Difference between revisions of "ENST00000499008.3"

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==Annotated Information==
 
==Annotated Information==
−
===Transcriptomic Nomeclature===
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===Transcriptomic Nomenclature===
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Please input transcriptomic nomeclature information here.
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''BDNF-AS'':BDNF antisense RNA 1 (HGNC nomenclature)
 +
 
 +
''BDNF-AS1'', ''BT2A'', ''BT2B'', ''BT2C'', ''BT2D'', ''NCRNA00049'', "non-protein coding RNA 49" <ref name="ref1" />
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 +
===Characteristics===
 +
[[File:Genomic organization of the human BDNF locus showing.jpg|right|thumb|400px'''Genomic organization of the human BDNF locus showing'''<ref name="ref1" />]]
 +
 
 +
''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" />
 +
 
 +
It belongs to the category of "Antisense" in lncRNA classification<ref name="ref1" />.
  
 
===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" />]]
 +
 
 +
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" />.
 +
 
 +
BDNF-AS represses chromatin by recruiting Polycomb Repressive Complex 2 (PRC2) to the BDNF promoter region<ref name="ref1" />.
  
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===Regulation===
 
−
Please input regulation information here.
 
  
 
===Expression===
 
===Expression===
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Please input expression information here.
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BDNF 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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{| class='wikitable' style="text-align:center"
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Please input allelic information and variation 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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===Evolution===
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===Diseases==
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Please input evolution information here.
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* Alzheimer’s disease, Parkinson’s disease and Fragile X syndrome<ref name="ref1" />.
  
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You can also add sub-section(s) at will.
 
  
 
==Labs working on this lncRNA==
 
==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" />.
  
 
==References==
 
