MIR4540 Gene

HGNC Family Non-coding RNAs
Name microRNA 4540
Description microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]
Summary
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nThe collection of abstracts provided centers on the role of TMEM67 in various ciliopathies, detailing its involvement in ciliary structure, signaling pathways (including both canonical and non‐canonical Wnt, Shh, and tyrosine kinase cascades), and developmental processes affecting multiple organs. None of these abstracts, however, include any direct reference to or data concerning the function of MIR4540. Consequently, there is no available evidence within these studies to infer or summarize a role for MIR4540."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "7"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn these studies, TMEM67 is highlighted as a key component of the ciliary transition zone, with its dysfunction linked to marked alterations in signaling activities (such as deregulated Wnt/β-catenin signaling and aberrant Shh pathway responses) that underlie the phenotypic variability seen in ciliopathy models. The research spans diverse experimental systems—from murine knockout models that recapitulate human syndromes like Meckel-Gruber and Joubert, to in vitro systems and zebrafish morphants—each demonstrating how TMEM67 dysfunction contributes to developmental malformations. Yet, even though microRNAs can be crucial regulators of gene expression in such pathways, none of the abstracts address a potential regulatory role for MIR4540."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nOverall, while the manuscripts provide valuable insights into the molecular mechanisms governing ciliary signaling and organ development via TMEM67, they do not shed light on a functional role for MIR4540. Further dedicated research would be required to determine if MIR4540 interacts with or influences these pathways, or if it has independent roles in the context of ciliopathies."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "4", "end_ref": "7"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Gayle B Collin, Jungyeon Won, Wanda L Hicks, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Meckelin is necessary for photoreceptor intraciliary transport and outer segment morphogenesis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Invest Ophthalmol Vis Sci (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1167/iovs.11-8766"}], "href": "https://doi.org/10.1167/iovs.11-8766"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22247471"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22247471"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Zakia A Abdelhamed, Gabrielle Wheway, Katarzyna Szymanska, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Variable expressivity of ciliopathy neurological phenotypes that encompass Meckel-Gruber syndrome and Joubert syndrome is caused by complex de-regulated ciliogenesis, Shh and Wnt signalling defects."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Hum Mol Genet (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/hmg/dds546"}], "href": "https://doi.org/10.1093/hmg/dds546"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23283079"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23283079"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Amanda C Leightner, Cynthia J Hommerding, Ying Peng, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The Meckel syndrome protein meckelin (TMEM67) is a key regulator of cilia function but is not required for tissue planar polarity."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Hum Mol Genet (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/hmg/ddt054"}], "href": "https://doi.org/10.1093/hmg/ddt054"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23393159"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23393159"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "E Du, Hong Li, Shunying Jin, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Evidence that TMEM67 causes polycystic kidney disease through activation of JNK/ERK-dependent pathways."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell Biol Int (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/cbin.10081"}], "href": "https://doi.org/10.1002/cbin.10081"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23456819"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23456819"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Sveva Romani, Barbara Illi, Roberta De Mori, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The ciliary proteins Meckelin and Jouberin are required for retinoic acid-dependent neural differentiation of mouse embryonic stem cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Differentiation (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.diff.2014.02.005"}], "href": "https://doi.org/10.1016/j.diff.2014.02.005"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24613594"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24613594"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Zakia A Abdelhamed, Subaashini Natarajan, Gabrielle Wheway, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The Meckel-Gruber syndrome protein TMEM67 controls basal body positioning and epithelial branching morphogenesis in mice via the non-canonical Wnt pathway."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Dis Model Mech (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1242/dmm.019083"}], "href": "https://doi.org/10.1242/dmm.019083"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26035863"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26035863"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Zakia A Abdelhamed, Dina I Abdelmottaleb, Mohammed E El-Asrag, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The ciliary Frizzled-like receptor Tmem67 regulates canonical Wnt/β-catenin signalling in the developing cerebellum via Hoxb5."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Sci Rep (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41598-019-41940-5"}], "href": "https://doi.org/10.1038/s41598-019-41940-5"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30931988"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30931988"}]}]}]}
NCBI Gene ID 100616278
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Download Associations
Predicted Functions View MIR4540's ARCHS4 Predicted Functions.
Co-expressed Genes View MIR4540's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View MIR4540's ARCHS4 Predicted Functions.

Functional Associations

MIR4540 has 429 functional associations with biological entities spanning 3 categories (molecular profile, cell line, cell type or tissue, gene, protein or microRNA) extracted from 8 datasets.

Click the + buttons to view associations for MIR4540 from the datasets below.

If available, associations are ranked by standardized value

Dataset Summary
CCLE Cell Line Gene CNV Profiles cell lines with high or low copy number of MIR4540 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
COSMIC Cell Line Gene CNV Profiles cell lines with high or low copy number of MIR4540 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
ENCODE Histone Modification Site Profiles histone modification site profiles with high histone modification abundance at MIR4540 gene from the ENCODE Histone Modification Site Profiles dataset.
ENCODE Transcription Factor Binding Site Profiles transcription factor binding site profiles with transcription factor binding evidence at the promoter of MIR4540 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
ENCODE Transcription Factor Targets transcription factors binding the promoter of MIR4540 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles cell lines with high or low copy number of MIR4540 gene relative to other cell lines from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles dataset.
MotifMap Predicted Transcription Factor Targets transcription factors regulating expression of MIR4540 gene predicted using known transcription factor binding site motifs from the MotifMap Predicted Transcription Factor Targets dataset.
Roadmap Epigenomics Histone Modification Site Profiles histone modification site profiles with high histone modification abundance at MIR4540 gene from the Roadmap Epigenomics Histone Modification Site Profiles dataset.