Our research

Signaling and Chromatin Dynamics  during cell development, differentiation, and disease

In metazoans, the discovery of cell type-specific, a non-random higher-order organization of chromatin and long-range intra- and interchromosomal interactions between genes and their regulatory element, point to the functional interplay between 3-Dimensional genome architecture and gene expression. Recent data suggest that active and repressed genes from different chromosomal regions spatially constrain and functionally organize in conjunction with RNA Pol II-enriched transcription factories or Polycomb group (PcG) enriched silencing factories respectively. Moreover, the chromatin architectural protein CTCF or/and cohesion mediates long-range chromatin interactions and are thought to bring distant chromatin elements to the sites of ongoing transcription. However, the causal relationships between genome architecture and gene expression in the context of various nuclear subdomains and epigenetic features at a genome-wide scale are yet to be determined. In this regard, we are interested to study the mechanism behind global interphase chromosomal positioning and its influence on the orchestration of preferential physical gene networks within the cell nucleus and their dynamic changes during the course of cellular development, differentiation and disease. In this study we use high-throughput genomic technologies, such as Chromosome Conformation Capture (3C) and related methods, utilizing a wide variety of genetic and cell line model systems (Embryonic stem cell differentiation, Differentiation of T-Lymphocyte sub-types) in combination with bioinformatics and other computational approaches. We anticipate that system-level understanding of the physical and functional organization of chromatin in the cell nucleus and its relation to various nuclear domains and epigenetic features are essential to our understanding of governing principles in the orchestration of cell type-specific gene expression programming.

Advertisements

Publications

 

  1. Sornapudi TR, Nayak R, Guthikonda PK, Pasupuleti AK, Kethaath S, Uppada V, Mondal S, Yellaboina S and Kurukuti S (2018). Comprehensive profiling of transcriptional networks specific for lactogenic differentiation of HC11 mammary epithelial cells. Scientific Reports. 8:11777.
  2.  Sornapudi TR, Nayak R, Guthikonda PK, Kethaath S, Yellaboina S and Kurukuti S (2018). RNA sequencing of murine mammary epithelial stem-like cells (Hc11) undergoing lactogenic differentiation and its comparison with embryonic stem cells. BMC Research Notes. 11-24.
  3. Parati sai Arun PV, Miryala SK, Rana A, Kurukuti S, Akhter Y and Yallaboina S. System-wide coordinates of higher order function in host-pathogen environment upon Mycobacterium tuberculosis infection. Scientific reports  5079 (2018).
  4. Nadella V, Aparna M, Sharma L, Yellaboina S, Balaji MV, Palaparthi P, Madhavi B M, Mourya R, Kurukuti S, Rudel T and Prakash H (2018). IAP antagonist controls polarization of macrophages during microbial challenge and sterile inflammatory responses. Front. Immunol. Inflammation, DOI: 10.3389/fimmu.2017.01792.
  5. Boya R, Yadavalli AD, Nikhat S, Kurukuti S, Palakodeti D & Pongubala JMR (2017). Nucleic Acids Res. 2017. 2:45 (19): 11070-11087)
  6. Zhou Y, Kurukuti S, Saffrey P, Vukovic M, Michie AM, Strogantsev R, West AG and Vetrie D (2013). Chromatic looping defines expression of TAL1 and its flanking genes and regulation in T-ALL. Blood.19;122(26):4199-209
  7. Sexton T, Kurukuti S, Mitchell JA, Umlauf D, Nagano T and Fraser P (2012). Sensitive detection of chromatin co-associations using enhanced chromosome conformation capture on chip  (e4C). Nature Protocols, 7(7):1335-50
  8. Raab JR, Chiu J, Zhu J, Katzman S, Kurukui S, Wade PA, Haussler D and Kamakaka RT (2012). Human tRNA genes function as chromatin insulators. The EMBO Journal, 31:330-350
  9. Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, Andrews A, Kurukuti S, Mitchell JA, Umlauf D, Dimitrova DS, Eskiw CH, Luo Y, Wei CH, Ruan Y, Bieker JJ, and Fraser P (2010). Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nature Genetics, 42(1): 53-61.
  10. Chakraborty A, Kurukuti S, and Raman R (2009). Involvement of androgen receptor gene in male gonad differentiation in Indian garden lizard, Calotes versicolor. Molecular and Cellular Endocrinology, 6(303): 1-2.
  11. Sexton T, Umalauf D, Kurukuti S, and Fraser P (2007). The role of transcription factories in the structure and dynamics of interphase chromatin. Seminars in Cell and Developmental Biology, 18(5): 691-697.
  12. Bergström R, Whitehead J, Kurukuti S, and Ohlsson R (2007). CTCF regulates asynchronous replication of the imprinted H19/Igf2 domain. Cell Cycle, 6(4): 450-454.
  13. Zhao Z, Tavoosidana G, Sjolinder M, Gondor A, Mariano P, Wang S, Kanduri C, Lexcano M, Sandhu KS, Singh U, Pant V, Tiwari V, Kurukuti S, and Ohlsson R (2006). Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra and inter-chromosomal interactions.  Nature Genetics, 38(11): 1341-7.
  14. Kurukuti S*, Tiwari VK*, Tavosidana G*, Pugacheva E, Murrell A, Zhao Z, Lobanenkov V, Reik W, and Ohlsson R (2006). CTCF binding at the H19 imprinting control region mediates maternally-inherited higher order chromatin conformation to restrict enhancer access to Igf2.   Proceedings of the National Academy of Sciences U.S.A., 103(28): 10684-10689. (*Co-first authors)
  15. Burke LJ, Zhang R, Bartkuhn M, Tiwari VK, Tavoosidana T, Kurukuti S, Weth C, Leers J, Niels, Galjart, Ohlsson R, and Renkawitz R (2005­). CTCF binding and higher order chromatin structure of the H19 locus is maintained in mitotic chromatin. The EMBO Journal, 24: 3291- 3300.
  16. Pant V, Kurukuti S, Pugacheva E, Shamsuddin S, Mariano P, Renkawitz R, Klenova E, Lobanenkov V, and Ohlsson R (2004). Mutation of a single CTCF target site within the H19 imprinting control region leads to loss of Igf2 imprinting and complex patterns of de novo methylation upon maternal inheritance. Molecular and Cellular Biology, 24(8): 3497-504.
  17. Kurukuti S, Ganesh S, and Raman R (2002). Evolutionarily conserved DMRT1 encodes alternatively spliced transcripts and shows dimorphic expression during gonadal differentiation in the lizard, Calotes versicolor. Mechanisms of Development, 119S, S55-S64.

