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A systematic survey of LU domain-containing proteins reveals a novel human gene, LY6A, which encodes the candidate ortholog of mouse Ly-6A/Sca-1 and is aberrantly expressed in pituitary tumors |
Dan Liu1,2, Chunhui Xu3, Yanting Liu4, Wen Ouyang1, Shaojian Lin4, Aining Xu1, Yuanliang Zhang1, Yinyin Xie1, Qiuhua Huang1, Weili Zhao1, Zhu Chen1, Lan Wang3, Saijuan Chen1(), Jinyan Huang1,5(), Zhe Bao Wu4,6(), Xiaojian Sun1() |
1. Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China 2. Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China 3. CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China 4. Department of Neurosurgery, Center of Pituitary Tumor, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China 5. Biomedical Big Data Center, First Affiliated Hospital, Zhejiang University School of Medicine, and Cancer Center, Zhejiang University, Hangzhou 310000, China 6. Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China |
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Abstract The Ly-6 and uPAR (LU) domain-containing proteins represent a large family of cell-surface markers. In particular, mouse Ly-6A/Sca-1 is a widely used marker for various stem cells; however, its human ortholog is missing. In this study, based on a systematic survey and comparative genomic study of mouse and human LU domain-containing proteins, we identified a previously unannotated human gene encoding the candidate ortholog of mouse Ly-6A/Sca-1. This gene, hereby named LY6A, reversely overlaps with a lncRNA gene in the majority of exonic sequences. We found that LY6A is aberrantly expressed in pituitary tumors, but not in normal pituitary tissues, and may contribute to tumorigenesis. Similar to mouse Ly-6A/Sca-1, human LY6A is also upregulated by interferon, suggesting a conserved transcriptional regulatory mechanism between humans and mice. We cloned the full-length LY6A cDNA, whose encoded protein sequence, domain architecture, and exon‒intron structures are all well conserved with mouse Ly-6A/Sca-1. Ectopic expression of the LY6A protein in cells demonstrates that it acts the same as mouse Ly-6A/Sca-1 in their processing and glycosylphosphatidylinositol anchoring to the cell membrane. Collectively, these studies unveil a novel human gene encoding a candidate biomarker and provide an interesting model gene for studying gene regulatory and evolutionary mechanisms.
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Keywords
LU domain-containing protein family
novel human gene
LY6A
pituitary tumor
biomarker
nonsynonymous SNP
GPI-anchored protein
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Corresponding Author(s):
Saijuan Chen,Jinyan Huang,Zhe Bao Wu,Xiaojian Sun
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Just Accepted Date: 03 February 2023
Online First Date: 15 March 2023
Issue Date: 28 July 2023
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|
1 |
AJ Feeney, U Hämmerling. Ala-1: a murine alloantigen of activated lymphocytes. Immunogenetics 1976; 3(1): 369–379
https://doi.org/10.1007/BF01576968
|
2 |
JN Woody, M Feldmann, PC Beverley, IF McKenzie. Expression of alloantigens LY-5 and LY-6 on cytotoxic effector cells. J Immunol 1977; 118(5): 1739–1743
