RNA Biology and Regeneration Lab
RNA Biology and Regeneration Lab

Research

RNA Biology & Regeneration Lab

Lab_Interest

A cell undergoes dynamic changes during its transition from one cell state to another, which happens during both tissue morphogenesis and stem cell function. However, the underlying mechanisms critical for these changes remain poorly understood. Our lab is interested in exploring the regulatory networks that fine-tune gene expression, such as post-transcriptional gene regulation. Often, the mere expression of an mRNA does not relate to its functionality, which suggest presence of certain “determinants” that dictate when and where these mRNAs should be translated. These regulatory networks involve coordination between miRNAs, several RNA binding proteins and various other RNA species. We employ a whole organism (using planarian Schmidtea mediterranea regeneration) approach coupled with in vitro data (embryonic stem cell differentiation) to understand these regulatory networks. Further, we employ a metabolomics and glycomics approach to understand regeneration and cell state transitions.

  



About Us

Lab Picture

Learn About our Team & Research.

Principal Investigator


Principal Investigator
Dasaradhi Palakodeti

Dasaradhi Palakodeti

Principal Investigator

dasaradhip at instem dot res dot in



Graduate Students


Graduate Student
Jahnavi

Jahnavi Kulkarni

jahnavik at instem dot res dot in
Education: MSc Biotechnology from Institute of Bioinformatics and Biotechnology from University of Pune.
As a cell progresses from one state to the other, it manifests changes at various levels- DNA, RNA, protein and of course, morphological. I am interested in studying the intracellular and intercellular ribosomal heterogeneity within cell types and understanding how it influences cell fate decisions.

Graduate Student
Srikar

Srikar Krishna G

srikark at instem dot res dot in
Education: MSc biotechnology from VIT, Vellore, Tamil Nadu.
I am broadly interested in understanding how genes are regulated in stem cells. I am currently looking into a novel class of small RNA called tRNA derived fragments (tRFs) in mouse embryonic stem cells.

Graduate Student
Vairavan

Vairavan Lakshmanan

vairavanl at instem dot res dot in
Education: B.Tech Bioinformatics from SASTRA University, Thanjavur, Tamil Nadu.
I am broadly interested in understanding mRNA’s fate. I am currently trying to understand gene regulation by non-coding region of mature mRNA (UTR's).In eukaryotes, 3’untranslated regions (3'UTRs) governs the stability, localization and translational efficiency of mRNA within the cell. The 3' UTRs also harvest majority of microRNA and RNA binding protein sites that consecutively perturb mRNA's fate and stability.



Graduate Student
Vinay

Vinay Kumar Dubey

vinaykd at ncbs dot res dot in
Education: Masters in Zoology from University of Delhi.
I am interested in understanding how positional information is specified along the medial-lateral axis in planarian flatworms.

Graduate Student
Namitha

Namita Mukundan

namitam at instem dot res dot in
Education: MSc Biotechnology from Amrita School of Biotechnology , Kerala.
Understanding the role of PolyA Binding Protein (Nuclear) in planarian homeostasis & regeneration.

Graduate Student
Souradeep

Souradeep

souradeeps at ncbs dot res dot in
Education: B.Tech Biotechnology from National Institute of Technology Durgapur.
I am a joint student between Das & Prof. R Sowdhamini (at NCBS). For my PhD I am interested in understanding how regeneration polarity is determined in planarian flatworms using both experimental & computational approaches.



Graduate Student
Arunabha

Arunabha Sarkar

arunabhas at ncbs dot res dot in
Education: Bachelors of Sciences from IISER, Kolkata.
Schmidtea mediterranea is a species of flatworm from phylum Platyhelminthes that are considered ‘almost immortal under the edge of knife’ (Dalyell, 1814, from Regeneration (book), T.H. Morgan, 1901).With the advent of molecular biology by the end of 20th century, the role of various small molecules inside a cell has been greatly extended from just secondary effectors and house keeping aspect. I am interested in finding out the roles of small molecules if any on neoblast regulation and differentiation. I am presently focussing my study on the role of small molecules 'methionine' and 'serotonin' for proper maintenance and function of planaria stem cells - the neoblast.

