Difference between revisions of "Lnc-MTHFSD-2:1"
Chunlei Yu (talk | contribs) (→Labs working on this lncRNA) |
Chunlei Yu (talk | contribs) |
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| − | LncRNA FOXF1-AS1, mapping 1.7 kb upstream of FOXF1, binds the Polycomb repressive complex PRC2. | + | LncRNA FOXF1-AS1, encoded in K3-K36 domains and mapping 1.7 kb upstream of FOXF1, binds the Polycomb repressive complex PRC2. |
==Annotated Information== | ==Annotated Information== | ||
| Line 5: | Line 5: | ||
FENDRR:FOXF1 adjacent non-coding developmental regulatory RNA (HGNC nonmenclature) | FENDRR:FOXF1 adjacent non-coding developmental regulatory RNA (HGNC nonmenclature) | ||
| + | ''lincFOXF1''<ref name="ref1" /> | ||
===Function=== | ===Function=== | ||
| − | + | [[File:Fendrr binds to the PRC2 and TrxG/MLL complexes and to target promoters.jpg|right|thumb|400px|'''Fendrr binds to the PRC2 and TrxG/MLL complexes and to target promoters'''<ref name="ref2" />]] | |
| − | FOXF1-AS1 may act as a transcriptional repressor <ref name=" | + | Mouse experiments suggest that Fendrr is essential for proper lateral mesoderm differentiation and can itself be considered to be a regulatory factor as a repressive role. Fendrr, by interacting with the PRC2 and TrxG/MLL complexes at a specific set of promoters, is required for fine-tuning of the GRN controlling the development of organs and tissues derived from the LPM <ref name="ref2" />. |
| + | |||
| + | FOXF1-AS1 may act as a transcriptional repressor <ref name="ref3" />. | ||
===Expression=== | ===Expression=== | ||
| − | LncRNA FOXF1-AS1 has the highest expression in human lungs and partially overlaps with the FOXF1 promoter <ref name=" | + | LncRNA FOXF1-AS1 has the highest expression in human lungs and partially overlaps with the FOXF1 promoter <ref name="ref3" />. |
==Labs working on this lncRNA== | ==Labs working on this lncRNA== | ||
| − | * Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany <ref name=" | + | * Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany <ref name="ref2" />. |
| − | * Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA <ref name=" | + | * Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA <ref name="ref3" />. |
==References== | ==References== | ||
<references> | <references> | ||
| − | <ref name="ref1">Grote P, Wittler L, Hendrix D, Koch F, Wahrisch S, Beisaw A, et al. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse[J]. Developmental cell. 2013,24(2):206-14.</ref>(1) | + | <ref name="ref1">Grote P, Wittler L, Hendrix D, Koch F, Wahrisch S, Beisaw A, et al. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse[J]. Developmental cell. 2013,24(2):206-14.</ref.>(1) |
| + | <ref name="ref2">Grote P, Wittler L, Hendrix D, Koch F, Wahrisch S, Beisaw A, et al. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse[J]. Developmental cell. 2013,24(2):206-14.</ref>(2) | ||
| − | <ref name=" | + | <ref name="ref3">Szafranski P, Dharmadhikari AV, Brosens E, Gurha P, Kolodziejska KE, Zhishuo O, et al. Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder[J]. Genome research. 2013,23(1):23-33.</ref>(3) |
</references> | </references> | ||
Revision as of 14:28, 9 April 2015
LncRNA FOXF1-AS1, encoded in K3-K36 domains and mapping 1.7 kb upstream of FOXF1, binds the Polycomb repressive complex PRC2.
Contents
Annotated Information
Transcriptomic Nomenclature
FENDRR:FOXF1 adjacent non-coding developmental regulatory RNA (HGNC nonmenclature)
lincFOXF1[1]
Function
File:Fendrr binds to the PRC2 and TrxG/MLL complexes and to target promoters.jpg
Fendrr binds to the PRC2 and TrxG/MLL complexes and to target promoters[2]
Mouse experiments suggest that Fendrr is essential for proper lateral mesoderm differentiation and can itself be considered to be a regulatory factor as a repressive role. Fendrr, by interacting with the PRC2 and TrxG/MLL complexes at a specific set of promoters, is required for fine-tuning of the GRN controlling the development of organs and tissues derived from the LPM [2].
FOXF1-AS1 may act as a transcriptional repressor [3].
Expression
LncRNA FOXF1-AS1 has the highest expression in human lungs and partially overlaps with the FOXF1 promoter [3].
Labs working on this lncRNA
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany [2].
