Postnatal dynamics of zeb2 expression in rat brain: Analysis of novel 3′ UTR sequence reveals a mir-9 interacting site

Journal of Molecular Neuroscience

Volumn 52, Issue 1, 2014, Pages 138-147

  Kropivšek, Klara ^a,b   Pickford, Jasmine ^a,c   Carter, David A ^a  

^a CARDIFF UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF ZURICH   (Switzerland)

^c UNIVERSITY OF BRISTOL   (United Kingdom)

Author keywords

Brain; miRNA; Rat; RNA; Transcription factor; Untranslated region

Indexed keywords

MICRORNA 9; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR ZEB2; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BRAIN; BRAIN CELL; BRAIN CORTEX; BRAIN DEVELOPMENT; CONTROLLED STUDY; DOWN REGULATION; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE LOCUS; GENE SEQUENCE; NONHUMAN; PROTEIN EXPRESSION; RAT; TRANSCRIPTION REGULATION;

RATTUS;

3' UNTRANSLATED REGIONS; ANIMALS; BRAIN; CELLS, CULTURED; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HOMEODOMAIN PROTEINS; MICRORNAS; NEURONS; RATS; RATS, SPRAGUE-DAWLEY; REPRESSOR PROTEINS; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

EID: 84895074579     PISSN: 08958696     EISSN: 15591166     Source Type: Journal    
DOI: 10.1007/s12031-013-0146-x     Document Type: Article

References (33)

