Difference between revisions of "TRERNA1"
(Created page with "==Annotated Information== ===Approved Symbol=== TRERNA1 ===Approved Name=== translation regulatory long non-coding RNA 1 ===Previous Symbols=== LINC00651 ===Synonyms=== ncRNA-...") |
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| + | ''TRERNA1'' translation regulatory long non-coding RNA 1 gene function as an Enhancer of ''SNAI1''. | ||
==Annotated Information== | ==Annotated Information== | ||
| − | === | + | ===Name=== |
| − | TRERNA1 | + | ''TRERNA1'': Translation regulatory long non-coding RNA 1 (HGNC nomenclarure), LINC00651 |
| − | === | + | |
| − | + | Synonyms: ncRNA-a7, treRNA | |
| − | === | + | |
| − | + | ===Characteristics=== | |
| − | === | + | ''TRERNA1'' is two exon transcript of 615 bp (GenBank) long non coding RNA that is located on human chromosome 20q13.13 <ref name="ref3" /><ref name="ref4" />. In 150 kb neighbor regions to TRERNA1 there are five protein-coding genes: SNAI1, UBE2V1, TMEM189, CEBPB, and RNF114 <ref name="ref3" />. ''TRERNA1'' transcript is spliced and polyadenylated <ref name="ref4" />. |
| − | + | ===Functions=== | |
| − | === | + | [[File: TRERNA1.jpg|right|thumb|400px|'''''TRERNA1'' as a regulator of SNAI1 expression.''' The relative position of the adjacent gene to the ''TRERNA1'' and the effects on mRNA levels for the surrounding genes after knockdown or enforced expression of TRERNA1 in MKN-28 and AGS cells <ref name="ref3" />.]] |
| − | + | ||
| − | === | + | ''TRERNA1'' fraction in the nucleus acts as an enhancer-like function to suppress CDH1 expression by enhancing transcription of the SNAI1 gene and epigenetically silencing the expression of CDH1 by binding to PRC2 <ref name="ref3" />. |
| − | + | ||
| − | === | + | ''TRERNA1'' promoted cell migration and invasion in gastric cancer (GC) <ref name="ref2" />. ''TRERNA1'' epigenetically silenced ''CDH1'' expression by physical association with EZH2 in GC cells <ref name="ref3" />. |
| − | + | ||
| − | === | + | ===Expression=== |
| − | + | ||
| − | === | + | ''TRERNA1'' is upregulated in gastric carcinogenesis <ref name="ref2" />. |
| − | + | ||
| + | ''TRERNA1'' is upregulated in paired clinical breast cancer primary and lymph node metastasis samples <ref name="ref4" /> . | ||
| + | |||
| + | ''TRERNA1'' is overexpression in chronic lymphocytic leukemia (CLL) and high expression is correlated with poor prognostic markers indicating that ''TRERNA1'' expression is part of an aggressive B-cell leukemia phenotype <ref name="ref5" />. | ||
| + | |||
| + | {| class='wikitable' style="text-align:center" | ||
| + | |- | ||
| + | ! | Experiment | ||
| + | ! | Forward primer | ||
| + | ! | Reverse primer | ||
| + | |- | ||
| + | | rowspan="1"|Quantitative PCR | ||
| + | | | 5'-CCGTTGGCTCCACAAACCT- 3' | ||
| + | | | 5'-CAGTGACAGTAGCAGGCATCCT- 3'<ref name="ref1" /> | ||
| + | |- | ||
| + | | rowspan="1"|PCR | ||
| + | | | 5′‐AATGAAAACACCAGGCCGGG‐3′ | ||
