Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus

The human 8q24 gene desert contains multiple enhancers that form tissue-specific long-range chromatin loops with the MYC oncogene, but how chromatin looping at the MYC locus is regulated remains poorly understood. Here we demonstrate that a long noncoding RNA (lncRNA), CCAT1-L, is transcribed specifically in human colorectal cancers from a locus 515 kb upstream of MYC. This lncRNA plays a role in MYC transcriptional regulation and promotes long-range chromatin looping. Importantly, the CCAT1-L locus is located within a strong super-enhancer and is spatially close to MYC. Knockdown of CCAT1-L reduced long-range interactions between the MYC promoter and its enhancers. In addition, CCAT1-L interacts with CTCF and modulates chromatin conformation at these loop regions. These results reveal an important role of a previously unannotated lncRNA in gene regulation at the MYC locus.

• Publication year

  2014

• Venue

  Cell Research

• Publication date

  2014-03-25

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1038/cr.2014.35PMID 24662484PMCID 4011346
• 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.

• Detection of a long non-coding RNA (CCAT1) in living cells and human adenocarcinoma of colon tissues using FIT-PNA molecular beacons.

  2014cited by this paper
• Architectural protein subclasses shape 3D organization of genomes during lineage commitment.

  2013cited by this paper
• Circular intronic long noncoding RNAs.

  2013cited by this paper
• Long noncoding RNAs usher in a new era in the biology of enhancers.

  2013cited by this paper
• In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures.

  2013cited by this paper
• ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering.

  2013cited by this paper
• The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells.

  2013cited by this paper
• Jpx RNA activates Xist by evicting CTCF.

  2013cited by this paper
• Enhancer transcripts mark active estrogen receptor binding sites

  2013cited by this paper
• Braveheart, a long noncoding RNA required for cardiovascular lineage commitment.

  2013cited by this paper
• Bivalent chromatin marks developmental regulatory genes in the mouse embryonic germline in vivo.

  2013cited by this paper
• Long Noncoding RNA MALAT1 Controls Cell Cycle Progression by Regulating the Expression of Oncogenic Transcription Factor B-MYB

  2013cited by this paper
• Master transcription factors and mediator establish super-enhancers at key cell identity genes.

  2013cited by this paper
• Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

  2013cited by this paper
• Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

  2013cited by this paper
• lincRNAs: genomics, evolution, and mechanisms.

  2013cited by this paper
• Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

  2013cited by this paper
• eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci.

  2013cited by this paper
• LncRNA-Dependent Mechanisms of Androgen Receptor-regulated Gene Activation Programs

  2013cited by this paper
• Selective inhibition of tumor oncogenes by disruption of super-enhancers.

  2013cited by this paper
• Super-enhancers in the control of cell identity and disease.

  2013cited by this paper
• Differential expression of colon cancer associated transcript1 (CCAT1) along the colonic adenoma-carcinoma sequence

  2013cited by this paper
• CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer

  2013cited by this paper
• Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions

  2013cited by this paper
• The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult.

  2012cited by this paper
• CTCF: insights into insulator function during development

  2012cited by this paper
• The hallmarks of cancer

  2012cited by this paper
• Mice Lacking a Myc Enhancer That Includes Human SNP rs6983267 Are Resistant to Intestinal Tumors

  2012cited by this paper
• The long-range interaction landscape of gene promoters

  2012cited by this paper
• A map of the cis-regulatory sequences in the mouse genome

  2012cited by this paper
• Long noncoding RNAs with snoRNA ends.

  2012cited by this paper
• LincRNA-p21 suppresses target mRNA translation.

  2012cited by this paper
• Genome regulation by long noncoding RNAs.

  2012cited by this paper
• Limitations and possibilities of low cell number ChIP-seq

  2012cited by this paper
• Colon cancer associated transcript‐1: A novel RNA expressed in malignant and pre‐malignant human tissues

  2012cited by this paper
• Single-tube linear DNA amplification for genome-wide studies using a few thousand cells

  2012cited by this paper
• An Integrated Encyclopedia of DNA Elements in the Human Genome

  2012cited by this paper
• Two-timing zinc finger transcription factors liaising with RNA.

