Publications

title

37. Faseela, E. E., Notani, D., & Sabarinathan, R. (2023). Replication stress underlies genomic instability at CTCF/cohesin-binding sites in cancer. BioRxiv, 2023.10.24.563697. https://doi.org/10.1101/2023.10.24.563697

 

36. Soota, D., Saravanan, B., Mann, R., Kharbanda, T., & Notani, D. (2023). RNA binding limits the ligand induced transcriptional potential of estrogen receptor-alpha (ERα). BioRxiv, 2023.08.10.552751. https://doi.org/10.1101/2023.08.10.552751

 

35. Mann, R., & Notani, D. (2023). Transcription factor condensates and signaling driven transcription. Nucleus (Austin, Tex.), 14(1), 2205758. https://doi.org/10.1080/19491034.2023.2205758

 

34. Sreenivas, D., Kumar, V., Kathirvel, K., Vadnala, R. N., Mishra, S., Shelar, B., Marate, S., CP, L., K, S. D., Bhardwaj, M., Pandit, A., Mayor, S., Ramakrishnan, U., & Notani, D. (2023). Genomic surveillance reveals circulation of multiple variants and lineages of SARS-CoV-2 during COVID-19 pandemic in Indian city of Bengaluru. BioRxiv, 2023.03.14.532352. 

 

33. Islam, Z., Saravanan, B., Walavalkar, K., Farooq, U., Singh, A. K., Radhakrishnan, S., Thakur, J., Pandit, A., Henikoff, S., & Notani, D. (2023). Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries. Genome research, 33(1), 1–17. https://doi.org/10.1101/gr.276643.122

 

32. Venkatesan, V., Christopher, A. C., Rhiel, M., Azhagiri, M. K. K., Babu, P., Walavalkar, K., Saravanan, B., Andrieux, G., Rangaraj, S., Srinivasan, S., Karuppusamy, K. V., Jacob, A., Bagchi, A., Pai, A. A., Nakamura, Y., Kurita, R., Balasubramanian, P., Pai, R., Marepally, S. K., Mohankumar, K. M., … Thangavel, S. (2023). Editing the core region in HPFH deletions alters fetal and adult globin expression for treatment of β-hemoglobinopathies. Molecular therapy. Nucleic acids, 32, 671–688. https://doi.org/10.1016/j.omtn.2023.04.024

 

31. Notani D. (2022). First glimpse of enhancers in gene regulation. Nature reviews. Genetics, 23(9), 522–523. https://doi.org/10.1038/s41576-022-00492-7

 

30. Farooq, U., & Notani, D. (2022). Transcriptional regulation of INK4/ARF locus by cis and trans mechanisms. Frontiers in cell and developmental biology, 10, 948351. https://doi.org/10.3389/fcell.2022.948351

 

29. Singh, A. K., Walavalkar, K., Tavernari, D., Ciriello, G., Notani, D., & Sabarinathan, R. (2022). Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers. BioRxiv, 2022.11.28.518229.

 

28. Farooq, U., & Notani, D. (2021). Optimized protocol to create deletion in adherent cell lines using CRISPR/Cas9 system. STAR protocols, 2(4), 100857. https://doi.org/10.1016/j.xpro.2021.100857

 

27. Blobel, G. A., Higgs, D. R., Mitchell, J. A., Notani, D., & Young, R. A. (2021). Testing the super-enhancer concept. Nature reviews. Genetics, 22(12), 749–755. https://doi.org/10.1038/s41576-021-00398-w

 

26. Mitra, R., Richhariya, S., Jayakumar, S., Notani, D., & Hasan, G. (2021). IP3-mediated Ca2+ signals regulate larval to pupal transition under nutrient stress through the H3K36 methyltransferase Set2. Development (Cambridge, England), 148(11), dev199018. https://doi.org/10.1242/dev.199018

 

25. Farooq, U., Saravanan, B., Islam, Z., Walavalkar, K., Singh, A. K., Jayani, R. S., Meel, S., Swaminathan, S., & Notani, D. (2021). An interdependent network of functional enhancers regulates transcription and EZH2 loading at the INK4a/ARF locus. Cell reports, 34(12), 108898. https://doi.org/10.1016/j.celrep.2021.108898

 

24. Walavalkar, K., Saravanan, B., Singh, A. K., Jayani, R. S., Nair, A., Farooq, U., Islam, Z., Soota, D., Mann, R., Shivaprasad, P. V., Freedman, M. L., Sabarinathan, R., Haiman, C. A., & Notani, D. (2020). A rare variant of African ancestry activates 8q24 lncRNA hub by modulating cancer associated enhancer. Nature communications, 11(1), 3598. https://doi.org/10.1038/s41467-020-17325-y

