Skip to main content

Advertisement

SpringerLink
Log in

A Novel Divergent Gene Transcription Paradigm—the Decisive, Brain-Specific, Neural |-Srgap2–Fam72a-| Master Gene Paradigm

  • Published:
Molecular Neurobiology Aims and scope Submit manuscript

Abstract

Brain development and repair largely depend on neural stem cells (NSCs). Here, we suggest that two genes, i.e., Srgap2 (SLIT-ROBO Rho GTPase–activating protein 2) and Fam72a (family with sequence similarity to 72, member A), constitute a single, NSC-specific, |-Srgap2–Fam72a-| master gene pair co-existing in reciprocal functional dependency. This gene pair has a dual, commonly used, intergenic region (IGR) promotor, which is a prerequisite in controlling human brain plasticity. We applied fluorescence cellular microscopy and fluorescence-activated cell sorting (FACS) to assess rat |-Srgap2–Fam72a-| master gene IGR promotor activity upon stimulation with two contrary growth factors: nerve growth factor (Ngf, a differentiation growth factor) and epidermal growth factor (Egf, a mitotic growth factor). We found that Ngf and Egf acted on the same IGR gene promotor element of the |-Srgap2–Fam72a-| master gene to mediate cell differentiation and proliferation, respectively. Ngf mediated Srgap2 expression and neuronal survival and differentiation while Egf activated Fam72a transcription and cell proliferation. Our data provide new insights into the specific regulation of the |-Srgap2–Fam72a-| master gene with its dual IGR promotor that controls two reverse-oriented functional-dependent genes located on opposite DNA strands. This structure represents a novel paradigm for controlling transcription of divergent genes in regulating NSC gene expression. This paradigm may allow for novel therapeutic approaches to restore or improve higher cognitive functions and cure cancers.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

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

Similar content being viewed by others

Abbreviations

Akt:

AK strain transforming, AKT serine/threonine kinase

ANOVA:

Analysis of variance

Atf1:

Activating transcription factor 1

Bad:

BCL2-associated agonist of cell death

Bak1:

BCL2-antagonist/killer 1

Bax:

BCL2-associated X

Bcl2:

B cell lymphoma 2

Bcl2l1:

Bcl2-like 1

Bid:

BH3-interacting domain death agonist

Braf:

B rapidly accelerated fibrosarcoma (B-Raf) proto-oncogene, serine/threonine kinase

BS:

Binding site

BSA:

Bovine serum albumin

Casp:

Caspase

Ccna/b/d/e:

Cyclin A/B/D/E

Cdk:

Cyclin-dependent kinase

Cdkn1a:

Cyclin-dependent kinase inhibitor 1A

Chr:

Chromosome

CMV:

Cytomegalovirus

CNS:

Central nervous system

Creb1:

cAMP-responsive element-binding protein 1

Cycs:

Cytochrome c, somatic

DAPI:

4′,6-Diamidino-2-phenylindole

DIC:

Differential interference contrast

DMEM:

Dulbecco’s modified Eagle’s medium

E:

Exon

E2f:

E2 transcription factor

EDTA:

Ethylenediaminetetraacetic acid

Egf:

Epidermal growth factor

Egfr:

Epidermal growth factor receptor

FACS:

Fluorescence-activated cell sorting

Fam72a:

Family with sequence similarity 72, member A

FBS:

Fetal bovine serum

Fos:

Finkel-Biskis-Jinkins (FBJ) murine osteosarcoma (Fos) proto-oncogene, activator protein 1 (AP-1) transcription factor subunit

GFP:

Green fluorescent protein

Hdac1:

Histone deacetylase 1

HEPES:

4-(2-Hydroxyethyl)-1-piperazineethanesulfonic acid

HS:

Horse serum

I:

Intron

IGR:

Intergenic region

IRES2:

Internal ribosome entry site 2

KCLB:

Korean cell line bank

Kmt5b/c:

Lysine methyltransferase 5B/C

Map2k:

Mitogen-activated protein kinase kinase

Mapk:

Mitogen-activated protein kinase

Mcl1:

Myeloid cell leukemia 1, BCL2 family apoptosis regulator

Mdm2:

Murine double minute 2 proto-oncogene

MOMP:

Mitochondrial outer membrane permeabilization

Mt1:

Metallothionein 1

Myc:

