RNA signatures in cell-fate decisions

Our research aims to uncover novel factors that modulate cellular pathways, particularly embryonic stem cell-fate.
We are engaged in developing potent crispr-cas9 based tools to explore functional long noncoding rnas  and develop strategies to utilize them as molecular diagnostic markers in diseases.

We are based in CSIR-Institute of genomics & integrative biology in new Delhi, India

Research in our lab focusses on three broad areas

Long noncoding RNAs (lncRNAs) are a class of RNAs that do not produce a functional protein product. Although there are a large number of them inside the cell, they are lowly expressed and are generally poorly understood in terms of function. In recent years, owing to the development of better strategies to identify and study them, lncRNAs have been implicated in a variety of different cellular pathways including disease progression. We are interested in studying functional lncRNAs that are implicated in certain types of cancer in the Indian population and develop strategies to utilize them as molecular biomarkers for early diagnosis and better prognostics.
Probably no other genome engineering technology has made such an impact on scientific progress as CRISPR-Cas9. The applicability of this system has extended from gene discovery to crop improvement, from studying disease models to identifying drug targets. Owing to its potential to become a gene therapy agent (an application where the system can be used to correct a faulty or defective gene in a diseased individual and offer a curative strategy) a lot of current research is aimed at increasing the specificity and efficiency of its action. Together with the lab of Souvik Maiti , we plan to tackle this using chemical biology approaches and develop alternate and potent DNA and RNA editing agents.
Embryonic stem (ES) cells originate from the inner cell mass of the blastocyst of female mammals. As one of the first cells formed in the body, they possess the power of pluripotency, a term that denotes the capability to give rise to virtually any other cell or tissue type in the body, be it a cardiomyocyte or a neuron. Hence ES cells offer a lot of promise for therapeutic purposes where they can potentially be used to generate a faulty or a defective organ if the right cues are given. This process is termed as lineage commitment. However, defining the lineage of an embryonic stem cell depends on the correct knowledge about the factors that control these processes so that these can be tweaked based on our needs. In our lab, we study some of these factors and try to better understand their roles during  development.


Arpit Mishra
  (Post Doctoral fellow - jointly  with Dr. Souvik Maiti)

"..I am broadly interested in understanding correlation between 3D genome
architecture and transcriptional regulation: how dynamics  in genome
organization plays role in different trancriptomic outcome.
I have completed my PhD from IGIB, where i tried to understand mechanism and regulatory impact of a novel mycobacterial genome architectural protein mIHF. I have expertise in area of protein biochemistry,
biophysics and NGS sequencing and analysis.

Currently i  am learning the tricks of cas9 genome editing tools and how I can use these tools in understanding my broader questions that how genome organization or different genomic architectures (Gquad) can act as global regulators. Out side of science I am interested in
trekking,  travelling and exploring newer places and discussing broad
areas ranging from socio-political issues to evolution.."

Mohd. Azhar
(PhD student - jointly with Dr. Souvik Maiti)

".. I did my Bachelors in Biomedical Sciences (ANDC, DU) and Master in Bioscience (JMI). I joined IGIB as a Ph.D student in 2015-16 session. Right now I am in a cool and best lab guided by the two cool and best PIs, Dr Souvik and Dr Debo. My topic of research is to look for the LincRNAs ( Long
intergenic non coding RNAs) directly involved in cancer. When I am not in the lab I love to see myself in a ground playing Cricket or partying with Friends. In future, I am seeing myself as a good professor with a kind and humble nature.."

Smita Nahar
(PhD student - jointly with Dr. Souvik Maiti)

"..Fascinated by the revolution created by CRISPR-Cas9 genome editing process, I am trying to edit these “editors” in a quest to make this system even more precise and efficient. Deeply interested in exploring the regulatory functions mediated by RNA adopting various structures, I am trying to study the outcome of the roles RNA structures play in CRISPR-Cas9 system. With a strong background in miRNA biology, I am also interested in finding small molecule modulators (magic bullets) of therapeutically important miRNAs in cancer. Being the senior most member of the lab, I try to ensure the smooth functioning of the lab and manage all lab activities from ordering reagents to organizing trips for recreation.."