| + | | | 5′‐TCTCACTCTCTCAA ATCGGC‐3′<ref name="ref4" /> | ||
| + | |- | ||
| + | | rowspan="1"|In Vitro Translation | ||
| + | | | GGC AGA GAC GGA GAA GAT GA | ||
| + | | | GCC TTA GAC TGT GAA ATT TTA TTG A <ref name="ref1" /> | ||
| + | |} | ||
| + | |||
| + | ===Regulation=== | ||
| + | Transcription factor, activating enhancer‑binding protein 4 (TFAP4) regulates ''TRERNA1'' by binding to the E‑box motifs in the TRERNA1 promoter <ref name="ref2" /> | ||
| + | |||
| + | ===Disease=== | ||
| + | * Breast cancer <ref name="ref4" /> | ||
| + | * Chronic lymphocytic leukemia (CLL) <ref name="ref5" /> | ||
| + | * Gastric cancer <ref name="ref2" /> | ||
| + | |||
| + | ==Lab working on this lncRNA== | ||
| + | * Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing 210009, China.<ref name="ref3" /> | ||
| + | * School of Life Science, Bengbu Medical College, Bengbu 233030, China.<ref name="ref3" /> | ||
| + | * Third Affiliated Hospital of Harbin Medical University (Harbin Medical University Cancer Hospital), Harbin 150040, China.<ref name="ref3" /> | ||
| + | * Department of Pathophysiology, Medical School of Southeast University, Nanjing 210009, China.<ref name="ref3" /> | ||
| + | * The Wistar Institute, Philadelphia, PA, USA.<ref name="ref4" /> | ||
| + | * University of Washington Medical Center, Seattle, WA, USA.<ref name="ref4" /> | ||
| + | * Department of Experimental Therapeutics, MD Anderson Cancer Center, Houston, TX, USA.<ref name="ref4" /> | ||
| + | * Drexel University College of Medicine, Philadelphia, PA, USA.<ref name="ref4" /> | ||
| + | * Max Planck Institute for Molecular Genetics, Berlin, Germany.<ref name="ref4" /> | ||
| + | * Division of Endocrine and Oncologic Surgery, Department of Surgery and Rena Rowan Breast Center, Perelman School of Medicine, Abramson Cancer | ||
| + | Center, University of Pennsylvania, Philadelphia, PA, USA.<ref name="ref4" /> | ||
| + | * Center for Research on Early Detection and Cure of Ovarian Cancer, University of Pennsylvania, Philadelphia, PA, USA.<ref name="ref4" /> | ||
| + | * Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA.<ref name="ref4" /> | ||
| + | * Department of Internal Medicine, Division of Hematology, Comprehensive Cancer Center at The Ohio State University, Columbus, OH, USA.<ref name="ref5" /> | ||
| + | * The Chronic Lymphocytic Leukemia (CLL) Research Consortium, La Jolla, CA, USA.<ref name="ref5" /> | ||
| + | ==References== | ||
| + | <references> | ||
| + | <ref name="ref1"> Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G et al. Long noncoding RNAs with enhancer-like function in human cells[J]. Cell. 2010, 143(1): 46-58. | ||
| + | </ref>(1) | ||
| + | <ref name="ref2"> Wu H, Liu X, Gong P, Song W, Zhou M, Li Y et al. Elevated TFAP4 regulates lncRNA TRERNA1 to promote cell migration and invasion in gastric cancer[J]. Oncology reports. 2018. | ||
| + | </ref>(2) | ||