Lab members

Principal Investigator

Sreenivasulu Kurukuti Ph.D. (BHU)

Professor
Department of Animal Biology
School of Life Sciences
University of Hyderabad
Hyderabad-500 046
A.P., India

Past experience:

Research Associate: Institute of Cancer Sci., University of Glasgow, United Kingdom (2008-11)

Research Scientist: The Babraham Institute, Cambridge, United Kingdom (2005-08)

Guest Scientist: Dept. of Development and Genetics, Uppsala Univ., Uppsala, Sweden (2003-05)

URL:http://www.uohyd.ernet.in/index.php/academics/2011-10-27-18-38-04/school-of-life-sciences/dept-animal-sciences/faculty?layout=edit&id=538

Present Lab Members

1. Mr. Prashanth Kumar Guthikonda- SRF

2. Ms. Rakhee Naik-SRF

3. Mr. Sukalpa Mondal-JRF

4. Mr. Srinivas Kethavath- SRF

5. Ms. Netrika Tiwari-JRF

6. Ms. Yuvasri-JRF

7. Mr. Satyanarayana-JRF

8. Ms. Jothisha-JRF (DBT)

9. Mr. Dharmapal-SRF (ICMR)

10. Ms. Gayatri-MSc-Project student

11. Ms. Shivani Navalaka-MSc-Project student

Ph.D. awarded Researchers

1.Mr. Trinadharao Sornapudi (Currently a postdoc at National Institute of Cancer, Bethesda, USA)

Past Lab Members

1. Ms. Pratyusha – M.Sc. project student (2012)- Completed

2. Ms. Susmita – M.Sc. project student (2012)-Completed

3. Mr. Avdesh – M.Sc. project student (2012)- Completed

4. Ms. Anisha Begum – M.Tech project student – (2012 )-Completed

5. Ms. Madhurima Vardhan- INSA Summer trainee – (2012) – Completed

6. Mr. Aditya Kumar-iMSc Project Student  – (2013) – Completed

7. Mr. Ananda Rao- MS.c  Project Student – (2013) – Completed

8. Ms. Tulasi- M.Sc Project Student – (2013) – Completed

9. Mr. Arun-INSA summer trainee – (2013) – Completed

10. Dr. Nalini – INSA summer trainee -(2013) – Completed

12. Mr. Faizan- M. Sc Project Student (2014)-Completed

13. Ms. Subhalaxmi Mohanthy-SRF (2014)-Completed

14. Ms. Keerthi Muralidharan- Summer trainee (2014)-Completed

15. Ms. Arya Aravaind- Summer trainee (2014)-Completed

16. Ms. Anusree Dey-Project Trainee (2014)-Completed

17. Mr. Rahul Kumar Vempati- Project assistant (2014)-Completed

18. Ms. Swati Thangariyal-MSc Project Student (2015)-Completed

19. Mr. Abhijith-INSA Summer trainee (2015)-Completed

20. Ms. Chandrika Konwar-INSA Summer trainee (2015)-Completed

21. Mr. Al Nihad Ahmad-INSA Summer trainee (2016)- Completed

22. Mr. Kalpanath Rai-MSc Project Student (2016)- Completed

23. Mr. Shailesh Keskar-MSc Project Student (2016)- Completed

24. Ms. Komal- MSc Project Student (2017)- Completed

25. Ms. Sree- MSc Project Student (2017)- Completed

27. Ms. Hashini- B. Tech Project Student (2017)- Completed

28. Ms. Devasmita-MSc-Project student (2017)-Completed

29. Dr. Kalyani-CSIR Research associated (2017)-Completed

30. MS. Naseema-MSc Project student (2018)-Completed

31. Ms. Yuvasri-MSc Project student (2018)- Completed

32. Mr. Raviteja-BTech Project student (2018)-Completed