Graduate Student
Mohamed

Mohamed Haroon

mohamedmh at instem dot res dot in
Education: B.Tech Biotechnology from Agriculture University, Coimbatore.
I am a collaborative student of Dr.Praveen Kumar Vemula and Das.Currently, I am developing novel cationic amphiphiles based delivery vectors for delivering biologicals to planarian cells. These novel amphiphiles would be then used for stable genome modification leading to transgenics in planaria.

Junior research fellow
Nivedita

Nivedita Hariharan

hnivedita at instem dot res dot in
Education: Masters in Bionformatics & Biotechnology from IBAB, Bangalore.
I am interested in exploring gene expression and its regulation at all levels, right from genomic variation to proteins, as the interplay among the various macromolecules is what makes the 'cell' a well-oiled machine.At present, I am studying the ​translational regulation in stem cells during early differentiation using an integrated 'omics' approach.



Post-Doctoral Fellows


Post Doc
Nathan

Sabarinath PS

sabarinathps at instem dot res dot in
Education: Phd(Biochemistry & Glycomics) from Sri chitra thirunal Institute for medical sciences & technology, Kerala.
In 2015 joined the lab as joint post-doctoral fellow under the supervision of Prof. Ramaswamy.S and Prof. Dasaradhi. P. Currently, I work on understanding the role of glycans in regeneration and tissue homeostasis using planaria as the model system. My work spans from characterizing the structure of glycans by mass spectrometry to elucidating the function using molecular biology approach.

Post Doc
Nishtha

Nishtha Nayyar

nishthan at instem dot res dot in
Education: PhD from ICGEB, Delhi.
What causes cells, tissues or organs to pattern along an anterio-posterior or dorso-ventral axis to form a tissue, organ or an individual is a question that has bewildered several regeneration and developmental biologists. I am interested to find the role of miRNAs in determining regeneration polarity in Planaria.

Post Doc
Rajdeep

Rajdeep Das

rajdeepd at instem dot res dot in
Education: PhD (Structural Proteomics) from St.John's Research Institute, Bangalore.
I am focusing on to understand the ribosomal heterogeneity in development of mouse embryonic stem cell using mass spectrometry based proteomics approach. Also, I will be focusing on posttranslational modifications of proteins using quantitative mass spectrometry. Additionally, I am interested to explore the structure-function relationship protein, protein-protein and protein-ligand interaction using Hydrogen/Deuterium exchange mass spectrometry (H/DX-MS) and ion mobility mass spectrometry (IMS) to provide a global picture of cellular function and biological processes in disease conditions.





Junior Research Fellows


Junior research fellow
Soundarya

Sai Sowndarya

saisowndarya at instem dot res dot in
Education: Masters in Biotechnology from Amrita Vishwa Vidyapeetham, Kerala.
Interested in understanding the role of polyA tails in Schmidtea mediterranea stem cells and during Regeneration.

Alumni

Niyanta Kumar Junior Research Fellow 2010-2012 PhD Student
University of Wisconsin-Madison
Srishti Baid Junior Research Fellow 2015-2017 PhD Student
University of kansas
Viraj Doddihal Masters dissertation Student 2014-2015 PhD Student
Stowers Institute for Medical Research
Giulia iFOM Exchange Student 2015-2016 Masters Student
iFOM, Italy
Aparna Nair Junior Research Fellow 2012-2014 PhD Student
CSIR Neet, Nagpur
Prathyusha Pavanram Junior Research Fellow 2012-2014 Research Assistant
Uniklinik RWTH, Aachen, Germany
Divya Sridhar Junior Research Fellow 2014-2016 PhD Student
University of Oxford
Pranavi Dasari Junior Research Fellow 2012-2014 Agastya International Foundation
Bangalore
Deepak Poduval Balakrishnan Junior Research Fellow 2012-2014 PhD Student
University of Bergen
Debayan Bose Junior Research Fellow 2012-2013 PhD Student
Academia Sinica
Davide Saroni iFOM Exchange Student 2015-2016 Completed Masters
Vidyanand Sasidharan Graduate Student 2012-2017 Post Doctral Fellow
Sánchez Lab, Stowers Institute for Medical Research
Dhiru Bansal Graduate Student 2012-2017 Post Doctral Fellow
Miska Lab, Gurdon Institute, Cambridge
Praveen Anand Post Doctral Fellow 2015-2016 Post Doctrol Fellow
Dana Farber Cancer Institute
Rosana Babu Post Doctrol Fellow 2016-2017 Post Doctrol Fellow
University of Hong Kong (HKU)
Anna Protasio Post Doctrol Fellow 2016-2018 Post Doctrol Fellow
University of Cambridge and Wellcome Trust Sanger Institute, UK.
Kaushik Iyer Junior Research Fellow 2017-2018 Pandorum Technologies, CCAMP, Bangalore.

