NANOGThe secret to immortality

Ka Yi, LingGenetics 677

04/28/09

Overview

Pluripotency

All about NanogGene decodingProtein translationNanog web

Future directions Image from http://www.cartoonstock.com/newscartoons/cartoonists/ato/lowres/aton305l.jpg

Star of immortality

Image obtained from Takahashi et al. (2007), Image obtained fromTakahashi et al. (2007) DOI 10.1016/j.cell.2007.11.019 and Lensch M. W. & Sullivan S. The cycle of developmental potency. Abcam(2008)

What’s the Nanog deal?

1)Pluripotent marker

2)Reprogramming factor

Image from: http://www.savagechickens.com/images/chickengoal.jpg

Deciphering Nanog

Image obtained fromHyslop et al. (2005) Stem Cells 2005;23:1035–1043,

NCBI MMDB, http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=61857 and Lensch M. W. & Sullivan S. The cycle of developmental potency. Abcam(2008)

What is pluripotency?

Pluripotency

Pluripotent

Multi-potent

Potency

Eg. ES cells, iPS cells

Eg. Adult stem cells

Forever Young

Image obtained from http://ific.uv.es/~lopes/pictures/kukuxumusu.jpg

Modified from http://www.csa.com/discoveryguides/stemcell/images/pluri.jpg

The Promise of Stem Cell Research

UnderstandingDevelopmenta

l Biology

Regenerative Medicine

Drug development

How to induce pluripotent cells

Figure from: http://graphics8.nytimes.com/images/2007/06/06/science/0607-nat-webCELL.gif

Nanog Sox2

Oct4Lin28

Necessary but not

SufficientImage obtained fromTakahashi (2007) DOI 10.1016/j.cell.2007.11.019

Goal: To learn the

mechanisms of Nanog function

Nanog

Image modified from http://i1.iofferphoto.com/img/item/489/760/11/discover_how_stuff_works.jpg

Learning lessons

Image from http://www.chrismadden.co.uk/genetics/dna-music.gif

Nanog signaling

Image from Applied Biosystems Gene Assist Pathway systems, http://www.ambion.com/tools/pathway/pathway.php?pathway=Nanog%20in%20Mammalian%20ESC%20Pluripotency

Multi-ome approach

Image from: http://innovech.files.wordpress.com/2007/11/genome3.jpg

DNA

Messenger RNA

Protein

Genome

Transcriptome

Proteome

Image modified from Stein (2001) and the Human Proteome Initiative. (2007) http://ca.expasy.org/sprot/hpi/hpi_desc.html Retrieved March 24, 2009. and

courtesy of Eva and Jessica’s Gen677 presentation

Fitting the pieces

Figure from http://www.ittc.ku.edu/bioinfo_seminar/images/wheel.gif

Chromosome hunting

GeneID: 79923

Size: 6661 base pairs

Chromosome: 12

Location: 12p13.31

Image obtained from GeneCards, http://www.genecards.org/cgi-bin/carddisp.pl?gene=NANOG&search=Nanogl

DNA motifs

What: Sex-determining region Y gene product (SRY) Consensus: AAACWAM Number of hits (Score above 99): 6

What: Homeo domain factor (Nkx-2.5/Csx), tinman homolog Consensus: TYAAGTG Number of hits (Score above 99): 7

Image obtained from Kyoto University Bioinformatics Centre, http://motif.genome.jp/

DNA motifs

What: CAP signal, transcription initiation Consensus: NCANNNNN Number of hits (Score above 99): 2

What: GATA binding factor-1 Consensus: SNNGATNNNNNumber of hits (Score above 99): -

(Score above 90): 12

Image obtained from Kyoto University Bioinformatics Centre, http://motif.genome.jp/

Nanog: DNA level

Image from Applied Biosystems Gene Assist Pathway systems, http://www.ambion.com/tools/pathway/pathway.php?pathway=Nanog%20in%20Mammalian%20ESC%20Pluripotency

NANOG protein crystals

Image obtained from STRING, http://string.embl.de/newstring_cgi/show_network_section.pl

FASTA number: NP_079141UniProtKB : Q9H9SOLength of protein: 305 aaSubcellular location: Nucleus

Nanog (Mus muculus)

Image obtained from NCBI MMDB, http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=61857

Homeobox domain

Pfam, SMART and prosite – similar predictions

Image from Prosite, http://www.expasy.ch/cgi-bin/prosite/ScanView.cgi?scanfile=89996073962.scan.gz and NCBI conserved domains, http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cl00084

Nanog signaling

Image from Applied Biosystems Gene Assist Pathway systems, http://www.ambion.com/tools/pathway/pathway.php?pathway=Nanog%20in%20Mammalian%20ESC%20Pluripotency

How does Nanog work?

