Anindya Dutta2020WEBProfessor
Chair, Department of Genetics


MBBS, Medicine
Christian Medical College, Vellore, India
Viral Oncology, The Rockefeller University, New York, NY
Cell Cycle, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Pathology, Brigham & Women's Hospital, Harvard Medical School


Lab Site

Research Disciplines

Bioinformatics and Genomics, Biotechnology, Cancer Biology, Epigenetics, Molecular Biology

Research Interests

Genomic Instability in Cancer Cells; Noncoding RNAs in differentiation and cancer; Bioinformatics of cancer outcome

Research Description

The current rotation projects in the lab relate to:

(1) Novel extrachromosomal circles of DNA in normal cells and cancer:

(2) Long noncoding RNAs that regulate cancer, e.g. DRAIC, or skeletal muscle differentiation, e.g. MUNC

(3) Novel short noncoding RNAs related to microRNAs: tRFs in the context of cancer.

(4) Bioinformatics for cancer:

Selected Publications

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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-κB Activation., 2020; Cancer research. 80(5) 950-963. PMID: 31900260 | PMCID: PMC7056510


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., 2020; Genome medicine. 12(1) 15. PMID: 32066500 | PMCID: PMC7027124


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., 2020; FASEB journal : official publication of the Federation of American Societies for Experimental Biology. () . PMID: 32277852


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., 2020; Science advances. 6(20) eaba2489. PMID: 32440553 | PMCID: PMC7228742


Chiu RWK, Dutta A, Hensson AG, Lo YMD, Mischel P, Regenberg B, What Is Extrachromosomal Circular DNA and What Does It Do?, 2020; Clinical chemistry. 66(6) 754-759. PMID: 32470125 | PMCID: PMC7259478


Chatrath A, Kiran M, Kumar P, Ratan A, Dutta A, The Germline Variants rs61757955 and rs34988193 Are Predictive of Survival in Lower Grade Glioma Patients., 2019; Molecular cancer research : MCR. 17(5) 1075-1086. PMID: 30651372 | PMCID: PMC6497557


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., 2019; Nucleic acids research. 47(9) 4586-4596. PMID: 30828735 | PMCID: PMC6511871


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., 2019; The Journal of biological chemistry. 294(45) 16930-16941. PMID: 31582561 | PMCID: PMC6851321


Cichewicz MA, Kiran M, Przanowska RK, Sobierajska E, Shibata Y, Dutta A, MUNC, an Enhancer RNA Upstream from the MYOD Gene, Induces a Subgroup of Myogenic Transcripts in trans Independently of MyoD., 2018; Molecular and cellular biology. 38(20) . PMID: 30037979 | PMCID: PMC6168980


Kiran S, Dar A, Singh SK, Lee KY, Dutta A, The Deubiquitinase USP46 Is Essential for Proliferation and Tumor Growth of HPV-Transformed Cancers., 2018; Molecular cell. 72(5) 823-835.e5. PMID: 30415951 | PMCID: PMC6294304


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., 2018; Molecular neurobiology. 56(7) 4786-4798. PMID: 30392137 | PMCID: PMC6499716


Paulsen T, Kumar P, Koseoglu MM, Dutta A, Discoveries of Extrachromosomal Circles of DNA in Normal and Tumor Cells., 2018; Trends in genetics : TIG. 34(4) 270-278. PMID: 29329720 | PMCID: PMC5881399


Reon BJ, Takao Real Karia B, Kiran M, Dutta A, LINC00152 Promotes Invasion through a 3'-Hairpin Structure and Associates with Prognosis in Glioblastoma., 2018; Molecular cancer research : MCR. 16(10) 1470-1482. PMID: 29991527 | PMCID: PMC6170721


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., 2018; RNA (New York, N.Y.). 24(8) 1093-1105. PMID: 29844106 | PMCID: PMC6049499


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., 2017; Molecular cell. 68(1) 61-75.e5. PMID: 28943310


Kumar P, Dillon LW, Shibata Y, Jazaeri AA, Jones DR, Dutta A, Normal and Cancerous Tissues Release Extrachromosomal Circular DNA (eccDNA) into the Circulation., 2017; Molecular cancer research : MCR. () . PMID: 28550083


Kumar P, Kuscu C, Dutta A, Biogenesis and Function of Transfer RNA-Related Fragments (tRFs)., 2016; Trends in biochemical sciences. 41(8) 679-89. PMID: 27263052 | PMCID: PMC5173347


Kuscu C, Dutta A, A Pro-metastatic tRNA Pathway., 2016; Cell. 165(6) 1314-1315. PMID: 27259143


Dutta A, Anindya Dutta., 2016; Current biology : CB. 25(23) R1112-4. PMID: 27027134


