Skip to main content

Global Transcriptome Profiling of Genes that Are Differentially Regulated During Differentiation of Mouse Embryonic Neural Stem Cells into Astrocytes

Journal of Molecular Neuroscience volume 55, pages 109–125 (2015)Cite this article

Abstract

Many genes are associated with the differentiation of neural stem cells (NSCs) into astrocytes, the most abundant and functionally diverse population of glial cells in the central nervous system, particularly in the brain. In the present study, we differentiated NSCs from the forebrain of embryonic day 14.5 mouse embryos into astrocytes over 1 and 7 days. We identified transcriptomes of NSCs and astrocytes using RNA sequencing and analyzed enriched gene networks, signal pathways, and ontology. To identify important regulators of differentiation, we performed gene clustering according to expression patterns and promoter CG types. Our data show that genes related to system development, including Fbln2, Bcan, Ncam1, Itih3, Tnr, and Vcan, regulate NSC differentiation through WNT/beta-catenin and epithelial to mesenchymal transition pathways. We identified many CG-rich promoter genes related to basic cellular maintenance such as transcription, translation, and structural components and CG-poor promoter genes that are highly associated with cell-type-specific functions or play important roles during development. Our study provides a foundation for further research on NSC differentiation and the future application of stem cells.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

USD 39.95

Price includes VAT (USA)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

References

  • Anderson JT (2005) RNA turnover: unexpected consequences of being tailed. Curr Biol CB 15(16):R635–R638. doi:10.1016/j.cub.2005.08.002

    CAS  Article  Google Scholar 

  • Andersson ER, Salto C, Villaescusa JC, Cajanek L, Yang S, Bryjova L, Nagy II, Vainio SJ, Ramirez C, Bryja V, Arenas E (2013) Wnt5a cooperates with canonical Wnts to generate midbrain dopaminergic neurons in vivo and in stem cells. Proc Natl Acad Sci U S A 110(7):E602–E610. doi:10.1073/pnas.1208524110

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Andres-Barquin PJ, Hernandez MC, Israel MA (1998) Injury selectively down-regulates the gene encoding for the Id4 transcription factor in primary cultures of forebrain astrocytes. Neuroreport 9(18):4075–4080

    CAS  PubMed  Article  Google Scholar 

  • Angelastro JM, Mason JL, Ignatova TN, Kukekov VG, Stengren GB, Goldman JE, Greene LA (2005) Downregulation of activating transcription factor 5 is required for differentiation of neural progenitor cells into astrocytes. J Neurosci Off J Soc Neurosci 25(15):3889–3899. doi:10.1523/jneurosci.3447-04.2005

    CAS  Article  Google Scholar 

  • Beckervordersandforth R, Tripathi P, Ninkovic J, Bayam E, Lepier A, Stempfhuber B, Kirchhoff F, Hirrlinger J, Haslinger A, Lie DC, Beckers J, Yoder B, Irmler M, Gotz M (2010) In vivo fate mapping and expression analysis reveals molecular hallmarks of prospectively isolated adult neural stem cells. Cell Stem Cell 7(6):744–758. doi:10.1016/j.stem.2010.11.017

    CAS  PubMed  Article  Google Scholar 

  • Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125(2):315–326. doi:10.1016/j.cell.2006.02.041

    CAS  PubMed  Article  Google Scholar 

  • Beutner C, Linnartz-Gerlach B, Schmidt SV, Beyer M, Mallmann MR, Staratschek-Jox A, Schultze JL, Neumann H (2013) Unique transcriptome signature of mouse microglia. Glia 61(9):1429–1442. doi:10.1002/glia.22524

    PubMed  Article  Google Scholar 

  • Brun M, Coles JE, Monckton EA, Glubrecht DD, Bisgrove D, Godbout R (2009) Nuclear factor I regulates brain fatty acid-binding protein and glial fibrillary acidic protein gene expression in malignant glioma cell lines. J Mol Biol 391(2):282–300. doi:10.1016/j.jmb.2009.06.041

