Chandrama Mukherjee

Assistant Professor

Academic

B.Sc.         Chemistry (Hons), Calcutta University, 1999

M.Sc.         Biochemistry (Molecular Biology as special paper), Calcutta University, 2001

Ph.D.         Bose Institute, Jadavpur University, 2008 on ‘Functional genomics of cell cycle control                          genes in Entamoeba histolytica’.

·       From a young age, I was passionate about pursuing a career in chemistry. However, my path shifted during my undergraduate studies when I enrolled in a special course on biochemistry. That course sparked a deep interest in understanding the physiological processes that underpin life, and for the first time, I felt a strong personal connection to the world of biology. During my M.Sc. in Biochemistry, I delved deeper into this realm through engaging coursework and hands-on practical classes. It was here that I realized science extends far beyond textbooks—it's a way to explore and understand the complexities of the real world.

·       Driven by curiosity, I entered the exciting field of molecular and cell biology, and pursued my Ph.D. under the mentorship of Prof. Anuradha Lohia, studying the regulation of the cell cycle and DNA replication in the human parasite Entamoeba histolytica. My doctoral training exposed me to the intricacies of parasite biology and the broader challenges of cell cycle regulation. It was a formative time that nurtured my scientific curiosity and prepared me for the next phase of my career.

·       During this period, I developed a keen interest in the interface of transcription and translation. To pursue this emerging area, I joined the Schoenberg Lab at The Ohio State University, USA, as a postdoctoral researcher, where I investigated the mechanisms of post-transcriptional regulation and mRNA decay in mammalian cells. This experience provided me with extensive training in mammalian cell culture and RNA biology, and allowed me to apply biochemical and molecular approaches to study gene regulation at the post-transcriptional level.

·       I also had a unique opportunity to explore clinical pharmacogenomics in Dr. Joseph Kitzmiller’s lab, gaining exposure to the translational aspects of research. There, I worked on understanding the differential effects of statins—cholesterol-lowering drugs—across various ethnic populations. Though brief, this experience broadened my scientific perspective and introduced me to the emerging field of personalized medicine, reinforcing the importance of linking basic science with clinical applications.

·       My time at OSU—surrounded by a vibrant RNA research community—was profoundly influential. Interacting with leading RNA biologists deepened my commitment to continue working in the field of RNA biology.

·       After spending nearly nine years abroad, I returned to India with a clear vision: to launch my own independent research program. I am grateful to the Department of Biotechnology (DBT), Government of India, for awarding me the Ramalingaswami Re-entry Fellowship, which provided the necessary support to establish my lab at the Department of Life Sciences initially and later in the Institute of Health Sciences, Presidency University.

·       Here, I lead the RNABio@Presi research group, where we explore RNA stability, decay, and translation, particularly under various stress conditions like arsenite stress, hypoxia. We work in close collaboration with CellBio@Presi, led by Dr. Shubhra Majumder, and other groups in our department. The Department of Life Sciences at Presidency is enriched by a vibrant student community and faculty working across diverse areas of biology—from molecules to organisms—which makes it an ideal environment for interdisciplinary collaboration.

·       This journey—spanning basic molecular biology, RNA biochemistry, translational research, and collaborative science—continues to shape my identity as a scientist and mentor. I remain committed to addressing fundamental questions in RNA biology while fostering the next generation of scientists.

Research Experience

PhD research brief (2001-2008)

The eukaryotic cell cycle follows strict control mechanisms that ensure faithful duplication and segregation of the genome. However, the cell division cycle of human parasite Entamoeba histolytica shows significant differences with this paradigm. Cells with multiple nuclei and nuclei with varying DNA content (1X-6X) lead to the heterogeneity in the genome content of axenically growing E. histolytica cells, suggesting the regulatory mechanisms of the typical cell cycle are either absent or different in this organism. During the course of my PhD, we strikingly found that the laboratory cultured (axenic) trophozoites of E. histolytica acquired ~ 20-30 fold higher nuclear DNA content compared to the clinical isolates (xenic E. histolytica), indicating that, E. histolytica trophozoites pass through several endo-reduplicative cycles (S-phase without mitosis) during axenisation (stage-conversion) probably due to adaptation with the in vitro culture condition. Thus, endo-reduplication of genome is a fundamental property of this protist parasite and we have also demonstrated that endo-reduplication of the genome occurred within one generation of E. histolytica cells. Our bioinformatics analyses showed that homologs of several proteins required for DNA replication, chromosome segregation or cell divisions were absent or significantly diverged in this organism. We showed that indecisive nature of cytokinesis which might give rise to accumulation of multi-nucleated cells is another key factor leading to the observed heterogeneity in the average DNA content of axenic E. histolytica cells. 