Phosphorylation

Image obtained from NetPhos 2.0 Server, http://www.cbs.dtu.dk/cgi-bin/nph-webface?jobid=netphos,49DE647502FAC760&opt=none

Dimerization

Drawing analogies

Animal stars

Image from: http://www.socialfiction.org/img/Enlarged_c_elegans.PNG, http://brembs.net/learning/drosophila/fly_down.jpg, http://64.207.144.142/movabletype/PETA2Daily/archives/kick1.PNG and http://images.forbes.com/images/2001/07/26/mice_400x300.jpg

Nanog in other organisms

Image obtained from NCBI Homologene, http://www.ncbi.nlm.nih.gov/sites/entrez

Phylogeny tree – Closeness of Nanog

Image from Deereeper A. et al. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W465-9. Epub 2008 Apr 19. (PubMed)

TreeFAM relations

Image from Treefamilies database, http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF337402

Comparing NANOG

orthologues

Homo sapiens Mus muculus

Image from STRING, http://string.embl.de/newstring_cgi/show_network_section.pl

Protein friends of Nanog

Table obtained from Lewitzky. M and Yamanaka S. (2007) Reprogramming somatic cells towards pluripotency by defined factors. Current Opinion in Biotechnology. 18: 467-473

Nanog Paralogues

Image obtained from GeneCard, http://www.genecards.org/cgi-bin/cardsearch.pl#results

Mutant phenotypes

Jaenisch paper

Table obtained from Boyer, L. A., Mathur, D. and Jaenisch R. (2006) Molecular control of pluripotency. Current Opinion in Genetics & Development. 16, 455-462

Nanog: protein level

Image from Applied Biosystems Gene Assist Pathway systems, http://www.ambion.com/tools/pathway/pathway.php?pathway=Nanog%20in%20Mammalian%20ESC%20Pluripotency

Pseudo Nanog related to cancer?

Inside view of crazy NANOG

Image taken from Siu et al.(2008)  DOI: 10.2353/ajpath.2008.080288

Inside view of looney NANOG

Image taken from Introduction to Reproductive Biology. http://www.sgul.ac.uk/depts/immunology/~dash/troph/trophoblast.jpg

NANOG gone looney

Image from SonoWorld (2009) Complete Molar Gestation: Role of Ultrasound, http://www.sonoworld.com/Article/ShowArticleImage.aspx?id=9098&Type=Paragraph and Mchumor, 

http://www.pioneer.net/~mchumor/00images/2192_pregnancy_cartoon.gif

Moving on

Image from http://grandtextauto.org/archives/newyorker.jpg

Image modified from Stein (2001) and the Human Proteome Initiative. (2007) http://ca.expasy.org/sprot/hpi/hpi_desc.html Retrieved March 24, 2009. and

courtesy of Eva and Jessica’s Gen677 presentation

Fitting the pieces

Figure from http://www.ittc.ku.edu/bioinfo_seminar/images/wheel.gif

GTD detection

Image from http://www.mchumor.com/00images/6575_biology_cartoon.gif

Confirmation assays

Function analysisNanog dimerPhosphorylation

Global outlookChemical geneticsTranscriptome sequencing

ReprogrammingImage modified from http://dcad.com.pl/image/dna1.jpg, http://www.dnastar.com/media/linegraphLrg.jpg and http://www.cs.usyd.edu.au/%7Eirena/arrayimage.jpg

Cures for tomorrow

Image from: http://gen677.weebly.com/uploads/8/6/5/7/865764/28942.jpg

Acknowledgements

Thank you:Ahna

for her kind help and guidance;

Genetics 677 for the kind peer feedbacks and

Jamie for the inspirational research!

Thank you!

Any questions?Image from http://www.newslettercartoons.com/freedaily/5651_todayT.gif and http://www.media-freaks.com/work/leilei/peterpan/peterpan-02.jpg