| + | <ref name="ref3"> Wu H, Hu Y, Liu X, Song W, Gong P, Zhang K et al. LncRNA TRERNA1 function as an enhancer of SNAI1 promotes gastric cancer metastasis by regulating epithelial-mesenchymal transition[J]. Molecular Therapy-Nucleic Acids. 2017, 8:291-299. | ||
| + | </ref>(3) | ||
| + | <ref name="ref4"> Gumireddy K, Li A, Yan J, Setoyama T, Johannes GJ, Ørom UA et al. Identification of a long non‐coding RNA‐associated RNP complex regulating metastasis at the translational step[J]. The EMBO journal. 2013, 32(20):2672-2684. | ||
| + | </ref>(4) | ||
| + | <ref name="ref5"> Miller CR, Ruppert AS, Fobare S, Chen TL, Liu C, Lehman A et al. The long noncoding RNA, treRNA, decreases DNA damage and is associated with poor response to chemotherapy in chronic lymphocytic leukemia[J]. Oncotarget. 2017, 8(16):25942. | ||
| + | </ref>(5) | ||
| + | </references> | ||
| + | |||
===Sequence=== | ===Sequence=== | ||
>gi|389565506|ref|NR_051976.1| Homo sapiens translation regulatory long non-coding RNA 1 (TRERNA1), long non-coding RNA | >gi|389565506|ref|NR_051976.1| Homo sapiens translation regulatory long non-coding RNA 1 (TRERNA1), long non-coding RNA | ||
<dnaseq>CCGTTCCTGCCTCCCACAGACACCTATTAAGTGCCTCCAGTTTTAGGAACTGGGTATAGATATGGCTGGGAACAAAATGGAAGAAAACAAAAACAAAAATCCCTGCCCTCATGGTGCTGACTCTCCTGTGGCAGAGACGGAGAAGATGAACAGGGATTTTATACCAGGCGTCAGAAGGGAACCAGTGCTAAAGAAAATGAAAACACCAGGCCGGGAGAGGCAGCTGGCATGCGGGCCGTGGTGGTTTTACGTGGCCGATTTGAGAGAGTGAGACCCCTGGGGTCTTGGAGCCAGGCCTGGGAAAAGCTACTTCACGTCAGGCCAGGGGCTGTAGCCCTGGCAACCTCCACTCCGCCTGGAAATCCTCCACCTCGGGGCCTCTCTTTGCCCAGACCTGGCCCAGGAGGAGCACATGGGAGCCGGGACCTTCCCAACAATCCTTGCCGTTGGCTCCACAAACCTCAGCCAGTCCTGCAACCTGGGATGCCTTTTCCACCAGGATGCCTGCTACTGTCACTGTTGTCATTAGATAATTAATGAACTATAATTAGAAATCATATCAATAAAATTTCACAGTCTAAGGCTGTTGAAATAGGAAAAAAAAAAAAAAAAAAA</dnaseq> | <dnaseq>CCGTTCCTGCCTCCCACAGACACCTATTAAGTGCCTCCAGTTTTAGGAACTGGGTATAGATATGGCTGGGAACAAAATGGAAGAAAACAAAAACAAAAATCCCTGCCCTCATGGTGCTGACTCTCCTGTGGCAGAGACGGAGAAGATGAACAGGGATTTTATACCAGGCGTCAGAAGGGAACCAGTGCTAAAGAAAATGAAAACACCAGGCCGGGAGAGGCAGCTGGCATGCGGGCCGTGGTGGTTTTACGTGGCCGATTTGAGAGAGTGAGACCCCTGGGGTCTTGGAGCCAGGCCTGGGAAAAGCTACTTCACGTCAGGCCAGGGGCTGTAGCCCTGGCAACCTCCACTCCGCCTGGAAATCCTCCACCTCGGGGCCTCTCTTTGCCCAGACCTGGCCCAGGAGGAGCACATGGGAGCCGGGACCTTCCCAACAATCCTTGCCGTTGGCTCCACAAACCTCAGCCAGTCCTGCAACCTGGGATGCCTTTTCCACCAGGATGCCTGCTACTGTCACTGTTGTCATTAGATAATTAATGAACTATAATTAGAAATCATATCAATAAAATTTCACAGTCTAAGGCTGTTGAAATAGGAAAAAAAAAAAAAAAAAAA</dnaseq> | ||
Revision as of 08:12, 21 November 2018
TRERNA1 translation regulatory long non-coding RNA 1 gene function as an Enhancer of SNAI1.
Contents
Annotated Information
Name
TRERNA1: Translation regulatory long non-coding RNA 1 (HGNC nomenclarure), LINC00651
Synonyms: ncRNA-a7, treRNA
Characteristics
TRERNA1 is two exon transcript of 615 bp (GenBank) long non coding RNA that is located on human chromosome 20q13.13 [1][2]. In 150 kb neighbor regions to TRERNA1 there are five protein-coding genes: SNAI1, UBE2V1, TMEM189, CEBPB, and RNF114 [1]. TRERNA1 transcript is spliced and polyadenylated [2].