Post-doctoral research brief (2008-2016)

I studied post-transcriptional control of gene expression through changes in mRNA translation and decay. The methylguanosine ‘cap’ (m7G) that is added by Capping Enzyme (CE) to all mRNAs plays a central role in translation initiation. Proteins that bind the cap facilitate splicing, polyadenylation, export and surveillance of mRNAs. The Schoenberg lab identified a cytoplasmic pool of CE (cCE) that, unlike nuclear CE, acts with an unidentified 5’-polynucleotide RNA kinase to restore the cap onto uncapped RNAs in the cytoplasm. My postdoctoral studies in the Schoenberg lab identified mRNA targets regulated by cytoplasmic capping. In the course of this work we also identified a cyclical process of decapping and recapping, termed ‘cap homeostasis’. Inhibition of cytoplasmic capping destabilized some target transcripts and caused the redistribution of other transcripts from translating polyribosomes to nontranslating messenger ribonucleoprotein fractions. The identification of cytoplasmic capping represents a paradigm shift in our understanding of the mRNA cycle and post-transcriptional gene expression. By demonstrating that a presumed irreversible process is in fact reversible, our finding expands upon the role of decapping in mRNA decay, and in doing describes a previously unrecognized post-transcriptional mechanism governing the cycling of mRNAs between active (translating) and inactive (non-translating) states. These targets encode proteins involved in nucleotide binding, RNA and protein localization and in regulation of cell cycle. While investigating the assembly of capping complex in cytoplasm, I identified Nck1, a cytoplasmic adaptor protein containing three SH3 and one SH2 domain as a cCE-interacting protein, and I showed Nck1 functions as the scaffold for assembling the cytoplasmic capping complex. I identified RNA methyl transferase as another component of cytoplasmic capping complex that likely adds the methyl group to capped RNA and other interesting candidate proteins as cCE interactors using LC-MS/MS. Identification of the mRNA targets and interactions of cytoplasmic Capping Enzyme leads to determine whether cytoplasmic capping is involved in the reactivation of mRNAs that are stored or silenced by microRNAs.

Post-doctoral research brief (2016-2017)

The 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase inhibitors or statins are recommended as candidate drugs for the treatment of hypercholesterolemia and prevention of cardiovascular disease. Though this drug has been used for long time effectively, potential side effects also have been reported worldwide. The level of efficacy of the drug as well as the potential side effects has been shown to vary with ethnicity. Primarily the single nucleotide polymorphisms (SNPs) contribute to the difference in drug efficacy. Our team has identified the SNPs responsible for this difference in African-American population. Further studies using large cohort of patients are required to understand the pharmacogenomics of statins to develop personalized medicine.

Current research

The generalized repression of cap-dependent translation is one of the earliest responses to cell stress. Non-translating mRNAs accumulate in stress granules (SGs) and processing bodies (PBs), and this is also associated with changes in the turnover of selected mRNAs. Thus, post-transcriptional reprogramming of mRNA translation and decay reconfigures the proteome during adverse environmental conditions as well as recovery from stress. Perturbations in RNA granule functions lead to pathological phenotypes observed in multiple neurodegenerative, immunological and infectious diseases, and SGs were recently shown to promote the formation of metastasis. Earlier work from our lab demonstrated that interfering with cytoplasmic capping reduced the ability of cells to recover from a brief oxidative stress. The concept of cytoplasmic capping is quite new and it starts to gain attention in last five years. Cytoplasmic capping impacts the transcriptome at the post-transcriptional level with addition of a cap at the 5’ end of uncapped RNA. Thus it may expand the proteome by generating new truncated proteins lacking 5’ terminus from recapped RNAs without affecting the transcriptome. This is a novel idea so far, but some studies across the world show evidences of new short proteins or peptides of unknown function. Earlier work demonstrated that interfering with cytoplasmic capping reduced the ability of cells to recover from a brief oxidative stress. Some of my preliminary data suggested a similar trend. Based on these findings, I hypothesize that recapping of mRNAs in the cytoplasm plays a central role in cellular recovery from stress. I will test my hypothesis using following aims.

Aim-1. What is the role of  cytoplasmic Capping Enzyme in response to stress?

