Difference between revisions of "ENST00000499008.3"

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Please input one-sentence summary here.
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''BDNF-AS'' which is approximately 200 kb downstream from the BDNF promoter and is located on the positive strand of chromosome-11,represses BDNF sense RNA transcription.
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==Annotated Information==
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===Name===
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''BDNF-AS'':BDNF antisense RNA 1 (HGNC nomenclature)
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''BDNF-AS1'', ''BT2A'', ''BT2B'', ''BT2C'', ''BT2D'', ''NCRNA00049'', "non-protein coding RNA 49" <ref name="ref1" />
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LncBook ID: HSALNT0288893.
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===Characteristics===
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[[File:Genomic organization of the human BDNF locus showing.jpg|right|thumb|400px|'''Genomic organization of the human BDNF locus showing'''<ref name="ref1" />]]
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''BDNF-AS'' is approximately 200 kb downstream from the BDNF promoter and it is located on the positive strand of chromosome-11. Transcription from this site gives rise to 16–25 splice variant long ncRNAs with 6–8 exons8. Exon-5 of ''BDNF-AS'', which contain 225-nucleotides of full complementarity to BDNF mRNA (overlapping) and exon-4 (non-overlapping) are common between all these variants . <ref name="ref1" />
  
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==Annotated Information==
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It belongs to the category of "Antisense" in lncRNA classification<ref name="ref1" />.
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===Transcriptomic Nomeclature===
 
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Please input transcriptomic nomeclature information here.
 
  
 
===Function===
 
===Function===
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Please input function information here.
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[[File:Antisense-mediated regulation of sense mRNA and protein.png|right|thumb|400px|'''Antisense-mediated regulation of sense mRNA and protein'''<ref name="ref1" />]]
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''BDNF-AS'' tonically represses BDNF sense RNA transcription by altering chromatin structure at the BDNF locus, which in turn reduces endogenous BDNF protein and function<ref name="ref1" />.
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''BDNF-AS'' represses chromatin by recruiting Polycomb Repressive Complex 2 (PRC2) to the BDNF promoter region<ref name="ref1" />.
  
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===Regulation===
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''BDNF-AS'' siRNA induces activation of the BDNF–TrkB–PI3K/Akt pathway following hypoxia/reoxygenation(H/R)-induced neurotoxicity<ref name="ref2" />.
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Please input regulation information here.
 
  
 
===Expression===
 
===Expression===
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Please input expression information here.
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''BDNF-AS'' mRNA levels are generally 10–100 fold higher than ''BDNF-AS'' transcript, except in testis, kidney, and heart, which contain equal or higher levels of ''BDNF-AS''. Both transcripts are expressed in brain, muscle and embryonic tissues. BDNF mRNA levels were relatively low in all post-natal tissues examined except in brain, bladder, heart, and skeletal muscle. In rhesus monkey and mouse tissues, both transcripts are co-expressed in many tissues, which suggest ''BDNF-AS'' potential for regulation of BDNF mRNA<ref name="ref1" />.
  
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===Allelic Information and Variation===
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BDNF expression was significantly downregulated in patients with cerebral
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Please input allelic information and variation information here.
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infarction, whereas the expression of ''BDNF-AS'' was significantly upregulated. In both human cortical neurons (HCN2) and human astrocytes, H/R significantly induced the expression of ''BDNF-AS'', but significantly decreased BDNF expression<ref name="ref2" />.
  
