Kusum K Singh

Assistant Professor

kusumsingh[AT*]iitg.ac.in

Research Areas:

Post-transcriptional gene regulation by RNA binding Proteins

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Welcome to RNA-Binding Proteins (RBPs) Laboratory

 

Starting from the time of birth of RNA molecules, many RNA-binding proteins (RBPs) associate with RNA to regulate its cytoplasmic fate. This assembly of RBPs on non-coding RNAs (ncRNAs) or mRNAs is referred to as ribonucleoprotein particles (RNPs). The dynamic interaction between different sets of RBPs and RNA molecules decides mRNA biogenesis, pre-mRNA processing, export, localization, translation and degradation. It is the deposition of RBPs on mRNAs that couples transcription with post-transcriptional events of gene expression. However, we donot have comprehensive idea about sequential assembly, composition and roles of many RBPs. Thus, our goal is to understand the assembly and functions of various mRNP interactome in order to decipher the molecular events at various stages of gene expression.

 

During splicing of premature mRNA, the spliceosome deposits a multiprotein complex termed Exon-Juction Complex (EJC) onto the mRNAs. The subunits that form the core EJC are eukaryotic translation initiation factor 4A3 (eIF4A3), Y14-MAGOH and barentz (BTZ, CAS3 or MLN51). Many proteins transiently interact with the core EJC and our focus of study is "Apoptosis and Splicing-Associated Protein (ASAP)" complex.

Components of both ASAP and EJC have been found to function in a wide range of activities pertaining to RNA metabolism including splicing, translation, nonsense-mediated mRNA decay (NMD) and Apoptosis.

Our Current Research Focus:

  • Understanding the functions of ASAP with respect to EJC in mRNA metabolism.
  • Elucidating the molecular involvement of RNA-binding proteins (RBPs) in various human diseases such as cancers, neurodevelopmental disorders.
  • Exploring the post-transcriptional gene regulations of different RBPs.
  • To investigate functional outcomes of isoform switching.

Academic Qualification:

 

2005-2009   Ph.D., Institute of Molecular Medicine, Heinrich Heine University, Duesseldorf, Germany.

2002-2003   Diploma, Institute Jules Guyot, University of Bourgogne, Dijon, France.

2000-2002   Masters in Biotechnology, Deen Dayal Upadhyay Gorakhpur University, India.

1997-2000   Bachelors in Biochemistry and vocational Biotechnology, St. Xavier’s College, University of Gujarat, India.   

 

Invited Talk/Symposium/Conference: 

19. Invited oral presentation "Protection splice sites", world congress on cancer at Mahatma Gandhi Medical College & Hospital, Jaipur, 4th Feb 2020.

18. Invited talk "Transcriptome integrity via RNPS1-EJC" at St. Xavier's College, Ahmedabad, 3rd Jan 2020.

17. Talk on "RNPS1 interaction partners", Caner Biology Conference at ILS, Bhubaneswar, 30th Nov 2019.

16. Invited talk on “Role of RNPS1 and EJC in protecting transcriptome “ at the International conference at Cotton college, Guwahati University, 1st June  2019.

15. Talk on “EJC suppresses spurious splice sites” at the 9th RNA Group Meeting, BHU Varanasi, 27th October 2017.

14. Talk on “RNA binding proteins” at NIAS-DST programme for Women Scientists, Bengaluru, 02nd March 2017.

13. The 8th RNA Group Meeting, “Splicing dependent mRNA binding of ASAP complexes” at  CSIR-CCMB Hyderabad, 8-10th January 2016.

12. SFB Meeting on RNA life span, Cologne University, Germany: 12-13th June 2013.

11. Quality Control-From molecules to Organelles at EMBL Heidelberg, Germany: 19-22nd September 2012.

10. SFB Meeting on post-transcriptional gene regulation, Dresden University, Germany: 17-19th October 2012.

9. RNA Meeting at RWTH Aachen University, Aachen, Germany: 16-18th April 2012.

8. Talk on "Functional characterization of p27 acetylation, at Zurich ETH, Switzerland, 27th May 2011.

7. Cell death meeting at Cold Spring Harbor Laboratory, NY, USA; 26-30th September 2007.

6. Autumn session of SFB612, SFB688 and GRK1089, Kaiserwerth, Düsseldorf, Germany; 30th September -2nd October 2007.

5. Symposium on “Day of Scientific talent” at Heinrich-Heine University of Düsseldorf, Germany; 22nd July 2007.

4. Talk on cardiovascular diseases and alternative splicing at spring workshop of GRK1089, Muenster, Germany; 29-30th June 2007.

3. Autumn session of SFB612 and GRK1089, Wermelskirchen, Germany; 11-12th December 2006.

2. Talk and poster on Alternative splicing and cardiovascular diseases at spring workshop of GRK1089, Bensberg, Germany; 9-10th June 2006.

1. Autumn session of SFB612 and GRK1089, Wermelskirchen, Germany; 4-5th November 2005.

                                                 

Professional Experience:

 

Jul 2015 onward       Assistant Professor, Department of Biosciences and Bioengineering, IIT Guwahati, Assam, India.

Jul 2011-Jul 2015     Postdoctoral research fellow, Institute of Genetics, University of Cologne, Germany.

Jun 2009-Oct 2009   Postdoctoral Fellow at Children’s Cancer Research Institute-UTHSCSA, San Antonio, Texas, USA.

Jul 2004-Apr 2005    Research fellow, Institute for Molecular Physiology & Biotechnology of plants (IMBIO), University of Bonn, Germany.

