Table 1.

List of genetic loci investigated using AP‐RISH for transcription in outer AF and NP cells in skeletally mature bovine IVDs

Functional category	Genetic locus	Gene symbol	Function	References
Structural proteins	Aggrecan	Acan	Major component of cartilage and IVD ECM Provides shock absorbing function of the NP	Watanabe et al. (1994), Day et al. (2004), Le Maitre et al. (2007)
	Biglycan	Bgn	Small leucine‐rich proteoglycan (SLRP) Role in ECM assembly	Schonherr et al. (1995), Fisher et al. (1989), Wilda et al. (2000), Marfia et al. (2014)
	Chondromodulin‐1	Chm1	Glycoprotein with anti‐angiogenesis properties	Hiraki & Shukunami (2000), Hiraki et al. (1991)
	Collagen Ia1	Col1a1	α1(I) chains of Collagen I heterotrimer	Pereira et al. (1993), Khillan et al. (1994), Aszodi et al. (1998)
	Collagen Ia2	Col1a2	α2(I) chain of Collagen I heterotrimer	Aszodi et al. (1998), Le Maitre et al. (2007)
	Collagen IIa1	Col2a1	α1(II) chains of Collagen II homotrimer	Vandenberg et al. (1991), Garofalo et al. (1991), Karsenty & Park (1995)
	Decorin	Dcn	Small leucine‐rich proteoglycan (SLRP) Role in ECM assembly	Iozzo et al. (1999), Wilda et al. (2000)
	Fibromodulin	Fmod	Small leucine‐rich proteoglycan (SLRP) Role in ECM assembly	Wilda et al. (2000), Jan et al. (2016)
	Heparan sulphate proteoglycan 2	Hspg2	Role in IVD development Structural similarity to Laminin α	Noonan et al. (1991), Sasaki et al. (1988), Melrose et al. (2001)
	Keratin 8	Krt8	Intermediate filament proteins	Bader et al. (1988), Moll et al. (2008)
	Keratin 18	Krt18	Intermediate filament proteins
	Keratin 19	Krt19	Intermediate filament proteins
	Laminin1	Lam1	Glycoprotein in basal lamina ECM Interacts with collagens, integrins and proteoglycans	Ekblom et al. (1998)
	Talin1	Tln1	Connects cells to the ECM	Critchley & Gingras (2008)
	Tenomodulin	Tnmd	ChM1 related transmembrane glycoprotein Tendon and tendon progenitor cell marker	Shukunami et al. (2001)
	Tenascin XB	Tnxb	Glycoprotein with anti‐adhesive properties Mutations associated with Ehlers Danlos Syndrome	Chiquet‐Ehrismann & Tucker (2011), Burch et al. (1997), Mao et al. (2002)
Transcription factors	Forkhead box F1	Foxf1	Required for the differentiation of the lateral plate mesoderm in mouse Proposed as NP specific in humans	Mahlapuu et al. (2001), Minogue et al. (2010b), Thorpe et al. (2016)
	Glioma‐associated oncogene 1	Gli1	Downstream mediator of Shh and Ihh signaling	Ahn & Joyner (2005), Buttitta et al. (2003)
	Glioma‐associated oncogene 3	Gli3	Downstream mediator of Shh and Ihh signaling Impact on Pax1, Pax9, and Sox9 expression	Buttitta et al. (2003), Shin et al. (1999)
	Myoblast determination protein 1	MyoD	Early differentiation marker for myogenic commitment Serves as marker of the non‐chondrogenic lineage	Rudnicki et al. (1993)
	Notochord	Noto	Involved in early notochord development Acts downstream of brachyury	Abdelkhalek et al. (2004), McCann et al. (2012)
	Paired box protein 1	Pax1	Synergistically regulate the development of the vertebral column in mice	Peters et al. (1999), Sivakamasundari et al. (2017)
	Paired box protein 9	Pax9
	Scleraxis	Scx	In connective tissues like tendons and ligaments Involved in regulating Tnmd expression Implicated in skeletogenesis during mouse embryonic development	Cserjesi et al. (1995), Shukunami et al. (2006, 2018), Schweitzer et al. (2001)
	Sex determining region Y‐box 5	Sox5	Crucial roles in organogenesis Key regulators of the chondrogenic pathway	Lefebvre et al. (2001), Lee et al. (2017), Smits et al. (2004), Barrionuevo et al. (2006), Ikeda et al. (2004), Chatterjee et al. (2014), Zhang et al. (2006)
	Sex determining region Y‐box 6	Sox6
	Sex determining region Y‐box 9	Sox9
