Publications
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167. Wilson B, Su Z, Kumar P, Dutta A. XRN2 suppresses aberrant entry of tRNA trailers into argonaute in humans and Arabidopsis. PLoS Genet. 2023, 19:e1010755. doi: 10.1371/journal.pgen.1010755. PMID: 37146074
166. Dutta A, Li H, Abounader R. Cryptic lncRNA-encoded ORFs: A hidden source of regulatory proteins. J Clin Invest. 2023 Mar 1. doi: 10.1172/JCI167271. PMID: 36856112
165. Su Z, Monshaugen I, Klungland A, Ougland R, Dutta A. Characterization of novel small non-coding RNAs and their modifications in bladder cancer using an updated small RNA-seq workflow. Front Mol Biosci. 2022 Jul 18. doi: 10.3389/fmolb.2022.887686. PMID: 35923465
164. Parikh R, Wilson B, Marrah L, Su Z, Saha S, Kumar P, Huang F, Dutta A. tRForest: a novel random forest-based algorithm for tRNA-derived fragment target prediction. NAR Genom Bioinform. 2022 May 30. doi: 10.1093/nargab/lqac037. PMID: 35664803
163. Su Z, Monshaugen I, Wilson B, Wang F, Klungland A, Ougland R, Dutta A. TRMT6/61A-dependent base methylation of tRNA-derived fragments regulates gene-silencing activity and the unfolded protein response in bladder cancer. Nat Commun. 2022 April 20. doi: 10.1038/s41467-022-29790-8. PMID: 35444240
162. Wilson B, Dutta A. Function and Therapeutic Implications of tRNA Derived Small RNAs. Front Mol Biosci. 2022 April 13. doi: 10.3389/fmolb.2022.888424. PMID: 35495621
161. Sahu D, Chatrath A, Ratan A, Dutta A. Integrated bioinformatic pipeline using whole-exome and RNAseq data to identify germline variants correlated with cancer. STAR Protoc. 2022 April 4. doi: 10.1016/j.xpro.2022.101273. PMID: 35403010
160. Przanowska RK, Weidmann CA, Saha S, Cichewicz MA, Jensen KN, Przanowski P, Irving PS, Janes KA, Guertin MJ, Weeks KM, Dutta A. Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors. Cell Rep. 2022 Feb 15. doi: 10.1016/j.celrep.2022.110361. PMID: 35172143
159. Kiran S, Wilson B, Saha S, Graff JA, Dutta A. HPVE6-USP46 Mediated Cdt2 Stabilization Reduces Set8 Mediated H4K20-Methylation to Induce Gene Expression Changes. Cancers. 2021 Dec 22. doi: 10.3390/cancers14010030. PMID: 35008200
158. Saha S, Zhang Y, Wilson B, Abounader R, Dutta A. A tumor suppressive long noncoding RNA, DRAIC, inhibits protein translation and induces autophagy by activating AMPK. J Cell Sci. 2021 Nov 18. doi: 10.1242/jcs.259306. PMID: 34746949
157. Paulsen T, Malapati P, Shibata Y, Wilson B, Eki R, Benamar M, Abbas T, Dutta A. MicroDNA levels are dependent on MMEJ, repressed by c-NHEJ pathway, and stimulated by DNA damage. Nucleic Acids Res. 2021 Nov 18. doi: 10.1093/nar/gkab984. PMID: 34718766
156. Su Z, Dutta A. De-stressing the T cells in need. Science. 2021 May 14. doi: 10.1126/science.abi7265. PMID: 33986167
155. Su Z, Saha S, Paulsen T, Kumar P, Dutta A. ATAC-Seq-based Identification of Extrachromosomal Circular DNA in Mammalian Cells and Its Validation Using Inverse PCR and FISH. Bio Protoc. 2021 May 5. doi: 10.21769/BioProtoc.4003. PMID: 34124304
154. Chatrath A, Ratan A, Dutta A. Germline variants predictive of tumor mutational burden and immune checkpoint inhibitor efficacy. iScience. 2021 Mar 4. doi: 10.1016/j.isci.2021.102248. PMID: 33786423
153. Lee KY, Dutta A. Chk1 promotes non-homologous end joining in G1 through direct phosphorylation of ASF1A. Cell Rep. 2021 Jan 26. doi: 10.1016/j.celrep.2020.108680. PMID: 33503415
152. Chatrath A, Ratan A, Dutta A. Germline Variants That Affect Tumor Progression. Trends Genet. 2020 Nov 14. doi: 10.1016/j.tig.2020.10.005. PMID: 33203571
151. Shibata E, Dutta A. A human cancer cell line initiates DNA replication normally in the absence of ORC5 and ORC2 proteins. J Biol Chem. 2020 Dec 11. doi: 10.1074/jbc.RA120.015450. PMID: 32989049
150. Su Z, Wilson B, Kumar P, Dutta A. Noncanonical Roles of tRNAs: tRNA Fragments and Beyond. Annu Rev Genet. 2020 Nov 23. doi: 10.1146/annurev-genet-022620-101840. PMID: 32841070
149. Kumar P, Kiran S, Saha S, Su Z, Paulsen T, Chatrath A, Shibata Y, Shibata E, Dutta A. ATAC-seq identifies thousands of extrachromosomal circular DNA in cancer and cell lines. Sci Adv. 2020 May 15. doi: 10.1126/sciadv.aba2489. PMID: 32440553
148. Przanowska RK, Sobierajska E, Su Z, Jensen K, Przanowski P, Nagdas S, Kashatus JA, Kashatus DF, Bhatnagar S, Lukens JR, Dutta A. miR-206 family is important for mitochondrial and muscle function, but not essential for myogenesis in vitro. FASEB J. 2020 Apr 11. doi: 10.1096/fj.201902855RR. [Epub ahead of print] PMID: 32277852