 

Visiting Faculty:

  •  The Institute for Genetics, University of Cologne, Germany (Aug 2018- Feb 2019).

  •  The Institute for Genetics, University of Cologne, Germany (May-July 2016).

 

Collaborations:

  •  Prof. Bithiah G. Jaganathan, Department of Biosciences and Bioengineering, IIT-Guwahati.

  •  Prof. Ashish Anand, Department of Computer Science and Engineering, IIT-Guwahati.

  •  Prof. Anil Mukund Limaye, Department of Biosciences and Bioengineering, IIT-Guwahati.

  •  Prof. Sachin Kumar, Department of Biosciences and Bioengineering, IIT-Guwahati.
  •  Prof. Niels H. Gehring, Institute for Genetics, University of Cologne, Germany.

 

Professional memberships:

  •  The RNA society
  •  Nano and molecular society

 

Teaching:           
 
 

BT-637: Genome Editing and Engineering (3-0-0-6) (July-Nov 2022)

BT-642: Alternative splicing and diseases (3-0-0-6)

BT-205: Cellular and Molecular Biology  (3-0-0-6)

BT-101: Introductory Biology (3-0-0-6)

BT-208: Molecular Biology and Genetic Engineering  (3-1-0-8)

BT-503: Advanced Genetic Engineering  (3-0-0-6)

BT-604: Enzymology (3-0-0-6)

BT-510: Analytical Biotechnology Laboratory (0-0-6-6)

BT-290: Biomolecular Analysis Laboratory (0-0-6-6)

BT-380: Molecular Biotechnology Laboratory  (0-0-6-6)

BT-600: M.Tech Seminar (0-0-2-2)

BT-520: Applied Biology & Bioengineering Laboratory (0-0-6-6)

 

 

Awards and Fellowships:

 

 2018     NER-DBT Overseas Associateship, Gov. of India (Aug 2018- Feb 2019).

 2016     Albert’s Reunion grant, University of Cologne, Germany (May-July 2016).

 2012     Fritz Thyssen Stiftung Grant, Cologne, Germany (Jul 2012-Jun 2015).

 2007     GRK1089 travel grant, Cold Spring Harbor, USA (Sep 2007).

 2005     DFG-GRK1089 Fellowship, Dusseldorf, Germany (Apr 2005-Mar 2008).

 2002     Campus France Fellowship, Dijon, France (Nov 2002-Dec 2003).

 2000     Grace Braganza Research Fellowship, Ahmedabad, India (Mar 2000).

 1995     Inter-State Talent Tests in Mathematics, Belgaum, India (Jan 1995).

 

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Journals


1. Rumela Mitra, Ayushi Rehman, Kusum Kumari Singh*, Bithiah Grace Jaganathan* "Multifaceted Roles of MAGOH Proteins", Molecular Biology Reports. DOI., Vol., MOLE-D-21-06677R1, P.P - , (2022)

2. Bhagyashree Deka, Pratap Chandra, Priyanka Yadav, Ayushi Rehman, Sweta Kumari, Ajaikumar B. Kunnumakkara and Kusum Kumari Singh "RNPS1 functions as an oncogenic splicing factor in cervical cancer cells", International Union of Biochemistry and Molecular Biology. DOI., Vol., , P.P - , (2022)

3. Bhagyashree Deka and Kusum K. Singh "Molecular cloning, expression and generation of a polyclonal antibody specific for RNPS1", Molecular Biology Reports. DOI.10.1007/s11033-022-07676-8, Vol.12, 4, P.P - , (2022)

4. Ayushi Rehman, Pratap Chandra, Kusum Kumari Singh "The MAGOH paralogs - MAGOH, MAGOHB and their multiple isoforms", Gene Reports. DOI.doi.org/10.1016/j.genrep.2021.101214, Vol.24, , P.P - , (2021)

5. Aparajita Dutta, Kusum K Singh, Ashish Anand. "SpliceViNCI: Visualizing the splicing of non-canonical introns through recurrent neural networks", Journal of Bioinformatics and Computational Biology. DOI.doi.org/10.1142/S0219720021500141, Vol.19, 04, P.P -215004 , (2021)

Conference Publication


1. Glory Basumata and Kusum Kumari Singh "Knockdown effect of MAGOHB on Alternative splicing via RNA-Seq Analysis", International Conference on Molecular Basis of Diseases and Therapeutics. Vol., , P.P - , (2019)

2. Glory Basumata and Kusum Kumari Singh "Effects of MAGOHB knockdown on Alternative splicing via RNA-Seq Analysis", Galaxy Community Conference 2019. Vol., , P.P - , (2019)

3. Glory Basumata "Training on RNA-Seq data analysis and gene ontology studies using various tools", International Workshop: Introduction to RNA-Seq and Functional Interpretation, EMBL-EBI, Hinxton, UK. Vol., , P.P - , (2019)

4. Volker Boehm, Thiago Britto-Borges, Anna-Lena Steckelberg, Kusum K. Singh, Jennifer V. Gerbracht, Elif Gueney, Lorea Blazquez, Janine Altmüller, Christoph Dieterich, Niels H. Gehring "Exon Junction Complexes Suppress Spurious Splice Sites to Safeguard Transcriptome Integrity", The 24th Annual Meeting of the RNA Society. Vol., , P.P - , (2019)

5. Aparajita Dutta, Tushar Dubey, Kusum Kumari Singh, Ashish Anand. "SpliceVec: distributed feature representations for splice junction prediction.", The Sixteenth Asia Pacific Bioinformatics Conference. Vol., , P.P - , (2018)



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