https://doi.org/10.4049/jimmunol.118.5.1739
pmid: 323358
|
3 |
EA Boyse, LJ Old. Some aspects of normal and abnormal cell surface genetics. Annu Rev Genet 1969; 3(1): 269–290
https://doi.org/10.1146/annurev.ge.03.120169.001413
|
4 |
BA Houlden, PM Hogarth, IF McKenzie. Interrelationships of the “Ly-6 complex” antigens. Immunogenetics 1986; 23(4): 226–232
https://doi.org/10.1007/BF00373017
pmid: 2422115
|
5 |
KP LeClair, RG Palfree, PM Flood, U Hammerling, A Bothwell. Isolation of a murine Ly-6 cDNA reveals a new multigene family. EMBO J 1986; 5(12): 3227–3234
https://doi.org/10.1002/j.1460-2075.1986.tb04633.x
pmid: 3028776
|
6 |
CL Loughner, EA Bruford, MS McAndrews, EE Delp, S Swamynathan, SK Swamynathan. Organization, evolution and functions of the human and mouse Ly6/uPAR family genes. Hum Genomics 2016; 10(1): 10
https://doi.org/10.1186/s40246-016-0074-2
pmid: 27098205
|
7 |
TP Gumley, IF McKenzie, MS Sandrin. Tissue expression, structure and function of the murine Ly-6 family of molecules. Immunol Cell Biol 1995; 73(4): 277–296
https://doi.org/10.1038/icb.1995.45
pmid: 7493764
|
8 |
H Reiser, H Oettgen, ET Yeh, C Terhorst, MG Low, B Benacerraf, KL Rock. Structural characterization of the TAP molecule: a phosphatidylinositol-linked glycoprotein distinct from the T cell receptor/T3 complex and Thy-1. Cell 1986; 47(3): 365–370
https://doi.org/10.1016/0092-8674(86)90593-3
pmid: 2876780
|
9 |
GJ Spangrude, S Heimfeld, IL Weissman. Purification and characterization of mouse hematopoietic stem cells. Science 1988; 241(4861): 58–62
https://doi.org/10.1126/science.2898810
pmid: 2898810
|
10 |
BE Welm, SB Tepera, T Venezia, TA Graubert, JM Rosen, MA Goodell. Sca-1(pos) cells in the mouse mammary gland represent an enriched progenitor cell population. Dev Biol 2002; 245(1): 42–56
https://doi.org/10.1006/dbio.2002.0625
pmid: 11969254
|
11 |
L Xin, DA Lawson, ON Witte. The Sca-1 cell surface marker enriches for a prostate-regenerating cell subpopulation that can initiate prostate tumorigenesis. Proc Natl Acad Sci USA 2005; 102(19): 6942–6947
https://doi.org/10.1073/pnas.0502320102
pmid: 15860580
|
12 |
CF Kim, EL Jackson, AE Woolfenden, S Lawrence, I Babar, S Vogel, D Crowley, RT Bronson, T Jacks. Identification of bronchioalveolar stem cells in normal lung and lung cancer. Cell 2005; 121(6): 823–835
https://doi.org/10.1016/j.cell.2005.03.032
pmid: 15960971
|
13 |
C Holmes, WL Stanford. Concise review: stem cell antigen-1: expression, function, and enigma. Stem Cells 2007; 25(6): 1339–1347
https://doi.org/10.1634/stemcells.2006-0644
pmid: 17379763
|
14 |
WL Stanford, S Haque, R Alexander, X Liu, AM Latour, HR Snodgrass, BH Koller, PM Flood. Altered proliferative response by T lymphocytes of Ly-6A (Sca-1) null mice. J Exp Med 1997; 186(5): 705–717
https://doi.org/10.1084/jem.186.5.705
pmid: 9271586
|
15 |
P Hanson, V Mathews, SH Marrus, TA Graubert. Enhanced green fluorescent protein targeted to the Sca-1 (Ly-6A) locus in transgenic mice results in efficient marking of hematopoietic stem cells in vivo. Exp Hematol 2003; 31(2): 159–167
https://doi.org/10.1016/S0301-472X(02)01021-4
pmid: 12591281
|
16 |
CY Ito, CY Li, A Bernstein, JE Dick, WL Stanford. Hematopoietic stem cell and progenitor defects in Sca-1/Ly-6A-null mice. Blood 2003; 101(2): 517–523