Nanda Kumar
(Project Fellow - jointly with Dr. Souvik Maiti)

"..I have completed my Masters degree in Genomics from School of Biological Sciences, Madurai Kamaraj University. I am currently involved in delineating the functional role of nuclear retained Long noncoding RNA (lncRNA) MALAT1 in tumor progression. Since the precise molecular mechanism that regulates gene expression and cellular dynamics is poorly understood, my goal is to unveil the molecular mechanisms of MALAT1 that governs tumor development. In my spare time I enjoy listening to songs and drawing. Sometimes I enjoy eating different varieties of food.."

Amrita Singh
(PhD student - jointly with Dr. Souvik Maiti)

"..This is Amrita, a PhD fellow in the lab. I have always had a keen
interest in studying cells at RNA level and I'm right now working on
understanding LncRNAs biology via triple helical structures. I presently
possess knowledge about basic molecular biology, mammalian cell culture
and biophysical techniques that help me move further in my research.
Having a knack for research and curiosity brimmed questions, I am
learning to develop more important skills such as patience and time
management, that I totally seem to lack! Apart from research, painting
had been my favourite pastime which I plan to revive soon.."

Meghali Aich 
(Project Fellow)

"..'Memories never die' they say, but can we recall all the experiences we go
through in our daily life? Neuroscience being one of my area of interest, I
am fascinated to understand the biology behind learning and memory. I
pursued Bachelors of Technology in Genetic Engineering from SRM
University, Chennai.
I am interested to study the role of long non-coding RNA mediated
epigenetic regulation of specific gene expression that facilitates acquisition
of new memories and retrieval of stored memories of learned experiences.
Using various molecular biology tools, I would like to study if modulating the
role of such lncs can induce memory based forgetting in post traumatic
stress disorder (PTSD in human) like animal models.
Besides the geeky side of me, I am equally excited about facing challenges
to overcome my fears. I love listening to music and do not fail to attempt a
new song. I am fond of travelling and participate in adventure sports. Being
a foodie, I often treat myself with different cuisines. I am passionate about
all my dreams and believe in making them come true.."

Saumya Sharma
(Project Fellow)

"..Since childhood, I have had a fascination for the night sky. I would wonder what lies into the oblivion of space, in between two or more stars. In one of my visits to my hometown in the foothills of Himalayas, I got the opportunity to view a starry night in the absence of light pollution. I observed what lied in the blank spaces were more and more of the stars. Originating from this incidence, my research interest lies in understanding the role of non-coding region of the genome, interspersed by the coding region, in regulating growth and development of an organism.
After my B.Sc. in Life Sciences from Miranda House College, I did a summer internship in the lab of Dr. Amulya K. Panda at the National Institute of Immunology. It motivated me to pursue a more research oriented M.Sc. in Biotechnology from the South Asian University. During my Master’s thesis research, under the supervision of Dr. Nirotpal Mrinal, I tried to understand the modulation in expression of mir genes by the overexpression of chromatin remodelling proteins FOXA1 & YY1, in a correlation with cancer. Now, at Dr. Debojyoti’s lab, I would work towards developing a molecular tool to perform genome editing that could overcome the shortcomings of CRISPR-Cas9 system, with a possibility to efficiently knockdown the expression of certain non-coding RNAs and thereby understanding their role in the normal and/or anomalous development of a cell and/or an organism. 
When not in lab, I could be seen eating, social networking, reading some novel or thinking of moonlighting as a stationary shop owner.."

Manoj Kumar
(PhD student - jointly with Dr. Souvik Maiti)

"Ever since I was a child, I was interested in learning about how things actually exist in nature. As a science student, I found myself asking several questions on life, our existence and always turned to biology for an explanation. I was particularly interested in therapeutic molecules such as various drugs, antibiotics, etc. This interest of mine was a stepping stone in the path of becoming a biochemist. After schooling I did my B.Sc. (Hons.) Biochemistry at University of Delhi and then completed my Masters at Department of Biochemistry, University of Delhi, South Campus. I just got into one of the best labs to work in, with Dr. Debojyoti Chakraborty. Here, I will be working on developing neural organoids associated to diseased condition and will try to correct these using cas9 system. Apart from academics, I play handball, basketball, cricket, badminton and have been selected twice for National level handball. If not in lab, you can catch me playing or chilling out with my lab mates and classmates in campus."