    CAS  PubMed  Article  Google Scholar 

  • Cahoy JD, Emery B, Kaushal A, Foo LC, Zamanian JL, Christopherson KS, Xing Y, Lubischer JL, Krieg PA, Krupenko SA, Thompson WJ, Barres BA (2008) A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J Neurosci Off J Soc Neurosci 28(1):264–278. doi:10.1523/JNEUROSCI.4178-07.2008

    CAS  Article  Google Scholar 

  • Chen H, Wang S, Chen L, Chen Y, Wu M, Zhang Y, Yu K, Huang Z, Qin L, Mo D (2013) MicroRNA-344 inhibits 3T3-L1 cell differentiation via targeting GSK3beta of Wnt/beta-catenin signaling pathway. FEBS Lett. doi:10.1016/j.febslet.2013.12.002

    Google Scholar 

  • Choi MR, Jung KH, Park JH, Das ND, Chung MK, Choi IG, Lee BC, Park KS, Chai YG (2011) Ethanol-induced small heat shock protein genes in the differentiation of mouse embryonic neural stem cells. Arch Toxicol 85(4):293–304. doi:10.1007/s00204-010-0591-z

    CAS  PubMed  Article  Google Scholar 

  • da Huang W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4(1):44–57. doi:10.1038/nprot.2008.211

    CAS  Article  Google Scholar 

  • Davis AA, Temple S (1994) A self-renewing multipotential stem cell in embryonic rat cerebral cortex. Nature 372(6503):263–266. doi:10.1038/372263a0

    CAS  PubMed  Article  Google Scholar 

  • Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA (2003) DAVID: database for annotation, visualization, and integrated discovery. Genome Biol 4(5):P3

    PubMed  Article  Google Scholar 

  • Foo LC, Dougherty JD (2013) Aldh1L1 is expressed by postnatal neural stem cells in vivo. Glia 61(9):1533–1541. doi:10.1002/glia.22539

    PubMed Central  PubMed  Article  Google Scholar 

  • Fujita T, Matsushita M, Endo Y (2004) The lectin-complement pathway–its role in innate immunity and evolution. Immunol Rev 198:185–202

    CAS  PubMed  Article  Google Scholar 

  • Gage FH (2000) Mammalian neural stem cells. Science 287(5457):1433–1438

    CAS  PubMed  Article  Google Scholar 

  • Gamsiz ED, Ouyang Q, Schmidt M, Nagpal S, Morrow EM (2012) Genome-wide transcriptome analysis in murine neural retina using high-throughput RNA sequencing. Genomics 99(1):44–51. doi:10.1016/j.ygeno.2011.09.003

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Han DM, Choi MR, Jung KH, Lee HT, Park JH, Ohn T, Chai YG (2012) Proteomic analysis of the copper ion-induced stress response in a human embryonic carcinoma cell line. Int J Toxicol 31(4):397–406. doi:10.1177/1091581812446869

    CAS  PubMed  Article  Google Scholar 

  • Hirai S, Miwa A, Ohtaka-Maruyama C, Kasai M, Okabe S, Hata Y, Okado H (2012) RP58 controls neuron and astrocyte differentiation by downregulating the expression of Id1-4 genes in the developing cortex. EMBO J 31(5):1190–1202. doi:10.1038/emboj.2011.486

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Hsieh FY, Ma TL, Shih HY, Lin SJ, Huang CW, Wang HY, Cheng YC (2013) Dner inhibits neural progenitor proliferation and induces neuronal and glial differentiation in zebrafish. Dev Biol 375(1):1–12. doi:10.1016/j.ydbio.2013.01.007

    CAS  PubMed  Article  Google Scholar 

  • Jovicic A, Roshan R, Moisoi N, Pradervand S, Moser R, Pillai B, Luthi-Carter R (2013) Comprehensive expression analyses of neural cell-type-specific miRNAs identify new determinants of the specification and maintenance of neuronal phenotypes. J Neurosci Off J Soc Neurosci 33(12):5127–5137. doi:10.1523/jneurosci.0600-12.2013