https://doi.org/10.1182/blood-2002-06-1918
pmid: 12393491
|
17 |
SB Bradfute, TA Graubert, MA Goodell. Roles of Sca-1 in hematopoietic stem/progenitor cell function. Exp Hematol 2005; 33(7): 836–843
https://doi.org/10.1016/j.exphem.2005.04.001
pmid: 15963860
|
18 |
JK Whitmire, B Eam, JL Whitton. Mice deficient in stem cell antigen-1 (Sca1, Ly-6A/E) develop normal primary and memory CD4+ and CD8+ T-cell responses to virus infection. Eur J Immunol 2009; 39(6): 1494–1504
https://doi.org/10.1002/eji.200838959
pmid: 19384870
|
19 |
ZX Zhang, WL Stanford, L Zhang. Ly-6A is critical for the function of double negative regulatory T cells. Eur J Immunol 2002; 32(6): 1584–1592
https://doi.org/10.1002/1521-4141(200206)32:6<1584::AID-IMMU1584>3.0.CO;2-2
pmid: 12115641
|
20 |
MA Jones, S DeWolf, V Vacharathit, M Yim, S Spencer, AK Bamezai. Investigating B cell development, natural and primary antibody responses in Ly-6A/Sca-1 deficient mice. PLoS One 2016; 11(6): e0157271
https://doi.org/10.1371/journal.pone.0157271
pmid: 27322740
|
21 |
M Bonyadi, SD Waldman, D Liu, JE Aubin, MD Grynpas, WL Stanford. Mesenchymal progenitor self-renewal deficiency leads to age-dependent osteoporosis in Sca-1/Ly-6A null mice. Proc Natl Acad Sci USA 2003; 100(10): 5840–5845
https://doi.org/10.1073/pnas.1036475100
pmid: 12732718
|
22 |
PO Mitchell, T Mills, RS O’Connor, ER Kline, T Graubert, E Dzierzak, GK Pavlath. Sca-1 negatively regulates proliferation and differentiation of muscle cells. Dev Biol 2005; 283(1): 240–252
https://doi.org/10.1016/j.ydbio.2005.04.016
pmid: 15901485
|
23 |
CL Epting, JE López, A Pedersen, C Brown, P Spitz, PC Ursell, HS Bernstein. Stem cell antigen-1 regulates the tempo of muscle repair through effects on proliferation of alpha7 integrin-expressing myoblasts. Exp Cell Res 2008; 314(5): 1125–1135
https://doi.org/10.1016/j.yexcr.2007.11.010
pmid: 18073129
|
24 |
G Upadhyay, Y Yin, H Yuan, X Li, R Derynck, RI Glazer. Stem cell antigen-1 enhances tumorigenicity by disruption of growth differentiation factor-10 (GDF10)-dependent TGF-β signaling. Proc Natl Acad Sci USA 2011; 108(19): 7820–7825
https://doi.org/10.1073/pnas.1103441108
pmid: 21518866
|
25 |
KK Long, M Montano, GK Pavlath. Sca-1 is negatively regulated by TGF-β1 in myogenic cells. FASEB J 2011; 25(4): 1156–1165
https://doi.org/10.1096/fj.10-170308
pmid: 21156809
|
26 |
HD Song, XJ Sun, M Deng, GW Zhang, Y Zhou, XY Wu, Y Sheng, Y Chen, Z Ruan, CL Jiang, HY Fan, LI Zon, JP Kanki, TX Liu, AT Look, Z Chen. Hematopoietic gene expression profile in zebrafish kidney marrow. Proc Natl Acad Sci USA 2004; 101(46): 16240–16245
https://doi.org/10.1073/pnas.0407241101
pmid: 15520368
|
27 |
XJ Sun, PF Xu, T Zhou, M Hu, CT Fu, Y Zhang, Y Jin, Y Chen, SJ Chen, QH Huang, TX Liu, Z Chen. Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes. PLoS One 2008; 3(1): e1499
https://doi.org/10.1371/journal.pone.0001499
pmid: 18231586
|
28 |
C Burge, S Karlin. Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997; 268(1): 78–94
https://doi.org/10.1006/jmbi.1997.0951
pmid: 9149143
|
29 |
MA Larkin, G Blackshields, NP Brown, R Chenna, PA McGettigan, H McWilliam, F Valentin, IM Wallace, A Wilm, R Lopez, JD Thompson, TJ Gibson, DG Higgins. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23(21): 2947–2948