  2012cited by this paper
• ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

  2012cited by this paper
• Single-tube linear DNA amplification (LinDA) for robust ChIP-seq

  2011cited by this paper
• Enhancer function: new insights into the regulation of tissue-specific gene expression

  2011cited by this paper
• CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells

  2011cited by this paper
• Functional and mechanistic diversity of distal transcription enhancers.

  2011cited by this paper
• Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting

  2011cited by this paper
• Noncoding RNA gene silencing through genomic integration of RNA destabilizing elements using zinc finger nucleases.

  2011cited by this paper
• Regulation of X-chromosome inactivation by the X-inactivation centre

  2011cited by this paper
• The relationship between transcription initiation RNAs and CCCTC-binding factor (CTCF) localization

  2011cited by this paper
• Genomewide characterization of non-polyadenylated RNAs

  2011cited by this paper
• Association of a novel long non‐coding RNA in 8q24 with prostate cancer susceptibility

  2011cited by this paper
• 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC

  2010cited by this paper
• A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

  2010cited by this paper
• Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA.

  2010cited by this paper
• Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

  2010cited by this paper
• Next-generation genomics: an integrative approach

  2010cited by this paper
• A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response.

  2010cited by this paper
• Long noncoding RNAs with enhancer-like function in human cells.

  2010cited by this paper
• Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors

  2010cited by this paper
• Long noncoding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

  2010cited by this paper
• CTCF: master weaver of the genome.

  2009cited by this paper
• The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling

  2009cited by this paper
• Automated microfluidic chromatin immunoprecipitation from 2,000 cells.

  2009cited by this paper
• The 8q24 cancer risk variant rs6983267 demonstrates long-range interaction with MYC in colorectal cancer

  2009cited by this paper
• ChIP–seq: advantages and challenges of a maturing technology

  2009cited by this paper
• How the c-myc promoter works and why it sometimes does not.

  2008cited by this paper
• Mapping networks of physical interactions between genomic elements using 5C technology

  2007cited by this paper
• Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth

  2007cited by this paper
• The complex language of chromatin regulation during transcription

  2007cited by this paper
• New cell lines from mouse epiblast share defining features with human embryonic stem cells

  2007cited by this paper
• Quantitative analysis of chromosome conformation capture assays (3C-qPCR)

  2007cited by this paper
• Comparison of sample preparation methods for ChIP-chip assays.

  2006cited by this paper
• Transcriptional regulatory elements in the human genome.

  2006cited by this paper
• RxFISH karyotype and MYC amplification in the HT‐29 colon adenocarcinoma cell line

  2003cited by this paper
• Having it both ways: transcription factors that bind DNA and RNA.

  2002cited by this paper
• Comprehensive karyotyping of the HT‐29 colon adenocarcinoma cell line

  2002cited by this paper
• Identification of c-MYC as a target of the APC pathway.

  1998cited by this paper

• Long noncoding RNAs as key regulators of autoimmunity.

  2026cites this paper
• Noncoding RNAs: A Novel Frontier in Liver Cancer Research and Therapy: Implications for Precision Oncology.

  2026cites this paper
• Deciphering the regulatory landscape of enhancer RNAs in health and disease

  2026influential citation
• Alternative transcription increases isoform complexity in Long Non-Coding RNAs and alters their functions in cancer

  2025cites this paper
• A transcription coupling model for how enhancers communicate with their target genes

  2025cites this paper
• Rewiring cancer epigenome: lncRNA as modulator of chromatin architecture and neoplastic transformation

  2025cites this paper
• Discovering the interactome, functions, and clinical relevance of enhancer RNAs in kidney renal clear cell carcinoma

  2025cites this paper
• Fluorescence imaging of MALAT1 expression using a Cy5.5-labeled antisense oligonucleotide in lung cancer and epidermal carcinoma cells

  2025cites this paper
• Long noncoding RNAs in plant chromatin 3D conformation dynamics.