    CAS  Article  Google Scholar 

  • Jungblut M, Tiveron MC, Barral S, Abrahamsen B, Knobel S, Pennartz S, Schmitz J, Perraut M, Pfrieger FW, Stoffel W, Cremer H, Bosio A (2012) Isolation and characterization of living primary astroglial cells using the new GLAST-specific monoclonal antibody ACSA-1. Glia 60(6):894–907. doi:10.1002/glia.22322

    PubMed  Article  Google Scholar 

  • Kamel G, Hoyos T, Rochard L, Dougherty M, Kong Y, Tse W, Shubinets V, Grimaldi M, Liao EC (2013) Requirement for frzb and fzd7a in cranial neural crest convergence and extension mechanisms during zebrafish palate and jaw morphogenesis. Dev Biol. doi:10.1016/j.ydbio.2013.06.012

    PubMed  Google Scholar 

  • Kang P, Lee HK, Glasgow SM, Finley M, Donti T, Gaber ZB, Graham BH, Foster AE, Novitch BG, Gronostajski RM, Deneen B (2012) Sox9 and NFIA coordinate a transcriptional regulatory cascade during the initiation of gliogenesis. Neuron 74(1):79–94. doi:10.1016/j.neuron.2012.01.024

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Katoh M (2006) Cross-talk of WNT and FGF signaling pathways at GSK3beta to regulate beta-catenin and SNAIL signaling cascades. Cancer Biol Ther 5(9):1059–1064

    CAS  PubMed  Article  Google Scholar 

  • Kettenmann H, Ransom BR (1988) Electrical coupling between astrocytes and between oligodendrocytes studied in mammalian cell cultures. Glia 1(1):64–73. doi:10.1002/glia.440010108

    CAS  PubMed  Article  Google Scholar 

  • Krencik R, Weick JP, Liu Y, Zhang ZJ, Zhang SC (2011) Specification of transplantable astroglial subtypes from human pluripotent stem cells. Nat Biotechnol 29(6):528–534. doi:10.1038/nbt.1877

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Laneve P, Gioia U, Andriotto A, Moretti F, Bozzoni I, Caffarelli E (2010) A minicircuitry involving REST and CREB controls miR-9-2 expression during human neuronal differentiation. Nucleic Acids Res 38(20):6895–6905. doi:10.1093/nar/gkq604

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Lim J, Thiery JP (2012) Epithelial-mesenchymal transitions: insights from development. Development 139(19):3471–3486. doi:10.1242/dev.071209

    CAS  PubMed  Article  Google Scholar 

  • Linhart C, Halperin Y, Shamir R (2008) Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets. Genome Res 18(7):1180–1189. doi:10.1101/gr.076117.108

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Liu HT, Tashmukhamedov BA, Inoue H, Okada Y, Sabirov RZ (2006) Roles of two types of anion channels in glutamate release from mouse astrocytes under ischemic or osmotic stress. Glia 54(5):343–357. doi:10.1002/glia.20400

    PubMed  Article  Google Scholar 

  • Marei HE, Ahmed AE, Michetti F, Pescatori M, Pallini R, Casalbore P, Cenciarelli C, Elhadidy M (2012) Gene expression profile of adult human olfactory bulb and embryonic neural stem cell suggests distinct signaling pathways and epigenetic control. PLoS One 7(4):e33542. doi:10.1371/journal.pone.0033542

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448(7153):553–560. doi:10.1038/nature06008

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Miyawaki T, Uemura A, Dezawa M, Yu RT, Ide C, Nishikawa S, Honda Y, Tanabe Y, Tanabe T (2004) Tlx, an orphan nuclear receptor, regulates cell numbers and astrocyte development in the developing retina. J Neurosci Off J Soc Neurosci 24(37):8124–8134. doi:10.1523/JNEUROSCI.2235-04.2004

    CAS  Article  Google Scholar 

  • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5(7):621–628. doi:10.1038/nmeth.1226

    CAS  PubMed  Article  Google Scholar 

  • Naka H, Nakamura S, Shimazaki T, Okano H (2008) Requirement for COUP-TFI and II in the temporal specification of neural stem cells in CNS development. Nat Neurosci 11(9):1014–1023. doi:10.1038/nn.2168