Myelocytomatosis viral oncogene

NCBI:

National Center for Biotechnology Information

NDR:

Nucleosome-depleted region

NEAA:

Non-essential amino acids

Ngf:

Nerve growth factor

NSC:

Neural stem cell

Ntrk1:

Neurotrophic receptor tyrosine kinase 1

P:

Phosphorylation

P/S:

Penicillin, streptomycin

pDNA:

Plasmid DNA

Pik3cg:

Phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma

PROMPT:

Promoter upstream transcript

Rap1:

Ras-related protein 1

Ras:

Rat sarcoma (RAS) proto-oncogene, GTPase

Rb:

Retinoblastoma (RB) transcriptional corepressor

RFP:

Red fluorescent protein

SEM:

Standard error of the mean

Srgap2:

SLIT-ROBO Rho GTPase–activating protein 2

Suv39h1:

Suppressor of variegation 3-9 homolog 1

TF:

Transcription factor

TFBS:

Transcription factor–binding sites

Tfdp1:

Transcription factor dimerization partner 1 (Dp-1)

Tp53:

Tumor protein 53

w/o:

Without

+:

Positive

References

  1. Raju TN (2000) The Nobel chronicles. 1986: Stanley Cohen (b 1922); Rita Levi-Montalcini (b 1909). Lancet 355(9202):506

    Article  CAS  PubMed  Google Scholar 

  2. Ribatti D (2016) The failed attribution of the Nobel Prize for Medicine or Physiology to Viktor Hamburger for the discovery of Nerve Growth Factor. Brain Res Bull 124:306–309. https://doi.org/10.1016/j.brainresbull.2016.02.019

    Article  CAS  PubMed  Google Scholar 

  3. Salazar-Roa M, Malumbres M (2017) Fueling the cell division cycle. Trends Cell Biol 27(1):69–81. https://doi.org/10.1016/j.tcb.2016.08.009

    Article  CAS  PubMed  Google Scholar 

  4. Dalton S (2015) Linking the cell cycle to cell fate decisions. Trends Cell Biol 25(10):592–600. https://doi.org/10.1016/j.tcb.2015.07.007

    Article  PubMed  PubMed Central  Google Scholar 

  5. Ajioka I (2014) Coordination of proliferation and neuronal differentiation by the retinoblastoma protein family. Develop Growth Differ 56(5):324–334. https://doi.org/10.1111/dgd.12127

    Article  CAS  Google Scholar 

  6. Hardwick LJ, Ali FR, Azzarelli R, Philpott A (2015) Cell cycle regulation of proliferation versus differentiation in the central nervous system. Cell Tissue Res 359(1):187–200. https://doi.org/10.1007/s00441-014-1895-8

    Article  CAS  PubMed  Google Scholar 

  7. Cheffer A, Tarnok A, Ulrich H (2013) Cell cycle regulation during neurogenesis in the embryonic and adult brain. Stem Cell Rev 9(6):794–805. https://doi.org/10.1007/s12015-013-9460-5

    Article  CAS  Google Scholar 

  8. Vaudry D, Stork PJ, Lazarovici P, Eiden LE (2002) Signaling pathways for PC12 cell differentiation: making the right connections. Science 296(5573):1648–1649. https://doi.org/10.1126/science.1071552

    Article  CAS  PubMed  Google Scholar 

  9. Counts SE, Mufson EJ (2017) Regulator of cell cycle (RGCC) expression during the progression of Alzheimer’s disease. Cell Transplant 26(4):693–702. https://doi.org/10.3727/096368916X694184

    Article  PubMed  PubMed Central  Google Scholar 

  10. Zhao CF, Liu Y, Ni YL, Yang JW, Hui HD, Sun ZB, Liu SJ (2013) SCIRR39 promotes neurite extension via RhoA in NGF-induced PC12 cells. Dev Neurosci 35(5):373–383. https://doi.org/10.1159/000350715

    Article  CAS  PubMed  Google Scholar 

  11. Mishra M, Akatsu H, Heese K (2011) The novel protein MANI modulates neurogenesis and neurite-cone growth. J Cell Mol Med 15(8):1713–1725. https://doi.org/10.1111/j.1582-4934.2010.01134.x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Mishra M, Manavalan A, Sze SK, Heese K (2012) Neuronal p60TRP expression modulates cardiac capacity. J Proteome 75(5):1600–1617. https://doi.org/10.1016/j.jprot.2011.11.034