https://doi.org/10.1093/bioinformatics/btm404
pmid: 17846036
|
30 |
K Tamura, G Stecher, D Peterson, A Filipski, S Kumar. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013; 30(12): 2725–2729
https://doi.org/10.1093/molbev/mst197
pmid: 24132122
|
31 |
H Yao, W Xie, Y Dai, Y Liu, W Gu, J Li, L Wu, J Xie, W Rui, B Ren, L Xue, Y Cheng, S Lin, C Li, H Tang, Y Wang, M Lou, X Zhang, R Hu, H Shang, J Huang, ZB Wu. TRIM65 determines the fate of a novel subtype of pituitary neuroendocrine tumors via ubiquitination and degradation of TPIT. Neuro-oncol 2022; 24(8): 1286–1297
https://doi.org/10.1093/neuonc/noac053
pmid: 35218667
|
32 |
XJ Sun, Z Wang, L Wang, Y Jiang, N Kost, TD Soong, WY Chen, Z Tang, T Nakadai, O Elemento, W Fischle, A Melnick, DJ Patel, SD Nimer, RG Roeder. A stable transcription factor complex nucleated by oligomeric AML1-ETO controls leukaemogenesis. Nature 2013; 500(7460): 93–97
https://doi.org/10.1038/nature12287
pmid: 23812588
|
33 |
N Liu, J Song, Y Xie, XL Wang, B Rong, N Man, MM Zhang, Q Zhang, FF Gao, MR Du, Y Zhang, J Shen, CH Xu, CL Hu, JC Wu, P Liu, YL Zhang, YY Xie, P Liu, JY Huang, QH Huang, F Lan, S Shen, SD Nimer, Z Chen, SJ Chen, RG Roeder, L Wang, XJ Sun. Different roles of E proteins in t(8;21) leukemia: E2-2 compromises the function of AETFC and negatively regulates leukemogenesis. Proc Natl Acad Sci USA 2019; 116(3): 890–899
https://doi.org/10.1073/pnas.1809327116
pmid: 30593567
|
34 |
MM Zhang, N Liu, YL Zhang, B Rong, XL Wang, CH Xu, YY Xie, S Shen, J Zhu, SD Nimer, Z Chen, SJ Chen, RG Roeder, F Lan, L Wang, QH Huang, XJ Sun. Destabilization of AETFC through C/EBPα-mediated repression of LYL1 contributes to t(8;21) leukemic cell differentiation. Leukemia 2019; 33(7): 1822–1827
https://doi.org/10.1038/s41375-019-0398-8
pmid: 30755707
|
35 |
YF Zhang, XL Wang, CH Xu, N Liu, L Zhang, YM Zhang, YY Xie, YL Zhang, QH Huang, L Wang, Z Chen, SJ Chen, RG Roeder, S Shen, K Xue, XJ Sun. A direct comparison between AML1-ETO and ETO2-GLIS2 leukemia fusion proteins reveals context-dependent binding and regulation of target genes and opposite functions in cell differentiation. Front Cell Dev Biol 2022; 10: 992714
https://doi.org/10.3389/fcell.2022.992714
pmid: 36158200
|
36 |
F Zhang, QY Zeng, H Xu, AN Xu, DJ Liu, NZ Li, Y Chen, Y Jin, CH Xu, CZ Feng, YL Zhang, D Liu, N Liu, YY Xie, SH Yu, H Yuan, K Xue, JY Shi, TX Liu, PF Xu, WL Zhao, Y Zhou, L Wang, QH Huang, Z Chen, SJ Chen, XL Zhou, XJ Sun. Selective and competitive functions of the AAR and UPR pathways in stress-induced angiogenesis. Cell Discov 2021; 7(1): 98
https://doi.org/10.1038/s41421-021-00332-8
pmid: 34697290
|
37 |
JL Rinn, HY Chang. Genome regulation by long noncoding RNAs. Annu Rev Biochem 2012; 81(1): 145–166
https://doi.org/10.1146/annurev-biochem-051410-092902
pmid: 22663078
|
38 |
EV Koonin. Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 2005; 39(1): 309–338
https://doi.org/10.1146/annurev.genet.39.073003.114725
pmid: 16285863
|
39 |
FJ Dumont, LZ Coker. Interferon-α/β enhances the expression of Ly-6 antigens on T cells in vivo and in vitro. Eur J Immunol 1986; 16(7): 735–740
https://doi.org/10.1002/eji.1830160704
pmid: 3487457
|
40 |