Aim-2. What is the impact of cellular stress on the recapped transcriptome?

Administrative Experience:

I am involved in different internal committees of the Institute of Health Scinces, Presidency University.

Teaching experiences:

I have been deeply influenced by my teachers throughout my academic journey, and their mentorship continues to inspire my own approach to teaching. In light of the rapid advancements in the fields of transcriptional and translational regulation and functional genomics, I am particularly passionate about teaching the biochemistry of gene expression to undergraduate and postgraduate students.

The course I envision focuses on providing both foundational knowledge and exposure to cutting-edge discoveries. The content would include, but not be limited to:

1.     Cellular organelles, with an emphasis on the structure and function of the nucleus

2.     Chromatin architecture and epigenetic modifications

3.     Molecular regulation of DNA replication, transcription, and translation

4.     Post-transcriptional control of gene expression

5.     Post-translational modifications, with a focus on RNA biochemistry, stress response pathways, and the emerging roles of non-coding RNAs

6.     Regulation of the eukaryotic cell cycle and checkpoint mechanisms in both normal and cancerous cells

As an educator, I strive to share recent scientific developments relevant to students' areas of study so they can relate theoretical concepts to real-world biological processes. My aim is to foster critical thinking, analytical skills, and intellectual independence—enabling students to learn beyond the boundaries of traditional classroom settings.

To complement theoretical learning with practical skills, I, along with my colleagues, organize a ‘Hands-on Training Course in Molecular Diagnostics’ every summer. This initiative provides students with laboratory exposure to modern techniques and analytical approaches used in molecular biology and diagnostics.

Above all, I believe teaching is not merely about information delivery but about inspiring students to ask questions, seek answers, and engage with science as an evolving and exciting discipline.

Taught courses (MSc) : Molecular Biology-Transcription and post transcriptional control

Cell Biology-Cell Cycle and its regulation

Bioethics-Research ethics, scientific misconduct, publication ethics, ethical use of bioresourses

Other courses: Last three years, myself along with two other colleauges are running hand on certificate course on 'Molecular Diagnostics'.

Professional experiences:

Ad hoc Reviewer- WIREs RNA, FEBS Letters, Cell Death and Discovery, iScience, CLMS journals

Judge- Denman Undergraduate Research Forum, Ohio State University (2013-2016)

Organizer- Member of the Organizing committee, Regional Young Investigators Meeting, Kolkata, 2019, 2023

I am looking for highly motivated and enthusiastic students preferably with UGC or CSIR JRF/ CSIR-LS or PhD category with DBT-JRF or ICMR-JRF fellowship to work in my group. Interested people may contact me at

chandrama.dbs@presiuniv.ac.in with their CV and research of interest.

Current lab members

1.      Anakshi Gayen                 M.Sc., SRF

2.      Avik Mukherjee                M.Sc., SRF

3.      Safirul Islam                     M.Sc., UGC-SRF

4.      Manisha Das                    M. Sc, JRF

Disseration student 

Ayan Ghosh, MSc Sem IV student, IHS, PU, 2024

Title Das, MSc Sem IV student, IHS, PU, 2024

Summer Interns (2025)

Souvik Sen, Ramakrishna Mission Vivekananda Centenary College, Rahara

Kunal Jana, Ramakrishna Mission Vivekananda Centenary College, Rahara

Srirup Samanta, Ulubria College

Past lab members

1. Saheli Saha                 PhD at IISC, Bengaluru

2. Arundhati Karmakar     Summer trainee; PU DLS, 3rd Sem UG student of 2017-20

3. Anurita Halder              Summer trainee; PU DLS, 3rd Sem UG student of 2017-20

 4. Ranu Soren                 M.Sc. dissertation student, PU DLS of 2017-19

5.  Soumi Saha                 M.Sc. dissertation student, PU DLS of 2017-19, Presently enrolled in PhD program at WBSU

6. Tithi Bhandari              Summer trainee, NISER, Odisha

7. Anirban Kundu           Summer trainee, Benaras Hindu University

8. Nivedita Mukherjee   M.Sc. dissertation student, PU DLS of 2018-20, presently doing PhD in NCBS, Bengaluru

9. Ananya Chatterjee               M.Sc. dissertation student, PU DLS of 2018-20, presently enrolled  in PhD program at IIT, Kharagpur