==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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</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 104:
 
sequence = <dnaseq>ATCGCGAGATCAGGAAGGTGGCCGAGTGTGTCGCCGCGGCCATCAGGCACTTCTCCTTCCTGCCCTTGTATGAAGAAGGATGTGTTTGCTTCCCCTTGTGCCATGATTGTAAATTTCCTGAGGCCTCCTCAGCCCTGCAGAACTGGGGTTATAGCCATGTGACTGATCTTCGTCCAAGAATATGTAAAGAAAAAGTGTTGAGTTGGCTTTTAGGGCTAGAGCAATGTATCTTAGGCTCACTTAAGGAAGCTGTAGAGATGAGCCCAAGGAGGGAAACCAGAAGAGCCCCCCAGGCTCACCAGTTGTTTGTTGGCTCCCTACAAACATGTCATTCAAGTGGCTAATCTTACAACAGCACAAATTCATCTAACCAGAAAGAGAAGAGGAGGCTCCAAAGGCACTTGACTACTGAGCATCACCCTGGACGTGTACAAGTCTGCGTCCTTATTGTTTTCTTCATTGGGCCGAACTTTCTGGTCCTCATCCAACAGCTCTTCTATCACGTGTTCGAAAGTGTCAGCCAATGATGTCAAGCCTCTTGAACCTGCCTTGGGCCCATTCACGCTCTCCAGAGTCCCATGGGTCCGCACACCTGGAGATACTCTATTATAGCAAAGAAGAAAGATAATTTCATTGAGCCATCCTGTTTTACAGTATTGAATTATTACCACAAGGTACCAACCATATATGCATACTTAATAGGGTATTTTGTCAAAACTATGCATGAAGGTCATTTGTTTGAGATGTCAGAACATTTTCCCGTGAGAAGATCTCATTGGGCATTGAAACAGAACCACATGCTCTTCAGACCAGCAACCGCGACTACCAAATACTCCTCTGTCAACTCTACTTGAGTAAGAACGCTTTCAATTAAGGCCTAAGTGTCAACATGCCTTTAAAAAAAATCGTGGTGACACAAAATCTTTCTTTTTAGCACCCAACAGAATCCCTTCAAAGCCTCGTGGTCTGACACCCTATGCTACGTGACTTGTGACCCATCCATTTGTCATGTTCTTCGGGAATGTGGCTAAGGGGCTAAGATGTGACTTGAAAAGAAAGGTAGAACAAGATCATCTCAAATTTATTATCAAGGAATAGTTCAGAAAACGACTTCAGACCACAGAGACAGCAGAACAGATGGTCCGGCATGGATAGAGCATCAGACACTCACAGACTGTGCCAACAAGAGCCATCGAGTCAAAACAGCCAAAGGAAGGAGGGTCATGGAATGGGTTCTCTCACACCAAACTGATGCCCAGAGGCCCTCAGCATGAATAACAAAGGCAACCAGACCCACAAGCCATACTGAGTGGATACAAAACCTATACCTAGGCTGACATCCCAAATGTGTGTGGCAAGTTAGATGATGATGGCACAAAAGACAGAACACCTTGCTTCTGGCCATTGTCAGCTCTTGGAAGAGAGCACACTTTTAGAGGAGCAGCTGCAAGGAGCCTGAGAACAAAACTGGAAATGTCTGTTATGAAAGCCTTCACAGGAAATTCTGCAAGTGGCAACGTGGGTCCATTCCGTGTGTGTCACTAGAGCTGGCGCAAGCCCATGGCCATGGTGAGGCAGCGTTTCCACTGGAACTAATCTGATACCTGCACCAGCTCTTGCAACTGTGCAGTGTTCCCACTGCAAACTACGGATGGGGTAAAAGACTGCTCACCTCCTATTTCTCATCTAATCTCACACACTCTGTTTGATGAGGCTATGGAGAAACAGGTCTTCTCATACACTAAAGGTGGGAGTACAAACAATTCAAGCCCTGTGCAGGACAATTAGGCAATACCTATCAAAATTATACATGATTTTTCCTGCTGACCCAGCAATTCCACTTCTGGGAATAATTGACAGATATAGGTGCATATGTACAAAATGATGGAAAGCTCTCTGGTATATATTAGTAAGTGATAAAACAAGGTGTAAAATAGTGTATATATGGCTACTACCTTTTGTTTTAAAAATGGGGGAAAATGGTGGAGCTTGCGGTGAGCCGAGATCGTGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAACAGGGTGGGGTGGGGGGGAAATAATAGTACATACTCATATTTACCTGTATCTATATAAAACACACTATCAAGGATTCACAAGAAACTAATACAAATGATCACCTTATAGATGGTATGTATTGGGGGATACTGAGGTGAGCAGGGTATAAGTGGGGCAAGACTTTTCAGTGTAAACTTCTTTTAAATTTTATTTTGATTTTTGAATAATGTAAATTAACTGTCAAATAATTAAATTAAAAATAACCAATTTATTAACAAAACA</dnaseq>|
 
