, Division of Plant Biology
PhD: University of Calcutta, 2001
2002-2003: Post Doctoral Fellow, Department of Plant Pathology, University of Missouri, Columbia, USA
2003-2005: Post Doctoral fellow, Department of Horticulture, Washington State University, USA
2005-2009: Research coordinator, School of Molecular Biosciences, Washington State University, USA
The highly complex structure of chromatin imparts
resistance to several nuclear processes. It is still an unsolved mystery as to
how several genes whose sequence might be buried in the complex chromatin
structure is accessed by nuclear factors during their expression in response to
endogenous and exogenous cues. Post-translation modification of histones
(epigenetic mark) as well as active chromatin remodelling guided by either ATP
dependent chromatin remodellers or histone chaperones play an important
regulatory role in activating or repressing gene expression by generating ‘open’
or ‘closed’ chromatin configuration inside the cell. Such dynamic changes in
the chromatin organization are essential for almost all cellular events like
transcription, replication, repair and DNA recombination. Stress response in
plants have been reported to exhibit similar dynamics at the epigenetic levels
which promotes the transcription of plethora of stress responsive genes to mount the response. Further, such stress-induced
epigenetic changes in the chromatin can lead to transient response or sustained
response where the new chromatin state are maintained as stress memory. It is
assumed that the stress memory induced due to epigenetic changes in the
chromatin, will provide a “primed state” to plants, for faster and stronger
response against subsequent environmental conditions.
Division of Plant Biology
P-1/12 C.I.T. Scheme VII-M
Kolkata - 700054, India
This project involves
the study of a novel class of high mobility group (HMG) protein ARID-HMG known
to modulate the chromatin structure during nuclear events. ARID-HMG proteins
contain both the AT rich interaction domain (ARID) and the HMG-box domain in a
Recent work has shown that ARID-HMG can bind different DNA topological forms, can bend DNA backbone and can also induce DNA supercoiling to facilitating nuclear processes [Roy et al, (2016) Plant Molecular Biology 92 (3), 371-388]. Identification of genome-wide targets and DNA recognition sequence of the Arabidopsis HMG-box protein during cold stress response using ChIP-on-chip was employed for further study. GO analysis shows genes belonging to abiotic stress response, cold response and root development were AtHMGB15 targets during cold stress. DNA binding and footprinting assays identified A(A/C)--ATA---(A/T)(A/T) as AtHMGB15 binding motif. Further, the expression of cold stress responsive genes decreased in athmgb15 knockout plants compared to wild-type. Taken together, binding enrichment of AtHMGB15 to the promoter and upstream to stress loci suggest an unexplored role of the protein in stress induced transcription regulation. [Mallik et al, (2020). BBA-Gene Regulatory Mechanisms 1863 (12), 194644]
Investigating the role of ARID-HMG in chromatin remodeling during plant development.
Explore the different epigenetic changes in plants to understand the transcription regulation of genes that are regulated during abiotic stress response.
Role of rice Trithorax factor, OsULT1, in regulating stress induced gene expression: Co-ordinated interplay between Polycomb group (PcG) and Trithorax group (TrxG) chromatin proteins regulates the spatiotemporal expression of target genes in higher eukaryotes. Rice Trithorax factor ULTRAPETALA 1 (OsULT1) specifically binds to the putative Polycomb response elements “GAGAG” of cold responsive genes, such as, OsDREB1b, to regulate the cold induced transcription. GAGAG is the recognition sequence for GAGA factor (GAF), Pipsqueak (Psq) as well as one of the major sites for PRC2 protein FIE occupancy. OsULT1 physically interacts with SET domain containing methyltransferase, OsTRX1 that methylates H3K4me3. These results collectively suggest that synchronised interaction between PcG and TrxG complex for PRE/TRE element is evolutionarily conserved mechanism throughout the kingdoms to mediated gene regulation [Royet al, 2019. BBA-Gene Regulatory Mechanisms 1862 (5), 582-597].
Low temperature a major abiotic stress, is known to adversely affect the
growth and development of rice plants, Oryza
sativa. Cellular reprogramming in response to cold stress involves
alteration of gene expression. Similar to other plant species originating in
tropical and sub-tropical areas, indica
rice is highly sensitive to low temperature that adversely affects its growth
and grain productivity. A transcriptome profile was generated for cold shock
treated seedlings of IR64 variety to identify early responsive transcripts that includes enrichment of genes involved in
altered membrane rigidity and electrolytic leakage, the onset of calcium
signaling, ROS generation and activation of stress responsive transcription
factors in IR64[Dasgupta, et al, 2020. BMC Genomics 21 (1), 425].