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA [3].
References
- ↑ Grote P, Wittler L, Hendrix D, Koch F, Wahrisch S, Beisaw A, et al. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse[J]. Developmental cell. 2013,24(2):206-14.</ref.>(1) <ref name="ref2">Grote P, Wittler L, Hendrix D, Koch F, Wahrisch S, Beisaw A, et al. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse[J]. Developmental cell. 2013,24(2):206-14.
- ↑ 2.0 2.1 2.2 Cite error: Invalid
<ref>tag; no text was provided for refs namedref2 - ↑ 3.0 3.1 3.2 Szafranski P, Dharmadhikari AV, Brosens E, Gurha P, Kolodziejska KE, Zhishuo O, et al. Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder[J]. Genome research. 2013,23(1):23-33.
Basic Information
| Transcript ID |
lnc-MTHFSD-2:1 |
| Source |
LNCipedia2.1 |
| Same with |
FENDRR ,FOXF1-AS1 |
| Classification |
intergenic |
| Length |
3099 nt |
| Genomic location |
chr16-:86508131..86542466 |
| Exon number |
4 |
| Exons |
86508131..86510805,86511492..86511657,86512311..86512362,86542261..86542466 |
| Genome context |
|
| Sequence |
000001 AGCAGACAGC GCGGGCTGGG AGCGCCGGCA AGGGCGGCCC TCGCGCACCT GGCTGCCAGC CCGCAGGGGG CTCGCACGCA 000080
000081 GACCTGCCCT TGCCACCTCA GCGCTCGGGT GCGGGCTGGG GGCGGTGGAG CCACGAAAGG TGGTGCCGAG AGCGGAGCGC 000160 000161 AGGACAGCGC AGGAGCCCCG GCGCATCGCG GCGCGCACAG ACCCAGGATT ACTTCATGCA CATAAAAGAA AACGCAACTA 000240 000241 CAGTGGACCC TGAACAACCT ATGGCCTGCA GCCACTGAAG AATGCTTGCA TAAGGAGCTC TTCTCTGCAC ATACCCCGAC 000320 000321 ACAGTGATGG TATCTTGCAG CTGCTGCTTC TGTCCAAGGC ACTGCAGCCT ACTCGTCAAA AGCCCGAAGC CCAGCTCTGC 000400 000401 CAGCAGTGCA CTGTGTGCTC TTAGGAAACA GAGAAGCAAA GAAGTTAGCA AGCTTGTTTT GGCAGAAGAA AAAACACAAA 000480 000481 ATACCCAACC ACAGATCCTC AAAAATATTG CTAAGCACTA ATTTTGCTAA CATGTTAGAC AGCCTTCGGA TCTAGGCAAT 000560 000561 CTTGTTCCTC AGCTGGAAAG AGTTCCTGCC AGCCATGTGA TTCCAAATCC ACCCTGGACA TATGGGGATA ATGAGAAAAT 000640 000641 CAGCTCCGGC CTTCCCTGGC CTTCCAGCCA AGTGAATGGG GGCATCCCCT GGTGCTTCAG CCCGGGGCCC ACCCAGAGGA 000720 000721 TGCTAGCTGG CCTGCAGAGG CCTCAACCAT GCCCTCCTGG ACTCAGGTAA GACTGAGGTT TCCATGCCCT CAAAACAATT 000800 000801 GTTCAGACAA AAACTCACTG CCCAGGTCAA AGTCACAGCA CCAGAAAGCC AACCTGAGGA TGAAGACAAA GCTCTTTGTT 000880 000881 GGCACAGTCC CCTGATCATT CGAGGTCAGC ATCTCCATCA AAATGGACCC AATGCTGAGG CAAGAAGGAG AACATCACTG 000960 000961 TTAAGAAGGT AATGAGTCAC AAATGCTATT TCGATGGTTT TCTTTGAAAG AAATACACAG AACCAAACCA ATTTTAATTA 001040 001041 AAGATCTTGT CTTTGTAATC AGGCAGCCAC AAATGAAGGC AAAACTGCTT TCATGTGGCA TAATATACAC AGAGCTGAAC 001120 001121 