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===Evolution===
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{| class='wikitable' style="text-align:center"
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Please input evolution information here.
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|-
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! | Primer name
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! | Sequence
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! | Application
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|-
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| rowspan="1"|Human BDNF-AS siRNA-1
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| | GGCTCACCAGTTGTTTGTT
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| | siRNA<ref name="ref1" />
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|-
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| rowspan="1"|Scramble siRNA-1
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| | AGCTCGCCAGTCGTTTATT
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| | Scrambled control<ref name="ref1" />
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|-
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| rowspan="1"|Human BDNF-AS siRNA-2
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| | GCAATGTATCTTAGGCTCA
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| | siRNA<ref name="ref1" />
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|-
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| rowspan="1"|Human BDNF-AS siRNA-3
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| | GCTAATCTTACAACAGCAC
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| | siRNA<ref name="ref1" />
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|-
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| rowspan="1"|Scramble siRNA-3
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| |ACTAAGCTTACAGCAGCGC
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| |Scrambled control<ref name="ref1" />
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|-
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| rowspan="1"|Human BDNF-AS siRNA-4
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| |TCCCTACAAACATGTCAT
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| |siRNA<ref name="ref1" />
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|-
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| rowspan="1"|Scramble siRNA-4
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| |GCCCGACAAACAAGTCAAT
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| |Scrambled control<ref name="ref1" />
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|-
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| rowspan="1"|Control siRNA
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| |CCUCUCCACGCGCAGUACATT
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| |Non-targeting control<ref name="ref1" />
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|-
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| rowspan="1"|Human BDNF-AS primer-F
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| |AGTGGCTAATATTACAACAGCACAA
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| |Real time PCR<ref name="ref1" />
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|-
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| rowspan="1"|Human BDNF-AS primer-R
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| |CTCAGTAGTCAAGTGCCTTTGGA
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| |Real time PCR<ref name="ref1" />
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|-
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| rowspan="1"|Human BDNF-AS probe
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| |CCTCCTCTTCTCTTTCTGGTTAG
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| |Real time PCR<ref name="ref1" />
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|}
  
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You can also add sub-section(s) at will.
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===Diseases===
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* Alzheimer’s disease, Parkinson’s disease and Fragile X syndrome<ref name="ref1" />.
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* Cerebral infarction<ref name="ref2" />.
  
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==Labs working on this lncRNA==
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===Labs working on this lncRNA===
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Please input related labs here.
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* Department of Psychiatry and Behavioral Sciences and Center for Therapeutic Innovation <ref name="ref1" />.
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* Department of Neurology, Guangzhou Zengcheng People’s Hospital and Boji Hospital of Sun Yat-Sen University, Guangzhou, People’s Republic of China<ref name="ref2" />.
  
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==References==
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===References===
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Please input cited references here.
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<references>
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<ref name="ref1"> Modarresi F, Faghihi MA, Lopez-Toledano MA, Fatemi RP, Magistri M, Brothers SP, et al. Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation[J]. Nature biotechnology. 2012,30(5):453-9
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</ref>(1)
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<ref name="ref2">
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Zhong J B, Li X, Zhong S M, et al. Knockdown of long noncoding antisense RNA brain-derived neurotrophic factor attenuates hypoxia/reoxygenation-induced nerve cell apoptosis through the BDNF–TrkB–PI3K/Akt signaling pathway[J]. Neuroreport, 2017, 28(14): 910-916.
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</ref>(2)
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</references>
  
 
{{basic|
 
{{basic|
 
tID = ENST00000499008.3|
 
tID = ENST00000499008.3|
 
source = Gencode19|
 
source = Gencode19|
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same = lnc-METTL15-4:4,NONHSAT018493|
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same = lnc-METTL15-4:4,NONHSAT018493,''BDNF-AS''|
 
classification = intergenic|
 
classification = intergenic|
 
length = 2324 nt|
 
length = 2324 nt|
Line 42: Line 112:
 