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., 2016; PLoS medicine. 13(12) e1002192. PMID: 27923049 | PMCID: PMC5140055


Reon BJ, Dutta A, Biological Processes Discovered by High-Throughput Sequencing., 2016; The American journal of pathology. () . PMID: 26828742


Shibata E, Kiran M, Shibata Y, Singh S, Kiran S, Dutta A, Two subunits of human ORC are dispensable for DNA replication and proliferation., 2016; eLife. 5() . PMID: 27906128 | PMCID: PMC5245961


Anaya J, Reon B, Chen WM, Bekiranov S, Dutta A, A pan-cancer analysis of prognostic genes., 2016; PeerJ. 3() e1499. PMID: 27047702 | PMCID: PMC4815555


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., 2015; Genes & development. 29(16) 1734-46. PMID: 26272819 | PMCID: PMC4561482


Sakurai K, Reon BJ, Anaya J, Dutta A, The lncRNA DRAIC/PCAT29 Locus Constitutes a Tumor-Suppressive Nexus., 2015; Molecular cancer research : MCR. 13(5) 828-38. PMID: 25700553 | PMCID: PMC4456356


Dillon LW, Kumar P, Shibata Y, Wang YH, Willcox S, Griffith JD, Pommier Y, Takeda S, Dutta A, Production of Extrachromosomal MicroDNAs Is Linked to Mismatch Repair Pathways and Transcriptional Activity., 2015; Cell reports. 11(11) 1749-59. PMID: 26051933 | PMCID: PMC4481157


Lee KY, Im JS, Shibata E, Park J, Handa N, Kowalczykowski SC, Dutta A, MCM8-9 complex promotes resection of double-strand break ends by MRE11-RAD50-NBS1 complex., 2015; Nature communications. 6() 7744. PMID: 26215093 | PMCID: PMC4525285


Lee KY, Dutta A, Initiation of replication in Xenopus egg extracts at a spatially defined origin., 2015; Cell cycle (Georgetown, Tex.). 14(15) 2391. PMID: 26091433 | PMCID: PMC4612457


Dey BK, Pfeifer K, Dutta A, The H19 long noncoding RNA gives rise to microRNAs miR-675-3p and miR-675-5p to promote skeletal muscle differentiation and regeneration., 2014; Genes & development. 28(5) 491-501. PMID: 24532688 | PMCID: PMC3950346


Floyd DH, Zhang Y, Dey BK, Kefas B, Breit H, Marks K, Dutta A, Herold-Mende C, Synowitz M, Glass R, Abounader R, 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., 2014; PloS one. 9(5) e96239. PMID: 24805821 | PMCID: PMC4013090


Shibata E, Dar A, Dutta A, CRL4Cdt2 E3 ubiquitin ligase and proliferating cell nuclear antigen (PCNA) cooperate to degrade thymine DNA glycosylase in S phase., 2014; The Journal of biological chemistry. 289(33) 23056-64. PMID: 24962565 | PMCID: PMC4132804


Dar A, Wu D, Lee N, Shibata E, Dutta A, 14-3-3 proteins play a role in the cell cycle by shielding cdt2 from ubiquitin-mediated degradation., 2014; Molecular and cellular biology. 34(21) 4049-61. PMID: 25154416 | PMCID: PMC4386460


Kumar P, Anaya J, Mudunuri SB, 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., 2014; BMC biology. 12() 78. PMID: 25270025 | PMCID: PMC4203973


Kumar P, Mudunuri SB, Anaya J, Dutta A, tRFdb: a database for transfer RNA fragments., 2014; Nucleic acids research. 43(0) D141-5. PMID: 25392422 | PMCID: PMC4383946


Mueller AC, Cichewicz MA, Dey BK, Layer R, Reon BJ, Gagan JR, Dutta A, MUNC, a long noncoding RNA that facilitates the function of MyoD in skeletal myogenesis., 2014; Molecular and cellular biology. 35(3) 498-513. PMID: 25403490 | PMCID: PMC4285423


Dey BK, Mueller AC, Dutta A, Long non-coding RNAs as emerging regulators of differentiation, development, and disease., 2014; Transcription. 5(4) e944014. PMID: 25483404 | PMCID: PMC4581346


Im JS, Keaton M, Lee KY, Kumar P, Park J, Dutta A, ATR checkpoint kinase and CRL1βTRCP collaborate to degrade ASF1a and thus repress genes overlapping with clusters of stalled replication forks., 2014; Genes & development. 28(8) 875-87. PMID: 24700029 | PMCID: PMC4003279


Negishi M, Wongpalee SP, Sarkar S, Park J, Lee KY, Shibata Y, Reon BJ, Abounader R, Suzuki Y, Sugano S, Dutta A, A New lncRNA, APTR, Associates with and Represses the CDKN1A/p21 Promoter by Recruiting Polycomb Proteins., 2014; PloS one. 9(4) e95216. PMID: 24748121 | PMCID: PMC3991591