    Article  CAS  Google Scholar 

  13. Greene LA, Tischler AS (1976) Establishment of a noradrenergic clonal line of rat adrenal pheochromocytoma cells which respond to nerve growth factor. Proc Natl Acad Sci U S A 73(7):2424–2428

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Jensch A, Thomaseth C, Radde NE (2017) Sampling-based Bayesian approaches reveal the importance of quasi-bistable behavior in cellular decision processes on the example of the MAPK signaling pathway in PC-12 cell lines. BMC Syst Biol 11(1):11. https://doi.org/10.1186/s12918-017-0392-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Offermann B, Knauer S, Singh A, Fernandez-Cachon ML, Klose M, Kowar S, Busch H, Boerries M (2016) Boolean modeling reveals the necessity of transcriptional regulation for bistability in PC12 cell differentiation. Front Genet 7:44. https://doi.org/10.3389/fgene.2016.00044

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Santos SD, Verveer PJ, Bastiaens PI (2007) Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate. Nat Cell Biol 9(3):324–330. https://doi.org/10.1038/ncb1543

    Article  CAS  PubMed  Google Scholar 

  17. Kutzner A, Pramanik S, Kim PS, Heese K (2015) All-or-(N) one - an epistemological characterization of the human tumorigenic neuronal paralogous FAM72 gene loci. Genomics 106(5):278–285. https://doi.org/10.1016/j.ygeno.2015.07.003

    Article  CAS  PubMed  Google Scholar 

  18. Brudvig JJ, Cain JT, Sears RM, Schmidt-Grimminger GG, Wittchen ES, Adler KB, Ghashghaei HT, Weimer JM (2018) MARCKS regulates neuritogenesis and interacts with a CDC42 signaling network. Sci Rep 8(1):13278. https://doi.org/10.1038/s41598-018-31578-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Charrier C, Joshi K, Coutinho-Budd J, Kim JE, Lambert N, de Marchena J, Jin WL, Vanderhaeghen P et al (2012) Inhibition of SRGAP2 function by its human-specific paralogs induces neoteny during spine maturation. Cell 149(4):923–935. https://doi.org/10.1016/j.cell.2012.03.034

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Fossati M, Pizzarelli R, Schmidt ER, Kupferman JV, Stroebel D, Polleux F, Charrier C (2016) SRGAP2 and its human-specific paralog co-regulate the development of excitatory and inhibitory synapses. Neuron 91(2):356–369. https://doi.org/10.1016/j.neuron.2016.06.013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Jiao Q, Wang L, Zhang Z, Wang Y, Yan H, Ma W, Jin W, Lu H et al (2016) Dynamic expression of srGAP2 in cell nuclei and cytoplasm during the differentiation of rat neural stem cells in vitro. Mol Med Rep 14(5):4599–4605. https://doi.org/10.3892/mmr.2016.5795

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Subramanian J, Nedivi E (2016) Filling the (SR)GAP in excitatory/inhibitory balance. Neuron 91(2):205–207. https://doi.org/10.1016/j.neuron.2016.07.008

    Article  CAS  PubMed  Google Scholar 

  23. Lucas B, Hardin J (2017) Mind the (sr)GAP - roles of Slit-Robo GAPs in neurons, brains and beyond. J Cell Sci 130(23):3965–3974. https://doi.org/10.1242/jcs.207456

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Benayoun BA, Pollina EA, Ucar D, Mahmoudi S, Karra K, Wong ED, Devarajan K, Daugherty AC et al (2014) H3K4me3 breadth is linked to cell identity and transcriptional consistency. Cell 158(3):673–688. https://doi.org/10.1016/j.cell.2014.06.027

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Nehar S, Mishra M, Heese K (2009) Identification and characterisation of the novel amyloid-beta peptide-induced protein p17. FEBS Lett 583(19):3247–3253. https://doi.org/10.1016/j.febslet.2009.09.018

    Article  CAS  PubMed  Google Scholar 

  26. Ho NTT, Kutzner A, Heese K (2017) Brain plasticity, cognitive functions and neural stem cells: a pivotal role for the brain-specific neural master gene |-SRGAP2-FAM72-|. Biol Chem 399(1):55–61. https://doi.org/10.1515/hsz-2017-0190