sequence = <dnaseq>ATCGCGAGATCAGGAAGGTGGCCGAGTGTGTCGCCGCGGCCATCAGGCACTTCTCCTTCCTGCCCTTGTATGAAGAAGGATGTGTTTGCTTCCCCTTGTGCCATGATTGTAAATTTCCTGAGGCCTCCTCAGCCCTGCAGAACTGGGGTTATAGCCATGTGACTGATCTTCGTCCAAGAATATGTAAAGAAAAAGTGTTGAGTTGGCTTTTAGGGCTAGAGCAATGTATCTTAGGCTCACTTAAGGAAGCTGTAGAGATGAGCCCAAGGAGGGAAACCAGAAGAGCCCCCCAGGCTCACCAGTTGTTTGTTGGCTCCCTACAAACATGTCATTCAAGTGGCTAATCTTACAACAGCACAAATTCATCTAACCAGAAAGAGAAGAGGAGGCTCCAAAGGCACTTGACTACTGAGCATCACCCTGGACGTGTACAAGTCTGCGTCCTTATTGTTTTCTTCATTGGGCCGAACTTTCTGGTCCTCATCCAACAGCTCTTCTATCACGTGTTCGAAAGTGTCAGCCAATGATGTCAAGCCTCTTGAACCTGCCTTGGGCCCATTCACGCTCTCCAGAGTCCCATGGGTCCGCACACCTGGAGATACTCTATTATAGCAAAGAAGAAAGATAATTTCATTGAGCCATCCTGTTTTACAGTATTGAATTATTACCACAAGGTACCAACCATATATGCATACTTAATAGGGTATTTTGTCAAAACTATGCATGAAGGTCATTTGTTTGAGATGTCAGAACATTTTCCCGTGAGAAGATCTCATTGGGCATTGAAACAGAACCACATGCTCTTCAGACCAGCAACCGCGACTACCAAATACTCCTCTGTCAACTCTACTTGAGTAAGAACGCTTTCAATTAAGGCCTAAGTGTCAACATGCCTTTAAAAAAAATCGTGGTGACACAAAATCTTTCTTTTTAGCACCCAACAGAATCCCTTCAAAGCCTCGTGGTCTGACACCCTATGCTACGTGACTTGTGACCCATCCATTTGTCATGTTCTTCGGGAATGTGGCTAAGGGGCTAAGATGTGACTTGAAAAGAAAGGTAGAACAAGATCATCTCAAATTTATTATCAAGGAATAGTTCAGAAAACGACTTCAGACCACAGAGACAGCAGAACAGATGGTCCGGCATGGATAGAGCATCAGACACTCACAGACTGTGCCAACAAGAGCCATCGAGTCAAAACAGCCAAAGGAAGGAGGGTCATGGAATGGGTTCTCTCACACCAAACTGATGCCCAGAGGCCCTCAGCATGAATAACAAAGGCAACCAGACCCACAAGCCATACTGAGTGGATACAAAACCTATACCTAGGCTGACATCCCAAATGTGTGTGGCAAGTTAGATGATGATGGCACAAAAGACAGAACACCTTGCTTCTGGCCATTGTCAGCTCTTGGAAGAGAGCACACTTTTAGAGGAGCAGCTGCAAGGAGCCTGAGAACAAAACTGGAAATGTCTGTTATGAAAGCCTTCACAGGAAATTCTGCAAGTGGCAACGTGGGTCCATTCCGTGTGTGTCACTAGAGCTGGCGCAAGCCCATGGCCATGGTGAGGCAGCGTTTCCACTGGAACTAATCTGATACCTGCACCAGCTCTTGCAACTGTGCAGTGTTCCCACTGCAAACTACGGATGGGGTAAAAGACTGCTCACCTCCTATTTCTCATCTAATCTCACACACTCTGTTTGATGAGGCTATGGAGAAACAGGTCTTCTCATACACTAAAGGTGGGAGTACAAACAATTCAAGCCCTGTGCAGGACAATTAGGCAATACCTATCAAAATTATACATGATTTTTCCTGCTGACCCAGCAATTCCACTTCTGGGAATAATTGACAGATATAGGTGCATATGTACAAAATGATGGAAAGCTCTCTGGTATATATTAGTAAGTGATAAAACAAGGTGTAAAATAGTGTATATATGGCTACTACCTTTTGTTTTAAAAATGGGGGAAAATGGTGGAGCTTGCGGTGAGCCGAGATCGTGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAACAGGGTGGGGTGGGGGGGAAATAATAGTACATACTCATATTTACCTGTATCTATATAAAACACACTATCAAGGATTCACAAGAAACTAATACAAATGATCACCTTATAGATGGTATGTATTGGGGGATACTGAGGTGAGCAGGGTATAAGTGGGGCAAGACTTTTCAGTGTAAACTTCTTTTAAATTTTATTTTGATTTTTGAATAATGTAAATTAACTGTCAAATAATTAAATTAAAAATAACCAATTTATTAACAAAACA</dnaseq>|
 
