Publications

1. Welter AL, Palani S, Machida Y, Schellenberg MJ, Machida YJ. The viral serpin SPI-1 directly inhibits the host cell serine protease FAM111A. J Biol Chem. 2025 Feb; 301 (2):108175 Epub 2025 Jan 10
   View PubMed
2. Erber L, Groehler AS 4th, Cyuzuzo CI, Baker-Wainwright J, Maskey RS, Li L, Machida YJ, Tretyakova N. SPRTN metalloprotease participates in repair of ROS-mediated DNA-protein crosslinks. Sci Rep. 2024 Dec 28; 14 (1):30919
   View PubMed
3. Palani S, Machida Y, Alvey JR, Mishra V, Welter AL, Cui G, Bragantini B, Botuyan MV, Cong ATQ, Mer G, Schellenberg MJ, Machida YJ. Dimerization-dependent serine protease activity of FAM111A prevents replication fork stalling at topoisomerase 1 cleavage complexes. Nat Commun. 2024 Mar 7; 15 (1):2064 Epub 2024 Mar 07
   View PubMed
4. Kelly RL, Huehls AM, Venkatachalam A, Huntoon CJ, Machida YJ, Karnitz LM. Intra-S phase checkpoint kinase Chk1 dissociates replication proteins Treslin and TopBP1 through multiple mechanisms during replication stress. J Biol Chem. 2022 Apr; 298 (4):101777 Epub 2022 Feb 26
   View PubMed
5. Welter AL, Machida YJ. Functions and evolution of FAM111 serine proteases. Front Mol Biosci. 2022; 9:1081166 Epub 2022 Dec 15
   View PubMed
6. Popay TM, Wang J, Adams CM, Howard GC, Codreanu SG, Sherrod SD, McLean JA, Thomas LR, Lorey SL, Machida YJ, Weissmiller AM, Eischen CM, Liu Q, Tansey WP. MYC regulates ribosome biogenesis and mitochondrial gene expression programs through its interaction with host cell factor-1. Elife. 2021 Jan 8; 10 Epub 2021 Jan 08
   View PubMed
7. Huang J, Zhou Q, Gao M, Nowsheen S, Zhao F, Kim W, Zhu Q, Kojima Y, Yin P, Zhang Y, Guo G, Tu X, Deng M, Luo K, Qin B, Machida Y, Lou Z. Tandem Deubiquitination and Acetylation of SPRTN Promotes DNA-Protein Crosslink Repair and Protects against Aging. Mol Cell. 2020 Sep 3; 79 (5):824-835.e5 Epub 2020 July 09
   View PubMed
8. Kojima Y, Machida YJ. DNA-protein crosslinks from environmental exposure: Mechanisms of formation and repair. Environ Mol Mutagen. 2020 Aug; 61 (7):716-729 Epub 2020 July 09
   View PubMed
9. Kojima Y, Machida Y, Palani S, Caulfield TR, Radisky ES, Kaufmann SH, Machida YJ. FAM111A protects replication forks from protein obstacles via its trypsin-like domain. Nat Commun. 2020 Mar 12; 11 (1):1318
   View PubMed
10. Kurmi K, Hitosugi S, Yu J, Boakye-Agyeman F, Wiese EK, Larson TR, Dai Q, Machida YJ, Lou Z, Wang L, Boughey JC, Kaufmann SH, Goetz MP, Karnitz LM, Hitosugi T. Tyrosine Phosphorylation of Mitochondrial Creatine Kinase 1 Enhances a Druggable Tumor Energy Shuttle Pathway. Cell Metab. 2018 Dec 4; 28 (6):833-847.e8 Epub 2018 Aug 30
    View PubMed
11. Maskey RS, Flatten KS, Sieben CJ, Peterson KL, Baker DJ, Nam HJ, Kim MS, Smyrk TC, Kojima Y, Machida Y, Santiago A, van Deursen JM, Kaufmann SH, Machida YJ. Spartan deficiency causes accumulation of Topoisomerase 1 cleavage complexes and tumorigenesis. Nucleic Acids Res. 2017 May 5; 45 (8):4564-4576
    View PubMed
12. Okino Y, Machida Y, Frankland-Searby S, Machida YJ. BRCA1-associated protein 1 (BAP1) deubiquitinase antagonizes the ubiquitin-mediated activation of FoxK2 target genes. J Biol Chem. 2015 Jan 16; 290 (3):1580-91 Epub 2014 Dec 01
    View PubMed
13. Maskey RS, Kim MS, Baker DJ, Childs B, Malureanu LA, Jeganathan KB, van Deursen JM, Machida YJ. Spartan deficiency causes genomic instability and progeroid phenotypes. Nat Commun. 2014 Dec 11; 5:5744
    View PubMed
14. Kim MS, Machida Y, Vashisht AA, Wohlschlegel JA, Pang YP, Machida YJ. Regulation of error-prone translesion synthesis by Spartan/C1orf124. Nucleic Acids Res. 2013 Feb 1; 41 (3):1661-8 Epub 2012 Dec 18
    View PubMed
15. Machida Y, Kim MS, Machida YJ. Spartan/C1orf124 is important to prevent UV-induced mutagenesis. Cell Cycle. 2012 Sep 15; 11 (18):3395-402 Epub 2012 Aug 16
    View PubMed
16. Shereda RD, Machida Y, Machida YJ. Human KIAA1018/FAN1 localizes to stalled replication forks via its ubiquitin-binding domain. Cell Cycle. 2010 Oct 1; 9 (19):3977-83 Epub 2010 Oct 01
    View PubMed
17. Machida Y, Vashisht AA, Wohlschlegel JA, Dutta A. The deubiquitinating enzyme BAP1 regulates cell growth via interaction with HCF-1. J Biol Chem. 2009 Dec 4; 284 (49):34179-88 Epub 2009 Oct 08
    View PubMed
18. Alpi A, Langevin F, Mosedale G, Machida YJ, Dutta A, Patel KJ. UBE2T, the Fanconi anemia core complex, and FANCD2 are recruited independently to chromatin: a basis for the regulation of FANCD2 monoubiquitination. Mol Cell Biol. 2007 Dec; 27(24):8421-30. Epub 2007 Oct 15.
