Особенности сайтов связывания miR-574-5р и miR-574-3р с mRNA генов-мишеней
Ключевые слова:
miRNA, mRNA, miR-574-5p, miR-574-3p, сайты связывания, гены-мишени.Аннотация
miR-574-5p және miR-574-3p нысана гендерінің mRNAмен байланысуы зерттелген. miR-574-5p байланысу сайттары 244 гендердің 3'UTR-нде, 20 гендердің 5'UTR-нде және екі геннің СDS-нде орналасқан. FGFRL1 және REM2 гендердің CDS-гі miR-574-5p байланысу сайттары жоғары ΔG/ΔGm мөлшерімен ақуыздарда HTHTHTHS және DTDMDTDT олигопептидтерді кодтайды. miR-574-3p байланысу сайттары GRK6, NACC2, SEC14L1 гендердің 3'UTR-нде, ZNF470 геннің 5'UTR-нде орналасқан. miR-574-5p көп нысана гендерінің mRNAда ΔG/ΔGm мөлшері 90%-дан жоғары бірнеше байланысу сайттары бар, олардың әрбіреуі екі нуклеотидтен кейін орналасқан. miR-574-5p және miR-574-3p экспрессиясы көп патологиялық жағдайларда, сонымен бірге онкологиялық аурулар кезінде олардың нысана гендерінің экспрессиясымен корреляцияланады. Изучено связывание miR-574-5p и miR-574-3p с mRNA их генов-мишеней. Сайты связывания miR-574-5p расположены в 3'UTR 244 генов, в 5'UTR 20 генов и в СDS двух генов. Сайты связывания miR-574-5p в CDS генов FGFRL1 и REM2 с наибольшей величиной ΔG/ΔGm кодируют олигопептиды HTHTHTHS и DTDMDTDT в соответствующих белках. Сайты связывания miR-574-3p расположены в 3'UTR генов GRK6, NACC2, SEC14L1 и в 5'UTR гена ZNF470. В большинстве mRNA генов мишеней miR-574-5p имеются множественные сайты связывания с величиной ΔG/ΔGm более 90%, последовательно расположенные через два нуклеотида. Изменение экспрессии miR-574-5p и miR-574-3p коррелирует с изменением экспрессии их генов мишеней при развитии многих патологий, в том числе и онкологических заболеваний. The binding of miR-574-5p and miR-574-3p with their target genes mRNAs was studied. miR-574-5p binding sites are located in the 3'UTR of 244 genes, in the 5'UTR of 20 genes and in the CDS of two genes. miR-574-5p binding sites in the CDS of REM2 and FGFRL1 genes with the high ΔG/ΔGm value encode oligopeptides HTHTHTHS and DTDMDTDT in the corresponding proteins. miR-574-3p binding sites are located in the 3'UTR of genes GRK6, NACC2, SEC14L1 and in the 5'UTR of the gene ZNF470. In the majority of miR-574-5p target genes mRNAs there are multiple binding sites with the ΔG/ΔGm value greater than 90%, which arranged located through two nucleotides. Changes in the miR-574-5p and miR-574-3p expression at many pathologies, including cancer, correlated with changes in the expression of their target genes.Библиографические ссылки
Литература
1 Ivashchenko A.T., Berillo O.A., Pyrkova A.Y., Niyazova R.Y. Binding sites of the miR-1273 family, miR-1285-3р and miR-5684 in human mRNAs // Proceedings of the 2014 International Conference on Chemical Engineering and Materials Science (CEMS '14), Venice, Italy, March. – 2014. – Р. 15-17.
2 Ivashchenko A., Berillo O., Pyrkova A., Niyazova R., Atambayeva Sh. Binding sites of mir-1273 family on the mRNA of target genes // Biomed research international. – 2014. – Vol. 2014. – P. 620530.
3 Ivashchenko A., Berillo O., Pyrkova A., Niyazova R., Atambayeva Sh. The properties of binding sites of miR-619-5p, miR-5095, miR-5096 and miR-5585-3p in the mRNAs of human genes // Biomed research international. – 2014. – 2014. – P. 720715.
