Table 1.
List of GRPAM genes and their ontology
| Gene | Ontology Wnt Signaling | Location of ChOP read w.r.t gene | Gene regulation on mrhl RNA silencing |
|---|---|---|---|
| Odz4 | Wnt signaling, Embryonic Development, differentiation, | Genic | Downregulated |
| Lamb3 | Wnt signaling, differentiation | Genic | Downregulated |
| Tsc22d1 | Wnt signaling, Tgf β signaling, | 51.5 kb upstream | Downregulated |
| Prickle1** | Wnt signaling, differentiation, development | 63.4 kb upstream | Upregulated |
| Znrf3 | Negative regulation of Wnt signaling, stem cell proliferation, tumor supressor | 132.3 kb upstream | Upregulated |
| Ostm1* | Activator of Wnt signaling, differentiation. | 22.2 kb upstream | Downregulated |
| Spermatogenesis | |||
| Sox8 | Sertoli cell function, germ cell differentiation (Also in Wnt signaling) | Promoter | Upregulated |
| Rarg | Retinoic acid signaling, spermatogenesis (Also in Wnt signaling) | 11.1 kb upstream | Upregulated |
| Spag16 | Spermatogenesis | Genic | Upregulated |
| Mael | Spermatogenesis, piRNA pathway, differentiation | 33 kb downstream | Upregulated |
| Spam1 | Spermatogenesis, sperm maturation | 27 kb upstream | Downregulated |
| Mageb16 | testis specific (adult), regulates differentiation in mouse ESCs | 122.5 kb upstream | Downregulated |
| Npepps*,** | Spermatogenesis, antigen processing. | 14.7 kb downstream | Upregulated |
| Cell Adhesion and Transport | |||
| Lrba | Oncogenesis, endosomal transport, | Promoter | Upregulated |
| Gabrg2 | Ion channel transport, post embryonic development | Genic | Upregulated |
| Kcnq5 | Ion transport | Genic | Downregulated |
| Grik2 | Ion transport, apoptosis | 440 kb upstream | Downregulated |
| Kcnh7 | Ion transport | 276 kb upstream | Downregulated |
| Cdh9** | Cell adhesion | 180.2 kb upstream | Upregulated |
| Nrxn1 | Cell adhesion, angiogenesis | Genic | Downregulated |
| Signaling | |||
| Palm | cAMP signaling, cytoskeleton | Genic | Upregulated |
| Rab40b** | Signaling, Protein transport, | Genic | Downregulated |
| Ksr1 | Ras/MAPK signaling, TNF signaling | Genic | Upregulated |
| Ssx2ip | Regulation of Rac signaling, Cell adhesion, | Genic | Downregulated |
| Adamts20 | Integrin signaling, Proteolysis, apoptosis, | 696 kb downstream | Downregulated |
| Sla2 | Calcium signaling, transcription, endocytosis | 0.54 kb downstream | Downregulated |
| Thbs4 | PDGF and PI3K/Akt signaling, Focal adhesion, | 25.5 kb downstream | Downregulated |
| Il1rapl1* | JNK pathway activation, RhoA signaling, differentiation, ion transport | Genic | Downregulated |
| Ppargc1a* | Signaling, differentiation | 183.8 kb downstream | Downregulated |
| Other Functions | |||
| Serpinb8 | Regulation of proteolysis | 0.7 Mb upstream | Downregulated |
| Bach2 | Cell cycle control, transcriptional repressor, differentiation | Genic | Upregulated |
| Zfp455* | Metal ion binding | 24.7 kb downstream | Upregulated |
| Mrpl32** | Ribosomal, translation | 75.75 kb downstream | Downregulated |
| Hhipl2 | Carbohydrate metabolism | 581 kb downstream | Upregulated |
| Myo18b* | Vasculogenesis, cardiac development | Genic | Downregulated |
| Stox2 | Not Annotated | Genic | Upregulated |
| H28 | Interferon induced | Promoter | Downregulated |
Genes that are physically associated with ChOP sequence reads and also showing perturbation of their expression following mrhl RNA down regulation in Gc1-Spg cells (GRPAM). These genes were identified by comparing the genes associated with the ChOP sequence reads (present study) and the transcriptome data from GSE19355. The physical position of occupancy of mrhl RNA with each of the GRPAM (total 37) and its functions are also given. Asterik (*) indicates the GRPAM loci which are not bound by p68. ** indicates the GRPAM loci where mrhl RNA occupancy is not perturbed upon p68 silencing.