Role of rice Trithorax factor, OsULT1, in regulating stress induced gene expression
Comparative epigenome during abiotic stress response
- Identification of genome-wide targets and DNA recognition sequence of the Arabidopsis HMG-box protein AtHMGB15 during cold stress response. R Mallik, P Prasad, A Kundu, S Sachdev, R Biswas, A Dutta, A Roy, J Mukhopadhyay, S K Bag, S Chaudhuri (2020). Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1863 (12), 194644.
- Understanding the early cold response mechanism in IR64 indica rice variety through comparative transcriptome analysis. P Dasgupta, A Das, S Datta, I Banerjee, S Tripathy, S Chaudhuri (2020). BMC Genomics 21 (1), 425.
- Rice Trithorax factor ULTRAPETALA 1 (OsULT1) specifically binds to “GAGAG” sequence motif present in Polycomb response elements. D Roy, J Chakrabarty, R Mallik, S Chaudhuri (2019). Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1862 (5), 582-597.
- High mobility group proteins: the multifaceted regulators of chromatin dynamics. R Mallik, A Kundu, S Chaudhuri (2018). The Nucleus 61 (3), 213-226.
- Molecular characterization of the 14-3-3 gene family in rice and its expression studies under abiotic stress. N Yashvardhini, S Bhattacharya, S Chaudhuri, DN Sengupta (2018). Planta 247 (1), 229-253.
- Understanding the role of DNA polymerase λ gene in different growth and developmental stages of Oryza sativa L. indica rice cultivars. S Sihi, S Maiti, S Bakshi, A Nayak, S Chaudhuri, DN Sengupta (2018). Plant physiology and biochemistry 120, 156-168.
- Molecular and biochemical characterization of a Vigna mungo MAP kinase associated with Mungbean Yellow Mosaic India Virus infection and deciphering its role in restricting the virus multiplication. A Patel, N Dey, S Chaudhuri, A Pal (2017). Plant Science 262, 127-140.
- Comparative analysis of Histone modifications and DNA methylation at OsBZ8 locus under salinity stress in IR64 and Nonabokra rice varieties A Paul, P Dasgupta, D Roy, S Chaudhuri (2017). Plant Molecular Biology 95 (1-2), 63-88.
- Deciphering the role of the AT-rich interaction domain and the HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana. A Roy, A Dutta, D Roy, P Ganguly, R Ghosh, R K Kar, A Bhunia, J Mukhobadhyay, S Chaudhuri (2016). Plant Molecular biology 92 (3), 371-388.
- Differential acetylation of histone H3 at the regulatory region of OsDREB1b promoter facilitates chromatin remodelling and transcription activation during cold stress. D Roy, A Paul, A Roy, R Ghosh, P Ganguly, S Chaudhuri (2014). PLoS One 9 (6), e100343
- Functional characterization of a serine-threonine protein kinase of Bambusabalcooa that implicates in cellulose overproduction and superior quality fiber formation. JS Ghosh, S Chaudhuri, NrisinghaDey and Amita Pal (2013). BMC Plant Biology, 13: 128 DOI:10.1186/1471-2229-13-128
- TLR signaling-mediated differential histone modification at IL-10 and IL-12 promoter region leads to functional impairments in tumor-associated macrophages. S Banerjee, K Halder, A Bose, P Bhattacharya, G Gupta, S Karmahapatra, S Das, S Chaudhuri, SB Majumdar, S Majumdar (2011). Carcinogenesis 32 (12), 1789-1797
- Arabinosylated lipoarabinomannan skews Th2 phenotype towards Th1 during Leishmania infection by chromatin modification: involvement of MAPK signaling. Bhattacharya P, Gupta G, Majumder S, Adhikari A, Banerjee S, Halder K, Majumdar SB, Ghosh M, Chaudhuri S, Roy S, Majumdar S (2011).PLoS One. 2011;6(9):e24141 DOI: 10.1371/journal.pone.0024141
- A calcium/calmodulin-regulated member of the receptor-like kinase confers cold tolerance in Plants. T Yang, S Chaudhuri, L Yang, L Du and B.W. Poovaiah (2010).J. Biol. Chem 285(10):7119-26.
- Histone H3 Lys79 Methylation is Required for Efficient Nucleotide Excision Repair in a Silenced Locus of Saccharomyces cerevisiae. S Chaudhuri, JJ. Wyrick, and M J. Smerdon. (2009).Nucleic acids research 37(5): 1690-1700
- Nodulation independent of rhizobia is induced by a calcium activated kinase lacking autoinhibition. C Gleason, S Chaudhuri, T Yang, A Munoz-Gutierrez , B. W. Poovaiah, G Oldroyd. (2006). Nature 441 (7097): 1149–1152
- Domain analysis of a groundnut calcium-dependent protein kinase: nuclear localization sequence in the junction domain is coupled with nonconsensus calcium binding domains. Raichaudhuri A, Bhattacharyya R, Chaudhuri S, Chakrabarti P, Dasgupta M. (2006). J. Biol. Chem., 281:10399-409.