Publications

  1. Krishna S, Palakodeti D ,Solana J Post-transcriptional regulation in planarian stem cells Seminars in Cell & Developmental Biology 2018 8 June. https://doi.org/10.1016/j.semcdb.2018.05.013

  2. Peruvemba SS, Babu P, Palakodeti D ,Subramanian R Identification of multiple isomeric core chitobiose-modified high mannose and paucimannose N-glycans in the planarian Schmidtea mediterranea J Biol Chem. 2018 Feb 23. pii: jbc.RA117.000782. doi: 10.1074/jbc.RA117.000782.

  3. Sasidharan V, Marepally S, Elliott A S, Baid S, Lakshmanan V, Nayyar N, Bansal D, Alvarado AS, Vemula P, Palakodeti D The miR-124 family of microRNAs is crucial for regeneration of the brain and visual system in the planarian Schmidtea mediterranea Development 2017.doi: 10.1242/dev.144758

  4. Bansal D, Kulkarni J, Nadahalli K, Lakshmanan V, Krishna S, Sasidharan V, Geo J, DilipKumar S, Pasricha R, Gulyani A, Raghavan S, Palakodeti D Cytoplasmic poly (A) binding protein (PABPC2) critically regulates epidermal maintenance and turnover in planarian Schmidtea mediterranea Development 2017. doi: 10.1242/dev.152942

  5. Boya R, Yadavalli AD, Nikhat S, Kurukuti S, Palakodeti D,Pongubala JM Developmentally regulated higher-order chromatin interactions orchestrate B cell fate commitment Nucleic Acids Research, 17 August 2017. https://doi.org/10.1093/nar/gkx722

  6. Yim D, Krishna S, Lakshmanan V, Koh J, Park EJ, Cheong KJ, Low LJ, Lim M, Ip J, Nah MJ, Tan I, Iyer G, Guo H, Sze KS, Raghavan S, Palakodeti D DasGupta R Dynamic expression of tRNA-derived small RNAs define cellular states bioRxiv July 1 2017. doi: https://doi.org/10.1101/158501

  7. Shettigar N, Joshi A,Dalmeida R, Gopalkrishna R, Chakravarthy A, Patnaik S, Mathew M, Palakodeti D, Gulyani A Hierarchies in light sensing and dynamic interactions between ocular and extraocular sensory networks in a flatworm Science Advances vol. 3 no. 7 28 July 2017.

  8. Arya D, Sachithanandan SP, Ross C, Palakodeti D, Li S, Krishna S.miRNA-182 regulates percentage of myeloid and erythroid cells in chronic myeloid leukemia. Cell Death and Disease. 2017 Jan 12;8(1):e2547.

  9. Lakshmanan V, Bansal D, Kulkarni J, Poduval D, Krishna S, Sasidharan V, Anand P, Seshasayee A, Palakodeti D. Genome-Wide Analysis of Polyadenylation Events in Schmidtea mediterranea. G3 (Bethesda). 2016 Aug 9. pii: g3.116.031120. doi:10.1534/g3.116.031120. [Epub ahead of print] PubMed PMID: 27489207.

  10. Natarajan N, Ramakrishnan P, Lakshmanan V, Palakodeti D, Rangiah K. A quantitative metabolomics peek into planarian regeneration. Analyst. 2015 May 21;140(10):3445-64. doi: 10.1039/c4an02037e. Epub 2015 Mar 27. PubMed PMID: 25815385.

  11. Rao RA, Dhele N, Cheemadan S, Ketkar A, Jayandharan GR, Palakodeti D, Rampalli S. Ezh2 mediated H3K27me3 activity facilitates somatic transition during human pluripotent reprogramming.Sci Rep. 2015 Feb 4;5:8229. doi: 10.1038/srep08229. PubMed PMID: 25648270; PubMed Central PMCID: PMC4316165.