sequence = <dnaseq>ATCGCGAGATCAGGAAGGTGGCCGAGTGTGTCGCCGCGGCCATCAGGCACTTCTCCTTCCTGCCCTTGTATGAAGAAGGATGTGTTTGCTTCCCCTTGTGCCATGATTGTAAATTTCCTGAGGCCTCCTCAGCCCTGCAGAACTGGGGTTATAGCCATGTGACTGATCTTCGTCCAAGAATATGTAAAGAAAAAGTGTTGAGTTGGCTTTTAGGGCTAGAGCAATGTATCTTAGGCTCACTTAAGGAAGCTGTAGAGATGAGCCCAAGGAGGGAAACCAGAAGAGCCCCCCAGGCTCACCAGTTGTTTGTTGGCTCCCTACAAACATGTCATTCAAGTGGCTAATCTTACAACAGCACAAATTCATCTAACCAGAAAGAGAAGAGGAGGCTCCAAAGGCACTTGACTACTGAGCATCACCCTGGACGTGTACAAGTCTGCGTCCTTATTGTTTTCTTCATTGGGCCGAACTTTCTGGTCCTCATCCAACAGCTCTTCTATCACGTGTTCGAAAGTGTCAGCCAATGATGTCAAGCCTCTTGAACCTGCCTTGGGCCCATTCACGCTCTCCAGAGTCCCATGGGTCCGCACACCTGGAGATACTCTATTATAGCAAAGAAGAAAGATAATTTCATTGAGCCATCCTGTTTTACAGTATTGAATTATTACCACAAGGTACCAACCATATATGCATACTTAATAGGGTATTTTGTCAAAACTATGCATGAAGGTCATTTGTTTGAGATGTCAGAACATTTTCCCGTGAGAAGATCTCATTGGGCATTGAAACAGAACCACATGCTCTTCAGACCAGCAACCGCGACTACCAAATACTCCTCTGTCAACTCTACTTGAGTAAGAACGCTTTCAATTAAGGCCTAAGTGTCAACATGCCTTTAAAAAAAATCGTGGTGACACAAAATCTTTCTTTTTAGCACCCAACAGAATCCCTTCAAAGCCTCGTGGTCTGACACCCTATGCTACGTGACTTGTGACCCATCCATTTGTCATGTTCTTCGGGAATGTGGCTAAGGGGCTAAGATGTGACTTGAAAAGAAAGGTAGAACAAGATCATCTCAAATTTATTATCAAGGAATAGTTCAGAAAACGACTTCAGACCACAGAGACAGCAGAACAGATGGTCCGGCATGGATAGAGCATCAGACACTCACAGACTGTGCCAACAAGAGCCATCGAGTCAAAACAGCCAAAGGAAGGAGGGTCATGGAATGGGTTCTCTCACACCAAACTGATGCCCAGAGGCCCTCAGCATGAATAACAAAGGCAACCAGACCCACAAGCCATACTGAGTGGATACAAAACCTATACCTAGGCTGACATCCCAAATGTGTGTGGCAAGTTAGATGATGATGGCACAAAAGACAGAACACCTTGCTTCTGGCCATTGTCAGCTCTTGGAAGAGAGCACACTTTTAGAGGAGCAGCTGCAAGGAGCCTGAGAACAAAACTGGAAATGTCTGTTATGAAAGCCTTCACAGGAAATTCTGCAAGTGGCAACGTGGGTCCATTCCGTGTGTGTCACTAGAGCTGGCGCAAGCCCATGGCCATGGTGAGGCAGCGTTTCCACTGGAACTAATCTGATACCTGCACCAGCTCTTGCAACTGTGCAGTGTTCCCACTGCAAACTACGGATGGGGTAAAAGACTGCTCACCTCCTATTTCTCATCTAATCTCACACACTCTGTTTGATGAGGCTATGGAGAAACAGGTCTTCTCATACACTAAAGGTGGGAGTACAAACAATTCAAGCCCTGTGCAGGACAATTAGGCAATACCTATCAAAATTATACATGATTTTTCCTGCTGACCCAGCAATTCCACTTCTGGGAATAATTGACAGATATAGGTGCATATGTACAAAATGATGGAAAGCTCTCTGGTATATATTAGTAAGTGATAAAACAAGGTGTAAAATAGTGTATATATGGCTACTACCTTTTGTTTTAAAAATGGGGGAAAATGGTGGAGCTTGCGGTGAGCCGAGATCGTGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAACAGGGTGGGGTGGGGGGGAAATAATAGTACATACTCATATTTACCTGTATCTATATAAAACACACTATCAAGGATTCACAAGAAACTAATACAAATGATCACCTTATAGATGGTATGTATTGGGGGATACTGAGGTGAGCAGGGTATAAGTGGGGCAAGACTTTTCAGTGTAAACTTCTTTTAAATTTTATTTTGATTTTTGAATAATGTAAATTAACTGTCAAATAATTAAATTAAAAATAACCAATTTATTAACAAAACA</dnaseq>|
 
