Anindya Dutta


  • MBBS, Christian Medical College, Vellore, India
  • PhD, The Rockefeller University, New York, NY
  • Postdoc, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
  • Resident, Brigham & Women’s Hospital, Harvard Medical School

Primary Appointment

  • Professor and Chair, Biochemistry and Molecular Genetics


Research Interest(s)

Genomic Instability in Cancer Cells; Noncoding RNAs in differentiation and cancer

Research Description

Our lab studies two different areas: genomic stability/instability in normal and cancer cells and the role of short and long noncoding RNAs in cell proliferation and differentiation. The projects in the lab are summarized below:

(1) DNA replication and response to DNA damage in human cells to determine how disorders in their regulation lead to genomic instability. For example, we have mapped hundreds of origins of replication in human cells, study how anti-cancer drugs impact on their activity and discover novel targets for ubiquitination important for genomic stability. We have discovered novel extrachromosomal circles of DNA, microDNAs, in normal cells and tissues and are analyzing how they contribute to cell function.

(2) MicroRNAs, novel non-micro short RNAs and long noncoding RNAs that regulate differentiation (muscle) or cancer progression (prostate). We discover RNAs that change during specific cellular transitions by cloning/high-throughput sequencing, determine whether the RNA is important for the biological transition and ascertain the mechanism of action of the RNA. We have discovered microRNAs and long noncoding RNAs critical for muscle differentiation and a new class of non-micro-short RNAs, tRFs , whose function is being investigated.