4 Ivashchenko A., Berillo O., Pyrkova A., Niyazova R., Atambayeva Sh. MiR-3960 binding sites with mRNA of human genes. // Bioinformation. – 2014. – Vol. 10(7). – P. 423-427.
5 Ivashchenko A., Berillo O., Pyrkova A., Niyazova R. and Atambayeva Sh. MiR-3960 binding sites with mRNA of human genes // Bioinformation. – 2014. – Vol. 10(7). – P. 423-427.
6 Berillo O., Regnier M., Ivashchenko A.T. miRAFinder and GeneAFinder scripts: large-scale searching for microRNA and
related information in indexed literature abstracts // Bioinformation. – 2014. – Vol. 10(8). – P. 539-543.
7 Berillo O., Regnier M., Ivashchenko A.T. TmiRUSite and TmiROSite scripts: searching for mRNA fragments with microRNA binding sites and their encoded for amino acid sequences // Bioinformation. – 2014. – Vol. 10(7). – P. 472-473.
8 Edel M.J., Menchon C., Menedez S., Consiglio A., Raya A., Izpisua Belmonte J.C. Rem2 GTPase maintains survival of human embryonic stem cells as well as enhancing reprogramming by regulating p53 and cyclin D1 // Genes & Development. – 2010. – Vol. 24(6). – P. 561-573.
9 Perfetti A., Greco S., Bugiardini E., Cardani R., Gaia P., Gaetano C., Meola G., Martelli F. Plasma microRNAs as biomarkers for myotonic dystrophy type 1 // Neuromuscular Disorders. – 2014. – Vol. 24(6). – P. 509-515.
10 Alvarez-Mora M.I., Rodriguez-Revenga L., Madrigal I., Torres-Silva F., Mateu-Huertas E., Lizano E., Friedländer M.R., Martí E., Estivill X., Milà M. MicroRNA expression profiling in blood from fragile X-associated tremor/ataxia syndrome patients // Genes, Brain and Behavior. – 2013. – Vol. 12(6). – P. 595-603.
11 Guérit D., Philipot D., Chuchana P., Toupet K., Brondello J.M., Mathieu M., Jorgensen C., Noël D. Sox9-regulated miRNA-574-3p inhibits chondrogenic differentiation of mesenchymal stem cells // PLoS One. – 2013. – Vol. 8(4). – e62582.
12 Kalabus J.L., Cheng Q., Blanco J.G. MicroRNAs differentially regulate carbonyl reductase 1 (CBR1) gene expression
dependent on the allele status of the common polymorphic variant rs9024 // PLoS One. – 2012. – Vol. 7(11). – e48622.
13 Li Q., Li X., Guo Z., Xu F., Xia J., Liu Z., Ren T. MicroRNA-574-5p was pivotal for TLR9 signaling enhanced tumor
progression via down-regulating checkpoint suppressor 1 in human lung cancer // PLoS One. – 2012. – Vol. 7(11). – e48278.
14 Yang M., Liu R., Sheng J., Liao J., Wang Y., Pan E., Guo W., Pu Y., Yin L. Differential expression profiles of microRNAs as potential biomarkers for the early diagnosis of esophageal squamous cell carcinoma // Oncology Reports. – 2013. – Vol.
29(1). – P. 169-176.
15 Su Y., Ni Z., Wang G., Cui J., Wei C., Wang J., Yang Q., Xu Y., Li F. Aberrant expression of microRNAs in gastric cancer and biological significance of miR-574-3p // International Immunopharmacology. – 2012. – Vol. 13(4). – P. 468-475.
16 Wang H., Meng K., Chen W., Feng D., Jia Y., Xie L. Serum miR-574-5p: a prognostic predictor of sepsis patients // Shock. – 2012. – Vol. 37(3). – P. 263-267.
17 Meyers-Needham M., Ponnusamy S., Gencer S., Jiang W., Thomas R.J., Senkal C.E., Ogretmen B. Concerted functions of HDAC1 and microRNA-574-5p repress alternatively spliced ceramide synthase 1 expression in human cancer cells // EMBO Molecular Medicine. – 2012. – Vol. 4(2). – Vol. 78-92.
18 Foss K.M., Sima C., Ugolini D., Neri M., Allen K.E., Weiss G.J. miR-1254 and miR-574-5p: serum-based microRNA biomarkers for early-stage non-small cell lung cancer // Journal of Thoracic Oncology. – 2011. – Vol. 6(3). – P. 482-488.
