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Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL INIST-CNRS Gene Section Review PPP6R3 (protein phosphatase 6 regulatory subunit 3) Luigi Cristiano Aesthetic and medical biotechnologies research unit, Prestige, Terranuova Bracciolini, Italy. [email protected]; [email protected] Published in Atlas Database: March 2019 Online updated version : http://AtlasGeneticsOncology.org/Genes/PPP6R3ID54550ch11q13.html Printable original version : http://documents.irevues.inist.fr/bitstream/handle/2042/70657/03-2019-PPP6R3ID54550ch11q13.pdf DOI: 10.4267/2042/70657 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2020 Atlas of Genetics and Cytogenetics in Oncology and Haematology Abstract bladder cancer, lung cancer, nodular fasciitis Protein phosphatase 6 regulatory subunit 3 Identity (PPP6R3) is a regulatory subunit of the PP6 holoenzyme complex involved in the turnover of Other names: Serine/threonine-protein phosphatase serine and threonine phosphorylation events during 6 regulatory subunit 3, chromosome 11 open reading mitosis. PPP6R3 shows abundant mRNA splicing frame 23 C11orf23, SAPS domain family member 3, variants and numerous functional protein isoforms. SAPS3, SAPLa, SAPL, SAP190, sporulation- PPP6R3 gene is often involved in abnormal induced transcript 4-associated protein, chromosomal translocations and it is found as a DKFZp781E2374, DKFZp781O2362, fusion gene partner in different kind of cancers. DKFZp781E17107, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712 Keywords PPP6R3, protein phosphatase 6 regulatory subunit 3, HGNC (Hugo): PPP6R3 C11orf23, SAPS, phosphorylation, breast cancer, Location: 11q13.2 Figure. 1. PPP6R3 gene and splicing variants/isoforms. The figure shows the locus on chromosome 11 of the PPP6R3 gene (reworked from https://www.ncbi.nlm.nih.gov/gene; http://grch37.ensembl.org; www.genecards.org) Atlas Genet Cytogenet Oncol Haematol. 2020; 24(2) 69 PPP6R3 (protein phosphatase 6 regulatory subunit 3) Cristiano L related protein 5) gene. Around the genomic locus of DNA/RNA PPP6R3 take place different promoter or enhancer transcriptional elements that are located at +0.5 kb, Description +837.9 kb and -359.7 kb. PPP6R3, alias protein phosphatase 6 regulatory subunit 3, is a protein coding gene that starts at Transcription 68,460,718 nt and ends at 68,615,334 nt from qter Exists a high number of spliced version of PPP6R3 (RefSeq NC_000011.10) and with a length of (Stefansson and Brautigan, 2006) and their main 154617 bp. It is proximal to LRP5 (LDL receptor characteristics are reported in Table.1 Leng Leng MW Varia Exon Isofor Name RefSeq (1) Transcript ID Type ht Alias RefSeq (2) ht (kDa pI nt s m (bp) (aa) ) PPP6R3-201 ENST0000026563 protein Isofor 88.9 4.4 (PPP6R3- Var.5 NM_018312 23 4992 - NP_060782 793 6.9 coding m 5 5 9 003) PPP6R3- ENST0000026563 202 (PPP6R Var.44 NR_147968.1 22 ncRNA 5124 - - - - - - 7.8 3-021) NM_0011641 Isofor NP_0011576 97.6 4.5 Var.6 5127 - 873 61 m 6 33 7 0 NM_0013523 Isofor NP_0013392 86.8 4.5 Var.21 4873 - 782 61 protein