147. Chatrath A, Przanowska R, Kiran S, Su Z, Saha S, Wilson B, Tsunematsu T, Ahn JH, Lee KY, Paulsen T, Sobierajska E, Kiran M, Tang X, Li T, Kumar P, Ratan A, Dutta A. The pan-cancer landscape of prognostic germline variants in 10,582 patients. Genome Medicine. 2020 Feb 17. doi: 10.1186/s13073-020-0718-7. PMID: 32066500
146. Su Z, Frost EL, Lammert CR, Przanowska RK, Lukens JR, Dutta A. tRNA-derived fragments and microRNAs in the maternal-fetal interface of a mouse maternal-immune-activation autism model. RNA Biol.2020 Jan 26. doi: 10.1080/15476286.2020.1721047. [Epub ahead of print] PMID: 31983265
145. Saha S, Kiran M, Kuscu C, Chatrath A, Wotton D, Mayo MW, Dutta A. Long noncoding RNA DRAIC inhibits prostate cancer progression by interacting with IKK to inhibit NF-kB activation. Cancer Res. 2020 Jan 3. pii: canres.3460.2019. doi: 10.1158/0008-5472.CAN-19-3460. [Epub ahead of print] PMID: 31900260
144. Su Z, Kuscu C, Malik A, Shibata E, Dutta A. Angiogenin generates specific stress-induced tRNA halves and is not involved in tRF-3-mediated gene silencing. J Biol Chem. 2019 Nov 8;294(45):16930-16941. doi: 10.1074/jbc.RA119.009272. PMID: 31582561
143. Paulsen T, Shibata Y, Kumar P, Dillon L, Dutta A. Small extrachromosomal circular DNAs, microDNA, produce short regulatory RNAs that suppress gene expression independent of canonical promoters. Nucleic Acids Res. 2019 May 21;47(9):4586-4596. doi: 10.1093/nar/gkz155. PMID: 30828735
142. Chatrath A, Kiran M, Kumar P, Ratan A, Dutta A. The Germline Variants rs6175955 and rs34988193 Are Predictive of Survival in Lower Grade Glioma Patients. Mol Cancer Research. 2019 May;17(5):1075-1086. doi: 10.1158/1541-7786.MCR-18-0996. PMID: 30651372
141. Kiran M, Chatrath A, Tang X, Keenan DM, Dutta A. A Prognostic Signature for Lower Grade Gliomas Based on Expression of Long Non-Coding RNAs. Mol Neurobiol. 2019 Jul;56(7):4786-4798. doi: 10.1007/s12035-018-1416-y. PMID: 30392137
140. Kiran S, Dar A, Singh SK, Lee KY, Dutta A. The Deubiquitinase USP46 Is Essential for Proliferation and Tumor Growth of HPV-Transformed Cancers. Mol Cell. 2018 Dec 6;72(5):823-835.e5. doi: 10.1016/j.molcel.2018.09.019. PMID: 30415951
139. Cichewicz MA, Kiran M, Przanowska RK, Sobierajska E, Shibata Y, Dutta A. MUNC, an eRNA upstream from the MYOD gene, induces a subgroup of myogenic transcripts in trans, independently of MyoD. Mol Cell Biol. 2018 Sep 28;38(20). pii: e00655-17. doi: 10.1128/MCB.00655-17. PMID: 30037979
138. Reon BJ, Takao Real Karia B, Kiran M, Dutta A. LINC00152 Promotes Invasion Through a 3'-hairpin Structure and Associates with Prognosis in Glioblastoma. Mol Cancer Res. 2018 Oct;16(10):1470-1482. doi: 10.1158/1541-7786.MCR-18-0322. PMID: 29991527
137. Kuscu C, Kumar P, Kiran M, Su Z, Malik A, Dutta A. tRNA fragments (tRFs) guide Ago to regulate gene expression post-transcriptionally in a Dicer-independent manner. RNA. 2018 Aug;24(8):1093-1105. PMID: 29844106
136. Paulsen T, Kumar P, Koseoglu MM, Dutta A. Discoveries of Extrachromosomal Circles of DNA in Normal and Tumor Cells. Trends Genet. 2018 Apr;34(4):270-278. PMID: 29329720
135. Abbas T, Dutta A. Regulation of Mammalian DNA Replication via the Ubiquitin-Proteasome System. Adv Exp Med Biol. 2017;1042:421-454. PMID: 29357069
134. Lee KY, Im JS, Shibata E, Dutta A. ASF1a Promotes Non-homologous End Joining Repair by Facilitating Phosphorylation of MDC1 by ATM at Double-Strand Breaks. Mol Cell. 2017 Oct 5;68(1):61-75.e5. PMID: 28943310
133. Kumar P, Kuscu C, Dutta A.Biogenesis and Function of Transfer RNA-Related Fragments (tRFs). Trends Biochem Sci. 2016 Aug;41(8):679-689. PMID: 27263052
132. Kumar P, Dillon L, Shibata Y, Jazaeri AA, Jones DR, Dutta A. Normal and Cancerous Tissues Release extrachromosomal circular DNA (eccDNA) into the Circulation. Molecular Cancer Res. 2017 Sep;15(9):1197-1205. doi: 10.1158/1541-7786.MCR-17-0095. PMID: 28550083
131. Shibata E, Kiran M, Shibata Y, Singh S, Kiran S, Dutta A. Two subunits of human ORC are dispensable for DNA replication and proliferation. Elife. 2016 Dec 1;5. pii: e19084. doi: 10.7554/eLife.19084. PMID: 27906128
130. Reon BJ, Anaya J, Zhang Y, Mandell J, Purow B, Abounader R, Dutta A. Expression of lncRNAs in Low-Grade Gliomas and Glioblastoma Multiforme: An In Silico Analysis. PLoS Med. 2016;13(12):e1002192. doi: 10.1371/journal.pmed.1002192. PMID: 27923049
129. Coleman KE, Grant GD, Haggerty RA, Brantley K, Shibata E, Workman BD, Dutta A, Varma D, Purvis JE, Cook JG. Sequential replication-coupled destruction at G1/S ensures genome stability. Genes Dev. 2015;29:1734-46. PMC4561482