}}
 
}}
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[[Category:Intergenic]][[Category:lnc-METTL15-4]]
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[[Category:Antisense]][[Category:lnc-METTL15-4]][[Category:NONHSAG007898]][[Category:ENSG00000245573.3]][[Category:Transcripts]]

Latest revision as of 14:35, 5 August 2019

BDNF-AS which is approximately 200 kb downstream from the BDNF promoter and is located on the positive strand of chromosome-11,represses BDNF sense RNA transcription.

Annotated Information

Name

BDNF-AS:BDNF antisense RNA 1 (HGNC nomenclature)

BDNF-AS1, BT2A, BT2B, BT2C, BT2D, NCRNA00049, "non-protein coding RNA 49" [1]

LncBook ID: HSALNT0288893.

Characteristics

Genomic organization of the human BDNF locus showing[1]

BDNF-AS is approximately 200 kb downstream from the BDNF promoter and it is located on the positive strand of chromosome-11. Transcription from this site gives rise to 16–25 splice variant long ncRNAs with 6–8 exons8. Exon-5 of BDNF-AS, which contain 225-nucleotides of full complementarity to BDNF mRNA (overlapping) and exon-4 (non-overlapping) are common between all these variants . [1]

It belongs to the category of "Antisense" in lncRNA classification[1].

Function

Antisense-mediated regulation of sense mRNA and protein[1]

BDNF-AS tonically represses BDNF sense RNA transcription by altering chromatin structure at the BDNF locus, which in turn reduces endogenous BDNF protein and function[1].

BDNF-AS represses chromatin by recruiting Polycomb Repressive Complex 2 (PRC2) to the BDNF promoter region[1].

BDNF-AS siRNA induces activation of the BDNF–TrkB–PI3K/Akt pathway following hypoxia/reoxygenation(H/R)-induced neurotoxicity[2].

Expression

BDNF-AS mRNA levels are generally 10–100 fold higher than BDNF-AS transcript, except in testis, kidney, and heart, which contain equal or higher levels of BDNF-AS. Both transcripts are expressed in brain, muscle and embryonic tissues. BDNF mRNA levels were relatively low in all post-natal tissues examined except in brain, bladder, heart, and skeletal muscle. In rhesus monkey and mouse tissues, both transcripts are co-expressed in many tissues, which suggest BDNF-AS potential for regulation of BDNF mRNA[1].

BDNF expression was significantly downregulated in patients with cerebral infarction, whereas the expression of BDNF-AS was significantly upregulated. In both human cortical neurons (HCN2) and human astrocytes, H/R significantly induced the expression of BDNF-AS, but significantly decreased BDNF expression[2].

Primer name Sequence Application
Human BDNF-AS siRNA-1 GGCTCACCAGTTGTTTGTT siRNA[1]
Scramble siRNA-1 AGCTCGCCAGTCGTTTATT Scrambled control[1]
Human BDNF-AS siRNA-2 GCAATGTATCTTAGGCTCA siRNA[1]
Human BDNF-AS siRNA-3 GCTAATCTTACAACAGCAC siRNA[1]
Scramble siRNA-3 ACTAAGCTTACAGCAGCGC Scrambled control[1]
Human BDNF-AS siRNA-4 TCCCTACAAACATGTCAT siRNA[1]
Scramble siRNA-4 GCCCGACAAACAAGTCAAT Scrambled control[1]
Control siRNA CCUCUCCACGCGCAGUACATT Non-targeting control[1]
Human BDNF-AS primer-F AGTGGCTAATATTACAACAGCACAA Real time PCR[1]
Human BDNF-AS primer-R CTCAGTAGTCAAGTGCCTTTGGA Real time PCR[1]
Human BDNF-AS probe CCTCCTCTTCTCTTTCTGGTTAG Real time PCR[1]

Diseases

  • Alzheimer’s disease, Parkinson’s disease and Fragile X syndrome[1].
  • Cerebral infarction[2].