    View PubMed
19. Machida YJ, Dutta A. The APC/C inhibitor, Emi1, is essential for prevention of rereplication. Genes Dev. 2007 Jan 15; 21(2):184-94.
    View PubMed
20. Sivaprasad U, Machida YJ, Dutta A. APC/C--the master controller of origin licensing? Cell Div. 2007; 2:8. Epub 2007 Feb 23.
    View PubMed
21. Machida YJ, Chen Y, Machida Y, Malhotra A, Sarkar S, Dutta A. Targeted comparative RNA interference analysis reveals differential requirement of genes essential for cell proliferation. Mol Biol Cell. 2006 Nov; 17(11):4837-45. Epub 2006 Sep 06.
    View PubMed
22. Machida YJ, Machida Y, Chen Y, Gurtan AM, Kupfer GM, D'Andrea AD, Dutta A. UBE2T is the E2 in the Fanconi anemia pathway and undergoes negative autoregulation. Mol Cell. 2006 Aug; 23(4):589-96.
    View PubMed
23. Teer JK, Machida YJ, Labit H, Novac O, Hyrien O, Marheineke K, Zannis-Hadjopoulos M, Dutta A. Proliferating human cells hypomorphic for origin recognition complex 2 and pre-replicative complex formation have a defect in p53 activation and Cdk2 kinase activation. J Biol Chem. 2006 Mar 10; 281(10):6253-60. Epub 2006 Jan 10.
    View PubMed
24. Inayoshi Y, Miyake K, Machida Y, Kaneoka H, Terajima M, Dohda T, Takahashi M, Iijima S. Mammalian chromatin remodeling complex SWI/SNF is essential for enhanced expression of the albumin gene during liver development. J Biochem. 2006 Feb; 139(2):177-88.
    View PubMed
25. Machida YJ, Hamlin JL, Dutta A. Right place, right time, and only once: replication initiation in metazoans. Cell. 2005 Oct 7; 123(1):13-24.
    View PubMed
26. Inayoshi Y, Kaneoka H, Machida Y, Terajima M, Dohda T, Miyake K, Iijima S. Repression of GR-mediated expression of the tryptophan oxygenase gene by the SWI/SNF complex during liver development. J Biochem. 2005 Oct; 138(4):457-65.
    View PubMed
27. Machida YJ, Teer JK, Dutta A. Acute reduction of an origin recognition complex (ORC) subunit in human cells reveals a requirement of ORC for Cdk2 activation. J Biol Chem. 2005 Jul 29; 280(30):27624-30 Epub 2005 Jun 7.
    View PubMed
28. Machida YJ, Dutta A. Cellular checkpoint mechanisms monitoring proper initiation of DNA replication. J Biol Chem. 2005 Feb 25; 280(8):6253-6. Epub 2004 Dec 09.
    View PubMed
29. Vaziri C, Saxena S, Jeon Y, Lee C, Murata K, Machida Y, Wagle N, Hwang DS, Dutta A. A p53-dependent checkpoint pathway prevents rereplication. Mol Cell. 2003 Apr; 11(4):997-1008.
    View PubMed
30. Dhar SK, Yoshida K, Machida Y, Khaira P, Chaudhuri B, Wohlschlegel JA, Leffak M, Yates J, Dutta A. Replication from oriP of Epstein-Barr virus requires human ORC and is inhibited by geminin. Cell. 2001 Aug 10; 106(3):287-96.
    View PubMed
31. Machida Y, Murai K, Miyake K, Iijima S. Expression of chromatin remodeling factors during neural differentiation. J Biochem. 2001 Jan; 129(1):43-9.
    View PubMed
32. Machida Y, Miyake K, Hattori K, Yamamoto S, Kawase M, Iijima S. Structure and function of a novel coliphage-associated sialidase. FEMS Microbiol Lett. 2000 Jan 15; 182(2):333-7.
    View PubMed
33. Machida Y, Hattori K, Miyake K, Kawase Y, Kawase M, Iijima S. Molecular cloning and characterization of a novel bacteriophage associated sialidase. J Biosci Bioeng. 2000; 90(1):62-8.
    View PubMed
34. Yamamoto S, Miyake K, Koike Y, Watanabe M, Machida Y, Ohta M, Iijima S. Molecular characterization of type-specific capsular polysaccharide biosynthesis genes of Streptococcus agalactiae type Ia. J Bacteriol. 1999 Sep; 181(17):5176-84.
    View PubMed
35. Miyake K, Machida Y, Hattori K, Iijima S. Characterization of a multidomain cellulase from an extremely thermophilic anaerobe strain NA10. J Ferment Bioeng. 1998; 85:289-96.
    
36. Miyake K, Muraki T, Hattori K, Machida Y, Watanabe M, Kawase M, Yoshida Y, Iijima S. Screening of bacteriophages producing Endo-N-acetylneuraminidase. J Ferment Bioeng. 1997; 84:90-3.