or regulatory RNA units could evolve.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-906) contains supplementary material, which is available to authorized users.

Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs.

Long noncoding RNAs (lncRNAs) are important regulators of cell fate, yet little is known about mechanisms controlling lncRNA expression. Here we show that transcription is quantitatively different for lncRNAs and mRNAs--as revealed by deficiency of Dicer (Dcr), a key RNase that generates microRNAs (miRNAs). Dcr loss in mouse embryonic stem cells led unexpectedly to decreased levels of hundreds of lncRNAs. The canonical Dgcr8-Dcr-miRNA pathway is required for robust lncRNA transcriptional initiation and elongation. Computational and genetic epistasis analyses demonstrated that Dcr activation of the oncogenic transcription factor cMyc is partly responsible for lncRNA expression. A quantitative metric of mRNA-lncRNA decoupling revealed that Dcr and cMyc differentially regulate lncRNAs versus mRNAs in diverse cell types and in vivo. Thus, numerous lncRNAs may be modulated as a class in development and disease, notably where Dcr and cMyc act.

Comparison of Long Noncoding RNA and mRNA Expression Profiles in Mesenchymal Stem Cells Derived from Human Periodontal Ligament and Bone Marrow

Mesenchymal stem cells (MSCs) in different anatomic locations possess diverse biological activities. Maintaining the pluripotent state and differentiation depend on the expression and regulation of thousands of genes, but it remains unclear which molecular mechanisms underlie MSC diversity. Thus, potential MSC applications are restricted. Long noncoding RNAs (lncRNAs) are implicated in the complex molecular circuitry of cellular processes. We investigated differences in lncRNA and mRNA expression profiles between bone marrow stem cells (BMSCs) and periodontal ligament stem cells (PDLSCs) with lncRNA microarray assays and bioinformatics analysis. In PDLSCs, numerous lncRNAs were significantly upregulated (n = 457) or downregulated (n = 513) compared to BMSCs. Furthermore, 1,578 mRNAs were differentially expressed. These genes implicated cellular pathways that may be associated with MSC characteristics, including apoptosis, MAPK, cell cycle, and Wnt signaling pathway. Signal-net analysis indicated that phospholipase C beta 4, filamin B beta, calcium/calmodulin-dependent protein kinase II gamma, and the ionotropic glutamate receptor, AMPA 1, had the highest betweenness centrality among significant genes in the differential gene profile network. A comparison between the coding-noncoding gene coexpression networks of PDLSCs and BMSCs identified chemokine (C-X-C motif) ligand 12 as a core regulatory factor in MSC biology. These results provided insight into the mechanisms underlying MSC biology.

Molecular versatility: the many faces and functions of noncoding RNA

Molecular versatility: the many faces and functions of noncoding RNA

Long noncoding RNAs regulate adipogenesis

The prevalence of obesity has led to a surge of interest in understanding the detailed mechanisms underlying adipocyte development. Many protein-coding genes, mRNAs, and microRNAs have been implicated in adipocyte development, but the global expression patterns and functional contributions of long noncoding RNA (lncRNA) during adipogenesis have not been explored. Here we profiled the transcriptome of primary brown and white adipocytes, preadipocytes, and cultured adipocytes and identified 175 lncRNAs that are specifically regulated during adipogenesis. Many lncRNAs are adipose-enriched, strongly induced during adipogenesis, and bound at their promoters by key transcription factors such as peroxisome proliferator-activated receptor γ (PPARγ) and CCAAT/enhancer-binding protein α (CEBPα). RNAi-mediated loss of function screens identified functional lncRNAs with varying impact on adipogenesis. Collectively, we have identified numerous lncRNAs that are functionally required for proper adipogenesis.

Developmental Changes in the Transcriptome of Human Cerebral Cortex Tissue: Long Noncoding RNA Transcripts

The human neocortex is characterized by protracted developmental intervals of synaptogenesis and myelination, which allow for an extended period of learning. The molecular basis of these and other postnatal developmental changes in the human cerebral cortex remain incompletely understood. Recently, a new large class of mammalian genes, encoding nonmessenger, long nonprotein-coding ribonucleic acid (lncRNA) molecules has been discovered. Although their function remains uncertain, numerous lncRNAs have primate-specific sequences and/or show evidence of rapid, lineage-specific evolution, making them potentially relevant to the evolution of unique human neural properties. To examine the hypothesis that lncRNA expression varies with age, potentially paralleling known developmental trends in synaptogenesis, myelination, and energetics, we quantified levels of nearly 6000 lncRNAs in 36 surgically resected human neocortical samples (primarily derived from temporal cortex) spanning infancy to adulthood. Our analysis identified 8 lncRNA genes with distinct developmental expression patterns. These lncRNA genes contained anthropoid-specific exons, as well as splice sites and polyadenylation signals that resided in primate-specific sequences. To our knowledge, our study is the first to describe developmental expression profiles of lncRNA in surgically resected in vivo human brain tissue. Future analysis of the functional relevance of these transcripts to neural development and energy metabolism is warranted.

Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs

The recent discovery that the human and other mammalian genomes produce thousands of long non-coding RNAs (lncRNAs) raises many fascinating questions. These mRNA-like molecules, which lack significant protein-coding capacity, have been implicated in a wide range of biological functions through diverse and as yet poorly understood molecular mechanisms. Despite some recent insights into how lncRNAs function in such diverse cellular processes as regulation of gene expression and assembly of cellular structures, by and large, the key questions regarding lncRNA mechanisms remain to be answered. In this review, we discuss recent advances in understanding the biology of lncRNAs and propose avenues of investigation that may lead to fundamental new insights into their functions and mechanisms of action. Finally, as numerous lncRNAs are dysregulated in human diseases and disorders, we also discuss potential roles for these molecules in human health.

Chromatin Isolation by RNA Purification (ChIRP)

Long noncoding RNAs are key regulators of chromatin states for important biological processes such as dosage compensation, imprinting, and developmental gene expression 1,2,3,4,5,6,7. The recent discovery of thousands of lncRNAs in association with specific chromatin modification complexes, such as Polycomb Repressive Complex 2 (PRC2) that mediates histone H3 lysine 27 trimethylation (H3K27me3), suggests broad roles for numerous lncRNAs in managing chromatin states in a gene-specific fashion 8,9. While some lncRNAs are thought to work in cis on neighboring genes, other lncRNAs work in trans to regulate distantly located genes. For instance, Drosophila lncRNAs roX1 and roX2 bind numerous regions on the X chromosome of male cells, and are critical for dosage compensation 10,11. However, the exact locations of their binding sites are not known at high resolution. Similarly, human lncRNA HOTAIR can affect PRC2 occupancy on hundreds of genes genome-wide 3,12,13, but how specificity is achieved is unclear. LncRNAs can also serve as modular scaffolds to recruit the assembly of multiple protein complexes. The classic trans-acting RNA scaffold is the TERC RNA that serves as the template and scaffold for the telomerase complex 14; HOTAIR can also serve as a scaffold for PRC2 and a H3K4 demethylase complex 13.Prior studies mapping RNA occupancy at chromatin have revealed substantial insights 15,16, but only at a single gene locus at a time. The occupancy sites of most lncRNAs are not known, and the roles of lncRNAs in chromatin regulation have been mostly inferred from the indirect effects of lncRNA perturbation. Just as chromatin immunoprecipitation followed by microarray or deep sequencing (ChIP-chip or ChIP-seq, respectively) has greatly improved our understanding of protein-DNA interactions on a genomic scale, here we illustrate a recently published strategy to map long RNA occupancy genome-wide at high resolution 17. This method, Chromatin Isolation by RNA Purification (ChIRP) (Figure 1), is based on affinity capture of target lncRNA:chromatin complex by tiling antisense-oligos, which then generates a map of genomic binding sites at a resolution of several hundred bases with high sensitivity and low background. ChIRP is applicable to many lncRNAs because the design of affinity-probes is straightforward given the RNA sequence and requires no knowledge of the RNA's structure or functional domains.

Chromatin Isolation by RNA Purification (ChIRP)

Long noncoding RNAs are key regulators of chromatin states for important biological processes such as dosage compensation, imprinting, and developmental gene expression 1,2,3,4,5,6,7. The recent discovery of thousands of lncRNAs in association with specific chromatin modification complexes, such as Polycomb Repressive Complex 2 (PRC2) that mediates histone H3 lysine 27 trimethylation (H3K27me3), suggests broad roles for numerous lncRNAs in managing chromatin states in a gene-specific fashion 8,9. While some lncRNAs are thought to work in cis on neighboring genes, other lncRNAs work in trans to regulate distantly located genes. For instance, Drosophila lncRNAs roX1 and roX2 bind numerous regions on the X chromosome of male cells, and are critical for dosage compensation 10,11. However, the exact locations of their binding sites are not known at high resolution. Similarly, human lncRNA HOTAIR can affect PRC2 occupancy on hundreds of genes genome-wide 3,12,13, but how specificity is achieved is unclear. LncRNAs can also serve as modular scaffolds to recruit the assembly of multiple protein complexes. The classic trans-acting RNA scaffold is the TERC RNA that serves as the template and scaffold for the telomerase complex 14; HOTAIR can also serve as a scaffold for PRC2 and a H3K4 demethylase complex 13. Prior studies mapping RNA occupancy at chromatin have revealed substantial insights 15,16, but only at a single gene locus at a time. The occupancy sites of most lncRNAs are not known, and the roles of lncRNAs in chromatin regulation have been mostly inferred from the indirect effects of lncRNA perturbation. Just as chromatin immunoprecipitation followed by microarray or deep sequencing (ChIP-chip or ChIP-seq, respectively) has greatly improved our understanding of protein-DNA interactions on a genomic scale, here we illustrate a recently published strategy to map long RNA occupancy genome-wide at high resolution 17. This method, Chromatin Isolation by RNA Purification (ChIRP) (Figure 1), is based on affinity capture of target lncRNA:chromatin complex by tiling antisense-oligos, which then generates a map of genomic binding sites at a resolution of several hundred bases with high sensitivity and low background. ChIRP is applicable to many lncRNAs because the design of affinity-probes is straightforward given the RNA sequence and requires no knowledge of the RNA's structure or functional domains.