1. Anders G, Mackowiak SD, Jens M, Maaskola J, Kuntzagk A, Rajewsky N, Landthaler M, Dieterich C (2012) doRiNA: a database of RNA interactions in post-transcriptional regulation. Nucleic Acids Res 40:D180-D186
2. Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215-233
3. Bolognani F, Contente-Cuomo T, Perrone-Bizzozero NI (2010) Novel recognition motifs and biological functions of the RNA-binding protein HuD revealed by genome-wide identification of its targets. Nuc Acids Res 38:117-130
4. Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel DP (2010) Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev 24:992-1009
5. Christoffersen NR, Silahtaroglu A, Orom UA, Kauppinen S, Lund AH (2007) miR-200b mediates post-transcriptional repression of ZFHX1B. RNA 13:1172-1178
6. Chew LJ, Murphy D, Carter DA (1994) Alternatively polyadenylated vasoactive intestinal peptide messenger ribonucleic acids are differentially regulated at the level of stability. Mol Endo 8:603-613
7. Dajas-Bailador F, Bonev B, Garcez P, Stanley P, Guillemot F, Papalopulu N (2012) microRNA-9 regulates axon extension and branching by targeting Map1b in mouse cortical neurons. Nat Neurosci 15:697-699
8. Dassi E, Malossini A, Re A, Mazza T, Tebaldi T, Caputi L, Quattrone A (2011) AURA: Atlas of UTR Regulatory Activity. Bioinformatics 28:142-144
9. Davies JS, Klein DC, Carter DA (2011) Selective genomic targeting by FRA-2/FOSL2 transcription factor: regulation of the Rgs4 gene is mediated by a variant activator protein 1 (AP-1) promoter sequence/CREB-binding protein (CBP) mechanism. J Biol Chem 286:15227-15239
10. Di Giammartino DC, Nishida K, Manley JL (2011) Mechanisms and consequences of alternative polyadenylation. Mol Cell 43:853-866
11. El-Kasti MM, Wells T, Carter DA (2012) A novel long-range enhancer regulates postnatal expression of Zeb2: implications for Mowat-Wilson syndrome phenotypes. Hum Mol Genet 21:5429-5442
12. Gregory PA, Bert AG, Paterson EL, Barry SC, Tsykin A, Farshid G, Vadas MA, Khew-Goodall Y, Goodall GJ (2008) The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1. Nat Cell Biol 10:593-601
13. Grillo G, Turi A, Licciulli F, Mignone F, Liuni S, Banfi S, Gennarino VA, Horner DS, Pavesi G, Picardi E, Pesole G (2010) UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res 38:D75-D80
14. Gruber AR, Fallmann J, Kratochvill F, Kovarik P, Hofacker IL (2011) AREsite: a database for the comprehensive investigation of AU-rich elements. Nucleic Acids Res 39:D66-D69
15. Ince-Dunn G, Okano HJ, Jensen KB, Park WY, Zhong R, Ule J, Mele A, Fak JJ, Yang C, Zhang C, Yoo J, Herre M, Okano H, Noebels JL, Darnell RB (2012) Neuronal Elav-like (Hu) proteins regulate RNA splicing and abundance to control glutamate levels and neuronal excitability. Neuron 75:1067-1080
16. Kedde M, van Kouwenhove M, Zwart W, Oude Vrielink JA, Elkon R, Agami RA (2010) Pumilio-induced RNA structure switch in p27-3′ UTR controls miR-221 and miR-222 accessibility. Nat Cell Biol 12:1014-1020
17. Kim KK, Adelstein RS, Kawamoto S (2009) Identification of neuronal nuclei (NeuN) as Fox-3, a new member of the Fox-1 gene family of splicing factors. J Biol Chem 284:31052-31061
18. Kim SW, Li Z, Moore PS, Monaghan AP, Chang Y, Nichols M, John B (2010) A sensitive non-radioactive northern blot method to detect small RNAs. Nucleic Acids Res 38:e98
19. Krichevsky AM, King KS, Donahue CP, Khrapko K, Kosik KS (2003) A microRNA array reveals extensive regulation of microRNAs during brain development. RNA 9:1274-1281
20. Lau P, Verrier JD, Nielsen JA, Johnson KR, Notterpek L, Hudson LD (2008) Identification of dynamically regulated microRNA and mRNA networks in developing oligodendrocytes. J Neurosci 28:11720-11730
21. Liu DZ, Ander BP, Tian Y, Stamova B, Jickling GC, Davis RR, Sharp FR (2012) Integrated analysis of mRNA and microRNA expression in mature neurons, neural progenitor cells and neuroblastoma cells. Gene 495:120-127
22. Lyck L, Krøigård T, Finsen B (2007) Unbiased cell quantification reveals a continued increase in the number of neocortical neurones during early post-natal development in mice. Eur J Neurosci 26:1749-1764
23. Ma L, Young J, Prabhala H, Pan E, Mestdagh P, Muth D, Teruya-Feldstein J, Reinhardt F, Onder TT, Valastyan S, Westermann F, Speleman F, Vandesompele J, Weinberg RA (2010) miR-9, a MYC/MYCN-activated microRNA, regulates E-cadherin and cancer metastasis. Nat Cell Biol 12:247-256
24. Man PS, Wells T, Carter DA (2007) Egr-1-d2EGFP transgenic rats identify transient populations of neurons and glial cells during postnatal brain development. Gene Expr Patterns 7:872-883
25. Moreau MP, Bruse SE, Jornsten R, Liu Y, Brzustowicz LM (2013) Chronological changes in microRNA expression in the developing human brain. PLoS One 8:e60480
26. Nelles L, Van de Putte T, van Grunsven L, Huylebroeck D, Verschueren K (2003) Organization of the mouse Zfhx1b gene encoding the two-handed zinc finger repressor Smad-interacting protein-1. Genomics 82:460-469
27. Prime G, Horn G, Sutor B (2000) Time-related changes in connexin mRNA abundance in the rat neocortex during postnatal development. Brain Res Dev Brain Res 119:111-125
28. Saito T, Sætrom P (2012) Target gene expression levels and competition between transfected and endogenous microRNAs are strong confounding factors in microRNA high-throughput experiments. Silence 3:3
29. Sangiao-Alvarellos S, Manfredi-Lozano M, Ruiz-Pino F, Navarro VM, Sánchez-Garrido MA, Leon S, Dieguez C, Cordido F, Matagne V, Dissen GA, Ojeda SR, Pinilla L, Tena-Sempere M (2013) Changes in hypothalamic expression of the Lin28/let-7 system and related microRNAs during postnatal maturation and after experimental manipulations of puberty. Endo 154:942-955
30. Seuntjens E, Nityanandam A, Miquelajauregui A, Debruyn J, Stryjewska A, Goebbels S, Nave KA, Huylebroeck D, Tarabykin V (2009) Sip1 regulates sequential fate decisions by feedback signaling from postmitotic neurons to progenitors. Nat Neurosci 12:1373-1380
31. Smibert P, Miura P, Westholm JO, Shenker S, May G, Duff MO, Zhang D, Eads BD, Carlson J, Brown JB, Eisman RC, Andrews J, Kaufman T, Cherbas P, Celniker SE, Graveley BR, Lai EC (2012) Global patterns of tissue-specific alternative polyadenylation in Drosophila. Cell Rep 1:277-289
32. van den Berghe V, Stappers E, Vandesande B, Dimidschstein J, Kroes R, Francis A, Conidi A, Lesage F, Dries R, Cazzola S, Berx G, Kessaris N, Vanderhaeghen P, van Ijcken W, Grosveld FG, Goossens S, Haigh JJ, Fishell G, Goffinet A, Aerts S, Huylebroeck D, Seuntjens E (2013) Directed migration of cortical interneurons depends on the cell-autonomous action of Sip1. Neuron 77:70-82
33. Zhang C, Darnell RB (2011) Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat Biotechnol 29:607-614