Functions
TRERNA1 as a regulator of SNAI1 expression. The relative position of the adjacent gene to the TRERNA1 and the effects on mRNA levels for the surrounding genes after knockdown or enforced expression of TRERNA1 in MKN-28 and AGS cells [1].
TRERNA1 fraction in the nucleus acts as an enhancer-like function to suppress CDH1 expression by enhancing transcription of the SNAI1 gene and epigenetically silencing the expression of CDH1 by binding to PRC2 [1].
TRERNA1 promoted cell migration and invasion in gastric cancer (GC) [3]. TRERNA1 epigenetically silenced CDH1 expression by physical association with EZH2 in GC cells [1].
Expression
TRERNA1 is upregulated in gastric carcinogenesis [3].
TRERNA1 is upregulated in paired clinical breast cancer primary and lymph node metastasis samples [2] .
TRERNA1 is overexpression in chronic lymphocytic leukemia (CLL) and high expression is correlated with poor prognostic markers indicating that TRERNA1 expression is part of an aggressive B-cell leukemia phenotype [4].
| Experiment | Forward primer | Reverse primer |
|---|---|---|
| Quantitative PCR | 5'-CCGTTGGCTCCACAAACCT- 3' | 5'-CAGTGACAGTAGCAGGCATCCT- 3'[5] |
| PCR | 5′‐AATGAAAACACCAGGCCGGG‐3′ | 5′‐TCTCACTCTCTCAA ATCGGC‐3′[2] |
| In Vitro Translation | GGC AGA GAC GGA GAA GAT GA | GCC TTA GAC TGT GAA ATT TTA TTG A [5] |
Regulation
Transcription factor, activating enhancer‑binding protein 4 (TFAP4) regulates TRERNA1 by binding to the E‑box motifs in the TRERNA1 promoter [3]
Disease
Lab working on this lncRNA
- Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing 210009, China.[1]
- School of Life Science, Bengbu Medical College, Bengbu 233030, China.[1]
- Third Affiliated Hospital of Harbin Medical University (Harbin Medical University Cancer Hospital), Harbin 150040, China.[1]
- Department of Pathophysiology, Medical School of Southeast University, Nanjing 210009, China.[1]
- The Wistar Institute, Philadelphia, PA, USA.[2]
- University of Washington Medical Center, Seattle, WA, USA.[2]
- Department of Experimental Therapeutics, MD Anderson Cancer Center, Houston, TX, USA.[2]
- Drexel University College of Medicine, Philadelphia, PA, USA.[2]
- Max Planck Institute for Molecular Genetics, Berlin, Germany.[2]
- Division of Endocrine and Oncologic Surgery, Department of Surgery and Rena Rowan Breast Center, Perelman School of Medicine, Abramson Cancer
Center, University of Pennsylvania, Philadelphia, PA, USA.[2]
- Center for Research on Early Detection and Cure of Ovarian Cancer, University of Pennsylvania, Philadelphia, PA, USA.[2]
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA.[2]
- Department of Internal Medicine, Division of Hematology, Comprehensive Cancer Center at The Ohio State University, Columbus, OH, USA.[4]
- The Chronic Lymphocytic Leukemia (CLL) Research Consortium, La Jolla, CA, USA.[4]
References
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 Wu H, Hu Y, Liu X, Song W, Gong P, Zhang K et al. LncRNA TRERNA1 function as an enhancer of SNAI1 promotes gastric cancer metastasis by regulating epithelial-mesenchymal transition[J]. Molecular Therapy-Nucleic Acids. 2017, 8:291-299.
- ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 Gumireddy K, Li A, Yan J, Setoyama T, Johannes GJ, Ørom UA et al. Identification of a long non‐coding RNA‐associated RNP complex regulating metastasis at the translational step[J]. The EMBO journal. 2013, 32(20):2672-2684.
