Difference between revisions of "BANCR"
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| − | BANCR, BRAF activated non-coding RNA,a 693-bp transcript on chromosome 9, | + | ''BANCR'', BRAF activated non-coding RNA,a 693-bp transcript on chromosome 9, serves as an important regulator in tumorigenesis. |
==Annotated Information== | ==Annotated Information== | ||
| Line 7: | Line 7: | ||
===Characteristics=== | ===Characteristics=== | ||
| − | ''BANCR'' is a four-exontranscript of 693 bp that is found in a 60 kb gene desert region on chromosome 9. The genes proximal to BANCR are not altered by changes in BANCR expression, indicating that | + | ''BANCR'' is a four-exontranscript of 693 bp that is found in a 60 kb gene desert region on chromosome 9. The genes proximal to ''BANCR'' are not altered by changes in ''BANCR'' expression, indicating that |
this lncRNA is not a cis regulator of neighbouring genes.<ref name="ref2" /> | this lncRNA is not a cis regulator of neighbouring genes.<ref name="ref2" /> | ||
| − | BANCR locus is enriched for chromatin marks associated with active transcription, and interestingly, the BANCR promoter was shown to be enriched for STAT1 transcription factor binding in HeLa-s3 cells (ENCODE ChIP-seq data). <ref name="ref2" /> | + | ''BANCR'' locus is enriched for chromatin marks associated with active transcription, and interestingly, the ''BANCR'' promoter was shown to be enriched for STAT1 transcription factor binding in HeLa-s3 cells (ENCODE ChIP-seq data). <ref name="ref2" /> |
===Function=== | ===Function=== | ||
| − | [[File:BANCR overexpression suppresses NSCLC cell invasion and metastasis by affecting EMT.jpg|right|thumb|400px|'''BANCR overexpression suppresses NSCLC cell invasion and metastasis by affecting EMT'''<ref name="ref1" />]] | + | [[File:BANCR overexpression suppresses NSCLC cell invasion and metastasis by affecting EMT.jpg|right|thumb|400px|'''''BANCR'' overexpression suppresses NSCLC cell invasion and metastasis by affecting EMT'''<ref name="ref1" />]] |
| − | ''BANCR'' inhibits migration and invasion of NSCLC cells and induces apoptosis, which possibly also | + | ''BANCR'' inhibits migration and invasion of NSCLC cells and induces apoptosis, which possibly also affectes EMT<ref name="ref1" />. |
| − | Downregulation of BANCR may be a negative prognostic factor for NSCLC patients, and indicative of poor survival rates and a higher risk for cancer metastasis<ref name="ref1" />. | + | Downregulation of ''BANCR'' may be a negative prognostic factor for NSCLC patients, and indicative of poor survival rates and a higher risk for cancer metastasis<ref name="ref1" />. |
''BANCR'' is a novel BRAFV600E-induced lncRNA that regulates melanoma cell migration in vitro in part by regulating expression of CXCL11.<ref name="ref2" />. | ''BANCR'' is a novel BRAFV600E-induced lncRNA that regulates melanoma cell migration in vitro in part by regulating expression of CXCL11.<ref name="ref2" />. | ||
| − | BANCR promotes proliferation in malignant melanoma by regulating MAPK pathway activation.<ref name="ref5" />. | + | ''BANCR'' promotes proliferation in malignant melanoma by regulating MAPK pathway activation.<ref name="ref5" />. |
| − | BANCR-regulated proliferation | + | ''BANCR''-regulated proliferation is not only ERK1/2-dependent but also JNK-dependent. <ref name="ref5" />. |
| + | |||
| + | ''BANCR'' regulates cell proliferation by targeting p21, and its effects were likely posttranscriptional. <ref name="ref7" />. | ||
===Regulation=== | ===Regulation=== | ||
| Line 35: | Line 37: | ||
===Expression=== | ===Expression=== | ||
| − | [[File: ''BANCR'' expression was downregulated and correlated with poor prognosis of NSCLC.jpg|right|thumb|400px|'''''BANCR'' expression | + | [[File: ''BANCR'' expression was downregulated and correlated with poor prognosis of NSCLC.jpg|right|thumb|400px|'''''BANCR'' expression is downregulated and correlated with poor prognosis of NSCLC''' <ref name="ref1" />.]] |