Jha S, Gupta A, Dar A, Dutta A, RVBs are required for assembling a functional TIP60 complex., 2013; Molecular and cellular biology. 33(6) 1164-74. PMID: 23297341 | PMCID: PMC3592018


Sun D, Layer R, Mueller AC, Cichewicz MA, Negishi M, Paschal BM, Dutta A, Regulation of several androgen-induced genes through the repression of the miR-99a/let-7c/miR-125b-2 miRNA cluster in prostate cancer cells., 2013; Oncogene. () . PMID: 23503464 | PMCID: PMC3915043


Abbas T, Keaton MA, Dutta A, Genomic instability in cancer., 2013; Cold Spring Harbor perspectives in biology. 5(3) a012914. PMID: 23335075 | PMCID: PMC3578360


Park J, Long DT, Lee KY, Abbas T, Shibata E, Negishi M, Luo Y, Schimenti JC, Gambus A, Walter JC, Dutta A, The MCM8-MCM9 complex promotes RAD51 recruitment at DNA damage sites to facilitate homologous recombination., 2013; Molecular and cellular biology. 33(8) 1632-44. PMID: 23401855 | PMCID: PMC3624244


Abbas T, Mueller AC, Shibata E, Keaton M, Rossi M, Dutta A, CRL1-FBXO11 promotes Cdt2 ubiquitylation and degradation and regulates Pr-Set7/Set8-mediated cellular migration., 2013; Molecular cell. 49(6) 1147-58. PMID: 23478445 | PMCID: PMC3615078


Terai K, Shibata E, Abbas T, Dutta A, Degradation of p12 Subunit by CRL4Cdt2 E3 Ligase Inhibits Fork Progression after DNA Damage., 2013; The Journal of biological chemistry. 288(42) 30509-14. PMID: 24022480 | PMCID: PMC3798521


Dey BK, Gagan J, Yan Z, Dutta A, miR-26a is required for skeletal muscle differentiation and regeneration in mice., 2012; Genes & development. 26(19) 2180-91. PMID: 23028144 | PMCID: PMC3465739


Gagan J, Dey BK, Layer R, Yan Z, Dutta A, Notch3 and Mef2c Are Mutually Antagonistic via Mkp1 and miR-1/206 in Differentiating Myoblasts., 2012; The Journal of biological chemistry. () . PMID: 23055528 | PMCID: PMC3504751


Dey BK, Mueller AC, Dutta A, Non-micro-short RNAs: the new kids on the block., 2012; Molecular biology of the cell. 23(24) 4664-7. PMID: 23239791 | PMCID: PMC3521675


Shibata Y, Kumar P, Layer R, Willcox S, Gagan JR, Griffith JD, Dutta A, Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues., 2012; Science (New York, N.Y.). 336(6077) 82-6. PMID: 22403181 | PMCID: PMC3703515


Gagan J, Dey BK, Dutta A, MicroRNAs regulate and provide robustness to the myogenic transcriptional network., 2012; Current opinion in pharmacology. 12(3) 383-8. PMID: 22386695 | PMCID: PMC3369106


Mueller AC, Sun D, Dutta A, The miR-99 family regulates the DNA damage response through its target SNF2H., 2012; Oncogene. () . PMID: 22525276 | PMCID: PMC3407337


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., 2011; Neoplasia (New York, N.Y.). 13(10) 899-911. PMID: 22028616 | PMCID: PMC3201567


Gagan J, Dey BK, Layer R, Yan Z, Dutta A, MicroRNA-378 targets the myogenic repressor MyoR during myoblast differentiation., 2011; The Journal of biological chemistry. 286(22) 19431-8. PMID: 21471220 | PMCID: PMC3103322


Mueller AC, Keaton MA, Dutta A, DNA replication: mammalian Treslin-TopBP1 interaction mirrors yeast Sld3-Dpb11., 2011; Current biology : CB. 21(16) R638-40. PMID: 21855008 | PMCID: PMC3523092


Keaton MA, Taylor CM, Layer RM, Dutta A, Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes., 2011; PloS one. 6(3) e17912. PMID: 21423757 | PMCID: PMC3056778


Abbas T, Dutta A, CRL4Cdt2: master coordinator of cell cycle progression and genome stability., 2011; Cell cycle (Georgetown, Tex.). 10(2) 241-9. PMID: 21212733 | PMCID: PMC3025761


Sarkar S, Dey BK, Dutta A, MiR-322/424 and -503 are induced during muscle differentiation and promote cell cycle quiescence and differentiation by down-regulation of Cdc25A., 2010; Molecular biology of the cell. 21(13) 2138-49. PMID: 20462953 | PMCID: PMC2893979