	Brachyury	T	Conserved function in bilateral animals Regulates notochord formation Biomarker for spine tumors (chordomas)	Tang et al. (2012), Nibu et al. (2013), Herrmann et al. (1990), Vujovic et al. (2006)
Signalling factors	Bone morphogenetic protein 4	Bmp4	Involved in bone and cartilage development Belongs to TGF‐beta superfamily	Nifuji et al. (1997), Wijgerde et al. (2005), Zhang et al. (2006)
	Growth differentiation factor 5	Gdf5	Related to BMP and TGF‐beta superfamily	Storm et al. (1994), Francis‐West et al. (1999)
	Indian hedgehog	Ihh	Involved in axial and appendicular skeleton development	Vortkamp et al. (1996), St‐Jacques et al. (1999), Ingham & McMahon (2001), Maeda et al. (2007)
	Sonic hedgehog	Shh	Linked to Bmp4 signaling Crucial in axial and appendicular skeleton development Absence results in aberrant vertebral column and NP development	DiPaola et al. (2005), Dahia et al. (2012), Chiang et al. (1996), Kraus et al. (2001), Ahn & Joyner (2005), Ingham & McMahon (2001), Choi et al. (2012)
Pluripotency and stem cell markers	Endoglin	Eng	Cell surface marker Part of a marker panel defining multipotent mesenchymal stromal cells	Dominici et al. (2006)
	Estrogen‐related receptor beta	Esrrb	Direct Nanog target Fibroblasts reprogramming factor	Feng et al. (2009), Festuccia et al. (2012), Doege et al. (2012)
	Nanog	Nanog	Guardian of pluripotency Levels correlate with the self‐renewal potential of stem cells	Mitsui et al. (2003), Chambers et al. (2007)
	Octamer‐binding transcription factor 4	Oct4	Essential for the pluripotency self‐renewal capacity of stem cells Fibroblasts reprogramming factor	Nichols et al. (1998), Niwa et al. (2009)
	Tyrosine phosphate receptor type C	Ptprc	Cell surface marker Part of a marker panel defining multipotent mesenchymal stromal cells	Dominici et al. (2006)
	Sex determining region Y‐box 2	Sox2	Essential for the pluripotency and self‐renewal capacity of stem cells Fibroblasts reprogramming factor	Niwa et al. (2009), Takahashi & Yamanaka (2006)
	Thymocyte differentiation antigen 1	Thy1	Cell surface marker Part of a marker panel defining multipotent mesenchymal stromal cells	Dominici et al. (2006)
	Zinc finger and SCAN domain containing 10	Zscan10	Associated with progenitor cell subpopulations or impact on their fate choice decisions in mouse	Wang et al. (2007), Kraus et al. (2014)
Metabolic context	Carbonic anhydrase 12	Ca12	Hypoxia induced enzyme Involved in pH balance Suggested as NP specific	Chiche et al. (2009), Power et al. (2011), Minogue et al. (2010b)
	Glyceraldehyde 3‐phosphate dehydrogenase	Gapdh	Catabolic enzyme in glycolysis	Seidler (2013), Lopa et al. (2016)
	Hypoxia‐inducible factor 1‐alpha	Hif1α	Hypoxia induced transcription factor Loss of function in mouse resulted in morphological abnormalities of the NP	Wuertz et al. (2008), Merceron et al. (2014)
	Lactate dehydrogenase A	LdhA	Catabolic enzyme involved in anaerobic energy production	Sudo et al. (1992a)
	Lactate dehydrogenase B	LdhB	Catabolic enzyme involved in anaerobic energy production	Sudo et al. (1992b)
	Malate dehydrogenase 2	Mdh2	Catabolic enzyme in the citric acid cycle	Bell et al. (2001)
Others	Annexin A4	Anxa4	Regulates ion channel activity Modulates the mobility of membrane proteins	Piljic & Schultz (2006)
	Ki67	Ki67	Proliferation marker found throughout the active cell cycle Immune positive cell clusters in degenerated disc	Johnson et al. (2001), Li et al. (2015)
	lnc RNA LOC101904175	LOC101904175	Long non‐coding RNA Orthologue of murine Klhl14as Downregulated in axial skeleton of Pax1/Pax9 mutant mouse embryos	Sivakamasundari et al. (2017), Kraus et al. (2018a)
	Synaptosomal‐associated protein 25	Snap25	Neuron‐specific in mouse hippocampus Functions in docking and membrane fusion of synaptic vesicles Suggested as NP marker	Zhao et al. (1994), Minogue et al. (2010a)