  2025cites this paper
• Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers

  2025cites this paper
• Frequent functional orthology of long noncoding RNAs and genomic loci associated with complex traits and disorders

  2025cites this paper
• The LncRNA lnc-POTEM-4:14 promotes HCC progression by interacting with FOXK1

  2025cites this paper
• A specific pluripotency-associated eRNA controls Nanog locus by shaping the epigenetic landscape and stabilizing enhancer–promoter interaction

  2025cites this paper
• A Super‐Enhancer‐Related Ferroptosis Signature Predicts Survival and Immune Microenvironment in Colon Cancer Based on Bioinformatics Analyses and Experimental Validation

  2025cites this paper
• Long Non-Coding RNAs and RNA-Binding Proteins in Pancreatic Cancer Development and Progression

  2025cites this paper
• Super-enhancer-associated long noncoding RNA lnc-SPI1U mediates SPI1 feedback regulation by interacting with HNRNPH1 and HNRNPF

  2025cites this paper
• Super-Enhancer-Driven HCG20 Promotes Pulmonary Hypertension Through U2AF2 Splicing.

  2025cites this paper
• The emerging roles of long non-coding RNAs in the nervous system

  2025cites this paper
• CRISPR live-cell imaging reveals chromatin dynamics and enhancer interactions at multiple non-repetitive loci.

  2025cites this paper
• The role of super-enhancer-driven lncRNAs in cancer

  2025cites this paper
• Biomolecules Interacting with Long Noncoding RNAs

  2025cites this paper
• Non-Coding RNAs in Cancer: Structure, Function, and Clinical Application

  2025cites this paper
• Dysregulation of lncRNAs in NK cells from breast cancer patients: implications for NK cell functions

  2025cites this paper
• An ensemble learning method combined with multiple feature representation strategies to predict lncRNA subcellular localizations

  2025cites this paper
• Tumor-associated long non-coding RNAs show variable expression across diffuse gliomas and effect on cell growth upon silencing in glioblastoma

  2025cites this paper
• Understanding lncRNAs: key regulators of myogenesis and lipogenesis in farm animals

  2025cites this paper
• Super-enhancer-driven SLCO4A1-AS1 is a new biomarker and a promising therapeutic target in glioblastoma

  2025cites this paper
• Multi-layered gene regulation by long non-coding RNAs: from chromatin to genome architecture.

  2025cites this paper
• Liquid Biopsy for Colorectal Cancer: Advancing Detection and Clinical Application

  2025cites this paper
• The roles of enhancer, especially super-enhancer-driven genes in tumor metabolism and immunity.

  2025cites this paper
• SNORA58 Facilitates Radioresistance via Suppressing JNK1‐Mediated Ferroptosis in Esophageal Squamous Cell Carcinoma

  2025cites this paper
• Epstein-Barr Virus Encoded lncRNAs Control the Viral Lytic Switch

  2025cites this paper
• Epigenetic regulators in cancer therapy and progression

  2025cites this paper
• NaRaDa: A comprehensive nascent RNA database

  2025cites this paper
• Chromatin-Associated RNAs Regulate Gene Expression and Chromatin Structure

  2025cites this paper
• Biological roles of enhancer RNA m6A modification and its implications in cancer

  2025cites this paper
• Ischemic stroke altered the expression profiles of super enhancer RNAs in mouse brain in a sexually dimorphic manner.

  2025cites this paper
• The role of long non‐coding RNAs in lung cancer metastasis: Molecular mechanisms, pathogenesis and clinical implications

  2025influential citation
• HSF1 promotes malignant phenotype in colorectal cancer via super-enhancer-driven lncRNA EXOSC10-AS1 and targeting HSF1 confers sensitivity to poly (ADP-ribose) polymerase inhibitor Niraparib.