128. Lee KY, Im JS, Shibata E, Park JH, Handa N, Kowalczykowski S and Dutta A. MCM8-9 complex promotes resection of double-strand break ends by Mre11-Rad50-Nbs1 complex. Nature Communications. 2015; 6:7744. PMC4525285
127. Dillon LW, Kumar P, Shibata Y, Wang YH, Willcox S, Griffith JD, Pommier Y, Takeda S, and Dutta A. Mismatch repair pathways and transcriptional activity are important for microDNA production. Cell Reports. 2015; 11:1749-59. PMC4481157
126. Sakurai K, Reon BJ, Anaya J, Dutta A. The lncRNA DRAIC/PCAT29 locus constitutes a tumor suppressive nexus. Mol Cancer Res. 2015. 13:828-38. PMC4456356
125. Hong S, Dutta A, Laimins LA. The acetyltransferase Tip60 is a critical regulator of the differentiation-dependent amplification of human papillomaviruses. J Virol. 2015. Apr 15;89(8):4668-75. doi: 10.1128/JVI.03455-14. PMID 25673709
124. Mueller AC, Cichewicz MA, Dey BK, Layer R, Reon BJ, Gagan JR and Dutta A. MUNC: A lncRNA that induces the expression of pro-myogenic genes in skeletal myogenesis. Mol. Cell Biol., 2015, 35:498-513. PMC4285423
123. Kumar P, Mudunuri SB, Anaya J and Dutta A. tRFdb: a database of transfer RNA fragments. Nucleic Acids Research, Nucleic Acids Res. 2015 Jan 28;43(Database issue):D141-5. doi: 10.1093/nar/gku1138.
122. Kumar P, Anaya J, Mudunuri SB and Dutta A. Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with Ago proteins to recognize specific RNA targets. BMC Biology, 2014, 12:78. doi: 10.1186/s12915-014-0078-0. PMC4203973
121. Dar A, Wu D, Lee N, Shibata E and Dutta A. 14-3-3 proteins play a role in the cell cycle by shielding Cdt2 from ubiquitin-mediated degradation. Mol. Cell Biol. 2014, 34:4049-61. PMC4386460.
120. Shibata E, Dar A and Dutta A. CRL4Cdt2 E3 Ubiquitin Ligase and PCNA Cooperate to Degrade Thymine DNA Glycosylase in S-phase. J Biol Chem. 2014, 289:23056-64. PMC4132804
119. Zhang Y, Kim J, Mueller AC, Dey B, Yang Y, Lee DH, Hachmann J, Finderle S, Park DM, Christensen J, Schiff D, Purow B, Dutta A, Abounader R. Multiple receptor tyrosine kinases converge on microRNA-134 to control KRAS, STAT5B, and glioblastoma. Cell Death Differ. 2014;21:720-34. PMC3978301
118. Floyd DH, Zhang Y, Dey BK, Kefas B, Breit H, Marks K, Dutta A, Herold-Mende C, Synowitz M, Glass R, Abounader R, and Purow BW. Novel anti-apoptotic microRNAs 582-5p and 363 promote human glioblastoma stem cell survival via direct inhibition of caspase 3, caspase 9, and Bim. PLoS One. 2014 ;9:e96239. PMC4013090
117. Negishi M, Wongpalee SP, Sarkar S, Park J, Lee KY, Shibata Y, Reon BJ, Abounader R, Suzuki Y, Sugano S and Dutta A. A new lncRNA, APTR, associates with and represses the CDKN1A/p21 promoter by recruiting Polycomb proteins. PLoS One, 2014; 9: e95216. PMC3991591
116. Im JS, Keaton M, Lee KY, Kumar P, Park J and Dutta A. ATR checkpoint kinase and CRL1βTRCP collaborate to degrade ASF1a and thus repress genes overlapping with clusters of stalled replication forks. Genes & Development. 2014; 28:875-87. PMC4003279
115. Dey BK, Pfeifer K, and Dutta A. The H19 long non-coding RNA gives rise to microRNAs miR-675-3p and -5p to promote skeletal muscle differentiation and regeneration. Genes & Development. 2014; 28:491-501. PMC3950346
114. Wagenseller AG, Shada A, D'Auria KM, Murphy C, Sun D, Molhoek KR, Papin JA, Dutta A, Slingluff CL Jr. MicroRNAs induced in melanoma treated with combination targeted therapy of Temsirolimus and Bevacizumab. J Transl Med. 2013;11:218. doi: 10.1186/1479-5876-11-218. PMC3853033
113. Terai K, Shibata E, Abbas T, Dutta A. Degradation of p12 by CRL4Cdt2 E3 ligase inhibits fork progression after DNA damage. J Biol Chem. 2013; 288:30509-14. PMC3798521
112. Jazaeri AA, Shibata E, Park J, Bryant JL, Conaway MR, Modesitt SC, Smith PG, Milhollen MA, Berger AJ, Dutta A. Overcoming platinum resistance in preclinical models of ovarian cancer using the neddylation inhibitor MLN4924. Molecular Cancer Therapeutics. 2013; 12:1958-67. PMC3795967
111. Dar A, Shibata E and Dutta A. Deubiquitination of Tip60 by USP7 Determines the Activity of the p53-Dependent Apoptotic Pathway. Mol Cell Biol. 2013; 33:3309-20. PMC3653351
110. Malhotra A, Shibata Y, Hall IM and Dutta A. Chromosomal structural variations during progression of a prostate epithelial cell line to a malignant metastatic state inactivate the NF2, NIPSNAP1, UGT2B17 and LPIN2 genes. Cancer Biol. Therapy, 2013;.epub 10.4161/cbt.25329 PMC3909553
109. Snow CJ, Dar A, Dutta A, Kehlenbach RH, Paschal BM. Defective nuclear import of Tpr in Progeria reflects the Ran sensitivity of large cargo transport. J Cell Biol. 2013; 201:541-57. PMC3653351