Jha S, Vande Pol S, Banerjee NS, Dutta AB, Chow LT, Dutta A, Destabilization of TIP60 by human papillomavirus E6 results in attenuation of TIP60-dependent transcriptional regulation and apoptotic pathway., 2010; Molecular cell. 38(5) 700-11. PMID: 20542002 | PMCID: PMC2886028


Terai K, Abbas T, Jazaeri AA, Dutta A, CRL4(Cdt2) E3 ubiquitin ligase monoubiquitinates PCNA to promote translesion DNA synthesis., 2010; Molecular cell. 37(1) 143-9. PMID: 20129063 | PMCID: PMC2818832


Abbas T, Shibata E, Park J, Jha S, Karnani N, Dutta A, CRL4(Cdt2) regulates cell proliferation and histone gene expression by targeting PR-Set7/Set8 for degradation., 2010; Molecular cell. 40(1) 9-21. PMID: 20932471 | PMCID: PMC2966975


Dey BK, Gagan J, Dutta A, miR-206 and -486 induce myoblast differentiation by downregulating Pax7., 2010; Molecular and cellular biology. 31(1) 203-14. PMID: 21041476 | PMCID: PMC3019853


Lin JJ, Milhollen MA, Smith PG, Narayanan U, Dutta A, NEDD8-targeting drug MLN4924 elicits DNA rereplication by stabilizing Cdt1 in S phase, triggering checkpoint activation, apoptosis, and senescence in cancer cells., 2010; Cancer research. 70(24) 10310-20. PMID: 21159650 | PMCID: PMC3059213


Abbas T, Dutta A, p21 in cancer: intricate networks and multiple activities., 2009; Nature reviews. Cancer. 9(6) 400-14. PMID: 19440234 | PMCID: PMC2722839


Shibata Y, Malhotra A, Bekiranov S, Dutta A, Yeast genome analysis identifies chromosomal translocation, gene conversion events and several sites of Ty element insertion., 2009; Nucleic acids research. 37(19) 6454-65. PMID: 19710036 | PMCID: PMC2770650


Lee YS, Shibata Y, Malhotra A, Dutta A, A novel class of small RNAs: tRNA-derived RNA fragments (tRFs)., 2009; Genes & development. 23(22) 2639-49. PMID: 19933153 | PMCID: PMC2779758


Jha S, Shibata E, Dutta A, Human Rvb1/Tip49 is required for the histone acetyltransferase activity of Tip60/NuA4 and for the downregulation of phosphorylation on H2AX after DNA damage., 2008; Molecular and cellular biology. 28(8) 2690-700. PMID: 18285460 | PMCID: PMC2293106


Abbas T, Sivaprasad U, Terai K, Amador V, Pagano M, Dutta A, PCNA-dependent regulation of p21 ubiquitylation and degradation via the CRL4Cdt2 ubiquitin ligase complex., 2008; Genes & development. 22(18) 2496-506. PMID: 18794347 | PMCID: PMC2546691


Lew DJ, Burke DJ, Dutta A, The immortal strand hypothesis: how could it work?, 2008; Cell. 133(1) 21-3. PMID: 18394982 | PMCID: 18394982


Hook SS, Lin JJ, Dutta A, Mechanisms to control rereplication and implications for cancer., 2007; Current opinion in cell biology. 19(6) 663-71. PMID: 18053699 | PMCID: PMC2174913


Machida YJ, Dutta A, The APC/C inhibitor, Emi1, is essential for prevention of rereplication., 2007; Genes & development. 21(2) 184-94. PMID: 17234884 | PMCID: PMC1770901


Lee YS, Dutta A, The tumor suppressor microRNA let-7 represses the HMGA2 oncogene., 2007; Genes & development. 21(9) 1025-30. PMID: 17437991 | PMCID: PMC1855228


Zhu W, Ukomadu C, Jha S, Senga T, Dhar SK, Wohlschlegel JA, Nutt LK, Kornbluth S, Dutta A, Mcm10 and And-1/CTF4 recruit DNA polymerase alpha to chromatin for initiation of DNA replication., 2007; Genes & development. 21(18) 2288-99. PMID: 17761813 | PMCID: PMC1973143


Zhu W, Dutta A, An ATR- and BRCA1-mediated Fanconi anemia pathway is required for activating the G2/M checkpoint and DNA damage repair upon rereplication., 2006; Molecular and cellular biology. 26(12) 4601-11. PMID: 16738325 | PMCID: PMC1489121


Kim HK, Lee YS, Sivaprasad U, Malhotra A, Dutta A, Muscle-specific microRNA miR-206 promotes muscle differentiation., 2006; The Journal of cell biology. 174(5) 677-87. PMID: 16923828 | PMCID: PMC2064311