  2025cites this paper
• Overrepresentation of Germline Immune-Related Gene Variants in Patients with Acquired Bone Marrow Failure

  2025cites this paper
• Targeting RNA binding proteins with small-molecule inhibitors: Advances, challenges, and therapeutic opportunities

  2025cites this paper
• Machine learning-based survival prediction in colorectal cancer combining clinical and biological features

  2025cites this paper
• SE‐lncRNAs in Cancer: Classification, Subcellular Localisation, Function and Corresponding TFs

  2024cites this paper
• Comprehensive review of LncRNA-mediated therapeutic resistance in non-small cell lung cancer

  2024cites this paper
• Diagnostics and Therapy for Malignant Tumors

  2024cites this paper
• Unraveling the Regulatory Role of HuR/microRNA Axis in Colorectal Cancer Tumorigenesis

  2024cites this paper
• Discovery of prognostic lncRNAs in colorectal cancer using spatial transcriptomics

  2024cites this paper
• The enhancer RNA, AANCR, regulates APOE expression in astrocytes and microglia.

  2024cites this paper
• RNA-Independent Regulatory Functions of lncRNA in Complex Disease

  2024cites this paper
• CASCADES, a novel SOX2 super‐enhancer‐associated long noncoding RNA, regulates cancer stem cell specification and differentiation in glioblastoma

  2024cites this paper
• CircNAP1L4 regulates pulmonary artery smooth muscle cell proliferation via the NAP1L4‐mediated super‐enhancer‐driven glycolysis gene hexokinase II (HK II) in pulmonary hypertension

  2024cites this paper
• DNA regulatory element cooperation and competition in transcription

  2024influential citation
• Unveiling the hidden gem: A review of long non-coding RNA NBAT-1 as an emerging tumor suppressor and prognostic biomarker in cancer.

  2024cites this paper
• Role of long non-coding RNAs in neurofibromatosis and Schwannomatosis: pathogenesis and therapeutic potential.

  2024cites this paper
• Automated Navigation of the lncRNA Transcriptome: A comprehensive SnakeMake based computational Pipeline for robust Identification of lncRNAs and their putative targets

  2024cites this paper
• Long non-coding RNAs: regulators of autophagy and potential biomarkers in therapy resistance and urological cancers

  2024cites this paper
• Long non-coding RNAs as pathophysiological regulators, therapeutic targets and novel extracellular vesicle biomarkers for the diagnosis of inflammatory bowel disease.

  2024cites this paper
• Effects of super-enhancers in cancer metastasis: mechanisms and therapeutic targets

  2024cites this paper
• Colorectal cancer microbiome programs DNA methylation of host cells by affecting methyl donor metabolism

  2024cites this paper
• Unraveling the ncRNA landscape that governs colorectal cancer: A roadmap to personalized therapeutics.

  2024cites this paper
• CRISPR-array-mediated imaging of non-repetitive and multiplex genomic loci in living cells

  2024cites this paper
• Superenhancer-driven circRNA Myst4 involves in pulmonary artery smooth muscle cell ferroptosis in pulmonary hypertension

  2024cites this paper
• Colon cancer-associated transcript 1 (CCAT1): A potential novel target in cancer therapy

  2024cites this paper
• Role of long noncoding RNAs in diabetes-associated peripheral arterial disease

  2024cites this paper
• CCAT1 lncRNA is chromatin-retained and post-transcriptionally spliced

  2024influential citation
• Chimera RNA transcribed from integrated HPV18 genome with adjacent host genomic region promotes oncogenic gene expression through condensate formation

  2024cites this paper
• Noncoding RNAs in skeletal development and disorders

  2024cites this paper
• Long non-coding RNA LIP interacts with PARP-1 influencing the efficiency of base excision repair

  2024cites this paper
• Effects of BRD4 inhibitor JQ1 on the expression profile of super-enhancer related lncRNAs and mRNAs in cervical cancer HeLa cells