| − | ''BANCR'' is overexpressed in melanoma cells and crucial for melanoma cell migration. Specifically, BANCR expression | + | ''BANCR'' is overexpressed in melanoma cells and crucial for melanoma cell migration. Specifically, BANCR expression is significantly lower at the later stages of tumor development, and in tumors that had undergone extensive metastasis<ref name="ref1" />. |
| − | ''BANCR'' is upregulated in Eosinophilic esophagitis (EoE) and | + | ''BANCR'' is upregulated in Eosinophilic esophagitis (EoE) and induces in interleukin-13 (IL-13)-treated primary esophageal epithelial cells.<ref name="ref6" /> |
| + | ''BANCR'' is downregulated in colorectal cancer tissues.<ref name="ref7" /> | ||
{| class='wikitable' style="text-align:center" | {| class='wikitable' style="text-align:center" | ||
|- | |- | ||
! | Experiment | ! | Experiment | ||
| − | |||
! | Forward primer | ! | Forward primer | ||
! | Reverse primer | ! | Reverse primer | ||
|- | |- | ||
| rowspan="1"|Quantitative PCR | | rowspan="1"|Quantitative PCR | ||
| − | | | | + | | | 5'-ACAGGACTCCATGGCAAACG- 3' |
| − | + | | | 5'-ATGAAGAAAGCCTGGTGCAGT- 3'<ref name="ref1" /> | |
| − | | | ATGAAGAAAGCCTGGTGCAGT<ref name="ref1" /> | ||
|- | |- | ||
| rowspan="1"|Knockdown | | rowspan="1"|Knockdown | ||
| − | |||
| | GGAAAUAGACUGCAGCACCAATT<ref name="ref1" /> | | | GGAAAUAGACUGCAGCACCAATT<ref name="ref1" /> | ||
| | _ | | | _ | ||
|- | |- | ||
| rowspan="1"|Quantitative PCR | | rowspan="1"|Quantitative PCR | ||
| − | | | | + | | | 5'-AGACCCCTGACCCTAAGGAA- 3' |
| − | | | | + | | | 5'-TGCTCTTTGCAGAGGTGAGA- 3'<ref name="ref6" /> |
| − | | | | + | |- |
| + | | rowspan="1"|qRT-PCR | ||
| + | | | 5'-ACAGGACTCCATGGCAAACG- 3' | ||
| + | | | 5'-ATGAAGAAAGCCTGGTGCAGT- 3'<ref name="ref7" /> | ||
|} | |} | ||
| Line 71: | Line 74: | ||
* Department of Dermatology, Inner Mongolia People's Hospital, Hohhot, Inner Mongolia Autonomous Region, China.<ref name="ref5" /> | * Department of Dermatology, Inner Mongolia People's Hospital, Hohhot, Inner Mongolia Autonomous Region, China.<ref name="ref5" /> | ||
* Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.<ref name="ref6" /> | * Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.<ref name="ref6" /> | ||
| + | * Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China; Taixing People's Hospital, Taixing, Jiangsu, PR China.<ref name="ref7" /> | ||
==References== | ==References== | ||
<references> | <references> | ||
| Line 82: | Line 86: | ||
<ref name="ref5"> Li R, Zhang L, Jia L, Duan Y, Li Y, Bao L, et al. Long non-coding RNA BANCR promotes proliferation in malignant melanoma by regulating MAPK pathway activation[J]. PloS one. 2014,9(6):e100893. </ref>(5) | <ref name="ref5"> Li R, Zhang L, Jia L, Duan Y, Li Y, Bao L, et al. Long non-coding RNA BANCR promotes proliferation in malignant melanoma by regulating MAPK pathway activation[J]. PloS one. 2014,9(6):e100893. </ref>(5) | ||
<ref name="ref6"> Sherrill JD, Kiran KC, Blanchard C, Stucke EM, Kemme KA, Collins MH, et al. Analysis and expansion of the eosinophilic esophagitis transcriptome by RNA sequencing[J]. Genes and immunity. 2014,15(6):361-9.</ref>(6) | <ref name="ref6"> Sherrill JD, Kiran KC, Blanchard C, Stucke EM, Kemme KA, Collins MH, et al. Analysis and expansion of the eosinophilic esophagitis transcriptome by RNA sequencing[J]. Genes and immunity. 2014,15(6):361-9.</ref>(6) | ||
| + | <ref name="ref7"> Shi Y, Liu Y, Wang J, Jie D, Yun T, Li W, et al. Downregulated Long Noncoding RNA BANCR Promotes the Proliferation of Colorectal Cancer Cells via Downregualtion of p21 Expression[J]. PloS one. 2015,10(4):e0122679.</ref>(7) | ||
</references> | </references> | ||
Revision as of 06:01, 30 June 2016
BANCR, BRAF activated non-coding RNA,a 693-bp transcript on chromosome 9, serves as an important regulator in tumorigenesis.
