BCYRN1

Summary

BCYRN1 (brain cytoplasmic RNA 1, HGNC:1022) is a long non-coding RNA gene on chromosome 2p21.

This gene, which encodes a neural small non-messenger RNA, is a member of the family of interspersed repetitive DNA, and its product represents an example of a primate tissue-specific RNA polymerase III transcript. The RNA sequence is divided into three domains: a 5’ portion homologous to the Alu Lm, a central adenosine-rich region, and the terminal 43-nt nonrepetitive domain. It is believed that this gene was retropositionally generated and recruited into a function regulating dendritic protein biosynthesis. At least two pseudogenes of this gene have been identified.

Source: NCBI Gene 618 — RefSeq curated summary.

At a glance

• Gene type: non-coding (lncRNA) — no protein product; not a drug target. Variant/disease associations are omitted (they would be positional, from an overlapping protein-coding gene).

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1022
Approved symbol	BCYRN1
Name	brain cytoplasmic RNA 1
Location	2p21
Locus type	RNA, long non-coding
Status	Approved
Aliases	BC200, BC200a, NCRNA00004, LINC00004
Ensembl gene	ENSG00000236824
Ensembl biotype	lncRNA
OMIM	606089
Entrez	618
RNAcentral	URS0000193C7E — lncRNA, 200 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 lncRNA

ENST00000418539

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000418539 — 1 exons

Exon	Start	End
ENSE00001641977	47335315	47335514

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 99.97.

Top tissues by expression

133 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
primary visual cortex	UBERON:0002436	99.97	gold quality
superior frontal gyrus	UBERON:0002661	99.97	gold quality
temporal lobe	UBERON:0001871	99.96	gold quality
amygdala	UBERON:0001876	99.96	gold quality
nucleus accumbens	UBERON:0001882	99.96	gold quality
Ammon’s horn	UBERON:0001954	99.96	gold quality
Brodmann (1909) area 9	UBERON:0013540	99.96	gold quality
hypothalamus	UBERON:0001898	99.95	gold quality
caudate nucleus	UBERON:0001873	99.94	gold quality
putamen	UBERON:0001874	99.94	gold quality
substantia nigra	UBERON:0002038	99.93	gold quality
right frontal lobe	UBERON:0002810	99.93	gold quality
cerebellum	UBERON:0002037	99.92	gold quality
cerebellar cortex	UBERON:0002129	99.92	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	99.92	gold quality
right hemisphere of cerebellum	UBERON:0014890	99.92	gold quality
cerebellar hemisphere	UBERON:0002245	99.91	gold quality
corpus callosum	UBERON:0002336	99.89	gold quality
anterior cingulate cortex	UBERON:0009835	99.89	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	99.87	gold quality
frontal cortex	UBERON:0001870	99.73	gold quality
cerebral cortex	UBERON:0000956	99.68	gold quality
brain	UBERON:0000955	99.63	gold quality
prefrontal cortex	UBERON:0000451	99.56	gold quality
colonic epithelium	UBERON:0000397	99.50	gold quality
hindlimb stylopod muscle	UBERON:0004252	99.43	gold quality
sural nerve	UBERON:0015488	99.37	gold quality
adrenal tissue	UBERON:0018303	99.25	gold quality
right adrenal gland	UBERON:0001233	98.54	gold quality
adenohypophysis	UBERON:0002196	98.47	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-HCAD-25	yes	10.05
E-ANND-3	no	1.69

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 40)