19 Guérit D., Philipot D., Chuchana P., Toupet K., Brondello J.M., Mathieu M., Jorgensen C., Noël D. Sox9-regulated miRNA-574-3p inhibits chondrogenic differentiation of mesenchymal stem cells // PLoS One. – 2013. – Vol. 8(4). – e62582.
20 Foss K.M., Sima C., Ugolini D., Neri M., Allen K.E., Weiss G.J. miR-1254 and miR-574-5p: serum-based microRNA biomarkers for early-stage non-small cell lung cancer // Journal of Thoracic Oncology. – 2011. – Vol. 6(3). – P. 482-488.
21 Li Q., Li X., Guo Z., Xu F., Xia J., Liu Z., Ren T. MicroRNA-574-5p was pivotal for TLR9 signaling enhanced tumor progression via down-regulating checkpoint suppressor 1 in human lung cancer // PLoS One. – 2012. – Vol. 7(11). – e48278.
22 Zhang T., Zhao D., Wang Q., Yu X., Cui Y., Guo L., Lu S.H. MicroRNA-1322 regulates ECRG2 allele specifically and acts as a potential biomarker in patients with esophageal squamous cell carcinoma // Molecular Carcinogenesis. – 2013. – Vol. 52(8). – P. 581-590.
23 Saito Y., Suzuki H., Tsugawa H., Nakagawa I., Matsuzaki J., Kanai Y., Hibi T. Chromatin remodeling at Alu repeats by epigenetic treatment activates silenced microRNA-512-5p with downregulation of Mcl-1 in human gastric cancer cells // Oncogene. – 2009. – Vol. 28(30). – P. 2738-2744.
24 Su Y., Ni Z., Wang G., Cui J., Wei C., Wang J., Yang Q., Xu Y., Li F. Aberrant expression of microRNAs in gastric cancer and biological significance of miR-574-3p // International Immunopharmacology. – 2012. – Vol. 13(4). – P. 468-475.
25 Chan W.L., Yuo C.Y., Yang W.K., Hung S.Y., Chang Y.S., Chiu C.C., Yeh K.T., Huang H.D., Chang J.G. Transcribed pseudogene ψPPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular carcinoma // Nucleic Acids Research. – 2013. – Vol. 41(6). – P. 3734-3747.
26 Jin Y., Yu Q., Zhou D., Chen L., Huang X., Xu G., Huang J., Gao X., Gao Y., Shen L. The mitochondrial DNA 9-bp deletion polymorphism is a risk factor for hepatocellular carcinoma in the Chinese population // Genet Testing and Molecular Biomarkers. – 2012. – Vol. 16(5). – P. 330-334.
27 di Martino E., Taylor C.F., Roulson J.A., Knowles M.A. An integrated genomic, transcriptional and protein investigation of FGFRL1 as a putative 4p16.3 deletion target in bladder cancer // Genes Chromosomes Cancer. – 2013. – Vol. 52(9). – P. 860-871.
28 Schild C., Trueb B. Aberrant expression of FGFRL1, a novel FGF receptor, in ovarian tumors // International Journal of Molecular Medicine. – 2005. – Vol. 16(6). – 1169-73.
29 Tsuchiya S., Fujiwara T Sato F Shimada Y Tanaka E Sakai Y Shimizu K Tsujimoto G. MicroRNA-210 regulates cancer cell proliferation through targeting fibroblast growth factor receptor-like 1 (FGFRL1) // Journal of Biological Chemistry. – 2011. – Vol. 286(1). – P. 420-428.
1 Ivashchenko A.T., Berillo O.A., Pyrkova A.Y., Niyazova R.Y. Binding sites of the miR-1273 family, miR-1285-3р and miR-5684 in human mRNAs // Proceedings of the 2014 International Conference on Chemical Engineering and Materials Science (CEMS '14), Venice, Italy, March. – 2014. – Р. 15-17.
2 Ivashchenko A., Berillo O., Pyrkova A., Niyazova R., Atambayeva Sh. Binding sites of mir-1273 family on the mRNA of target genes // Biomed research international. – 2014. – Vol. 2014. – P. 620530.