FJ Dumont, RC Boltz. The augmentation of surface Ly-6A/E molecules in activated T cells is mediated by endogenous interferon-gamma. J Immunol 1987; 139(12): 4088–4095
https://doi.org/10.4049/jimmunol.139.12.4088
pmid: 3121727
|
41 |
Y Luo, BC Hitz, I Gabdank, JA Hilton, MS Kagda, B Lam, Z Myers, P Sud, J Jou, K Lin, UK Baymuradov, K Graham, C Litton, SR Miyasato, JS Strattan, O Jolanki, JW Lee, FY Tanaka, P Adenekan, E O’Neill, JM Cherry. New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. Nucleic Acids Res 2020; 48(D1): D882–D889
https://doi.org/10.1093/nar/gkz1062
pmid: 31713622
|
42 |
Consortium GTEx. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 2020; 369(6509): 1318–1330
https://doi.org/10.1126/science.aaz1776
pmid: 32913098
|
43 |
L Lorenzi, HS Chiu, F Avila Cobos, S Gross, PJ Volders, R Cannoodt, J Nuytens, K Vanderheyden, J Anckaert, S Lefever, AP Tay, EJ de Bony, W Trypsteen, F Gysens, M Vromman, T Goovaerts, TB Hansen, S Kuersten, N Nijs, T Taghon, K Vermaelen, KR Bracke, Y Saeys, T De Meyer, NP Deshpande, G Anande, TW Chen, MR Wilkins, A Unnikrishnan, K De Preter, J Kjems, J Koster, GP Schroth, J Vandesompele, P Sumazin, P Mestdagh. The RNA Atlas expands the catalog of human non-coding RNAs. Nat Biotechnol 2021; 39(11): 1453–1465
https://doi.org/10.1038/s41587-021-00936-1
pmid: 34140680
|
44 |
I Donangelo, SG Ren, T Eigler, C Svendsen, S Melmed. Sca1+ murine pituitary adenoma cells show tumor-growth advantage. Endocr Relat Cancer 2014; 21(2): 203–216
https://doi.org/10.1530/ERC-13-0229
pmid: 24481638
|
45 |
ES Lander, LM Linton, B Birren, C Nusbaum, MC Zody, J Baldwin, K Devon, K Dewar, M Doyle, W FitzHugh, R Funke, D Gage, K Harris, A Heaford, J Howland, L Kann, J Lehoczky, R LeVine, P McEwan, K McKernan, J Meldrim, JP Mesirov, C Miranda, W Morris, J Naylor, C Raymond, M Rosetti, R Santos, A Sheridan, C Sougnez, Y Stange-Thomann, N Stojanovic, A Subramanian, D Wyman, J Rogers, J Sulston, R Ainscough, S Beck, D Bentley, J Burton, C Clee, N Carter, A Coulson, R Deadman, P Deloukas, A Dunham, I Dunham, R Durbin, L French, D Grafham, S Gregory, T Hubbard, S Humphray, A Hunt, M Jones, C Lloyd, A McMurray, L Matthews, S Mercer, S Milne, JC Mullikin, A Mungall, R Plumb, M Ross, R Shownkeen, S Sims, RH Waterston, RK Wilson, LW Hillier, JD McPherson, MA Marra, ER Mardis, LA Fulton, AT Chinwalla, KH Pepin, WR Gish, SL Chissoe, MC Wendl, KD Delehaunty, TL Miner, A Delehaunty, JB Kramer, LL Cook, RS Fulton, DL Johnson, PJ Minx, SW Clifton, T Hawkins, E Branscomb, P Predki, P Richardson, S Wenning, T Slezak, N Doggett, JF Cheng, A Olsen, S Lucas, C Elkin, E Uberbacher, M Frazier, RA Gibbs, DM Muzny, SE Scherer, JB Bouck, EJ Sodergren, KC Worley, CM Rives, JH Gorrell, ML Metzker, SL Naylor, RS Kucherlapati, DL Nelson, GM Weinstock, Y Sakaki, A Fujiyama, M Hattori, T Yada, A Toyoda, T Itoh, C Kawagoe, H Watanabe, Y Totoki, T Taylor, J Weissenbach, R Heilig, W Saurin, F Artiguenave, P Brottier, T Bruls, E Pelletier, C Robert, P Wincker, DR Smith, L Doucette-Stamm, M Rubenfield, K Weinstock, HM Lee, J Dubois, A Rosenthal, M Platzer, G Nyakatura, S Taudien, A Rump, H Yang, J Yu, J Wang, G Huang, J Gu, L Hood, L Rowen, A Madan, S Qin, RW Davis, NA Federspiel, AP Abola, MJ Proctor, RM Myers, J Schmutz, M Dickson, J Grimwood, DR Cox, MV Olson, R Kaul, C