• potential of BC200 expression to serve as a molecular tool in the diagnosis and/or prognosis of breast cancer. (PMID:15240511)
• We further showed that the promoter can be active in human neuroblastoma SH-SY5Y cells and reduced expression of targeted protein, although the BC1 RNA gene is a rodent-specific gene. (PMID:16054886)
• Dendritic BC200 was studied in aging and in Alzheimer disease. (PMID:17553964)
• Protein interaction analysis of senataxin and the ALS4 L389S mutant yields insights into senataxin post-translational modification and uncovers mutant-specific binding with a brain cytoplasmic RNA-encoded peptide. (PMID:24244371)
• BCYRN1 has direct affinity for RHAU in vitro. (PMID:26740632)
• BC200 knockout suppresses tumor cell growth in vitro and in vivo by expression of the pro-apoptotic Bcl-xS isoform. (PMID:27277684)
• BC200 RNA interacts with hnRNP E1 and E2 mainly through its unique 3’ C-rich domain. (PMID:28027391)
• Results suggest that BC200 RNA up-regulates S100A11 expression by stabilizing the S100A11 mRNA at the post-transcriptional level, and this upregulation of S100A11 contributes to the ability of BC200 RNA to increase cancer cell motility. (PMID:28277927)
• BC200 expression is elevated in proliferating cultured cells regardless of origin.BC200 expression is largely restricted to the cytoplasm.BC200 role in cancer cell survival and proliferation. (PMID:28651607)
• Data show that increases in both RNA stability and transcription contribute to the upregulation of BC200 RNA in cancer cells. Since BC200 RNA role in promoting metastasis, its biosynthetic regulation should be related to cancer pathogenesis. Results provide a molecular basis for the regulation of BC200 RNA biosynthesis and improve the understanding of BC200 RNA-mediated regulatory networks in cancer. (PMID:28761139)
• This work establishes the potential of BC200 RNA detection in blood to serve as a molecular indicator of invasive breast malignancy. (PMID:29967012)
• Findings confirmed that inhibition of BC200 significantly suppressed BACE1 expression. BC200 may act as a basic regulating factor to induce cell apoptosis in the process of Alzheimer’s disease through mediating BACE1. (PMID:29979260)
• The presented combination of experimental and bioinformatic approaches not only enabled the determination of the most reliable secondary and tertiary structures of human BC200 RNA (largely in agreement with the previous phylogenetic model), but also verified the compatibility and potential disadvantages of utilizing in silico structure prediction programs. (PMID:30072491)
• BCYRN1 knockdown significantly inhibited the proliferation and apoptosis of colorectal cancer cells and NPR3 was identified to be a target of BCYRN1 and was downregulated by BCYRN1 knockdown. (PMID:30114690)
• CSDE1 binds directly to BC200 RNA.CSDE1 and BC200 expression levels are mutually dependent. (PMID:30247708)
• Mechanistically, BC200 directly interacted with cyclin E2 and promoted CDK2-cyclin E2 complex formation. Upregulation of cell cycle-related genes in hepatocellular carcinoma samples was positively correlated with BC200 expression. Our collective findings support the utility of a potential therapeutic strategy involving targeting of BC200 for the treatment of hepatocellular carcinoma. (PMID:30400024)
• Long Non-Coding RNA Brain Cytoplasmic RNA 1 Acts as an Oncogene and Regulates Cell Proliferation and Metastasis in Non-Small Cell Lung Cancer. (PMID:30486938)
• BC200 is highly expressed in NSCLC, which is positively correlated with tumor stage and metastasis of NSCLC patients. (PMID:30779077)
• findings provide the first evidence for impaired Pol III transcription in cellular models of POLR3-HLD and identify several candidate effectors, including BC200 RNA, having a potential role in oligodendrocyte biology and involvement in the disease (PMID:30898877)
• Esophageal cancer related gene-4 inhibits the migration and proliferation of oral squamous cell carcinoma through BC200 lncRNA/MMP-9 and -13 signaling pathway. (PMID:31152845)
• Analysis of BC200 RNA was performed to identify functional RNA motifs responsible for its translationalinhibition activity. Various RNA variants were assayed for their ability to inhibit translation of luciferase mRNA in vitro. We found that the 111-200-nucleotide region consisting of part of the Alu domain as well as the A/C-rich domain is most effective for translation inhibition. (PMID:31234958)
• BC200 RNA sequences are highly heterogeneous in cancer cells by virtue of multiple adenine nucleotide insertions in the internal A-rich region. (PMID:31250622)
• High BCYRN1 expression is associated with hepatocellular carcinoma pathogenesis. (PMID:31339046)
• Long non-coding RNA BC200 (BC200) is upregulated in nulliparous women, and breast cancer cells and tissue. When overexpressed in luminal and triple negative breast cancer cell lines, BC200 shows increased proliferation, migration, and invasion in vitro. In vivo, overexpression of BC200 increases tumor size. (PMID:31646972)
• BCYRN1 is correlated with progression and prognosis in gastric cancer. (PMID:31652309)
• Clinical significance of lncRNA BCYRN1 in colorectal cancer and its role in cell metastasis. (PMID:31773686)
• Effect of lncRNABC200 on proliferation and migration of liver cancer cells in vitro and in vivo. (PMID:31894342)
• Long noncoding RNA BCYRN1 promotes prostate cancer progression via elevation of HDAC11. (PMID:32705287)
• Targeting BC200/miR218-5p Signaling Axis for Overcoming Temozolomide Resistance and Suppressing Glioma Stemness. (PMID:32784466)
• LncRNA BCYRN1 inhibits glioma tumorigenesis by competitively binding with miR-619-5p to regulate CUEDC2 expression and the PTEN/AKT/p21 pathway. (PMID:32978519)
• LncRNA BCYRN1-induced autophagy enhances asparaginase resistance in extranodal NK/T-cell lymphoma. (PMID:33391513)
• The noncoding RNA BC200 associates with polysomes to positively regulate mRNA translation in tumor cells. (PMID:33410401)
• Tumor-derived exosomal BCYRN1 activates WNT5A/VEGF-C/VEGFR3 feedforward loop to drive lymphatic metastasis of bladder cancer. (PMID:34323412)
• The HNF4alpha-BC200-FMR1-Positive Feedback Loop Promotes Growth and Metastasis in Invasive Mucinous Lung Adenocarcinoma. (PMID:34654723)
• LncRNA BC200/miR-150-5p/MYB positive feedback loop promotes the malignant proliferation of myelodysplastic syndrome. (PMID:35136029)
• LncRNA BCYRN1 promotes cell migration and invasion of non-small cell lung cancer via the miR-30b-3p/ROCK1 axis. (PMID:35225646)
• The Long Non-Coding BC200 Is a Novel Circulating Biomarker of Parathyroid Carcinoma. (PMID:35586620)
• Long Noncoding RNA Brain Cytoplasmic RNA 1 Induces Cisplatin-Resistance of Cervical Cancer Cells by Sponging MicroRNA-330-5p and Upregulating High-Mobility Group Box 3. (PMID:35705019)
• Long Noncoding RNA BCYRN1 Recruits BATF to Promote TM4SF1 Upregulation and Enhance HCC Cell Proliferation and Invasion. (PMID:35730016)
• Long Non-Coding RNA BCYRN1 Drives Cellular Processes to Promote Asthma Development. (PMID:38224673)

Cross-species orthologs

0 orthologs

Protein

Non-coding RNA — no protein product; not a drug target.

Function

No curated pathway, Gene-Ontology, or interaction data.

Disease & clinical

No curated disease, variant, or cancer-driver associations.

Drugs & pharmacology

No drug or pharmacology data — not an established drug target.