m 18 90 8 2 NM_0013523 coding Isofor NP_0013392 97.6 4.5 Var.28 5211 - 873 68 m 6 97 7 0 PPP6R3-203 Var. NM_0013523 ENST0000039380 Isofor NP_0013393 97.6 4.5 (PPP6R3- 24 5233 - 873 35 75 0.6 m 6 04 7 0 001) Var.41 NR_147965 4942 - - - - - - Var.43 NR_147967 5401 - - - - - - Var.45 NR_147969 ncRNA 5235 - - - - - - Var.46 NR_147970 4978 - - - - - - Var.47 NR_147971 5362 - - - - - - A, NM_0011641 Isofor NP_0011576 98.4 4.5 Var.4 5145 C11orf23 879 60 m 4 32 9 4 a, SAPLa NM_0013523 Isofor NP_0013392 73.1 4.4 Var.7 5052 - 664 47 m 7 76 5 4 NM_0013523 Isofor NP_0013392 95.2 4.5 Var.10 5037 - 850 50 m 8 79 6 5 NM_0013523 Isofor NP_0013392 96.4 4.5 Var.12 5073 - 862 52 m 10 81 5 5 NM_0013523 Isofor NP_0013392 79.5 4.4 Var.13 4704 - 717 53 m 11 82 3 9 NM_0013523 Isofor NP_0013392 99.4 4.5 Var.14 5281 - 889 54 m 12 83 7 3 PPP6R3- NM_0013523 ENST0000039380 protein Isofor NP_0013392 99.4 4.5 204 (PPP6R Var.16 25 5154 - 889 56 1.7 coding m 12 85 7 3 3-005) NM_0013523 Isofor NP_0013392 96.2 4.5 Var.20 5194 - 860 60 m 17 89 5 4 A, NM_0013523 Isofor NP_0013392 98.4 4.5 Var.24 5251 C11orf23 879 64 m 4 93 9 4 a, SAPLa NM_0013523 Isofor NP_0013392 72.1 4.4 Var.29 5149 - 654 69 m 20 98 6 5 NM_0013523 Isofor NP_0013392 87.6 4.5 Var.30 4891 - 788 70 m 21 99 9 6 NM_0013523 Isofor NP_0013393 96.4 4.5 Var.31 5200 - 862 71 m 10 00 5 5 NM_0013523 Isofor NP_0013393 97.7 4.5 Var.32 5233 - 873 72 m 24 01 3 4 Atlas Genet Cytogenet Oncol Haematol. 2020; 24(2) 70 PPP6R3 (protein phosphatase 6 regulatory subunit 3) Cristiano L NM_0013523 Isofor NP_0013393 96.2 4.5 Var.33 5067 - 860 73 m 17 02 5 4 NM_0013523 Isofor NP_0013393 84.4 4.5 Var.34 4804 - 759 74 m 22 03 7 8 NM_0013523 Isofor NP_0013393 95.2 4.5 Var.36 5164 - 850 76 m 8 05 6 5 NM_0013523 Isofor NP_0013393 97.7 4.5 Var.37 5106 - 873 77 m 24 06 3 4 NM_0013523 Isofor NP_0013393 84.4 4.5 Var.38 4931 - 759 78 m 22 07 7 8 A, NM_0013523 Isofor NP_0013393 98.4 4.5 Var.39 5390 C11orf23 879 79 m 4 08 9 4 a, SAPLa NM_0013523 Isofor NP_0013393 95.2 4.5 Var.40 5142 - 850 80 m 8 09 6 5 Var.42 NR_147966 ncRNA 5392 - - - - - - NM_0011641 Isofor NP_0011576 94.4 4.5 Var.2 5040 - 844 63 m 2 35 4 1 PPP6R3-205 NM_0013523 ENST0000052484 protein Isofor NP_0013392 83.6 4.5 (PPP6R3- Var.15 23 4786 - 753 55 5.5 coding m 13 84 5 4 026) NM_0013523 Isofor NP_0013392 94.4 4.5 Var.23 5146 - 844 63 m 2 92 4 1 NM_0011641 Isofor NP_0011576 96.9 4.5 Var.1 5109 - 867 62 m 1 34 6 1 NM_0013523 Isofor NP_0013392 96.9 4.5 Var.8 5284 - 867 48 m 1 77 6 1 NM_0013523 Isofor NP_0013392 84.8 4.5 Var.11 4822 - 765 51 m 9 80 4 4 PPP6R3- NM_0013523 ENST0000052490 protein Isofor NP_0013392 90.1 4.4 206 (PPP6R Var.18 24 4902 - 805 58 4.5 coding m 15 87 4 9 3-007) NM_0013523 Isofor NP_0013392 87.1 4.5 Var.19 4885 - 786 59 m 16 88 5 2 NM_0013523 Isofor NP_0013392 95.6 4.5 Var.22 5129 - 856 62 m 19 91 3 2 NM_0013523 Isofor NP_0013392 95.6 4.5 Var.25 5055 - 856 65 m 19 94 3 2 ENST0000052505 retained PPP6R3-207 - - 4 513 - - - - - - 0.5 intron ENST0000052515 retained PPP6R3-208 - - 2 582 - - - - - - 2.1 intron ENST0000052542 nonsens PPP6R3-209 - - 8 830 - - - - - - 1.5 e md ENST0000052630 retained PPP6R3-210 - - 10 4134 - - - - - - 7.5 intron ENST0000052657 retained PPP6R3-211 - - 4 489 - - - - - - 4.1 intron ENST0000052659 nonsens PPP6R3-212 - - 5 570 - - - - - - 3.1 e md ENST0000052706 retained PPP6R3-213 - - 4 573 - - - - - - 9.5 intron PPP6R3- NM_0013523 ENST0000052740 protein Isofor NP_0013392 94.5 4.5 214 (PPP6R Var.26 22 5019 - 844 66 3.6 coding m 23 95 5 6 3-020) PPP6R3- ENST0000052863 215 (PPP6R - - 5 (?) 