- Calcium/calmodulin up-regulates a cytoplasmic receptor-like kinase in plants. T Yang, S Chaudhuri, L Yang, Y Chen, and B. W. Poovaiah. (2004). J. Biol. Chem., 279: 42552-42559
- Identification of regulators of hrp/hop genes of Erwiniacarotovora ssp. carotovora and characterization of HrpLEcc(sigma LEcc), an alternative sigma factor. A Chatterjee, Y Cui, S Chaudhuri and A Chatterjee (2002).Molecular Plant Pathology 3(5), 359-370
- Exogenous auxin depletion renders Arachis hypogea suspension culture sensitive to water loss without affecting cell growth. Seal, A., Hazra A., Nag, R., Chaudhuri, S. and DasGupta, M (2001).Plant Cell Reports. 20(6): 567 – 573
- Autophosphorylation Dependent Activation of a Calcium Dependent Protein Kinase from Arachis hypogea Plant. S Chaudhuri, A Seal & M DasGupta (1999). Plant Physiology 120: 859-866
- Analysis of DNA Methylation Profile in Plants by Chop-PCR. P Dasgupta, S Chaudhuri (2019). Plant Innate Immunity, Methods in Molecular Biology, Springer Protocols, Humana Press, 79-90.
- Change in Nucleosome Dynamics During Stress Responses in Plants A Paul, S Chaudhuri (2019). Plant Innate Immunity, Methods in Molecular Biology, Springer Protocols, Humana Press, 91-100.
- CDPKS in plant signaling networks- Progress in research on Groundnut CDPK. In “Signal transduction in plants” (S.K. Sopory; R. Oelmuller and S. C. Maheshwari, Eds.). M DasGupta and S Chaudhuri (2001). Kluwer academic Press, Page 145-156.
1. Involved in teaching of Cell Biology, Plant biology Course of Integrated M.Sc. PhD Course in Life Science (Bose Institute).
2. Involved in taking Pre-Ph.D course work classes for research scholars in Bose Institute.
|Ruby Biswas||Junior Research Fellow||Division of Plant Biology||Centenary||25693254|
|Sonal Sachdev||Junior Research Fellow||Division of Plant Biology||Centenary||25693297||sonalsachdev|
Ms. Pratiti Dasgupta email@example.com
Ms. Jinia Chakrabarty firstname.lastname@example.org
Ms Sonal Sachdev email@example.com
Ms Ruby Biswas firstname.lastname@example.org
Dr. Sudip Saha
Assistant professor at Techno India University, West Bengal
Joined NIAB-Cambridge, UK
Post-doctoral Fellow at Durham University, UK
Dr. Amit Paul
Post-doctoral Fellow at UCLA, USA
Dr. Rwitie Mallik
2019: Dr Shubho Chaudhuri received the SERB-ITS grant for poster presentation at Plant Biology 2019 (hosted by ASPB) in San Jose, California, USA in August, 2019.
2018: Ms. Pratiti Dasgupta received the SERB-ITS grant for poster presentation at Keystone Symposia meeting on Chromatin Architecture and Chromosome Organization held at Whistler Conference Centre, BC, Canada in March, 2018.
2017: Ms Adrita Roy received the best poster award [International symposium on Insights to Plant Biology,]
for PhD position enrollment
Positions available: Four position available (JRF)
RA: Interested candidates can directly contact email@example.com
Our group at Bose Institute, Kolkata is seeking for highly motivated doctoral research candidates, who are interested to work in understanding the molecular events instrumental in plant development and plant response to external cues at genetic and epigenetic levels. The group is currently involved in understanding the regulation in Arabidopsis thaliana and rice (Oryza sativa) plant species.
Our work has the following focus areas:
1. To explore the different epigenetic changes in plants to understand the transcription regulation of genes that are regulated during abiotic stress response.
2. To identify the chromatin state (modifications) that can be transferred to the offspring as stress memory for better stress perception and adaptability, in cases of repeated stress cycles.
3. Study the mechanism of chromatin remodelling in plants (with emphasis on HMG superfamily) to understand the transcription regulation of genes that are regulated by endogenous and exogenous cues.
We are looking for
prospective candidates for filling up four vacancies in the above-mentioned
areas of research.
- Master Degree or equivalent degree in either of the following: Biotechnology, Biochemistry, Botany, Genetics, Microbiology, Life Sciences.
- Candidates must have an award of a valid JRF (CSIR-UGC JRF/ DBT-JRF/ DST-INSPIRE/ DBT-BINC or equivalent). Candidates, currently in their final year of their Master’s degree and in possession of an award of a JRF can apply. If selected, they will be asked to submit their final degree certificate at the time of joining.
Interested candidates are encouraged to apply.
Application related query and submissions (application letter along with Curriculum Vitae) may be directly addressed to the lab supervisor
Dr Shubho Chaudhuri at firstname.lastname@example.org