108. Park J, Long DT, Lee KY, Abbas T, Shibata E, Negishi M, Luo Y, Schimenti JC, Gambus A, Walter JC and Dutta A. The MCM8-9 complex promotes RAD51 recruitment at DNA damage sites to facilitate homologous recombination. Mol Cell Biol. 2013; 33:1632-44. PMC3624244
107. Abbas T, Mueller AC, Shibata E, Keaton M, Rossi M and Dutta A.CRL1-FBXO11 promotes Cdt2 ubiquitylation and degradation and regulates Pr-Set7/Set8-mediated cellular migration. Molecular Cell. 2013. 49:1147-58. PMC3615078
106. Sun D, Layer R, Mueller AC, Cichewicz M, Negishi M, Paschal BM and Dutta A. Regulation of several androgen-induced genes through the repression miR 99a/let-7c/miR 125-b-2 miRNA cluster in prostate cancer cells. Oncogene. 2014;33:1448-57 PMC3915043 (Epub 2013)
105. Jha S, Gupta A, Dar A and Dutta A. RVBs are required for assembling a functional TIP60 complex. Mol Cell Biol. 2013, 33:1164-74. PMC3592018
104. Gupta A, Jha S, Engel DA, Ornelles DA and Dutta A. Tip60 degradation by adenovirus relieves transcriptional repression of viral transcriptional activator E1A. Oncogene. 2013; 32:5017-25. doi: 10.1038/onc.2012.534. [Epub 2012] PMC3955737
103. Gagan JR, Dey BK, Layer R, Yan Z and Dutta A. Notch3 and Mef2c Are Mutually Antagonistic via Mkp1 and miR-1/206 in Differentiating Myoblasts. J. Biol. Chem. 2012; 287:40360-70. PMC3504751
102. Dey BK, Gagan JR, Yan Z, Dutta A. MiR-26a is required for skeletal muscle differentiation and regeneration in mice. Genes & Development. 2012; 26:2180-2191. PMC3465739
101. Mueller AC, Sun D, Dutta A. The miR-99 family regulates the DNA damage response through its target SNF2H. Oncogene. 2013; 32:1164-72 PMC3407337 (Epub 2012)
100. Shibata Y, Kumar P, Layer R, Willcox S, Gagan JR, Griffith JD, Dutta A. Extrachromosomal MicroDNAs and Chromosomal Microdeletions in Normal Tissues. Science. 2012; 336:82-6 F1000 citation. PMC3703515
99. Jazaeri AA, Bryant JL, Park H, Li H, Dahiya N, Stoler MH, Ferriss JS, Dutta A. Molecular requirements for transformation of fallopian tube epithelial cells into serous carcinoma. Neoplasia. 2011; 13:899-911. PMC3201567
98. Van Rechem C, Black JC, Abbas TA, Allen A, Rinehart CA, Yuan GC, Dutta A, Whetstine JR. The SKP1 - Cul1 - F-box and Leucine-rich repeat protein 4 (SCF-FbxL4) ubiquitin ligase regulates lysine demethylase 4A (KDM4A)/Jumonji domain-containing 2A (JMJD2A). J Biol Chem. 2011; 286:30462-70. PMC3162406
97. Shibata E, Abbas T, Huang X, Wohlschlegel JA and Dutta A. Selective ubiquitylation of p21 and Cdt1 by UbcH8 and Ube2G ubiquitin-conjugating enzymes via the CRL4-Cdt2 ubiquitin ligase complex. Mol. Cell Biol., 2011; 31:3136-45 PMC3147600
96. Gagan JR, Dey BK, Layer R, Yan Z and Dutta A. MICRORNA-378 targets the myogenic repressor MyoR during myoblast differentiation, J. Biol. Chem., 2011; 286:19431-8. PMC3103322
95. Keaton M and Dutta A. Nuclear Scaffold Attachment Sites within ENCODE Regions Associate with Actively Transcribed Genes, PLOS One, 2011; 6 : e17912. PMC3056778
94. Karnani N and Dutta A. The effect of the intra-S-phase checkpoint on origins of replication in human cells. Genes & Development, 2011; 25:621-33. PMC3059835
93. Mesner LD, Valsakumar V, Karnani N, Dutta A, Hamlin JL, Bekiranov S. Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription. Genome Res., 2011, 21:377-89. (F1000 citation) PMC3044852
92. Sun D, Lee YS, Malhotra A, Kim HK, Matecic M, Evans C, Jensen RV, Moskaluk CA and Dutta A. miR-99 family of microRNAs suppresses the expression of prostate specific antigen and prostate cancer cell proliferation. Cancer Research, 2011; 71:1313-24. PMC3523179
91. Dey BK, Gagan J and Dutta A. MiR-206 and -486 induce myoblast differentiation by downregulating Pax7. Mol. Cell Biol., 2011, 31:203-14. PMC3019853
90. Lin JJ, Milhollen MA, Smith PG, Narayanan U and Dutta A. NEDD8-targeting drug MLN4924 elicits DNA rereplication by stabilizing Cdt1 in S phase, triggering checkpoint activation, apoptosis, and senescence in cancer cells. Cancer Research, 2010, 70:10310-20. PMC3059213
89. Abbas T, Shibata E, Park J, Jha S, Karnani N and Dutta A. CRL4Cdt2 Regulates Cell Proliferation and Histone Gene Expression by Targeting PR-Set7/Set8 for Degradation. Molecular Cell, 2010, 40: 9-21. (Featured Article, F1000 citation, Perspective in Molecular Cell, Research Highlight in Nature Reviews MCB) PMC2966975
88. Shibata Y, Malhotra A and Dutta A. Detection of DNA fusion junctions for BCR-ABL translocations by Anchored ChromPET. Genome Med. 2010, 2:70. PMC3092121 (Highly Accessed)
87. Jha S, Vande Pol S, Banerjee NS, Dutta AB, Chow LT, and Dutta A. Destabilization of TIP60 by human papillomavirus E6 results in attenuation of TIP60 dependent transcriptional regulation and apoptotic pathway. Molecular Cell, 2010, 38:700-11 (F1000 citation) PMC2886028