    Article  CAS  PubMed  Google Scholar 

  27. Guo C, Zhang X, Fink SP, Platzer P, Wilson K, Willson JK, Wang Z, Markowitz SD (2008) Ugene, a newly identified protein that is commonly overexpressed in cancer and binds uracil DNA glycosylase. Cancer Res 68(15):6118–6126. https://doi.org/10.1158/0008-5472.CAN-08-1259

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Heese K (2013) The protein p17 signaling pathways in cancer. Tumour Biol 34(6):4081–4087. https://doi.org/10.1007/s13277-013-0999-1

    Article  CAS  PubMed  Google Scholar 

  29. Pramanik S, Kutzner A, Heese K (2015) Lead discovery and in silico 3D structure modeling of tumorigenic FAM72A (p17). Tumour Biol 36(1):239–249. https://doi.org/10.1007/s13277-014-2620-7

    Article  CAS  PubMed  Google Scholar 

  30. Marko TA, Shamsan GA, Edwards EN, Hazelton PE, Rathe SK, Cornax I, Overn PR, Varshney J et al (2016) Slit-Robo GTPase-Activating Protein 2 as a metastasis suppressor in osteosarcoma. Sci Rep 6:39059. https://doi.org/10.1038/srep39059

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Ho NT, Kim PS, Kutzner A, Heese K (2017) Cognitive functions: human vs. animal - 4:1 advantage |-FAM72-SRGAP2-|. J Mol Neurosci 61(4):603–606. https://doi.org/10.1007/s12031-017-0901-5

    Article  CAS  PubMed  Google Scholar 

  32. Chen Y, Pai AA, Herudek J, Lubas M, Meola N, Jarvelin AI, Andersson R, Pelechano V et al (2016) Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters. Nat Genet 48(9):984–994. https://doi.org/10.1038/ng.3616

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Lacadie SA, Ibrahim MM, Gokhale SA, Ohler U (2016) Divergent transcription and epigenetic directionality of human promoters. FEBS J 283(23):4214–4222. https://doi.org/10.1111/febs.13747

    Article  CAS  PubMed  Google Scholar 

  34. Ibrahim MM, Karabacak A, Glahs A, Kolundzic E, Hirsekorn A, Carda A, Tursun B, Zinzen RP et al (2018) Determinants of promoter and enhancer transcription directionality in metazoans. Nat Commun 9(1):4472. https://doi.org/10.1038/s41467-018-06962-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Sulistio YA, Lee HK, Jung SJ, Heese K (2018) Interleukin-6-mediated induced pluripotent stem cell (iPSC)-derived neural differentiation. Mol Neurobiol 55(4):3513–3522. https://doi.org/10.1007/s12035-017-0594-3

    Article  CAS  PubMed  Google Scholar 

  36. Bennett JO, Briggs WL (2008) Using and understanding mathematics: a quantitative reasoning approach. Pearson Addison Wesley, Reading

    Google Scholar 

  37. Rahane CS, Kutzner A, Heese K (2019) A cancer tissue-specific FAM72 expression profile defines a novel glioblastoma multiform (GBM) gene-mutation signature. J Neuro-Oncol. https://doi.org/10.1007/s11060-018-03029-3

  38. Rahane CS, Kutzner A, Heese K (2019) Establishing a human adrenocortical carcinoma (ACC)-specific gene mutation signature. Cancer Genet 230:1–12. https://doi.org/10.1016/j.cancergen.2018.10.005

    Article  CAS  PubMed  Google Scholar 

  39. Dennis MY, Nuttle X, Sudmant PH, Antonacci F, Graves TA, Nefedov M, Rosenfeld JA, Sajjadian S et al (2012) Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. Cell 149(4):912–922. https://doi.org/10.1016/j.cell.2012.03.033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Sporny M, Guez-Haddad J, Kreusch A, Shakartzi S, Neznansky A, Cross A, Isupov MN, Qualmann B et al (2017) Structural history of human SRGAP2 proteins. Mol Biol Evol 34(6):1463–1478. https://doi.org/10.1093/molbev/msx094

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Lin T, Islam O, Heese K (2006) ABC transporters, neural stem cells and neurogenesis--a different perspective. Cell Res 16(11):857–871. https://doi.org/10.1038/sj.cr.7310107