Labs working on this lncRNA

  • Department of Psychiatry and Behavioral Sciences and Center for Therapeutic Innovation [1].
  • Department of Neurology, Guangzhou Zengcheng People’s Hospital and Boji Hospital of Sun Yat-Sen University, Guangzhou, People’s Republic of China[2].

References

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 1.19 1.20 Modarresi F, Faghihi MA, Lopez-Toledano MA, Fatemi RP, Magistri M, Brothers SP, et al. Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation[J]. Nature biotechnology. 2012,30(5):453-9
  2. ↑ 2.0 2.1 2.2 2.3 Zhong J B, Li X, Zhong S M, et al. Knockdown of long noncoding antisense RNA brain-derived neurotrophic factor attenuates hypoxia/reoxygenation-induced nerve cell apoptosis through the BDNF–TrkB–PI3K/Akt signaling pathway[J]. Neuroreport, 2017, 28(14): 910-916.

Basic Information

Transcript ID

ENST00000499008.3

Source

Gencode19

Same with

lnc-METTL15-4:4,NONHSAT018493,BDNF-AS

Classification

intergenic

Length

2324 nt

Genomic location

chr11+:27528399..27699354

Exon number

8

Exons

27528399..27528445,27561567..27561663,27605816..27605884,27661392..27661552,27679788..27680009,27680718..27680775,27696844..27697687,27698529..27699354

Genome context

Sequence
000001 ATCGCGAGAT CAGGAAGGTG GCCGAGTGTG TCGCCGCGGC CATCAGGCAC TTCTCCTTCC TGCCCTTGTA TGAAGAAGGA 000080
000081 TGTGTTTGCT TCCCCTTGTG CCATGATTGT AAATTTCCTG AGGCCTCCTC AGCCCTGCAG AACTGGGGTT ATAGCCATGT 000160
000161 GACTGATCTT CGTCCAAGAA TATGTAAAGA AAAAGTGTTG AGTTGGCTTT TAGGGCTAGA GCAATGTATC TTAGGCTCAC 000240
000241 TTAAGGAAGC TGTAGAGATG AGCCCAAGGA GGGAAACCAG AAGAGCCCCC CAGGCTCACC AGTTGTTTGT TGGCTCCCTA 000320
000321 CAAACATGTC ATTCAAGTGG CTAATCTTAC AACAGCACAA ATTCATCTAA CCAGAAAGAG AAGAGGAGGC TCCAAAGGCA 000400
000401 CTTGACTACT GAGCATCACC CTGGACGTGT ACAAGTCTGC GTCCTTATTG TTTTCTTCAT TGGGCCGAAC TTTCTGGTCC 000480
000481 TCATCCAACA GCTCTTCTAT CACGTGTTCG AAAGTGTCAG CCAATGATGT CAAGCCTCTT GAACCTGCCT TGGGCCCATT 000560
000561 CACGCTCTCC AGAGTCCCAT GGGTCCGCAC ACCTGGAGAT ACTCTATTAT AGCAAAGAAG AAAGATAATT TCATTGAGCC 000640
000641 ATCCTGTTTT ACAGTATTGA ATTATTACCA CAAGGTACCA ACCATATATG CATACTTAAT AGGGTATTTT GTCAAAACTA 000720
000721 TGCATGAAGG TCATTTGTTT GAGATGTCAG AACATTTTCC CGTGAGAAGA TCTCATTGGG CATTGAAACA GAACCACATG 000800
000801 CTCTTCAGAC CAGCAACCGC GACTACCAAA TACTCCTCTG TCAACTCTAC TTGAGTAAGA ACGCTTTCAA TTAAGGCCTA 000880
000881 AGTGTCAACA TGCCTTTAAA AAAAATCGTG GTGACACAAA ATCTTTCTTT TTAGCACCCA ACAGAATCCC TTCAAAGC