86. Sarkar S, Dey BK and Dutta A. MiR-322/424 and 503 are induced during muscle differentiation and promote cell-cycle quiescence and differentiation by downregulation of Cdc25A. Mol. Biol. Cell. 2010, 21:2138-49. PMC2893979
85. Jazaeri AA, Ferriss JS, Bryant JL, Dalton MS, Dutta A. Evaluation of EVI1 and EVI1s (Delta324) as potential therapeutic targets in ovarian cancer. Gynecol Oncol. 2010, 118:189-95
84. Karnani N, Taylor CM, Malhotra A and Dutta A. Genomic study of replication initiation in human chromosomes reveals the influence of transcription regulation and chromatin structure on origin selection. Mol. Biol. Cell. 2010; 21:393-404 PMC2814785
83. Terai K, Abbas T, Jazaeri AA and Dutta A. CRL4Cdt2 E3 ubiquitin ligase monoubiquitinates PCNA to promote translesion DNA synthesis. Molecular Cell, 2010; 37:143-149. PMC2818832
82. Machida YJ, Machida Y, Vashisht A, Wohlschlegel JA and Dutta A. The Deubiquitinating Enzyme BAP1 Regulates Cell Growth via Interaction with HCF-1. J. Biol. Chem., 2009; 284:34179-88. PMC2797188
81. Lee YS, Shibata Y, Malhotra A and Dutta A. A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes & Development, 2009; 23:2639-49. PMC2779758
80. Shibata Y, Malhotra A, Bekiranov S and Dutta A. Yeast genome analysis identifies chromosomal translocation, gene conversion events and several sites of Ty element insertion. Nucleic Acids Research, 2009: 37:6454-65. PMC2770650
79. Torreira E, Jha S, López-Blanco JR, Arias-Palomo E, Chacón P, Cañas C, Ayora S, Dutta A and Llorca O. Architecture of the pontin/reptin complex, essential in the assembly of several macromolecular complexes. Structure, 2008: 16:1511-20. PMC2577609
78. Abbas T, Sivaprasad U, Terai K, Amador V, Pagano M and Dutta A. PCNA-dependent regulation of p21 ubiquitylation and degradation via the CRL4-cdt2 ubiquitin ligase complex. Genes & Development, 2008; 22:2496-506. PMC2546691
77. Lew DJ, Burke DJ and Dutta A. The immortal strand hypothesis: How could it work? Cell, 2008; 133:21-23.
76. Jha S, Shibata E and Dutta A. Human Rvb1/Tip49 is required for the HAT activity of TIP60/NuA4 and for the downregulation of phosphorylation on H2AX after DNA damage. Mol. Cell. Biol. 2008; 28:2690-700. PMC2293106
75. Teer JK and Dutta A. Human Cdt1 lacking the evolutionarily conserved region that interacts with MCM2-7 is capable of inducing re-replication. J. Biol. Chem. 2008; 283:6817-25.
74. Deng Z, Dheekollu J, Broccoli D, Dutta A and Lieberman PM. The Origin Recognition Complex Localizes to Telomere Repeats and Prevents Telomere-Circle Formation. Current Biology. 2007; 17:1989-95.
73. Alpi A, Langevin F, Mosedale G, Machida YJ, Dutta A and Patel KJ. UBE2T, the FA core complex and FANCD2 are recruited independently to chromatin: A basis for the regulation of FANCD2 monoubiquitination. Mol Cell Biol. 2007; 27:8421-30
72. Lin JJ and Dutta A. ATR pathway is the primary pathway for activating G2/M checkpoint induction after re-replication. J. Biol. Chem. 2007; 282:30357-62 (Highlighted as “Research Highlight” in Nature Structural and Molecular Biology, 14:1061)
71. Zhu W, Ukomadu C, Jha S, Senga T, Dhar SK, Wohlschlegel JA, Nutt LK, Kornbluth S and Dutta A. Mcm10 and And-1/CTF4 recruit DNA polymerase α to chromatin for initiation of DNA replication. . Genes & Development, 2007; 21:2288-99. (F1000 citation)
70. ENCODE project consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project consortium. Nature, 2007; 447: 799-816. (Our group provided and analyzed the DNA replication data for the consortium; F1000 citation.) PMC2212820
69. Lee YS and Dutta A. The tumor suppressor microRNA let-7 represses the HMGA2 oncogene. Genes & Development, 2007; 21:1025-30. (Accompanied by a Perspectives essay). PMC1855228
68. Abbas T, Jha S, Sherman NE and Dutta A. Autocatalytic Phosphorylation of CDK2 at the Activating Thr160. Cell Cycle, 2007; 6:843-52. (F1000 citation)
67. Machida YJ and Dutta A. The APC/C Inhibitor, Emi1, Is Essential for Prevention of Rereplication. Genes & Development, 2007; 21:184-194. (F1000 citation) PMC1770901
66. Karnani N, Taylor C M, Malhotra A and Dutta A. Pan-S replication patterns and chromosomal domains defined by genome tiling arrays of ENCODE genomic areas. Genome Research, 2007; 17 : 865-76. (F1000 citation)
65. Machida Y J, Chen Y, Machida Y, Malhotra A, Sarkar S and Dutta A. Targeted Comparative RNAi (TARCOR) Analysis Reveals Differential Requirement of Genes Essential for Cell Proliferation. Mol. Biol. Cell. 2006; 17: 4837–4845.