Raymond, N Shimizu, K Kawasaki, S Minoshima, GA Evans, M Athanasiou, R Schultz, BA Roe, F Chen, H Pan, J Ramser, H Lehrach, R Reinhardt, WR McCombie, la Bastide M de, N Dedhia, H Blöcker, K Hornischer, G Nordsiek, R Agarwala, L Aravind, JA Bailey, A Bateman, S Batzoglou, E Birney, P Bork, DG Brown, CB Burge, L Cerutti, HC Chen, D Church, M Clamp, RR Copley, T Doerks, SR Eddy, EE Eichler, TS Furey, J Galagan, JG Gilbert, C Harmon, Y Hayashizaki, D Haussler, H Hermjakob, K Hokamp, W Jang, LS Johnson, TA Jones, S Kasif, A Kaspryzk, S Kennedy, WJ Kent, P Kitts, EV Koonin, I Korf, D Kulp, D Lancet, TM Lowe, A McLysaght, T Mikkelsen, JV Moran, N Mulder, VJ Pollara, CP Ponting, G Schuler, J Schultz, G Slater, AF Smit, E Stupka, J Szustakowki, D Thierry-Mieg, J Thierry-Mieg, L Wagner, J Wallis, R Wheeler, A Williams, YI Wolf, KH Wolfe, SP Yang, RF Yeh, F Collins, MS Guyer, J Peterson, A Felsenfeld, KA Wetterstrand, A Patrinos, MJ Morgan, Jong P de, JJ Catanese, K Osoegawa, H Shizuya, S Choi, YJ Chen, J; International Human Genome Sequencing Consortium Szustakowki. Initial sequencing and analysis of the human genome. Nature 2001; 409(6822): 860–921
https://doi.org/10.1038/35057062
pmid: 11237011
|
46 |
JC Venter, MD Adams, EW Myers, PW Li, RJ Mural, GG Sutton, HO Smith, M Yandell, CA Evans, RA Holt, JD Gocayne, P Amanatides, RM Ballew, DH Huson, JR Wortman, Q Zhang, CD Kodira, XH Zheng, L Chen, M Skupski, G Subramanian, PD Thomas, J Zhang, Miklos GL Gabor, C Nelson, S Broder, AG Clark, J Nadeau, VA McKusick, N Zinder, AJ Levine, RJ Roberts, M Simon, C Slayman, M Hunkapiller, R Bolanos, A Delcher, I Dew, D Fasulo, M Flanigan, L Florea, A Halpern, S Hannenhalli, S Kravitz, S Levy, C Mobarry, K Reinert, K Remington, J Abu-Threideh, E Beasley, K Biddick, V Bonazzi, R Brandon, M Cargill, I Chandramouliswaran, R Charlab, K Chaturvedi, Z Deng, Francesco V Di, P Dunn, K Eilbeck, C Evangelista, AE Gabrielian, W Gan, W Ge, F Gong, Z Gu, P Guan, TJ Heiman, ME Higgins, RR Ji, Z Ke, KA Ketchum, Z Lai, Y Lei, Z Li, J Li, Y Liang, X Lin, F Lu, GV Merkulov, N Milshina, HM Moore, AK Naik, VA Narayan, B Neelam, D Nusskern, DB Rusch, S Salzberg, W Shao, B Shue, J Sun, Z Wang, A Wang, X Wang, J Wang, M Wei, R Wides, C Xiao, C Yan, A Yao, J Ye, M Zhan, W Zhang, H Zhang, Q Zhao, L Zheng, F Zhong, W Zhong, S Zhu, S Zhao, D Gilbert, S Baumhueter, G Spier, C Carter, A Cravchik, T Woodage, F Ali, H An, A Awe, D Baldwin, H Baden, M Barnstead, I Barrow, K Beeson, D Busam, A Carver, A Center, ML Cheng, L Curry, S Danaher, L Davenport, R Desilets, S Dietz, K Dodson, L Doup, S Ferriera, N Garg, A Gluecksmann, B Hart, J Haynes, C Haynes, C Heiner, S Hladun, D Hostin, J Houck, T Howland, C Ibegwam, J Johnson, F Kalush, L Kline, S Koduru, A Love, F Mann, D May, S McCawley, T McIntosh, I McMullen, M Moy, L Moy, B Murphy, K Nelson, C Pfannkoch, E Pratts, V Puri, H Qureshi, M Reardon, R Rodriguez, YH Rogers, D Romblad, B Ruhfel, R Scott, C Sitter, M Smallwood, E Stewart, R Strong, E Suh, R Thomas, NN Tint, S Tse, C Vech, G Wang, J Wetter, S Williams, M Williams, S Windsor, E Winn-Deen, K Wolfe, J Zaveri, K Zaveri, JF Abril, R Guigó, MJ Campbell, KV Sjolander, B Karlak, A Kejariwal, H Mi, B Lazareva, T Hatton, A Narechania, K Diemer, A Muruganujan, N Guo, S Sato, V