 

23. Walavalkar, K., & Notani, D. (2020). Beyond the coding genome: non-coding mutations and cancer. Frontiers in bioscience (Landmark edition), 25(10), 1828–1838. https://doi.org/10.2741/4879

 

22. Saravanan, B., Soota, D., Islam, Z., Majumdar, S., Mann, R., Meel, S., Farooq, U., Walavalkar, K., Gayen, S., Singh, A. K., Hannenhalli, S., & Notani, D. (2020). Ligand dependent gene regulation by transient ERα clustered enhancers. PLoS genetics, 16(1), e1008516. https://doi.org/10.1371/journal.pgen.1008516

 

21. Rodrigues, C., Pattabiraman, C., Vijaykumar, A., Arora, R., Narayana, S. M., Kumar, R. V., Notani, D., Varga-Weisz, P., & Krishna, S. (2019). A SUV39H1-low chromatin state characterises and promotes migratory properties of cervical cancer cells. Experimental cell research, 378(2), 206–216. https://doi.org/10.1016/j.yexcr.2019.02.010

 

20. Jayani, R. S., Singh, A., & Notani, D. (2017). Isolation of Nuclear RNA-Associated Protein Complexes. Methods in molecular biology (Clifton, N.J.), 1543, 187–193. https://doi.org/10.1007/978-1-4939-6716-2_9

 

19. Li, W., Notani, D., & Rosenfeld, M. G. (2016). Enhancers as non-coding RNA transcription units: recent insights and future perspectives. Nature reviews. Genetics, 17(4), 207–223. https://doi.org/10.1038/nrg.2016.4

 

18. Han, Y., Rand, K. A., Hazelett, D. J., Ingles, S. A., Kittles, R. A., Strom, S. S., Rybicki, B. A., Nemesure, B., Isaacs, W. B., Stanford, J. L., Zheng, W., Schumacher, F. R., Berndt, S. I., Wang, Z., Xu, J., Rohland, N., Reich, D., Tandon, A., Pasaniuc, B., Allen, A., … Haiman, C. A. (2016). Prostate Cancer Susceptibility in Men of African Ancestry at 8q24. Journal of the National Cancer Institute, 108(7), djv431. https://doi.org/10.1093/jnci/djv431

 

17. Telese F, Ma Q, Perez PM, Notani D, Oh S, Li W, Comoletti D, Ohgi KA, Taylor H, Rosenfeld MG. LRP8-Reelin-Regulated Neuronal Enhancer Signature Underlying Learning and Memory Formation. Neuron. 2015 May 6;86(3):696-710. doi: 10.1016/j.neuron.2015.03.033. Epub 2015 Apr 16.

Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486257/

 

16. Li W, Lam MT, Notani D. Enhancer RNAs. Cell Cycle. 2014;13(20):3151-2.doi: 10.4161/15384101.2014.962860.

Link: https://www.tandfonline.com/doi/full/10.4161/15384101.2014.962860

 

15. Skowronska-Krawczyk D, Ma Q, Schwartz M, Scully K, Li W, Liu Z, Taylor H, Tollkuhn J, Ohgi KA, Notani D, Kohwi Y, Kohwi-Shigematsu T and Rosenfeld MG. Required enhancer-matrin-3 network interactions for a homeodomain transcription program. Nature. 2014 Aug 3. doi: 10.1038/nature1357. Link: https://www.nature.com/articles/nature13573

 

14. Li W*, Notani D*, Ma Q, Tanasa B, Nunez E, Chen AY, Merkurjev D, Zhang J, Ohgi K, Song X, Oh S, Kim H-S, Glass CK, and Rosenfeld MG. Functional Importance of eRNAs for Estrogen-dependent Transcriptional Activation Events. Nature. 2013. 498(7455):516-20. (* Equal Contribution) Recommended by Faculty of 1000 Biology.Comment In: Redmond AM, Carroll JS. Enhancer-derived RNAs: 'spicing up' transcription programs. EMBO J. 2013. 32(15):2096-8. Research Highlight: Carlos A Melo, Nicolas Léveillé, and Reuven Agami. eRNAs reach the heart of transcription. Cell Research. 2013. doi: 10.1038/cr.2013.97.

Link: https://www.nature.com/articles/nature12210

 

13. Dunkel Y, Ong A, Notani D, Mittal Y, Lam M, Mi X, Ghosh P. STAT3 protein up-regulates Gα-interacting vesicle-associated protein (GIV)/Girdin expression, and GIV enhances STAT3 activation in a positive feedback loop during wound healing and tumor invasion/metastasis. J Biol Chem. 2012. 287(50):41667-83.