Selected Publications

  • Kumar P, Dillon L, Shibata Y, Jazaeri A, Jones D, Dutta A. Normal and Cancerous Tissues Release Extrachromosomal Circular DNA (eccDNA) into the Circulation. Molecular cancer research : MCR. 2017. PMID: 28550083
  • Lee K, Im J, Shibata E, Dutta A. ASF1a Promotes Non-homologous End Joining Repair by Facilitating Phosphorylation of MDC1 by ATM at Double-Strand Breaks. Molecular cell. 2017;68(1): 61-75.e5. PMID: 28943310
  • Anindya Dutta. Current biology : CB. 2016;25(23): R1112-4. PMID: 27027134
  • Anaya J, Reon B, Chen W, Bekiranov S, Dutta A. A pan-cancer analysis of prognostic genes. PeerJ. 2016;3 e1499. PMID: 27047702 | PMCID: PMC4815555
  • Kumar P, Kuscu C, Dutta A. Biogenesis and Function of Transfer RNA-Related Fragments (tRFs). Trends in biochemical sciences. 2016;41(8): 679-89. PMID: 27263052 | PMCID: PMC5173347
  • Kuscu C, Dutta A. A Pro-metastatic tRNA Pathway. Cell. 2016;165(6): 1314-1315. PMID: 27259143
  • Reon B, 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 medicine. 2016;13(12): e1002192. PMID: 27923049 | PMCID: PMC5140055
  • Reon B, Dutta A. Biological Processes Discovered by High-Throughput Sequencing. The American journal of pathology. 2016. 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. eLife. 2016;5. PMID: 27906128 | PMCID: PMC5245961
  • Coleman K, Grant G, Haggerty R, Brantley K, Shibata E, Workman B, Dutta A, Varma D, Purvis J, Cook J. Sequential replication-coupled destruction at G1/S ensures genome stability. Genes & development. 2015;29(16): 1734-46. PMID: 26272819 | PMCID: PMC4561482
  • Dillon L, Kumar P, Shibata Y, Wang Y, Willcox S, Griffith J, Pommier Y, Takeda S, Dutta A. Production of Extrachromosomal MicroDNAs Is Linked to Mismatch Repair Pathways and Transcriptional Activity. Cell reports. 2015;11(11): 1749-59. PMID: 26051933 | PMCID: PMC4481157
  • Lee K, Dutta A. Initiation of replication in Xenopus egg extracts at a spatially defined origin. Cell cycle (Georgetown, Tex.). 2015;14(15): 2391. PMID: 26091433 | PMCID: PMC4612457
  • Lee K, Im J, Shibata E, Park J, Handa N, Kowalczykowski S, Dutta A. MCM8-9 complex promotes resection of double-strand break ends by MRE11-RAD50-NBS1 complex. Nature communications. 2015;6 7744. PMID: 26215093 | PMCID: PMC4525285
  • Sakurai K, Reon B, Anaya J, Dutta A. The lncRNA DRAIC/PCAT29 Locus Constitutes a Tumor-Suppressive Nexus. Molecular cancer research : MCR. 2015;13(5): 828-38. PMID: 25700553 | PMCID: PMC4456356
  • 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. Molecular and cellular biology. 2014;34(21): 4049-61. PMID: 25154416 | PMCID: PMC4386460
  • Dey B, Mueller A, Dutta A. Long non-coding RNAs as emerging regulators of differentiation, development, and disease. Transcription. 2014;5(4): e944014. PMID: 25483404 | PMCID: PMC4581346
  • Dey B, 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. Genes & development. 2014;28(5): 491-501. PMID: 24532688 | PMCID: PMC3950346
  • Floyd D, Zhang Y, Dey B, Kefas B, Breit H, Marks K, Dutta A, Herold-Mende C, Synowitz M, Glass R, Abounader R, Purow B. 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(5): e96239. PMID: 24805821 | PMCID: PMC4013090
  • Im J, Keaton M, Lee K, 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. Genes & development. 2014;28(8): 875-87. PMID: 24700029 | PMCID: PMC4003279
  • Kumar P, Anaya J, Mudunuri S, 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. PMID: 25270025 | PMCID: PMC4203973
  • Kumar P, Mudunuri S, Anaya J, Dutta A. tRFdb: a database for transfer RNA fragments. Nucleic acids research. 2014;43 D141-5. PMID: 25392422 | PMCID: PMC4383946
  • Mueller A, Cichewicz M, Dey B, Layer R, Reon B, Gagan J, Dutta A. MUNC, a long noncoding RNA that facilitates the function of MyoD in skeletal myogenesis. Molecular and cellular biology. 2014;35(3): 498-513. PMID: 25403490 | PMCID: PMC4285423
  • Negishi M, Wongpalee S, Sarkar S, Park J, Lee K, Shibata Y, Reon B, Abounader R, Suzuki Y, Sugano S, Dutta A. A New lncRNA, APTR, Associates with and Represses the CDKN1A/p21 Promoter by Recruiting Polycomb Proteins. PloS one. 2014;9(4): e95216. PMID: 24748121 | PMCID: PMC3991591
  • 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. The Journal of biological chemistry. 2014;289(33): 23056-64. PMID: 24962565 | PMCID: PMC4132804
  • Abbas T, Keaton M, Dutta A. Genomic instability in cancer. Cold Spring Harbor perspectives in biology. 2013;5(3): a012914. PMID: 23335075 | PMCID: PMC3578360
  • Abbas T, Mueller A, Shibata E, Keaton M, Rossi M, Dutta A. CRL1-FBXO11 promotes Cdt2 ubiquitylation and degradation and regulates Pr-Set7/Set8-mediated cellular migration. Molecular cell. 2013;49(6): 1147-58. PMID: 23478445 | PMCID: PMC3615078
  • Jha S, Gupta A, Dar A, Dutta A. RVBs are required for assembling a functional TIP60 complex. Molecular and cellular biology. 2013;33(6): 1164-74. PMID: 23297341 | PMCID: PMC3592018
  • Park J, Long D, Lee K, Abbas T, Shibata E, Negishi M, Luo Y, Schimenti J, Gambus A, Walter J, Dutta A. The MCM8-MCM9 complex promotes RAD51 recruitment at DNA damage sites to facilitate homologous recombination. Molecular and cellular biology. 2013;33(8): 1632-44. PMID: 23401855 | PMCID: PMC3624244
  • Sun D, Layer R, Mueller A, Cichewicz M, Negishi M, Paschal B, 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. Oncogene. 2013. PMID: 23503464 | PMCID: PMC3915043
  • Terai K, Shibata E, Abbas T, Dutta A. Degradation of p12 Subunit by CRL4Cdt2 E3 Ligase Inhibits Fork Progression after DNA Damage. The Journal of biological chemistry. 2013;288(42): 30509-14. PMID: 24022480 | PMCID: PMC3798521