- ↑ 3.0 3.1 3.2 3.3 Wu H, Liu X, Gong P, Song W, Zhou M, Li Y et al. Elevated TFAP4 regulates lncRNA TRERNA1 to promote cell migration and invasion in gastric cancer[J]. Oncology reports. 2018.
- ↑ 4.0 4.1 4.2 4.3 Miller CR, Ruppert AS, Fobare S, Chen TL, Liu C, Lehman A et al. The long noncoding RNA, treRNA, decreases DNA damage and is associated with poor response to chemotherapy in chronic lymphocytic leukemia[J]. Oncotarget. 2017, 8(16):25942.
- ↑ 5.0 5.1 Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G et al. Long noncoding RNAs with enhancer-like function in human cells[J]. Cell. 2010, 143(1): 46-58.
Sequence
>gi|389565506|ref|NR_051976.1| Homo sapiens translation regulatory long non-coding RNA 1 (TRERNA1), long non-coding RNA
000001 CCGTTCCTGC CTCCCACAGA CACCTATTAA GTGCCTCCAG TTTTAGGAAC TGGGTATAGA TATGGCTGGG AACAAAATGG 000080
000081 AAGAAAACAA AAACAAAAAT CCCTGCCCTC ATGGTGCTGA CTCTCCTGTG GCAGAGACGG AGAAGATGAA CAGGGATTTT 000160
000161 ATACCAGGCG TCAGAAGGGA ACCAGTGCTA AAGAAAATGA AAACACCAGG CCGGGAGAGG CAGCTGGCAT GCGGGCCGTG 000240
000241 GTGGTTTTAC GTGGCCGATT TGAGAGAGTG AGACCCCTGG GGTCTTGGAG CCAGGCCTGG GAAAAGCTAC TTCACGTCAG 000320
000321 GCCAGGGGCT GTAGCCCTGG CAACCTCCAC TCCGCCTGGA AATCCTCCAC CTCGGGGCCT CTCTTTGCCC AGACCTGGCC 000400
000401 CAGGAGGAGC ACATGGGAGC CGGGACCTTC CCAACAATCC TTGCCGTTGG CTCCACAAAC CTCAGCCAGT CCTGCAACCT 000480
000481 GGGATGCCTT TTCCACCAGG ATGCCTGCTA CTGTCACTGT TGTCATTAGA TAATTAATGA ACTATAATTA GAAATCATAT 000560
000561 CAATAAAATT TCACAGTCTA AGGCTGTTGA AATAGGAAAA AAAAAAAAAA AAAAA
000081 AAGAAAACAA AAACAAAAAT CCCTGCCCTC ATGGTGCTGA CTCTCCTGTG GCAGAGACGG AGAAGATGAA CAGGGATTTT 000160
000161 ATACCAGGCG TCAGAAGGGA ACCAGTGCTA AAGAAAATGA AAACACCAGG CCGGGAGAGG CAGCTGGCAT GCGGGCCGTG 000240
000241 GTGGTTTTAC GTGGCCGATT TGAGAGAGTG AGACCCCTGG GGTCTTGGAG CCAGGCCTGG GAAAAGCTAC TTCACGTCAG 000320
000321 GCCAGGGGCT GTAGCCCTGG CAACCTCCAC TCCGCCTGGA AATCCTCCAC CTCGGGGCCT CTCTTTGCCC AGACCTGGCC 000400
000401 CAGGAGGAGC ACATGGGAGC CGGGACCTTC CCAACAATCC TTGCCGTTGG CTCCACAAAC CTCAGCCAGT CCTGCAACCT 000480
000481 GGGATGCCTT TTCCACCAGG ATGCCTGCTA CTGTCACTGT TGTCATTAGA TAATTAATGA ACTATAATTA GAAATCATAT 000560
000561 CAATAAAATT TCACAGTCTA AGGCTGTTGA AATAGGAAAA AAAAAAAAAA AAAAA