sequence = <dnaseq>ATCGCGAGATCAGGAAGGTGGCCGAGTGTGTCGCCGCGGCCATCAGGCACTTCTCCTTCCTGCCCTTGTATGAAGAAGGATGTGTTTGCTTCCCCTTGTGCCATGATTGTAAATTTCCTGAGGCCTCCTCAGCCCTGCAGAACTGGGGTTATAGCCATGTGACTGATCTTCGTCCAAGAATATGTAAAGAAAAAGTGTTGAGTTGGCTTTTAGGGCTAGAGCAATGTATCTTAGGCTCACTTAAGGAAGCTGTAGAGATGAGCCCAAGGAGGGAAACCAGAAGAGCCCCCCAGGCTCACCAGTTGTTTGTTGGCTCCCTACAAACATGTCATTCAAGTGGCTAATCTTACAACAGCACAAATTCATCTAACCAGAAAGAGAAGAGGAGGCTCCAAAGGCACTTGACTACTGAGCATCACCCTGGACGTGTACAAGTCTGCGTCCTTATTGTTTTCTTCATTGGGCCGAACTTTCTGGTCCTCATCCAACAGCTCTTCTATCACGTGTTCGAAAGTGTCAGCCAATGATGTCAAGCCTCTTGAACCTGCCTTGGGCCCATTCACGCTCTCCAGAGTCCCATGGGTCCGCACACCTGGAGATACTCTATTATAGCAAAGAAGAAAGATAATTTCATTGAGCCATCCTGTTTTACAGTATTGAATTATTACCACAAGGTACCAACCATATATGCATACTTAATAGGGTATTTTGTCAAAACTATGCATGAAGGTCATTTGTTTGAGATGTCAGAACATTTTCCCGTGAGAAGATCTCATTGGGCATTGAAACAGAACCACATGCTCTTCAGACCAGCAACCGCGACTACCAAATACTCCTCTGTCAACTCTACTTGAGTAAGAACGCTTTCAATTAAGGCCTAAGTGTCAACATGCCTTTAAAAAAAATCGTGGTGACACAAAATCTTTCTTTTTAGCACCCAACAGAATCCCTTCAAAGCCTCGTGGTCTGACACCCTATGCTACGTGACTTGTGACCCATCCATTTGTCATGTTCTTCGGGAATGTGGCTAAGGGGCTAAGATGTGACTTGAAAAGAAAGGTAGAACAAGATCATCTCAAATTTATTATCAAGGAATAGTTCAGAAAACGACTTCAGACCACAGAGACAGCAGAACAGATGGTCCGGCATGGATAGAGCATCAGACACTCACAGACTGTGCCAACAAGAGCCATCGAGTCAAAACAGCCAAAGGAAGGAGGGTCATGGAATGGGTTCTCTCACACCAAACTGATGCCCAGAGGCCCTCAGCATGAATAACAAAGGCAACCAGACCCACAAGCCATACTGAGTGGATACAAAACCTATACCTAGGCTGACATCCCAAATGTGTGTGGCAAGTTAGATGATGATGGCACAAAAGACAGAACACCTTGCTTCTGGCCATTGTCAGCTCTTGGAAGAGAGCACACTTTTAGAGGAGCAGCTGCAAGGAGCCTGAGAACAAAACTGGAAATGTCTGTTATGAAAGCCTTCACAGGAAATTCTGCAAGTGGCAACGTGGGTCCATTCCGTGTGTGTCACTAGAGCTGGCGCAAGCCCATGGCCATGGTGAGGCAGCGTTTCCACTGGAACTAATCTGATACCTGCACCAGCTCTTGCAACTGTGCAGTGTTCCCACTGCAAACTACGGATGGGGTAAAAGACTGCTCACCTCCTATTTCTCATCTAATCTCACACACTCTGTTTGATGAGGCTATGGAGAAACAGGTCTTCTCATACACTAAAGGTGGGAGTACAAACAATTCAAGCCCTGTGCAGGACAATTAGGCAATACCTATCAAAATTATACATGATTTTTCCTGCTGACCCAGCAATTCCACTTCTGGGAATAATTGACAGATATAGGTGCATATGTACAAAATGATGGAAAGCTCTCTGGTATATATTAGTAAGTGATAAAACAAGGTGTAAAATAGTGTATATATGGCTACTACCTTTTGTTTTAAAAATGGGGGAAAATGGTGGAGCTTGCGGTGAGCCGAGATCGTGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAACAGGGTGGGGTGGGGGGGAAATAATAGTACATACTCATATTTACCTGTATCTATATAAAACACACTATCAAGGATTCACAAGAAACTAATACAAATGATCACCTTATAGATGGTATGTATTGGGGGATACTGAGGTGAGCAGGGTATAAGTGGGGCAAGACTTTTCAGTGTAAACTTCTTTTAAATTTTATTTTGATTTTTGAATAATGTAAATTAACTGTCAAATAATTAAATTAAAAATAACCAATTTATTAACAAAACA</dnaseq>|
 
}}
 
}}
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[[Category:Intergenic]][[Category:lnc-METTL15-4]][[Category:NONHSAG007898]][[Category:ENSG00000245573.3]][[Category:Transcripts]]
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[[Category:Antisense]][[Category:lnc-METTL15-4]][[Category:NONHSAG007898]][[Category:ENSG00000245573.3]][[Category:Transcripts]]

Revision as of 05:12, 9 April 2015

Please input one-sentence summary here.

Annotated Information

Transcriptomic Nomenclature

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

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

Characteristics

400pxGenomic 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].


Expression

BDNF 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].


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].


Labs working on this lncRNA

  • Department of Psychiatry and Behavioral Sciences and Center for Therapeutic Innovation [1].

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

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 TTCAAAGCCT 000960
000961 CGTGGTCTGA CACCCTATGC TACGTGACTT GTGACCCATC CATTTGTCAT GTTCTTCGGG AATGTGGCTA AGGGGCTAAG 001040
001041 ATGTGACTTG AAAAGAAAGG TAGAACAAGA TCATCTCAAA TTTATTATCA AGGAATAGTT CAGAAA</