64. Sivaprasad U, Abbas T and Dutta A. Differential efficacy of HMG CoA reductase inhibitors on the cell cycle of prostate cancer cells. Molecular Cancer Therapeutics, 2006; 5: 2310-6.
63. Machida Y J, Machida Y, Chen Y, Gurtan A, Kupfer G M, D’Andrea A D and Dutta A. UBE2T is the E2 in the Fanconi Anemia Pathway and Undergoes Negative Autoregulation. Molecular Cell, 2006; 23, 589-96.
62. Kim HK, Lee YS, Sivaprasad U, Malhotra A and Dutta A. Muscle-specific microRNA miR-206 promotes muscle differentiation. J. Cell Biol. 2006; 174, 677-687. (Cover Image and News Highlight in JCB; Research Highlight in Nature, 2006: 443, 4-5; F1000) PMC2064311
61. Zhu W and Dutta A. An ATR, BRCA1 mediated Fanconi Anemia pathway is required for activating the G2/M checkpoint and DNA damage repair upon re-replication. Mol. Cell. Biol. 2006; 26, 4601-11.
60. Ernkvist M, Aase K, Ukomadu C, Wohlschlegel J, Blackman R, Veitonmaki N, Bratt A, Dutta A and Holmgren L p130-Angiomotin associates with actin and controls endothelial cell shape. FEBS Journal, 2006; 273, 2000-11
59. Teer J K, Machida Y J, Labit H, Novac O, Hyrien O, Marheineke K, Zannis-Hadjopoulos M and Dutta A. Proliferating human cells hypomorphic for Orc2 and pre-RC formation have a defect in p53 activation and CDK2 kinase activation. J. Biol. Chem. 2006; 281, 6253-60.
58. Senga T, Sivaprasad U, Zhu W, Park J H, Arias E E, Walter J C and Dutta A. PCNA is a co-factor for Cdt1 degradation by CUL4/DDB1 mediated N-terminal ubiquitination. J. Biol. Chem. 2006; 281, 6246-52. (F1000)
57. Takeda D Y, Shibata Y, Parvin J D and Dutta A. Recruitment of ORC or CDC6 is sufficient to create an artificial origin of replication in mammalian cells. Genes & Development. 2005; 19, 2827-36. (Research Highlight in Nature Reviews Genetics and Nature Reviews MCB; F1000) PMC1315390.
56. Machida Y J, Teer J K and Dutta A. Acute reduction of an ORC subunit in human cells reveals a requirement of ORC for CDK2 activation. J. Biol. Chem. 2005; 280, 27624-27630.
55. Takeda D Y, Parvin J D and Dutta A. Degradation of Cdt1 during S phase is SKP2 independent and is required for efficient progression of mammalian cells through S phase. J. Biol. Chem. 2005; 280, 23416-23423.
54. Jeon Y, Bekiranov S, Karnani N, Kapranov P, Ghosh S, MacAlpine D, Lee C, Hwang DS, Gingeras T and Dutta A. Temporal profile of replication of human chromosomes. Proc. Natl. Acad. Sci. USA. 2005; 102, 6419-6424.
53. Lee YS, Kim HK, Chung S, Kim KS, and Dutta A. Depletion of human microRNA miR-125b reveals that it is critical for the proliferation of differentiated cells but not for the down-regulation of putative targets during differentiation. J Biol Chem. 2005; 280, 16635-16641.
52. ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 2004;306, 636-640.
51. Jónsson Z O, Jha S, Wohlschlegel J A and Dutta A. Rvb1p/Rvb2p recruit Arp5p and assemble a functional Ino80 chromatin remodeling complex. Molecular Cell, 2004; 16, 465-477.
50. Saxena S, Yuan P, Dhar SK, Senga T, Takeda D, Robinson H, Kornbluth SA, Swaminathan K and Dutta A. A dimerized coiled-coil domain and an adjoining part of geminin interact with two sites on Cdt1 for replication inhibition. Molecular Cell, 2004; 15, 245-258.
49. Zhu W, Chen Y and Dutta A. Re-replication by depletion of geminin is seen regardless of p53 status and activates a G2/M checkpoint. Mol. Cell. Biol. 2004; 24, 7140-7150. (Cover Image)
48. Yoshida K, Oyaizu N, Dutta A and Inoue I. The destruction box of human Geminin is critical for proliferation and tumor growth in human colon cancer cells. Oncogene. 2004; 23, 58-70.
47. Saxena S, Jonsson Z O and Dutta A. Small RNAs with imperfect match to endogenous mRNA repress translation: implications for off-target activity of siRNA in mammalian cells. J. Biol. Chem. 2003; 278, 44312-44319.