538 - - - - - - 5.5 3-012) ENST0000052917 retained PPP6R3-216 - - 4 500 - - - - - - 2.1 intron Atlas Genet Cytogenet Oncol Haematol. 2020; 24(2) 71 PPP6R3 (protein phosphatase 6 regulatory subunit 3) Cristiano L PPP6R3- ENST0000052934 217 (PPP6R - - 4 (?) 603 - - - - - - 4.5 3-011) PPP6R3- B, NM_0011641 ENST0000052971 protein Isofor NP_0011576 88.9 4.4 218 (PPP6R Var.3 23 3426 C11orf23 791 64 0.5 coding m 3 36 1 8 3-004) b, SAPLb PPP6R3- ENST0000052990 219 (PPP6R - - 7 (?) 826 - - - - - - 7.5 3-009) processe ENST0000053042 d PPP6R3-220 - - 5 560 - - - - - - 7.5 transcri pt PPP6R3-221 ENST0000053073 (PPP6R3- - - 2 (?) 576 - - - - - - 4.1 025) PPP6R3- ENST0000053124 222 (PPP6R - - 5 (?) 687 - - - - - - 4.1 3-013) ENST0000053143 retained PPP6R3-223 - - 2 590 - - - - - - 2.1 intron PPP6R3-224 ENST0000053312 (PPP6R3- - - 4 (?) 551 - - - - - - 7.5 027) PPP6R3- NM_0013523 ENST0000053419 protein Isofor NP_0013392 68.1 4.4 225 (PPP6R Var.17 16 5150 - 619 57 0.5 coding m 14 86 2 2 3-018) PPP6R3- ENST0000053453 226 (PPP6R - - 19 (?) 2968 - - - - - - 4.5 3-008) Table.1 Alterative splicing variants and isoforms of PPP6R3. (reworked from http://grch37.ensembl.org; ttps://www.ncbi.nlm.nih.gov; https://web.expasy.org/protparam/; https://www.uniprot.org). ncRNA = non-coding RNA; nonsense md = nonsense mediated decay; (?) = undetermined; MW = molecular weight; pI = theoretical pI. Pseudogene contrary, PPP6R3 protein is found at high levels in lung, bladder, spleen and pancreas (Ziembik et al., Currently, pseudogenes for PPP6R3 have not been 2017). detected in the human genome. Localisation Protein PPP6R3 localize in various subcellular compartments: it is present mainly in the cytoplasm Description but it is also found in Golgi apparatus, nucleoplasm, PPP6R3 encodes the protein phosphatase 6 nucleus and associated with the plasma membrane regulatory subunit 3, which belongs to protein (Stefansson et al., 2008; phosphatase 6 (PP6) complex (York et al., 2014; https://www.ncbi.nlm.nih.gov). Guergnon et al., 2009) in which there are also PPP6R1, PPP6R2 and PPP6C proteins. Function PP6 complex is a member of the PP2A subfamily of PPP6R3 is a subunit of protein phosphatase 6 (PP6), protein phosphatases and shows a Sit4-associated a trimeric holoenzyme of the family of protein domain (SAPS domain) (Stefansson and phosphoprotein phosphatases (PPPs), involved in the Brautigan, 2006).
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  • Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses

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    medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened.