    Article  CAS  PubMed  Google Scholar 

  42. Islam O, Gong X, Rose-John S, Heese K (2009) Interleukin-6 and neural stem cells: more than gliogenesis. Mol Biol Cell 20(1):188–199. https://doi.org/10.1091/mbc.E08-05-0463

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Islam O, Loo TX, Heese K (2009) Brain-derived neurotrophic factor (BDNF) has proliferative effects on neural stem cells through the truncated TRK-B receptor, MAP kinase, AKT, and STAT-3 signaling pathways. Curr Neurovasc Res 6(1):42–53

    Article  CAS  PubMed  Google Scholar 

  44. Pramanik S, Sulistio YA, Heese K (2017) Neurotrophin signaling and stem cells-implications for neurodegenerative diseases and stem cell therapy. Mol Neurobiol 54(9):7401–7459. https://doi.org/10.1007/s12035-016-0214-7

    Article  CAS  PubMed  Google Scholar 

  45. Mesner PW, Winters TR, Green SH (1992) Nerve growth factor withdrawal-induced cell death in neuronal PC12 cells resembles that in sympathetic neurons. J Cell Biol 119(6):1669–1680

    Article  CAS  PubMed  Google Scholar 

  46. Katoh S, Mitsui Y, Kitani K, Suzuki T (1996) Nerve growth factor rescues PC12 cells from apoptosis by increasing amount of bcl-2. Biochem Biophys Res Commun 229(2):653–657. https://doi.org/10.1006/bbrc.1996.1859

    Article  CAS  PubMed  Google Scholar 

  47. Vaghefi H, Hughes AL, Neet KE (2004) Nerve growth factor withdrawal-mediated apoptosis in naive and differentiated PC12 cells through p53/caspase-3-dependent and -independent pathways. J Biol Chem 279(15):15604–15614. https://doi.org/10.1074/jbc.M311500200

    Article  CAS  PubMed  Google Scholar 

  48. Moriguchi T, Gotoh Y, Nishida E (1995) Activation of two isoforms of mitogen-activated protein kinase kinase in response to epidermal growth factor and nerve growth factor. Eur J Biochem 234(1):32–38

    Article  CAS  PubMed  Google Scholar 

  49. Zhang BH, Guan KL (2000) Activation of B-Raf kinase requires phosphorylation of the conserved residues Thr598 and Ser601. EMBO J 19(20):5429–5439. https://doi.org/10.1093/emboj/19.20.5429

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Saba-El-Leil MK, Fremin C, Meloche S (2016) Redundancy in the world of MAP kinases: all for one. Front Cell Dev Biol 4:67. https://doi.org/10.3389/fcell.2016.00067

    Article  PubMed  PubMed Central  Google Scholar 

  51. Vaghefi H, Neet KE (2004) Deacetylation of p53 after nerve growth factor treatment in PC12 cells as a post-translational modification mechanism of neurotrophin-induced tumor suppressor activation. Oncogene 23(49):8078–8087. https://doi.org/10.1038/sj.onc.1207953

    Article  CAS  PubMed  Google Scholar 

  52. Nayak G, Cooper GM (2012) p53 is a major component of the transcriptional and apoptotic program regulated by PI 3-kinase/Akt/GSK3 signaling. Cell Death Dis 3:e400. https://doi.org/10.1038/cddis.2012.138

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank Hanyang University for providing a scholarship to Ms. N. T. T. H.

Funding

This study was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF), which was funded by the Ministry of Education (2015R1D1A1A01057243).

Author information

Authors and Affiliations

  1. Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea

    Nguyen Thi Thanh Ho & Klaus Heese

  2. Department of Information Systems, College of Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 133-791, Republic of Korea

    Arne Kutzner

Authors
  1. Nguyen Thi Thanh Ho
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Arne Kutzner
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Klaus Heese
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Klaus Heese.

Ethics declarations

Conflict of Interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ho, N.T.T., Kutzner, A. & Heese, K. A Novel Divergent Gene Transcription Paradigm—the Decisive, Brain-Specific, Neural |-Srgap2–Fam72a-| Master Gene Paradigm. Mol Neurobiol 56, 5891–5899 (2019). https://doi.org/10.1007/s12035-019-1486-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12035-019-1486-5

Keywords

Search

Navigation