Shivaksh Ahluwalia
(Senior Project Fellow) - currently in IIT Delhi (PhD)

* co-first author, # co- corresponding author


  1. CRISPR/Cas9 and the era of targeted genome engineering
       *Amrita Singh, *#Debojyoti Chakraborty and #Souvik Maiti. Chemical Society Reviews (2016)
   2. LncRNA Panct1 maintains mouse embryonic stem cell identity by recruiting TOBF1 to Oct-Sox sequences in early G1
       Debojyoti Chakraborty, Maciej Paszkowski-Rogacz, Nicolas Berger, Li Ding, Jovan Mircetic et al  (under revision)
   3. Inactivation of cancer mutations utilizing CRISPR/Cas9
       Christina Gebler, Tim Lohoff, Maciej Paszkowski-Rogacz, Jovan Mircetic, Debojyoti Chakraborty et al. Journal of National Cancer Institute (2016)

   4. Directed evolution of Brec1: A broad-range recombinase that inactivates HIV-1 in patient-specific humanized mice
       Janet Karpinski, Ilona Hauber, Jan Chemnitz, Carola Schäfer, Maciej Paszkowski-Rogacz, Deboyoti Chakraborty  et al. Nature Biotechnology
   5. Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells
       Li Ding, Maciej Paszkowski-Rogacz, Maria Winzi, Debojyoti Chakraborty, Mirko Theis et al. Cell Systems (2015)

   6. Targeting Human Long-Noncoding Transcripts by Endoribonuclease-prepared siRNAs
       Mirko Theis, Maciej Paszkowski-Rogacz, Ina Weisswange, Debojyoti Chakraborty, Frank Buchholz. Journal of Biomolecular Screening (2015)
   7. Universal Tre (uTre) recombinase specifically targets the majority of HIV-1 isolates
        Janet Karpinski, Jan Chemnitz, Ilona Hauber Josephine Abi-Ghanem, Maciej Paszkowski-Rogacz, Vineeth Surendranath, Deboyoti Chakraborty
       et  al. Journal of the International AIDS Society (2014)

   8. Combined RNAi and localization for functionally dissecting long noncoding RNAs
       Debojyoti Chakraborty, Dennis Kappei, Mirko Theis, Anja Nitzsche, Li Ding, Maciej Paszkowski-Rogacz et al. Nature Methods (2012)


22-25 March 2017

The first CRISPR Workshop is here. Registration open!

For more details and registration:


Summer 2016

Meghali and Saumya have joined the lab as Project Assistants. Welcome Meghali and Saumya!
Shivaksh joined the PhD programme at IIT Delhi; all the best to him!
Manoj joined the lab as a PhD student after making it through the IGIB interviews. Wecome to the group!

December 2016

Amrita's CRISPR review has made it to the cover of Chemical Society Reviews! Congratulations to everyone who put their efforts into this.
Dr. Debojyoti Chakraborty heads a RNA Biology group at CSIR-Institute of Genomics and Integrative Biology where he currently holds a Senior Scientist position.

He finished his Masters in Molecular Biology from West Bengal University of Technology, Kolkata and completed his PhD from Max Planck Institute of Molecular Cell Biology & Genetics in Dresden under Frank Buchholz. Following a post doctoral stint at the Medical Faculty in TU Dresden, he returned to India to setup his own lab at IGIB.

Dr. Chakraborty has been nominated for a Wellcome Trust Early Career Fellowship (2016) and a INSPIRE Faculty Award (2015).

Besides his academic interests, Dr. Chakraborty is an  acclaimed sitarist and has performed widely in India and abroad ( www.debojyotichakraborty.com )

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If you are interested in joining us and perform cutting edge research bordering on stem cell biology and genome engineering, please write a one page synopsis explaining your research interests and the specific scientific question you wish to address and send to:

CSIR-Institute of Genomics and Integrative Biology,
Mathura Road,
New Delhi - 110025
Tel +911129879129
Page last updated: January 2017