Link: https://www.jbc.org/article/S0021-9258(20)43816-5/fulltext

 

12. Notani D, Ramanujam PL, Kumar PP, Gottimukkala KP, Kumar-Sinha C, Galande S.N-terminal PDZ-like domain of chromatin organizer SATB1 contributes towards its function as transcription regulator. J Biosci. 2011. 36(3):461-9.

Link: https://link.springer.com/article/10.1007/s12038-011-9091-4

 

11. Harismendy O*, Notani D*, Song X, Rahim NG, Tanasa B, Heintzman N, Ren B, Fu XD, Topol EJ, Rosenfeld MG, Frazer KA. 9p21 DNA variants associated with coronary artery disease impair interferon-γ signaling response. Nature. 2011. 470(7333):264-8. (* Equal Contribution) Recommended by Faculty of 1000 Biology.

Link: https://www.nature.com/articles/nature09753

 

10. Lakshminarayana Reddy CN, Vyjayanti VN, Notani D, Galande S and Kotamraju S. Down-regulation of the global regulator SATB1 by statins in COLO205 colon cancer cells. Molecular Medicine Reports. 2010. 3(5)857-861. Link: https://pubmed.ncbi.nlm.nih.gov/21472326/

 

9. Vempati RK, Jayani RS, Notani D, Sengupta A, Galande S, Haldar D. p300 mediated acetylation of histone H3 lysine 56 functions in DNA damage response in mammals. J Biol Chem. 2010. 285(37):28553-64. Link: https://www.jbc.org/article/S0021-9258(20)52707-5/fulltext

 

8. Notani D, Limaye AS, Kumar PP, Galande S. Phosphorylation-Dependent regulation of SATB1, the higher-order chromatin organizer and global gene regulator. Methods Mol Biol. 2010. 647:317-35.

Link: https://link.springer.com/protocol/10.1007/978-1-60761-738-9_20

 

7. Ahlfors H, Limaye A, Elo LL, Tuomela S, Burute M, Gottimukkala K, Notani D, Rasool O, Galande S, Lahesmaa R. SATB1 dictates expression of multiple genes including IL-5 involved in human T helper cell differentiation. Blood. 2010.116(9):1443-53.

Link: https://ashpublications.org/blood/article/116/9/1443/103905/SATB1-dictates-expression-of-multiple-genes

 

6. Notani D, Gottimukkala KP, Jayani RS, Limaye A, Damle MV, Mehta S, Purbey PK, Joseph J and Galande S. Global regulator SATB1 recruits β-catenin and mediates Wnt/β-catenin response. PLoS Biol. 2010. 8(1):e1000296. Synopsis: Sedwick, C. SATB1 makes a splash in T cell Wnt signaling. PLoS Biol. 2010. e1000295. doi:10.1371/journal.pbio.1000295.

Link: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000296

 

5. Purbey PK, Singh S, Notani D, Kumar PP, Limaye AS, Galande S. Acetylation-dependent interaction of SATB1 and CtBP1 mediates transcriptional repression by SATB1. Mol. Cell. Biol. 2009. 29:1321-37.

Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643834/

 

4. Galande S, Purbey PK, Notani D, and Kumar PP. The third dimension of gene regulation: Organization of dynamic chromatin loopscape by SATB1. Curr. Opin. Genet. Dev. 2007. 17: 408-417.

Link: https://pubmed.ncbi.nlm.nih.gov/17913490/

 

3. Kumar PP, Mehta S, Purbey PK, Notani D, Jayani RS, Purohit HJ, Raje DV, Ravi DS, Bhonde RR, Mitra D, and Galande S. SATB1-Binding Sequences and Alu-Like Motifs Define a Unique Chromatin Context in the Vicinity of Human Immunodeficiency Virus Type 1 Integration Sites. J Virol. 2007. 81:5617-5627.

Link: https://pubmed.ncbi.nlm.nih.gov/17376900/

 

2. Kumar PP, Bischof O, Purbey PK, Notani D, Urlaub U, Dejean A, and Galande S. Functional interaction between PML and SATB1 regulated chromatin loop architecture and transcription of the MHC class I locus. Nat. Cell Biol. 2007. 9: 45-56.

Link: https://pubmed.ncbi.nlm.nih.gov/17173041/

 

1. Kumar PP, Purbey PK, Sinha CK, Notani D, Limaye A, Jayani RS, and Galande S. Phosphorylation of SATB1, a global gene regulator, acts as a molecular switch regulating its transcriptional activity in vivo. Mol Cell. 2006. 22:231-243.

Link: https://pubmed.ncbi.nlm.nih.gov/16630892/