10. Sourav Mukherjee    Project assistant, currently enrolled in PhD program  in Bombay IIT

11.      Saitali Laha Roy  Project Assistant, currently enrolled in PhD program in Bombay IIT

12. Souvik Chakraborty M.Sc. dissertation student, PU SBT of 2019-2021

13. Somnath Panda, 4th Sem, MSc in Biotechnology, Maulana abul kalam university of technology, West Bengal

14. Piyush Jaiswal,  1st Sem, MSc in Human Genetics & Molecular Biology, Bharathiar University, Coimbatore, Tamil Nadu

15. Nilabhra Ghosh, 1 st Sem, MSc in Biotechnology, Viswa Bharati University

16. Moumita Ghosh, 1st Sem, MSc in Biotechnology, Amity University, Kolkata

17. Adrit Biswas, 4th Sem, BSc in Microbiology,  Ramkrishna Mission Vivekananda Centenary College, Rahara

18. Aryan Mukherjee, 4th Sem, Bsc in LifeScince, Presidency University, Kolkata

19. Pinaki Ghosh, MSc Sem IV student, IHS, PU, 2024, dissertation student

20. Arpita Patra, MSc Sem IV student, IHS, PU, 2024, dissertation student

American Heart Association : 2013-2015

RNA Society: 2009-Present

RNA group (India): 2022-Present

Guest Editor of Frontiers in Genetics and Development

Reviewer: MDPI, NAR Cancer, Khorana summer program

Publications (in reverse chronological order)

Islam S and Mukherjee C. Hypoxia inducible factor HIF1α elevates expression of mRNA capping enzyme during cobalt chloride-induced hypoxia. BBA Gene Regulatory Mechanism (in press).

Ghosh P; Islam I and  Mukherjee C. (2024) Preprint: Identification of transcriptome-wide cobalt chloride-induced hypoxia-responsive long noncoding RNAs regulated by cytoplasmic mRNA capping enzyme.

Chakraborty P. and Mukherjee C. (2024) The interplay of metabolic and epigenetic players in disease development. Biochem Biophy Res Communication 29: 734:150621.

Islam S. and Mukherjee C. (2024) Preprint: Hypoxia inducible factor HIF1α elevates expression of mRNA capping enzyme during cobalt chloride-induced hypoxia..

Gayen A., Mukherjee A., Kumar K., Majumder S., Chakrabarti S., and Mukherjee C. (2024) The mRNA-capping enzyme localizes to stress granules in the cytoplasm and maintains cap homeostasis of target mRNAs. Journal of Cell Science 137(11): jcs261578.

Dutta A., Halder P., Gayen A,,  Mukherjee A,  Mukherjee C.,  and Majumder S*. (2023) Increase in primary cilia number and length upon VDAC1 depletion contributes to attenuated proliferation of cancer cells. Exp Cell Res. June 3

 Gayen A., Mukherjee A., Majumder S.  and Mukherjee C*. (2023)Preprint: mRNA capping enzyme exports to cytoplasm, localizes to stress granules and maintains cap homeostasis of the target mRNAs

Mukherjee A., Islam S., Kieser R.E., Kiss D.L., Mukherjee C.* (2023) Long non-coding RNAs are substrates for cytoplasmic capping enzyme. FEBS Letters. March 1

Islam, S and Mukherjee C. (2022) Molecular regulation of hypoxia through the lenses of non- codingRNAs and epitranscriptome. WIREs RNA (online publication:July 3, 2022). https://doi.org/10.1002/wrna.1750

Mukherjee, N. and Mukherjee C. (2021) Germ cell ribonucleoprotein granules in different clades
of life: From insects to mammals. WIREs RNA, e1642.

Mukherjee C., Sweet K. M., Luzum J. A., Abdel-Rasoul M., Christman M.F. and Kitzmiller J.P. (2017) Clinical pharmacogenomics: patient perspectives of pharmacogenomic testing and the incidence of actionable test results in a chronic disease cohort. Personalized Medicine, 14: 5.

Trotman J., Giltmier A., Mukherjee C., and Schoenberg D.R. (2017) RNA guanine-7- methyltransferase catalyzes the methylation of cytoplasmically recapped RNAs. Nucleic Acids Research, 45(18) 10726–10739.

Kitzmiller J.P., Mikulik E.B, Dauki A.M., Mukherjee C. and Luzum J.A. (2016) Pharmacogenomics of statins: understanding susceptibility to adverse effects. Pharmacogenomics and Personalized Medicine, 2016: 9: 97–106.