Contents
Annotated Information
Name
BANCR: BRAF-activated non-protein coding RNA (HGNC nomenclature) LINC00586[1]
Characteristics
BANCR is a four-exontranscript of 693 bp that is found in a 60 kb gene desert region on chromosome 9. The genes proximal to BANCR are not altered by changes in BANCR expression, indicating that this lncRNA is not a cis regulator of neighbouring genes.[2]
BANCR locus is enriched for chromatin marks associated with active transcription, and interestingly, the BANCR promoter was shown to be enriched for STAT1 transcription factor binding in HeLa-s3 cells (ENCODE ChIP-seq data). [2]
Function
BANCR overexpression suppresses NSCLC cell invasion and metastasis by affecting EMT[1]
BANCR inhibits migration and invasion of NSCLC cells and induces apoptosis, which possibly also affectes EMT[1].
Downregulation of BANCR may be a negative prognostic factor for NSCLC patients, and indicative of poor survival rates and a higher risk for cancer metastasis[1].
BANCR is a novel BRAFV600E-induced lncRNA that regulates melanoma cell migration in vitro in part by regulating expression of CXCL11.[2].
BANCR promotes proliferation in malignant melanoma by regulating MAPK pathway activation.[3].
BANCR-regulated proliferation is not only ERK1/2-dependent but also JNK-dependent. [3].
BANCR regulates cell proliferation by targeting p21, and its effects were likely posttranscriptional. [4].
Regulation
Histone acetylation is a key factor in controlling lncRNA BANCR expression[1].
Diseases
- Non-small cell lung cancer(NSCLC)[1]
- Osteosarcoma[5]
- Hepatocellular carcinoma[6]
- Malignant melanoma[3]
- Eosinophilic esophagitis[7]
Expression
BANCR expression is downregulated and correlated with poor prognosis of NSCLC [1].
BANCR is overexpressed in melanoma cells and crucial for melanoma cell migration. Specifically, BANCR expression is significantly lower at the later stages of tumor development, and in tumors that had undergone extensive metastasis[1].
BANCR is upregulated in Eosinophilic esophagitis (EoE) and induces in interleukin-13 (IL-13)-treated primary esophageal epithelial cells.[7]
BANCR is downregulated in colorectal cancer tissues.[4]
| Experiment | Forward primer | Reverse primer |
|---|---|---|
| Quantitative PCR | 5'-ACAGGACTCCATGGCAAACG- 3' | 5'-ATGAAGAAAGCCTGGTGCAGT- 3'[1] |
| Knockdown | GGAAAUAGACUGCAGCACCAATT[1] | _ |
| Quantitative PCR | 5'-AGACCCCTGACCCTAAGGAA- 3' | 5'-TGCTCTTTGCAGAGGTGAGA- 3'[7] |
| qRT-PCR | 5'-ACAGGACTCCATGGCAAACG- 3' | 5'-ATGAAGAAAGCCTGGTGCAGT- 3'[4] |
Labs working on this lncRNA
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing 210029, People's Republic of China. [1]
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, California 94304, USA; The Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA.[2]
- Department of Orthopedics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.[5]
- Department of Gastroenterology, Qi-Lu Hospital, Shandong University, Jinan, 250012, Shan Dong Province, People's Republic of China.[6]
- Department of Dermatology, Inner Mongolia People's Hospital, Hohhot, Inner Mongolia Autonomous Region, China.[3]
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.[7]
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China; Taixing People's Hospital, Taixing, Jiangsu, PR China.[4]
References
- ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 Sun M, Liu XH, Wang KM, Nie FQ, Kong R, Yang JS, et al. Downregulation of BRAF activated non-coding RNA is associated with poor prognosis for non-small cell lung cancer and promotes metastasis by affecting epithelial-mesenchymal transition[J]. Molecular cancer. 2014,13:68.
- ↑ 2.0 2.1 2.2 2.3 Flockhart RJ, Webster DE, Qu K, Mascarenhas N, Kovalski J, Kretz M, et al. BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration[J]. Genome research. 2012,22(6):1006-14.
- ↑ 3.0 3.1 3.2 3.3 Li R, Zhang L, Jia L, Duan Y, Li Y, Bao L, et al. Long non-coding RNA BANCR promotes proliferation in malignant melanoma by regulating MAPK pathway activation[J]. PloS one. 2014,9(6):e100893.