3 Ivashchenko A., Berillo O., Pyrkova A., Niyazova R., Atambayeva Sh. The properties of binding sites of miR-619-5p, miR-5095, miR-5096 and miR-5585-3p in the mRNAs of human genes // Biomed research international. – 2014. – 2014. – P. 720715.
4 Ivashchenko A., Berillo O., Pyrkova A., Niyazova R., Atambayeva Sh. MiR-3960 binding sites with mRNA of human genes. // Bioinformation. – 2014. – Vol. 10(7). – P. 423-427.
5 Ivashchenko A., Berillo O., Pyrkova A., Niyazova R. and Atambayeva Sh. MiR-3960 binding sites with mRNA of human genes // Bioinformation. – 2014. – Vol. 10(7). – P. 423-427.
6 Berillo O., Regnier M., Ivashchenko A.T. miRAFinder and GeneAFinder scripts: large-scale searching for microRNA and
related information in indexed literature abstracts // Bioinformation. – 2014. – Vol. 10(8). – P. 539-543.
7 Berillo O., Regnier M., Ivashchenko A.T. TmiRUSite and TmiROSite scripts: searching for mRNA fragments with microRNA binding sites and their encoded for amino acid sequences // Bioinformation. – 2014. – Vol. 10(7). – P. 472-473.
8 Edel M.J., Menchon C., Menedez S., Consiglio A., Raya A., Izpisua Belmonte J.C. Rem2 GTPase maintains survival of human embryonic stem cells as well as enhancing reprogramming by regulating p53 and cyclin D1 // Genes & Development. – 2010. – Vol. 24(6). – P. 561-573.
9 Perfetti A., Greco S., Bugiardini E., Cardani R., Gaia P., Gaetano C., Meola G., Martelli F. Plasma microRNAs as biomarkers for myotonic dystrophy type 1 // Neuromuscular Disorders. – 2014. – Vol. 24(6). – P. 509-515.
10 Alvarez-Mora M.I., Rodriguez-Revenga L., Madrigal I., Torres-Silva F., Mateu-Huertas E., Lizano E., Friedländer M.R., Martí E., Estivill X., Milà M. MicroRNA expression profiling in blood from fragile X-associated tremor/ataxia syndrome patients // Genes, Brain and Behavior. – 2013. – Vol. 12(6). – P. 595-603.
11 Guérit D., Philipot D., Chuchana P., Toupet K., Brondello J.M., Mathieu M., Jorgensen C., Noël D. Sox9-regulated miRNA-574-3p inhibits chondrogenic differentiation of mesenchymal stem cells // PLoS One. – 2013. – Vol. 8(4). – e62582.
12 Kalabus J.L., Cheng Q., Blanco J.G. MicroRNAs differentially regulate carbonyl reductase 1 (CBR1) gene expression
dependent on the allele status of the common polymorphic variant rs9024 // PLoS One. – 2012. – Vol. 7(11). – e48622.
13 Li Q., Li X., Guo Z., Xu F., Xia J., Liu Z., Ren T. MicroRNA-574-5p was pivotal for TLR9 signaling enhanced tumor
progression via down-regulating checkpoint suppressor 1 in human lung cancer // PLoS One. – 2012. – Vol. 7(11). – e48278.
14 Yang M., Liu R., Sheng J., Liao J., Wang Y., Pan E., Guo W., Pu Y., Yin L. Differential expression profiles of microRNAs as potential biomarkers for the early diagnosis of esophageal squamous cell carcinoma // Oncology Reports. – 2013. – Vol.
29(1). – P. 169-176.
15 Su Y., Ni Z., Wang G., Cui J., Wei C., Wang J., Yang Q., Xu Y., Li F. Aberrant expression of microRNAs in gastric cancer and biological significance of miR-574-3p // International Immunopharmacology. – 2012. – Vol. 13(4). – P. 468-475.
16 Wang H., Meng K., Chen W., Feng D., Jia Y., Xie L. Serum miR-574-5p: a prognostic predictor of sepsis patients // Shock. – 2012. – Vol. 37(3). – P. 263-267.