TAGTTTTCCC ATAAAAGGGC AGGTTCTTTT CTTCAAATAA GAAAAGAGTT TGTTCCTAAC AATATGGGGG ATGCAACAGA 001200 001201 AAGCTGTCTT TTGCAAAGTA TAAAATTGCA GATCCTCCCG TGGAAGCCAT TTCTTGATGC TAAACCAATG CGAACGTTTG 001280 001281 CCAAACGCAC ATGCGAGCCG GGATTATCCT ACCCTTTGAG ATTAGACATG TGATCCTGAT TTTTAAGTGA AAAACGCAGC 001360 001361 CAGAGGCCAA ATAAACATAC CTACAAGTAC ATCGAAAGCT CAAATGGTTG AGAAATGATT GTAACACACC CCGGTGTGTA 001440 001441 TTTCTGAGGA AGAATCAACA TGCACATGGA AATTGATGTT TTGATTTTTA ATTTTAAAAC GACGACAGAA CTGAAATACC 001520 001521 TCCCCTAACT AGGTCCACTG AAACCAGTGA GGAGATAATC ATTTTCAGTT AAATATGCAT GTAATTTAAT AATCCACAGA 001600 001601 TGGAAAATGC ATTTGAGGTG GACTGAACAC AGCCAGGAGT TTTTGCTTAT CGACAGCACT GAATCCTGCC TTGACTAGAG 001680 001681 AGACTCGTCA TGTGATCAAC TGTGGCCAGA GGGCATCCTG CAGACAGCTC CTGTCACACC ACACTGACCA GACTCTTATG 001760 001761 AGTATTTAAG CATCTTCAGG GAAGCGATTG ACTGTCTTAT AATGGTCTTA CAAGTACGGA ACTTTATTAC CTGCTAATAA 001840 001841 TCAGAGCACA TGATGGCACA ATAGAATATA CGAGTGAAGT TCTAAATGCA AGGTTGTTCT TATTCTGTGA GTGGCAAAAC 001920 001921 TCATGCAGTG AGCAGATAAA GCTGGCAGGA GGCATTGGCG CCCTAATGCT GGGCACTAAC CACCTGCCCG GACTGCGAAT 002000 002001 ATCTGTTGGG TCCTTTCTAT ATCTGGTCTA TTCTCGTGTT TGATTATATC CTGGTGGCAA GAATAGCAAA ATCAACTCTC 002080 002081 CTTCCTATCC CATGTGGAGA GGCATGATTT GAGTCAGAGA GCATTATCCT CTCTGCGTTA TCCAACCCCA TGTCCCATGA 002160 002161 TGCACTTTGT AGACAAGCAA GTGTCCCTGG TGGAGAATCC ACAGCCACAC ATCCTCATTG GTTGCAAGGA TCAGTGTCCA 002240 002241 ATATCTACTG CCATGATCAT TCTCAGTTTT ACATCCACAG AGCTTCATAG AATTCTAACA CCACAGGTCC AAGTAGAGGT 002320 002321 TTTGGCCTCA GAGTGGGCTA GATTCCACCT CTGACAGCAG CTGTGGGACT GTTTTTCCAT CTGTAAAATG GAGACAAGAG 002400 002401 TATCACCTAC CTCATGGTGT TGGTGGGATC GTTAAACAGA ATTCCGATCA TGAAACCCTT AGCCTGCTCC CTGCATAGGC 002480 002481 TGCATGCGCT CAGTGAGCTA TGGCTCTGTT TCATGCTGAC TTTACCATCA TGTAAGCAGT TTTAAAAATG CTAGAAGCTT 002560 002561 TAGTCATAGA ATTACCATAT GATACAGCCT ACTGCAGAGT CCAGAGGCTG AGGCAGGAGA GTTACTTGAA CCTGGGAGGC 002640 002641 GGAGGTTGCA GTGAGCCAAG ATCGCGCCAC TGCACTCCAG CCTGGGCAAC AGAGTGAGAT TCTGTCTCAA CACAAAAAAG 002720 002721 AAGACATGTG TCCCCATCAC AGTATCATAC AGAGTGCTTC CACTGCCCTA AAATACCCTG TGCTCTTCCT ATTCATCCCT 002800 002801 CTCTTCAACC CCAGCAACCA CTGATCCTTT TACCATCTCC ATGGTTTTGC CTTTCCCAGA ATGTCATATT GTTGGAATCA 002880 002881 TACGCTATGT AGCCTTTGCA AATGGGCTTC TTTCACCGAG CAATGTGCAT TGAAGGTGCC TCTATGACTT TTCAAGGGTT 002960 002961 GATAGCTCAT TCCTTTTTAT TGCTAAATAA TATTCCATTG TCTGAATGTA CCACATTTTG TTTATCCATT CACCTACTAA 003040 003041 AGGACATCTT GGTTGCTTCC AAGTTTGGGC AATTATAAAT AAAACTGCTA TAAACATTG |