- ↑ 4.0 4.1 4.2 4.3 Shi Y, Liu Y, Wang J, Jie D, Yun T, Li W, et al. Downregulated Long Noncoding RNA BANCR Promotes the Proliferation of Colorectal Cancer Cells via Downregualtion of p21 Expression[J]. PloS one. 2015,10(4):e0122679.
- ↑ 5.0 5.1 Peng ZQ, Lu RB, Xiao DM, Xiao ZM. Increased expression of the lncRNA BANCR and its prognostic significance in human osteosarcoma[J]. Genetics and molecular research : GMR. 2016,15(1).
- ↑ 6.0 6.1 Zhou T, Gao Y. Increased expression of LncRNA BANCR and its prognostic significance in human hepatocellular carcinoma[J]. World journal of surgical oncology. 2016,14(1):8.
- ↑ 7.0 7.1 7.2 7.3 Sherrill JD, Kiran KC, Blanchard C, Stucke EM, Kemme KA, Collins MH, et al. Analysis and expansion of the eosinophilic esophagitis transcriptome by RNA sequencing[J]. Genes and immunity. 2014,15(6):361-9.
Sequence
>gi|392973718|ref|NR_047671.2| Homo sapiens BRAF-activated non-protein coding RNA (BANCR), long non-coding RNA
000001 ATTCCCTTAC TTTCTTAATA AACTCGCTTT CACTTTATGG ATTCAACTGT AATTCTTTCT TGTGTGAGAT CCAAGAACCT 000080
000081 TCTTGTAGGG TCTGGATTGG GACCCTTTTC TGGTAACATC TTCCTGGTGA CCATGAAGGG ACAATACTGA AGAGACCCCT 000160
000161 GACCCTAAGG AAATAGACTG CAGCACCAAT GGGCCAACTT TGGGGCGATC ATCTTGCCCA GAAACATCAT GTTGAAACTC 000240
000241 TTGGTCAGAG GTTGGATGAA AGCTGACAGG GTCCATCCAG GAGCAAGTTT GAGCCTTGCC AGTTCCATTT TGGGTGCTGA 000320
000321 GTGGAGTGGC GACTATAGCA AACCTGTGAT CTCTGGCTGC TGCTCAGAAG AAACAAGAGG GAGGGATGAA TAATGTAAAA 000400
000401 CTCTGGATCA ATATTCTAAT TCTGAGCCTC TATTGGAATC AGCTAGCAAC CACATATCAG CTTGGTTTCA ACAGTTTCCC 000480
000481 AGTTCATGCT GCTGAGAAGT TCAGAGTCAA ACCTGAATCT CACCTCTGCA AAGAGCACAG GACTCCATGG CAAACGTTGT 000560
000561 ATATACGCAA GTCATCCCTG GCACCACATT GATTTACTGC ACCAGGCTTT CTTCATTGTG ATGATGTTCT CTCTCTTTTC 000640
000641 TAAAAAAAAA ATAAAAATAA AATTTAAAAA ATCCTAAAAA AAAAAAAA
000081 TCTTGTAGGG TCTGGATTGG GACCCTTTTC TGGTAACATC TTCCTGGTGA CCATGAAGGG ACAATACTGA AGAGACCCCT 000160
000161 GACCCTAAGG AAATAGACTG CAGCACCAAT GGGCCAACTT TGGGGCGATC ATCTTGCCCA GAAACATCAT GTTGAAACTC 000240
000241 TTGGTCAGAG GTTGGATGAA AGCTGACAGG GTCCATCCAG GAGCAAGTTT GAGCCTTGCC AGTTCCATTT TGGGTGCTGA 000320
000321 GTGGAGTGGC GACTATAGCA AACCTGTGAT CTCTGGCTGC TGCTCAGAAG AAACAAGAGG GAGGGATGAA TAATGTAAAA 000400
000401 CTCTGGATCA ATATTCTAAT TCTGAGCCTC TATTGGAATC AGCTAGCAAC CACATATCAG CTTGGTTTCA ACAGTTTCCC 000480
000481 AGTTCATGCT GCTGAGAAGT TCAGAGTCAA ACCTGAATCT CACCTCTGCA AAGAGCACAG GACTCCATGG CAAACGTTGT 000560
000561 ATATACGCAA GTCATCCCTG GCACCACATT GATTTACTGC ACCAGGCTTT CTTCATTGTG ATGATGTTCT CTCTCTTTTC 000640
000641 TAAAAAAAAA ATAAAAATAA AATTTAAAAA ATCCTAAAAA AAAAAAAA