46. Ukomadu C and Dutta A. p21 dependent inhibition of colon cancer cell growth by mevastatin is independent of inhibition of G1 cyclin-dependent kinases. J. Biol. Chem. 2003; 278, 43586.
45. Vaziri C, Saxena S, Jeon Y, Lee C, Murata K, Machida Y, Wagle N, Hwang D S and Dutta A. A p53 dependent checkpoint pathway prevents re-replication. Molecular Cell 2003; 11, 997-1008. (Cover Image)
44. Ukomadu C and Dutta A. Inhibition of cdk2 activating phosphorylation by mevastatin. J. Biol. Chemistry 2003; 278, 4840-4846.
43. Wohlschlegel J A, Kutok J L , Weng A P and Dutta A. Expression of geminin as a marker of cell proliferation in normal tissues and malignancies. Am. J. Pathology 2002; 161, 267-273.
42. Wohlschlegel J A, Dhar SK, Prokhorova TA, Dutta A* and Walter J*. Xenopus Mcm10 binds to origins of DNA replication after Mcm2-7 and stimulates binding of Cdc45. Molecular Cell. 2002; 9, 233-240. * Co-corresponding authors. (F1000)
41. Chaudhuri B, Xu H, Todorov I, Dutta A and Yates J L. Human DNA replication initiation factors, ORC and MCM, associate with oriP of Epstein-Barr virus. . Proc Natl Acad Sci U S A. 2001; 98, 10085-10089.
40. Dhar S K, Yoshida K, Machida Y, Khaira P, Chaudhuri B, Wohlschlegel J A, Leffak M, Yates J and Dutta A. Replication from oriP of Epstein-Barr Virus requires human ORC and is inhibited by geminin. Cell, 2001; 106, 287-296.
39. Dhar S K, Delmolino L M and Dutta A. Architecture of the human Origin Recognition Complex. J Biol. Chemistry, 2001; 276, 29067-29071.
38. Delmolino L M, Saha P and Dutta A. Multiple mechanisms regulate subcellular localization of human CDC6: NLS, NES and phosphorylation. J.Biol. Chemistry. 2001; 276, 26947-26954.
37. Wohlschlegel J A, Dwyer B, Takeda D and Dutta A. A mutational analysis of the Cy motif from p21 reveals sequence degeneracy and specificity for different cyclin-dependent kinases. Mol. Cell. Biol. 2001; 21, 4868-4874.
36. Yoshida K, Kuo F, George E L, Sharpe A H and Dutta A. Requirement of CDC45 for postimplantation mouse development. Mol. Cell. Biol. 2001; 21, 4598-4603.
35. Jonsson Z O, Dhar S K, Narlikar G, Auty R, Wagle N, Pellman D, Pratt R E, Kingston R and Dutta A. Rvb1p and Rvb2p are essential components of a chromatin remodeling complex that regulates transcription of over 5% of yeast genes. J. Biol. Chemistry. 2001; 276,16279-16288.
34. Takeda D, Wohlschlegel J A, and Dutta A. A bipartite substrate recognition motif for cyclin-dependent kinases. J. Biol. Chemistry. 2001; 276, 1993-1997.
33. Wohlschlegel J A, Dwyer B, Dhar S K, Cvetic C, Walter J and Dutta A. Inhibition of eukaryotic DNA replication by geminin binding to Cdt1. Science. 2000; 290, 2309-2312. (Accompanied by Perspectives essay in Science)
32. Yamaguchi R and Dutta A. Proteasome inhibitors alter the orderly progression of DNA synthesis in S phase of HeLa cells and lead to re-replication of DNA. Exptl. Cell Research. 2000; 261, 271-283.
31. Thome K C, Dhar S K, Quintana D G, Delmolino L, Shahsafaei A and Dutta A. Subsets of human ORC subunits are expressed in non-proliferating cells and associate with non-ORC proteins. J. Biol. Chemistry. 2000; 275, 35233-35241.
30. Dhar S K and Dutta A. Identification of the human ORC6 homolog. J. Biol. Chemistry. 2000; 275, 34983-34988.
29. Datta M W, Renshaw A A, Dutta A, Hoffman M A and Loughlin KR. Evaluation of cyclin expression in testicular germ cell tumors: cyclin E correlates with tumor type, advanced clinical stage, and pulmonary metastasis. Modern Pathology. 2000; 13, 667-672
28. Pinto S, Quintana D G, Smith P, Mihalik R M, Hou Z -H, Boynton S, Jones C J, Hendricks M, Velinzon K, Wohlschlegel J A, Austin R J, Lane W S, Tully T* and Dutta A*. latheo encodes a subunit of the Origin Recognition Complex and disrupts neuronal proliferation and adult olfactory memory when mutant. Neuron. 1999; 23, 45-54. * Co-corresponding authors.
27. Quade B J, Park J J, Crum C P, Sun D, Dutta A. In vivo cyclin E expression as a marker for early cervical neoplasia. Modern Pathology. 1998; 11, 1238-1246.
26. Qiu X B, Lin Y L, Thome K C, Pian P, Schlegel B P, Weremowicz S, Parvin J D, Dutta A. An Eukaryotic RuvB-like Protein (RUVBL1) Essential for Growth. J. Biol. Chemistry 1998; 273, 27786-27793.
25.Quintana DG, Thome KC, Hou ZH, Ligon AH, Morton C C and Dutta A. ORC5L, a new member of the human Origin Recognition Complex, is deleted in uterine leiomyomas and malignant myeloid diseases. J. Biol. Chemistry 1998; 273, 27137-27145.