Kiss D., Kenji O.*, Dougherty J.*, Mukherjee C.*, Bundschuh R., and Schoenberg D.R. (2015) Cap homeostasis is independent of poly(A) tail length. Nucleic Acid Research, 44(1): 304-14. (* equal contribution).

Mukherjee C., Bakthavachalu B., and Schoenberg D.R. (2014) The cytoplasmic capping complex assembles on adapter protein Nck1 bound to the proline-rich C-terminus of mammalian capping enzyme. PLoS Biology, 12(8): e1001933.

Mukherjee C.*, Patil D.P.*, Kennedy B.A., Bakthavachalu B., Bundschuh R., Schoenberg D.R. (2012) Identification of cytoplasmic capping targets reveals a role for cap homeostasis in translation and mRNA stability. Cell Reports, 2(3): 674-84. (* equal contribution); Selected as ‘Resource’ article.

Mukherjee C.*, Majumder S.*, and Lohia A. (2009) Inter-cellular variation in DNA content of Entamoeba histolytica originates from temporal and spatial uncoupling of cytokinesis from the nuclear duplication cycle. PLoS Neglected Tropical Disease, 3(4): e409. (* equal contribution) (Image selected for ‘Cover Photo’); Selected for discussion in the ‘Editor’s Choice’ section, Science, 324(5931): 1119.

Mukherjee C., Clark C.G., and Lohia A. (2008) Entamoeba shows reversible variation in ploidy under different growth conditions and between life cycle phases. PLoS Neglected Tropical Disease, 2(8): e281.

Clark C.G., Alsmark U.C.M., Hofer M., Saito-Nakano Y., Ali V., Marion S., Weber C., Mukherjee C., Bruchhaus I., Tannich E., Leippe M., Sicheritz-Ponten T., Foster P.G., Samuelson J., Noël C., Hirt R.P., Embley T.M., Gilchrist C.A., Mann B.J., Singh U., Ackers J.P., Bhattacharya S., Bhattacharya A., Lohia A., Guillén N., Duchêne M., Nozaki T., and Hall N. (2007)Structure and Content of the Entamoeba histolytica Genome. Advances in Parasitology, 65: 51-190.

Loftus B., Anderson I., Davies R., Alsmark U.C., Samuelson J., Amedeo P., Roncaglia P., Berriman M., Hirt R.P., Mann B.J., Nozaki T, Suh B., Pop M., Duchene M., Ackers J., Tannich E., Leippe M., Hofer M., Bruchhaus I., Willhoeft U., Bhattacharya A., Chillingworth T., Churcher C., Hance Z., Harris B., Harris D., Jagels K., Moule S., Mungall K., Ormond D., Squares R., Whitehead S., Quail M.A., Rabbinowitsch E., Norbertczak H., Price C., Wang Z., Guillen N., Gilchrist C., Stroup S.E., Bhattacharya S., Lohia A., Foster P.G., Sicheritz-Ponten T., Weber C., Singh U., Mukherjee C., El-Sayed N.M., Petri W.A. Jr., Clark C.G., Embley T.M., Barrell B., Fraser C.M., and Hall N. (2005) The genome of the protist parasite Entamoeba histolytica. Nature, 433: 865-868. 

Das S., Mukherjee C., Sinha P., and Lohia A. (2005) Constitutive association of Mcm 2-3-5 proteins with chromatin in Entamoeba histolytica. Cellular Microbiology, 7: 259-267.

Other publications, reviews

Abstract 1121: Identifying novel cytoplasmic mRNA capping enzyme-targeted, hypoxia-responsive RNAs in hypoxic osteosarcoma cellular model: A plausible therapeutic approach

Islam S, Bakshi U,  Mukherjee  C- Journal of Biological Chemistry, 2024

Editorial: Role of non-coding RNAs in development and metastasis of solid tumours
B Roy, S Dutta, C Mukherjee*
Frontiers in Cell and Developmental Biology 
 

Lohia A., Mukherjee C., Majumder S., and Ghosh Dastider P. (2007) Genome re-duplication and irregular segregation occur during the cell cycle of Entamoeba histolytica. Bioscience Reports, 27: 373-384. (Review)

Mukherjee C., Majumder S., Ghosh Dastider P. and Lohia A. (2007) Endoreplication and irregular division lead to heterogeneity of genome content in Entamoeba histolytica. Tropical Medicine & International Health, 12: 30-31. (Brief report).