  • Dey B, Gagan J, Yan Z, Dutta A. miR-26a is required for skeletal muscle differentiation and regeneration in mice. Genes & development. 2012;26(19): 2180-91. PMID: 23028144 | PMCID: PMC3465739
  • Dey B, Mueller A, Dutta A. Non-micro-short RNAs: the new kids on the block. Molecular biology of the cell. 2012;23(24): 4664-7. PMID: 23239791 | PMCID: PMC3521675
  • Gagan J, Dey B, Dutta A. MicroRNAs regulate and provide robustness to the myogenic transcriptional network. Current opinion in pharmacology. 2012;12(3): 383-8. PMID: 22386695 | PMCID: PMC3369106
  • Gagan J, Dey B, Layer R, Yan Z, Dutta A. Notch3 and Mef2c Are Mutually Antagonistic via Mkp1 and miR-1/206 in Differentiating Myoblasts. The Journal of biological chemistry. 2012. PMID: 23055528 | PMCID: PMC3504751
  • Mueller A, Sun D, Dutta A. The miR-99 family regulates the DNA damage response through its target SNF2H. Oncogene. 2012. PMID: 22525276 | PMCID: PMC3407337
  • Shibata Y, Kumar P, Layer R, Willcox S, Gagan J, Griffith J, Dutta A. Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues. Science (New York, N.Y.). 2012;336(6077): 82-6. PMID: 22403181 | PMCID: PMC3703515
  • Abbas T, Dutta A. CRL4Cdt2: master coordinator of cell cycle progression and genome stability. Cell cycle (Georgetown, Tex.). 2011;10(2): 241-9. PMID: 21212733 | PMCID: PMC3025761
  • Gagan J, Dey B, Layer R, Yan Z, Dutta A. MicroRNA-378 targets the myogenic repressor MyoR during myoblast differentiation. The Journal of biological chemistry. 2011;286(22): 19431-8. PMID: 21471220 | PMCID: PMC3103322
  • Jazaeri A, Bryant J, Park H, Li H, Dahiya N, Stoler M, Ferriss J, Dutta A. Molecular requirements for transformation of fallopian tube epithelial cells into serous carcinoma. Neoplasia (New York, N.Y.). 2011;13(10): 899-911. PMID: 22028616 | PMCID: PMC3201567
  • Keaton M, Taylor C, Layer R, Dutta A. Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes. PloS one. 2011;6(3): e17912. PMID: 21423757 | PMCID: PMC3056778
  • Mueller A, Keaton M, Dutta A. DNA replication: mammalian Treslin-TopBP1 interaction mirrors yeast Sld3-Dpb11. Current biology : CB. 2011;21(16): R638-40. PMID: 21855008 | PMCID: PMC3523092
  • 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. Molecular cell. 2010;40(1): 9-21. PMID: 20932471 | PMCID: PMC2966975
  • Dey B, Gagan J, Dutta A. miR-206 and -486 induce myoblast differentiation by downregulating Pax7. Molecular and cellular biology. 2010;31(1): 203-14. PMID: 21041476 | PMCID: PMC3019853
  • Jha S, Vande Pol S, Banerjee N, Dutta A, Chow L, Dutta A. Destabilization of TIP60 by human papillomavirus E6 results in attenuation of TIP60-dependent transcriptional regulation and apoptotic pathway. Molecular cell. 2010;38(5): 700-11. PMID: 20542002 | PMCID: PMC2886028
  • Lin J, Milhollen M, Smith P, 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. Cancer research. 2010;70(24): 10310-20. PMID: 21159650 | PMCID: PMC3059213
  • Sarkar S, Dey B, Dutta A. MiR-322/424 and -503 are induced during muscle differentiation and promote cell cycle quiescence and differentiation by down-regulation of Cdc25A. Molecular biology of the cell. 2010;21(13): 2138-49. PMID: 20462953 | PMCID: PMC2893979
  • Terai K, Abbas T, Jazaeri A, Dutta A. CRL4(Cdt2) E3 ubiquitin ligase monoubiquitinates PCNA to promote translesion DNA synthesis. Molecular cell. 2010;37(1): 143-9. PMID: 20129063 | PMCID: PMC2818832
  • Abbas T, Dutta A. p21 in cancer: intricate networks and multiple activities. Nature reviews. Cancer. 2009;9(6): 400-14. PMID: 19440234 | PMCID: PMC2722839
  • Lee Y, Shibata Y, Malhotra A, Dutta A. A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes & development. 2009;23(22): 2639-49. PMID: 19933153 | PMCID: PMC2779758
  • Shibata Y, Malhotra A, Bekiranov S, Dutta A. Yeast genome analysis identifies chromosomal translocation, gene conversion events and several sites of Ty element insertion. Nucleic acids research. 2009;37(19): 6454-65. PMID: 19710036 | PMCID: PMC2770650
  • 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. Genes & development. 2008;22(18): 2496-506. PMID: 18794347 | PMCID: PMC2546691
  • 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. Molecular and cellular biology. 2008;28(8): 2690-700. PMID: 18285460 | PMCID: PMC2293106
  • Lew D, Burke D, Dutta A. The immortal strand hypothesis: how could it work? Cell. 2008;133(1): 21-3. PMID: 18394982 | PMCID: 18394982
  • Hook S, Lin J, Dutta A. Mechanisms to control rereplication and implications for cancer. Current opinion in cell biology. 2007;19(6): 663-71. PMID: 18053699 | PMCID: PMC2174913
  • Lee Y, Dutta A. The tumor suppressor microRNA let-7 represses the HMGA2 oncogene. Genes & development. 2007;21(9): 1025-30. PMID: 17437991 | PMCID: PMC1855228
  • Machida Y, Dutta A. The APC/C inhibitor, Emi1, is essential for prevention of rereplication. Genes & development. 2007;21(2): 184-94. PMID: 17234884 | PMCID: PMC1770901
  • Zhu W, Ukomadu C, Jha S, Senga T, Dhar S, Wohlschlegel J, Nutt L, Kornbluth S, Dutta A. Mcm10 and And-1/CTF4 recruit DNA polymerase alpha to chromatin for initiation of DNA replication. Genes & development. 2007;21(18): 2288-99. PMID: 17761813 | PMCID: PMC1973143
  • Kim H, Lee Y, Sivaprasad U, Malhotra A, Dutta A. Muscle-specific microRNA miR-206 promotes muscle differentiation. The Journal of cell biology. 2006;174(5): 677-87. PMID: 16923828 | PMCID: PMC2064311
  • 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. Molecular and cellular biology. 2006;26(12): 4601-11. PMID: 16738325 | PMCID: PMC1489121