24.Renshaw A A, Loughlin K R, Dutta A. Cyclin A and Mib1 (Ki67) as markers of proliferation in primary renal neoplasms. Modern Pathology. 1998; 10, 963-966.
23. Saha P, Thome K C, Yamaguchi R, Hou Z H., Weremowicz S and Dutta A. The human homolog of Saccharomyces cerevisiae CDC45. J. Biol. Chemistry 1998; 273, 18205-18209.
22. Saha P, Chen J, Thome K C, Lawlis S J, Hou Z H, Hendricks M, Parvin J D, Dutta A. The human CDC6/Cdc18 associates with Orc1 and cyclin-cdk and is selectively eliminated from the nucleus at the onset of S phase. Mol. Cell. Biol. 1998; 18, 2758-2767.
21. Lin Y L, Shivji M K K, Chen C, Kolodner R, Wood R D, Dutta A. The evolutionarily conserved zinc finger motif in the largest sub-unit of human RPA is required for DNA replication and mismatch repair but not for nucleotide excision repair. J. Biol. Chemistry 1998; 273, 1453-1461.
20. Quintana DG, Hou ZH, Thome KC, Hendricks M, Saha P, Dutta A. Identification of a novel subunit of the human origin recognition complex with homology to yeast Orc4. J. Biol. Chemistry 1997; 272, 28247-28251.
19. Saha P, Eichbaum Q, Silberman E D, Mayer B J, Dutta A. p21/CIP1 and Cdc25A, competition between an inhibitor and an activator of cyclin dependent kinases. Mol. Cell. Biol. 1997; 17, 4338-4345.
18. Chen J, Chen S, Saha P and Dutta A. p21 disrupts the recruitment of human Fen1 by proliferating cell nuclear antigen into the DNA replication apparatus. Proc. Natl. Acad. Sci. USA. 1996; 93, 11597-11602.
17. Mashal R D, Lester S, Corless C, Richie J P, Chandra R, Propert K J, Dutta A. Expression of cell-cycle regulated proteins in prostate cancer. Cancer Research. 1996; 56, 4159-4163.
16. Chen J, Saha P, Kornbluth S, Dynlacht B, Dutta A. Cyclin binding motifs are essential for the function of p21/CIP1. Mol. Cell. Biol. 1996; 16, 4673-4682.
15. Henricksen L A, Carter T, Dutta A, Wold M S. Phosphorylation of human replication protein A by the DNA-dependent protein kinase is involved in the modulation of DNA replication. Nucleic Acids Research. 1996; 24, 3107-3112.
14. Leiter L M, Chen J, Marathe T, Tanaka M, Dutta A. Loss of transactivation and transrepression function, and not RPA binding, alters growth suppression by p53. Oncogene. 1996; 12, 2661-2668.
13. Lin Y-L, Chen C, Keshav K F, Winchester E, Dutta A. Dissection of functional domains of the human DNA replication protein complex Replication Protein A. J. Biol. Chemistry. 1996; 271, 17190-17198.
12.Chen J, Peters R, Saha P, Lee P, Theodoras A, Pagano M, Wagner G, Dutta A. A 39 amino acid fragment of the cell cycle regulator p21 is sufficient to bind PCNA and partially inhibit DNA replication in vivo. Nucleic Acids Research. 1996; 24, 1727-1733.
11. Keshav K F, Chen C, Dutta A. Rpa4, a homolog of the 34 kDa subunit of the replication protein A complex. Mol. Cell. Biol. 1995; 15, 3119-3128.
10. Dutta A, Chandra R, Leiter L M, Lester S. Cyclins as markers of tumor proliferation and angiogenesis: immunocytochemical studies in breast cancer. Proc Natl Acad Sci USA. 1995; 92, 5386-5390.
9. Chen J, Jackson P K, Kirschner M W, and Dutta A. Separate domains of p21 involved in the inhibition of cdk kinase and PCNA. Nature. 1995; 374, 386-388
8. Dutta A, Ruppert J M, Aster J C, Winchester E. Inhibition of DNA replication factor RPA by p53. Nature. 1993; 365, 79-82. (Accompanied by News and Views piece in Nature)
7. Dutta A, Stillman B. cdc2 family kinases phosphorylate a human cell DNA replication factor, RPA, and activate DNA replication. EMBO J. 1992; 11, 2189-2199.
6. Dutta A, Hamaguchi M, Hanafusa H. Serum independence of transcription from the promoter of an avian retrovirus in v-src transformed cells is a primary, intracellular effect of increased tyrosine phosphorylation. Proc Natl Acad Sci U S A. 1990; 87, 608-612.
5. Dutta A, Stoeckle M Y, Hanafusa H. Serum and v-src increase the level of CCAAT binding factor required for transcription from a retroviral LTR. Genes & Dev. 1990; 4, 243-254.
4. Prywes R, Dutta A, Cromlish J A, Roeder R G. Phosphorylation of serum response factor, a factor that binds to the serum response element upstream of the c-fos promoter. Proc Natl Acad Sci USA. 1988; 85, 7206-7210.
3. Dutta A, Dorai T, Hanafusa H. The putative trans-activator in the MA gag region of Rous sarcoma virus is not required for cell transformation. J Virol. 1988; 62, 4767-4769.
2. Dutta A, Majumder H K. Effects of monosaccharides on uptake of Leishmania donovani promastigotes by murine macrophages. Indian Jl Biochem Biophys. 1986; 23, 1-4.
1. Dutta A, Wang L-H, Hanafusa T, Hanafusa H. Partial nucleotide sequence of Rous sarcoma virus-29 provides evidence that the original Rous sarcoma virus was replication defective. J Virol. 1985; 55, 728-735.