FIRRE Gene

HGNC Family Non-coding RNAs
Name firre intergenic repeating RNA element
Description This gene produces a long RNA containing a repeating sequence. This RNA interacts with heterogeneous nuclear ribonucleoprotein U and coats chromosomes, where it plays an important role in the maintenance of repressive chromatin. This transcript can also act post-transcriptionally to regulate the stability of mRNAs during the innate immune response. [provided by RefSeq, Dec 2017]
Summary
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Its transcription is induced via NF-κB signaling in cells such as macrophages and intestinal epithelial cells, where FIRRE, by interacting with heterogeneous nuclear ribonucleoprotein U (hnRNPU), enhances the expression of inflammatory genes through posttranscriptional stabilization of mRNAs via AU-rich element targeting."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n FIRRE activity has also been implicated in tumorigenesis. In diffuse large B-cell lymphoma and colorectal cancer, aberrant upregulation of FIRRE promotes oncogenic behaviors. In these settings, FIRRE facilitates tumor cell proliferation by activating pathways such as Wnt/β-catenin—via promoting the nuclear translocation of β-catenin—or by stabilizing transcripts like BECN1 through its interaction with RNA-binding proteins such as PTBP1."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": " Furthermore, differential FIRRE expression may have prognostic significance, as higher levels have been associated with improved overall survival in certain colorectal cancer patient cohorts."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "9"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Collectively, these findings support a context-dependent role for FIRRE in regulating nuclear architecture, inflammatory responses, and oncogenic processes, underscoring its importance as a multifunctional regulatory RNA in both normal physiology and disease.\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Fan Yang, Xinxian Deng, Wenxiu Ma, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genome Biol (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/s13059-015-0618-0"}], "href": "https://doi.org/10.1186/s13059-015-0618-0"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25887447"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25887447"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "A Rasim Barutcu, Philipp G Maass, Jordan P Lewandowski, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Commun (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41467-018-03614-0"}], "href": "https://doi.org/10.1038/s41467-018-03614-0"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29654311"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29654311"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "He Fang, Giancarlo Bonora, Jordan P Lewandowski, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Commun (2020)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41467-020-19879-3"}], "href": "https://doi.org/10.1038/s41467-020-19879-3"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "33247132"}], "href": "https://pubmed.ncbi.nlm.nih.gov/33247132"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Ezgi Hacisuleyman, Loyal A Goff, Cole Trapnell, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Struct Mol Biol (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nsmb.2764"}], "href": "https://doi.org/10.1038/nsmb.2764"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24463464"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24463464"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Yajing Lu, Xu Liu, Minghong Xie, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The NF-κB-Responsive Long Noncoding RNA FIRRE Regulates Posttranscriptional Regulation of Inflammatory Gene Expression through Interacting with hnRNPU."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Immunol (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.4049/jimmunol.1700091"}], "href": "https://doi.org/10.4049/jimmunol.1700091"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28993514"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28993514"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Jordan P Lewandowski, James C Lee, Taeyoung Hwang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Commun (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41467-019-12970-4"}], "href": "https://doi.org/10.1038/s41467-019-12970-4"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31723143"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31723143"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Xue Shi, Zhongguang Cui, Xiaodan Liu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "LncRNA FIRRE is activated by MYC and promotes the development of diffuse large B-cell lymphoma via Wnt/β-catenin signaling pathway."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biochem Biophys Res Commun (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.bbrc.2019.01.105"}], "href": "https://doi.org/10.1016/j.bbrc.2019.01.105"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30739786"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30739786"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Yajie Wang, Zhengyang Li, Shizan Xu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "LncRNA FIRRE functions as a tumor promoter by interaction with PTBP1 to stabilize BECN1 mRNA and facilitate autophagy."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell Death Dis (2022)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41419-022-04509-1"}], "href": "https://doi.org/10.1038/s41419-022-04509-1"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "35110535"}], "href": "https://pubmed.ncbi.nlm.nih.gov/35110535"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Jia-Jun Qiu, Jing-Bin Yan "}, {"type": "b", "children": [{"type": "t", "text": "Long non-coding RNA LINC01296 is a potential prognostic biomarker in patients with colorectal cancer."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Tumour Biol (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s13277-015-3448-5"}], "href": "https://doi.org/10.1007/s13277-015-3448-5"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25894381"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25894381"}]}]}]}
Synonyms LINC01200
NCBI Gene ID 286467
API
Download Associations
Predicted Functions View FIRRE's ARCHS4 Predicted Functions.
Co-expressed Genes View FIRRE's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View FIRRE's ARCHS4 Predicted Functions.

Functional Associations

FIRRE has 381 functional associations with biological entities spanning 4 categories (functional term, phrase or reference, disease, phenotype or trait, cell line, cell type or tissue, gene, protein or microRNA) extracted from 11 datasets.

Click the + buttons to view associations for FIRRE from the datasets below.

If available, associations are ranked by standardized value

Dataset Summary
Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles tissues with high or low expression of FIRRE gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq tissue samples with high or low expression of FIRRE gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles tissues with high or low expression of FIRRE gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
CCLE Cell Line Gene CNV Profiles cell lines with high or low copy number of FIRRE gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
CellMarker Gene-Cell Type Associations cell types associated with FIRRE gene from the CellMarker Gene-Cell Type Associations dataset.
GEO Signatures of Differentially Expressed Genes for Gene Perturbations gene perturbations changing expression of FIRRE gene from the GEO Signatures of Differentially Expressed Genes for Gene Perturbations dataset.
GEO Signatures of Differentially Expressed Genes for Kinase Perturbations kinase perturbations changing expression of FIRRE gene from the GEO Signatures of Differentially Expressed Genes for Kinase Perturbations dataset.
GTEx Tissue-Specific Aging Signatures tissue samples with high or low expression of FIRRE gene relative to other tissue samples from the GTEx Tissue-Specific Aging Signatures dataset.
Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles cell lines with high or low copy number of FIRRE gene relative to other cell lines from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles dataset.
LOCATE Predicted Protein Localization Annotations cellular components predicted to contain FIRRE protein from the LOCATE Predicted Protein Localization Annotations dataset.
MGI Mouse Phenotype Associations 2023 phenotypes of transgenic mice caused by FIRRE gene mutations from the MGI Mouse Phenotype Associations 2023 dataset.