  • (P -Value<0.05, Fold Change≥1.4), 4 Vs. 0 Gy Irradiation

    (P -Value<0.05, Fold Change≥1.4), 4 Vs. 0 Gy Irradiation

    Table S1: Significant differentially expressed genes (P -Value<0.05, Fold Change≥1.4), 4 vs. 0 Gy irradiation Genbank Fold Change P -Value Gene Symbol Description Accession Q9F8M7_CARHY (Q9F8M7) DTDP-glucose 4,6-dehydratase (Fragment), partial (9%) 6.70 0.017399678 THC2699065 [THC2719287] 5.53 0.003379195 BC013657 BC013657 Homo sapiens cDNA clone IMAGE:4152983, partial cds. [BC013657] 5.10 0.024641735 THC2750781 Ciliary dynein heavy chain 5 (Axonemal beta dynein heavy chain 5) (HL1). 4.07 0.04353262 DNAH5 [Source:Uniprot/SWISSPROT;Acc:Q8TE73] [ENST00000382416] 3.81 0.002855909 NM_145263 SPATA18 Homo sapiens spermatogenesis associated 18 homolog (rat) (SPATA18), mRNA [NM_145263] AA418814 zw01a02.s1 Soares_NhHMPu_S1 Homo sapiens cDNA clone IMAGE:767978 3', 3.69 0.03203913 AA418814 AA418814 mRNA sequence [AA418814] AL356953 leucine-rich repeat-containing G protein-coupled receptor 6 {Homo sapiens} (exp=0; 3.63 0.0277936 THC2705989 wgp=1; cg=0), partial (4%) [THC2752981] AA484677 ne64a07.s1 NCI_CGAP_Alv1 Homo sapiens cDNA clone IMAGE:909012, mRNA 3.63 0.027098073 AA484677 AA484677 sequence [AA484677] oe06h09.s1 NCI_CGAP_Ov2 Homo sapiens cDNA clone IMAGE:1385153, mRNA sequence 3.48 0.04468495 AA837799 AA837799 [AA837799] Homo sapiens hypothetical protein LOC340109, mRNA (cDNA clone IMAGE:5578073), partial 3.27 0.031178378 BC039509 LOC643401 cds. [BC039509] Homo sapiens Fas (TNF receptor superfamily, member 6) (FAS), transcript variant 1, mRNA 3.24 0.022156298 NM_000043 FAS [NM_000043] 3.20 0.021043295 A_32_P125056 BF803942 CM2-CI0135-021100-477-g08 CI0135 Homo sapiens cDNA, mRNA sequence 3.04 0.043389246 BF803942 BF803942 [BF803942] 3.03 0.002430239 NM_015920 RPS27L Homo sapiens ribosomal protein S27-like (RPS27L), mRNA [NM_015920] Homo sapiens tumor necrosis factor receptor superfamily, member 10c, decoy without an 2.98 0.021202829 NM_003841 TNFRSF10C intracellular domain (TNFRSF10C), mRNA [NM_003841] 2.97 0.03243901 AB002384 C6orf32 Homo sapiens mRNA for KIAA0386 gene, partial cds.
  • An Integrated Platform to Systematically Identify Causal Variants 2 and Genes for Polygenic Human Traits

    An Integrated Platform to Systematically Identify Causal Variants 2 and Genes for Polygenic Human Traits

    bioRxiv preprint doi: https://doi.org/10.1101/813618; this version posted January 15, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 An integrated platform to systematically identify causal variants 2 and genes for polygenic human traits. 3 Damien J. Downes1, Ron Schwessinger1,2,*, Stephanie J. Hill1,*, Lea Nussbaum1,*, Caroline 4 Scott1, Matthew E. Gosden1, Priscila P. Hirschfeld1, Jelena M. Telenius1,2, Chris Q. 5 Eijsbouts1,3,4, Simon J. McGowan2, Antony J. Cutler4,5, Jon Kerry1, Jessica L. Davies6, 6 Calliope A. Dendrou4,6, Jamie R.J. Inshaw5, Martin S.C. Larke1, A. Marieke Oudelaar1,2, 7 Yavor Bozhilov1, Andrew J. King1, Richard C. Brown2, Maria C. Suciu1, James O.J. Davies1, 8 Philip Hublitz7, Chris Fisher1, Ryo Kurita8, Yukio Nakamura9, Gerton Lunter2, Stephen 9 Taylor2, Veronica J. Buckle1, John A. Todd5, Douglas R. Higgs1, & Jim R. Hughes1,2,†. 10 11 * These authors contributed equally: Ron Schwessinger, Stephanie J. Hill, Lea Nussbaum. 12 13 † Corresponding author: [email protected] 14 15 Affiliations: 16 1 MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, 17 Radcliffe Department of Medicine, University of Oxford, Oxford, UK 18 2 MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of 19 Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, 20 UK