17 Meyers-Needham M., Ponnusamy S., Gencer S., Jiang W., Thomas R.J., Senkal C.E., Ogretmen B. Concerted functions of HDAC1 and microRNA-574-5p repress alternatively spliced ceramide synthase 1 expression in human cancer cells // EMBO Molecular Medicine. – 2012. – Vol. 4(2). – Vol. 78-92.
18 Foss K.M., Sima C., Ugolini D., Neri M., Allen K.E., Weiss G.J. miR-1254 and miR-574-5p: serum-based microRNA biomarkers for early-stage non-small cell lung cancer // Journal of Thoracic Oncology. – 2011. – Vol. 6(3). – P. 482-488.
19 Guérit D., Philipot D., Chuchana P., Toupet K., Brondello J.M., Mathieu M., Jorgensen C., Noël D. Sox9-regulated miRNA-574-3p inhibits chondrogenic differentiation of mesenchymal stem cells // PLoS One. – 2013. – Vol. 8(4). – e62582.
20 Foss K.M., Sima C., Ugolini D., Neri M., Allen K.E., Weiss G.J. miR-1254 and miR-574-5p: serum-based microRNA biomarkers for early-stage non-small cell lung cancer // Journal of Thoracic Oncology. – 2011. – Vol. 6(3). – P. 482-488.
21 Li Q., Li X., Guo Z., Xu F., Xia J., Liu Z., Ren T. MicroRNA-574-5p was pivotal for TLR9 signaling enhanced tumor progression via down-regulating checkpoint suppressor 1 in human lung cancer // PLoS One. – 2012. – Vol. 7(11). – e48278.
22 Zhang T., Zhao D., Wang Q., Yu X., Cui Y., Guo L., Lu S.H. MicroRNA-1322 regulates ECRG2 allele specifically and acts as a potential biomarker in patients with esophageal squamous cell carcinoma // Molecular Carcinogenesis. – 2013. – Vol. 52(8). – P. 581-590.
23 Saito Y., Suzuki H., Tsugawa H., Nakagawa I., Matsuzaki J., Kanai Y., Hibi T. Chromatin remodeling at Alu repeats by epigenetic treatment activates silenced microRNA-512-5p with downregulation of Mcl-1 in human gastric cancer cells // Oncogene. – 2009. – Vol. 28(30). – P. 2738-2744.
24 Su Y., Ni Z., Wang G., Cui J., Wei C., Wang J., Yang Q., Xu Y., Li F. Aberrant expression of microRNAs in gastric cancer and biological significance of miR-574-3p // International Immunopharmacology. – 2012. – Vol. 13(4). – P. 468-475.
25 Chan W.L., Yuo C.Y., Yang W.K., Hung S.Y., Chang Y.S., Chiu C.C., Yeh K.T., Huang H.D., Chang J.G. Transcribed pseudogene ψPPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular carcinoma // Nucleic Acids Research. – 2013. – Vol. 41(6). – P. 3734-3747.
26 Jin Y., Yu Q., Zhou D., Chen L., Huang X., Xu G., Huang J., Gao X., Gao Y., Shen L. The mitochondrial DNA 9-bp deletion polymorphism is a risk factor for hepatocellular carcinoma in the Chinese population // Genet Testing and Molecular Biomarkers. – 2012. – Vol. 16(5). – P. 330-334.
27 di Martino E., Taylor C.F., Roulson J.A., Knowles M.A. An integrated genomic, transcriptional and protein investigation of FGFRL1 as a putative 4p16.3 deletion target in bladder cancer // Genes Chromosomes Cancer. – 2013. – Vol. 52(9). – P. 860-871.
28 Schild C., Trueb B. Aberrant expression of FGFRL1, a novel FGF receptor, in ovarian tumors // International Journal of Molecular Medicine. – 2005. – Vol. 16(6). – 1169-73.
29 Tsuchiya S., Fujiwara T Sato F Shimada Y Tanaka E Sakai Y Shimizu K Tsujimoto G. MicroRNA-210 regulates cancer cell proliferation through targeting fibroblast growth factor receptor-like 1 (FGFRL1) // Journal of Biological Chemistry. – 2011. – Vol. 286(1). – P. 420-428.
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Современные проблемы биомедицины и биофизики