    CAS  PubMed  Article  Google Scholar 

  • Nieto-Estevez V, Pignatelli J, Arauzo-Bravo MJ, Hurtado-Chong A, Vicario-Abejon C (2013) A global transcriptome analysis reveals molecular hallmarks of neural stem cell death, survival, and differentiation in response to partial FGF-2 and EGF deprivation. PLoS One 8(1):e53594. doi:10.1371/journal.pone.0053594

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Obayashi S, Tabunoki H, Kim SU, Satoh J (2009) Gene expression profiling of human neural progenitor cells following the serum-induced astrocyte differentiation. Cell Mol Neurobiol 29(3):423–438. doi:10.1007/s10571-008-9338-2

    CAS  PubMed  Article  Google Scholar 

  • Park JH, Choi MR, Park KS, Kim SH, Jung KH, Chai YG (2012) The characterization of gene expression during mouse neural stem cell differentiation in vitro. Neurosci Lett 506(1):50–54. doi:10.1016/j.neulet.2011.10.046

    CAS  PubMed  Article  Google Scholar 

  • Pekny M, Nilsson M (2005) Astrocyte activation and reactive gliosis. Glia 50(4):427–434. doi:10.1002/glia.20207

    PubMed  Article  Google Scholar 

  • Pino D, Choe Y, Pleasure SJ (2011) Wnt5a controls neurite development in olfactory bulb interneurons. ASN Neurol 3(3):e00059. doi:10.1042/an20100038

    Google Scholar 

  • Rowitch DH, Kriegstein AR (2010) Developmental genetics of vertebrate glial-cell specification. Nature 468(7321):214–222. doi:10.1038/nature09611

    CAS  PubMed  Article  Google Scholar 

  • Samanta J, Kessler JA (2004) Interactions between ID and OLIG proteins mediate the inhibitory effects of BMP4 on oligodendroglial differentiation. Development 131(17):4131–4142. doi:10.1242/dev.01273

    CAS  PubMed  Article  Google Scholar 

  • Sancho-Martinez I, Baek SH, Izpisua Belmonte JC (2012) Lineage conversion methodologies meet the reprogramming toolbox. Nat Cell Biol 14(9):892–899. doi:10.1038/ncb2567

    CAS  PubMed  Article  Google Scholar 

  • Sanosaka T, Namihira M, Asano H, Kohyama J, Aisaki K, Igarashi K, Kanno J, Nakashima K (2008) Identification of genes that restrict astrocyte differentiation of midgestational neural precursor cells. Neuroscience 155(3):780–788. doi:10.1016/j.neuroscience.2008.06.039

    CAS  PubMed  Article  Google Scholar 

  • Sanosaka T, Namihira M, Nakashima K (2009) Epigenetic mechanisms in sequential differentiation of neural stem cells. Epigenetics Off J DNA Methylation Soc 4(2):89–92

    CAS  Article  Google Scholar 

  • Singh SK, Wilczynska KM, Grzybowski A, Yester J, Osrah B, Bryan L, Wright S, Griswold-Prenner I, Kordula T (2011) The unique transcriptional activation domain of nuclear factor-I-X3 is critical to specifically induce marker gene expression in astrocytes. J Biol Chem 286(9):7315–7326. doi:10.1074/jbc.M110.152421

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Skreka K, Schafferer S, Nat IR, Zywicki M, Salti A, Apostolova G, Griehl M, Rederstorff M, Dechant G, Huttenhofer A (2012) Identification of differentially expressed non-coding RNAs in embryonic stem cell neural differentiation. Nucleic Acids Res 40(13):6001–6015. doi:10.1093/nar/gks311

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Swiss VA, Nguyen T, Dugas J, Ibrahim A, Barres B, Androulakis IP, Casaccia P (2011) Identification of a gene regulatory network necessary for the initiation of oligodendrocyte differentiation. PLoS One 6(4):e18088. doi:10.1371/journal.pone.0018088