  12. Vyas N, Walvekar A, Tate D, Lakshmanan V, Bansal D, Lo Cicero A, Raposo G, Palakodeti D, Dhawan J. Vertebrate Hedgehog is secreted on two types of extracellular vesicles with different signaling properties. Sci Rep. 2014 Dec 8;4:7357. doi: 10.1038/srep07357. PubMed PMID: 25483805; PubMed Central PMCID: PMC4258658.

  13. Rangiah K, Palakodeti D. Comprehensive analysis of neurotransmitters from regenerating planarian extract using an ultrahigh-performance liquid chromatography/mass spectrometry/selected reaction monitoring method. Rapid Commun Mass Spectrom. 2013 Nov 15;27(21):2439-52. doi: 10.1002/rcm.6706. PubMed PMID: 24097401.

  14. Sasidharan V, Lu YC, Bansal D, Dasari P, Poduval D, Seshasayee A, Resch AM, Graveley BR, Palakodeti D. Identification of neoblast and regeneration-specific miRNAs in the planarian Schmidtea mediterranea. RNA. 2013 Oct;19(10):1394-404. doi: 10.1261/rna.038653.113. Epub 2013 Aug 23. PubMed PMID: 23974438; PubMed Central PMCID: PMC3854530.

  15. Krishna S, Nair A, Cheedipudi S, Poduval D, Dhawan J, Palakodeti D, Ghanekar Y. Deep sequencing reveals unique small RNA repertoire that is regulated during head regeneration in Hydra magnipapillata. Nucleic Acids Res. 2013 Jan 7;41(1):599-616. doi: 10.1093/nar/gks1020. Epub 2012 Nov 19. PubMed PMID: 23166307; PubMed Central PMCID: PMC3592418.

  16. Resch AM, Palakodeti D, Lu YC, Horowitz M, Graveley BR. Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea. PLoS One. 2012;7(4):e34447. doi: 10.1371/journal.pone.0034447. Epub 2012 Apr 4. PubMed PMID: 22496805; PubMed Central PMCID: PMC3319590.

  17. Resch AM, Palakodeti D. Small RNA pathways in Schmidtea mediterranea. Int J Dev Biol. 2012;56(1-3):67-74. doi: 10.1387/ijdb.113436ar. Review. PubMed PMID: 22450996.

  18. Hollenbach JP, Resch AM, Palakodeti D, Graveley BR, Heinen CD. Loss of DNA mismatch repair imparts a selective advantage in planarian adult stem cells. PLoS One. 2011;6(7):e21808. doi: 10.1371/journal.pone.0021808. Epub 2011 Jul 1. PubMed PMID: 21747960; PubMed Central PMCID: PMC3128615.

  19. Eipper-Mains JE, Kiraly DD, Palakodeti D, Mains RE, Eipper BA, Graveley BR. microRNA-Seq reveals cocaine-regulated expression of striatal microRNAs. RNA. 2011 Aug;17(8):1529-43. doi: 10.1261/rna.2775511. Epub 2011 Jun 27. PubMed PMID: 21708909; PubMed Central PMCID: PMC3153976.

  20. Lu YC, Smielewska M, Palakodeti D, Lovci MT, Aigner S, Yeo GW, Graveley BR. Deep sequencing identifies new and regulated microRNAs in Schmidtea mediterranea.RNA. 2009 Aug;15(8):1483-91. doi: 10.1261/rna.1702009. Epub 2009 Jun 24. PubMed PMID: 19553344; PubMed Central PMCID: PMC2714757.

  21. Palakodeti D, Smielewska M, Lu YC, Yeo GW, Graveley BR. The PIWI proteins SMEDWI-2 and SMEDWI-3 are required for stem cell function and piRNA expression in planarians. RNA. 2008 Jun;14(6):1174-86. doi: 10.1261/rna.1085008. Epub 2008 May 2. PubMed PMID: 18456843; PubMed Central PMCID: PMC2390803.

  22. Palakodeti D, Smielewska M, Graveley BR. MicroRNAs from the Planarian Schmidtea mediterranea: a model system for stem cell biology. RNA. 2006 Sep;12(9):1640-9. Epub 2006 Jul 18. PubMed PMID: 16849698; PubMed Central PMCID: PMC1557691.



Funding

Our work would not be possible without the generous funding from those listed below


Get in Touch

Join the team!!
JRF/SRF and post-doc applications are welcome !
Interested candidates write to Dr.Dasaradhi Palakodeti


If you are interested in our work and want to contact us.

Contact Details