  2024cites this paper
• An Emerging Role for Enhancer RNAs in Brain Disorders

  2024cites this paper
• The role of long non-coding RNA in hepatocellular carcinoma

  2024cites this paper
• Bioinformatics analysis proposes a possible role for long noncoding RNA MIR17HG in retinoblastoma

  2024cites this paper
• Long Noncoding RNA RP11-278A23.1, a Potential Modulator of p53 Tumor Suppression, Contributes to Colorectal Cancer Progression

  2024cites this paper
• Super enhancer lncRNAs: a novel hallmark in cancer

  2024cites this paper
• Bivalent activity of super-enhancer RNA LINC02454 controls 3D chromatin structure and regulates glioma sensitivity to temozolomide

  2024cites this paper
• Cell type specific long non-coding RNA targets identified by integrative analysis of single-cell and bulk colorectal cancer transcriptomes

  2024cites this paper
• Reciprocal interactions between lncRNAs and MYC in colorectal cancer: partners in crime

  2024cites this paper
• 3D epigenomics and 3D epigenopathies

  2024cites this paper
• MIAT LncRNA: A multifunctional key player in non-oncological pathological conditions

  2024cites this paper
• Integrated enhancer regulatory network by enhancer–promoter looping in gastric cancer

  2024cites this paper
• Long non‑coding RNAs as diagnostic and prognostic biomarkers for colorectal cancer (Review)

  2024cites this paper
• Exploring the lncRNA-VEGF axis: Implications for cancer detection and therapy.

  2023cites this paper
• The nexus of long noncoding RNAs, splicing factors, alternative splicing and their modulations

  2023cites this paper
• Super-enhancer RNA m^6A promotes local chromatin accessibility and oncogene transcription in pancreatic ductal adenocarcinoma

  2023cites this paper
• Transcriptional activation of the Myc gene by glucose in β-cells requires a ChREBP-dependent 3-D chromatin interaction between the Myc and Pvt1 genes

  2023cites this paper
• eRNAbase: a comprehensive database for decoding the regulatory eRNAs in human and mouse

  2023cites this paper
• Lnc AC016727.1/BACH1/HIF-1 α signal loop promotes the progression of non-small cell lung cancer

  2023cites this paper
• The Roles of Long Noncoding RNA in Depression.

  2023cites this paper
• From carcinogenesis to therapeutic avenues: lncRNAs and mTOR crosstalk in lung cancer.

  2023cites this paper
• METTL3‐stabilized super enhancers‐lncRNA SUCLG2‐AS1 mediates the formation of a long‐range chromatin loop between enhancers and promoters of SOX2 in metastasis and radiosensitivity of nasopharyngeal carcinoma

  2023cites this paper
• Hnrnpk is essential for embryonic limb bud development as a transcription activator and a collaborator of insulator protein Ctcf

  2023cites this paper
• Super-enhancers complexes zoom in transcription in cancer

  2023cites this paper
• lncRNAs: the abyss being gazed back.

  2023cites this paper
• Long non-coding RNAs in lung cancer: Unraveling the molecular modulators of MAPK signaling.

  2023cites this paper
• A risk model constructed using 14 N6-methyladenosine-related lncRNAs as a new prognostic marker that correlates with the immunomodulatory effect and drug sensitivity in colorectal cancer

  2023cites this paper
• The Talented LncRNAs: Meshing into Transcriptional Regulatory Networks in Cancer

  2023influential citation
• LncRNAs: the good, the bad, and the unknown.

  2023cites this paper
• Super-enhancer landscape rewiring in cancer: The epigenetic control at distal sites.

  2023cites this paper
• Enhancers are genes that express organizational RNAs

  2023cites this paper
• The relationship between long non-coding RNAs and Wnt/β-catenin signaling pathway in the pathogenesis of Alzheimer's disease.

  2023cites this paper