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Tan PP, French L, Pavlidis P (2013) Neuron-enriched gene expression patterns are regionally anti-correlated with oligodendrocyte-enriched patterns in the adult mouse and human brain. Front Neurosci 7:5. doi:10.3389/fnins.2013.00005

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Tanaka S, Terada K, Nohno T (2011) Canonical Wnt signaling is involved in switching from cell proliferation to myogenic differentiation of mouse myoblast cells. J Mol Signal 6:12. doi:10.1186/1750-2187-6-12

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Telese F, Gamliel A, Skowronska-Krawczyk D, Garcia-Bassets I, Rosenfeld MG (2013) “Seq-ing” insights into the epigenetics of neuronal gene regulation. Neuron 77(4):606–623. doi:10.1016/j.neuron.2013.01.034

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Ueno T, Ito J, Hoshikawa S, Ohori Y, Fujiwara S, Yamamoto S, Ohtsuka T, Kageyama R, Akai M, Nakamura K, Ogata T (2012) The identification of transcriptional targets of Ascl1 in oligodendrocyte development. Glia 60(10):1495–1505. doi:10.1002/glia.22369

    PubMed  Article  Google Scholar 

  • Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1):57–63. doi:10.1038/nrg2484

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, Rahl PB, Lee TI, Young RA (2013) Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153(2):307–319. doi:10.1016/j.cell.2013.03.035

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B (2013) Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153(5):1134–1148. doi:10.1016/j.cell.2013.04.022

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Yamashita R, Wakaguri H, Sugano S, Suzuki Y, Nakai K (2010) DBTSS provides a tissue specific dynamic view of transcription start sites. Nucleic Acids Res 38(Database issue):D98–D104. doi:10.1093/nar/gkp1017

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Zhang HM, Chen H, Liu W, Liu H, Gong J, Wang H, Guo AY (2012) AnimalTFDB: a comprehensive animal transcription factor database. Nucleic Acids Res 40(Database issue):D144–D149. doi:10.1093/nar/gkr965

    CAS  PubMed Central  PubMed  Article  Google Scholar 

Download references

Acknowledgment

This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIP) (No.2011-0030049).

Author information

Authors and Affiliations

  1. Department of Molecular and Life Science, Hanyang University, Ansan, 426-791, Korea

    Dalmuri Han, Mi Ran Choi, Kyoung Hwa Jung, Se kye Kim, Jin Choul Chai, Young Seek Lee & Young Gyu Chai

  2. Department of Nanobiotechnology, Hanyang University, Seoul, 131-791, Korea

    Young Gyu Chai

  3. Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea

    Namshin Kim

Authors
  1. Dalmuri Han
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mi Ran Choi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kyoung Hwa Jung
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Namshin Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Se kye Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jin Choul Chai
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Young Seek Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Young Gyu Chai
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Young Gyu Chai.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Figure S1
figure 7figure 7figure 7

Signaling pathway genes that showed enriched expression during 7-day differentiation (A) Signaling pathways during 7-day differentiation (B) Map of top scoring signaling pathways during 7-day differentiation (C), (D) mRNA expression of genes related to the Tgf-b pathway (C) and growth factors (D) in NSCs, differentiated cells, and primary cultured astrocytes by qRT-PCR. * Significantly different from NSCs by one-way ANOVA with HSD test (*P < 0.05, n = 3). (GIF 23 kb)

(GIF 85 kb)

(GIF 24 kb)

Full size image

High resolution image (TIFF 3052 kb)

High resolution image (TIFF 11839 kb)

High resolution image (TIFF 4010 kb)

Table S1

(XLSX 11.4 kb)

Table S2

(XLSX 8.30 mb)

Table S3

(XLSX 191 kb)

Table S4

(XLSX 86.8 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Han, D., Choi, M.R., Jung, K.H. et al. Global Transcriptome Profiling of Genes that Are Differentially Regulated During Differentiation of Mouse Embryonic Neural Stem Cells into Astrocytes. J Mol Neurosci 55, 109–125 (2015). https://doi.org/10.1007/s12031-014-0382-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12031-014-0382-8

Keywords

  • Neural stem cells
  • Astrocytes
  • Cell differentiation
  • TGF beta
  • WNTs