Bafna, S Istrail, R Lippert, R Schwartz, B Walenz, S Yooseph, D Allen, A Basu, J Baxendale, L Blick, M Caminha, J Carnes-Stine, P Caulk, YH Chiang, M Coyne, C Dahlke, Mays A Deslattes, M Dombroski, M Donnelly, D Ely, S Esparham, C Fosler, H Gire, S Glanowski, K Glasser, A Glodek, M Gorokhov, K Graham, B Gropman, M Harris, J Heil, S Henderson, J Hoover, D Jennings, C Jordan, J Jordan, J Kasha, L Kagan, C Kraft, A Levitsky, M Lewis, X Liu, J Lopez, D Ma, W Majoros, J McDaniel, S Murphy, M Newman, T Nguyen, N Nguyen, M Nodell, S Pan, J Peck, M Peterson, W Rowe, R Sanders, J Scott, M Simpson, T Smith, A Sprague, T Stockwell, R Turner, E Venter, M Wang, M Wen, D Wu, M Wu, A Xia, A Zandieh, X Zhu. The sequence of the human genome. Science 2001; 291(5507): 1304–1351
https://doi.org/10.1126/science.1058040
pmid: 11181995
|
47 |
RA Raff. Evo-devo: the evolution of a new discipline. Nat Rev Genet 2000; 1(1): 74–79
https://doi.org/10.1038/35049594
pmid: 11262880
|
48 |
AM Sinclair, EA Dzierzak. Cloning of the complete Ly-6E.1 gene and identification of DNase I hypersensitive sites corresponding to expression in hematopoietic cells. Blood 1993; 82(10): 3052–3062
https://doi.org/10.1182/blood.V82.10.3052.3052
pmid: 8219196
|
49 |
A McLysaght, D Guerzoni. New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation. Philos Trans R Soc Lond B Biol Sci 2015; 370(1678): 20140332
https://doi.org/10.1098/rstb.2014.0332
|
50 |
JP Adelman, CT Bond, J Douglass, E Herbert. Two mammalian genes transcribed from opposite strands of the same DNA locus. Science 1987; 235(4795): 1514–1517
https://doi.org/10.1126/science.3547652
pmid: 3547652
|
51 |
S Katayama, Y Tomaru, T Kasukawa, K Waki, M Nakanishi, M Nakamura, H Nishida, CC Yap, M Suzuki, J Kawai, H Suzuki, P Carninci, Y Hayashizaki, C Wells, M Frith, T Ravasi, KC Pang, J Hallinan, J Mattick, DA Hume, L Lipovich, S Batalov, PG Engström, Y Mizuno, MA Faghihi, A Sandelin, AM Chalk, S Mottagui-Tabar, Z Liang, B Lenhard, C; RIKEN Genome Exploration Research Group; Genome Science Group (Genome Network Project Core Group); FANTOM Consortium Wahlestedt. Antisense transcription in the mammalian transcriptome. Science 2005; 309(5740): 1564–1566
https://doi.org/10.1126/science.1112009
pmid: 16141073
|
52 |
EJ Strobel, AM Yu, JB Lucks. High-throughput determination of RNA structures. Nat Rev Genet 2018; 19(10): 615–634
https://doi.org/10.1038/s41576-018-0034-x
pmid: 30054568
|
53 |
JF Hu, D Yim, D Ma, SM Huber, N Davis, JM Bacusmo, S Vermeulen, J Zhou, TJ Begley, MS DeMott, SS Levine, Crécy-Lagard V de, PC Dedon, B Cao. Quantitative mapping of the cellular small RNA landscape with AQRNA-seq. Nat Biotechnol 2021; 39(8): 978–988
https://doi.org/10.1038/s41587-021-00874-y
pmid: 33859402
|
54 |
Y Kong, H Hu, Y Shan, Z Zhou, K Zen, Y Sun, R Yang, Z Fu, X Chen. Accurate quantification of 3′-terminal 2′-O-methylated small RNAs by utilizing oxidative deep sequencing and stem-loop RT-qPCR. Front Med 2022; 16(2): 240–250
https://doi.org/10.1007/s11684-021-0909-7
pmid: 35416629
|
55 |
G Upadhyay. Emerging role of lymphocyte antigen-6 family of genes in cancer and immune cells. Front Immunol 2019; 10: 819
https://doi.org/10.3389/fimmu.2019.00819
pmid: 31068932
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