Department of Biosciences and Bioengineering : Indian Institute of Technology Guwahati

Kusum K Singh

Assistant Professor

kusumsingh[AT*]iitg.ac.in

Research Areas:

Post-transcriptional gene regulation by RNA binding Proteins

Web page:

Welcome to RNA-Binding Proteins (RBPs) Laboratory

Upcoming 12th RNA Meeting at IIT Guwahati (22nd - 24th May 2024)

https://www.iitg.ac.in/biotech/rna2024/index.html

Starting from the 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 called ribonucleoprotein particles (RNPs). The dynamic interaction between RBPs and RNA molecules decides mRNA biogenesis, pre-mRNA processing, export, localization, translation, and degradation—the deposition of RBPs on mRNAs couples transcription with post-transcriptional gene expression events. However, we do not have a comprehensive idea about the sequential assembly, composition, and roles of many RBPs. Thus, our goal is to understand the assembly and functions of various mRNP interactomes to decipher the molecular events at different stages of gene expression.

During the splicing of premature mRNA, the spliceosome deposits a multiprotein complex termed Exon-Juction Complex (EJC) onto the mRNAs. The core EJC subunits 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 the study is the "Apoptosis and Splicing-Associated Protein (ASAP)" complex.

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

Our Current Research Focus:

Understanding the functions of ASAP concerning EJC in mRNA metabolism.
Elucidating the molecular involvement of RNA-binding proteins (RBPs) in various human diseases such as cancers, and 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:

26. Invited oral presentation "Role of RNPS1 in cervical cancer", National Centre for Cell Science, Pune. 1^st to 3^rd December 2022.

25. Attended EMBO/EMBL Symposium: The complex life of RNA in Virtual mode from 12^th to 15^th October 2022.

24. Attended Cold Spring Harbor Laboratory Conference on Regulatory and Noncoding RNAs in the virtual mode from 17^th to 21^st May 2022.

23. Attended EMBO-INDIA NCCS PUNE RNA Binding Proteins: from RNA binding to condensation and Aggregation Conference in Virtual mode from 07th to 11th February 2022.

22. Attended EMBL Conference on The Non-Coding Genome in Virtual mode from 13th to 15th October 2021.

21. Attended the 26th Annual Meeting of the RNA Society in virtual mode, May 25th to June 04^th, 2021.

20. Attended the 25th Annual Meeting of the RNA Society in virtual mode, May 25th to 31st, 2020.

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, 8-10 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 2010-Jul 2015 Postdoctoral research fellow, Institute of Genetics, University of Cologne, Germany.

Apr 2010-June 2011 Postdoctoral research fellow, Institute for Biochemistry and Molecular Biology, RWTH Aachen, Germany.

Jul 2009-Oct 2009 Postdoctoral research fellow, Childrens Cancer Research Institute-UTHSC, San Antonio, Texas.

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

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

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 2023)

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) (Jan - May 2024)

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).

Journals

1. Priyanka Yadav, Raja Tamilselvan, M Harita, Kusum Kumari Singh "MicroRNA-mediated regulation of nonsense-mediated mRNA decay factors: Insights into microRNA prediction tools and profiling techniques", Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms. DOI.https://doi.org/10.1016/j.bbagrm.2024.195022, Vol.1867, 2, P.P 195022-195032 , (2024)

2. Sweta Kumari, Bhagyashree Deka, and Kusum Kumari Singh "Serine-rich domain of RNPS1 functions in activation of alternative splicing", Genes to Cells. DOI. 10.1111/gtc.13036 , Vol., PMID: 37204171 , P.P - , (2023)

3. Aparajita Dutta , Kusum Kumari Singh , Ashish Anand "Identification of Splice Junctions Across Species Using BLSTM Model", ACM DIGITAL LIBRARY. DOI.https://dl.acm.org/doi/10.1145/3589437.3589438, Vol., , P.P 1-6 , (2023)

4. Sweta Kumari, Ayushi Rehman, Pratap Chandra, Kusum K. Singh "Functional role of SAP18 protein: From transcriptional repression to splicing regulation", Cell Biochemistry and Function. DOI. https://doi.org/10.1002/cbf.3830, Vol., , P.P - , (2023)

5. Bhagyashree Deka, Kusum K Singh "Identification of Candidate RNA Binding Proteins Associated with RNPS1 3’UTR", Healthcare Research and Related Technologies. DOI.10.1007/978-981-99-4056-1_2, Vol., , P.P - , (2023)

Conference Publication

1. Harita M, Bhagyashree Deka, Kusum K Singh . "Identification of candidate RNA binding proteins associated with RNPS1 mRNA.", 11th RNA Group Meeting. Vol., , P.P - , (2022)

2. Raja T "", Hands-on workshop on CRISPR/Cas technology and genome editing, National Center for Biological Sciences, Bangalore. Vol., , P.P - , (2022)

3. Sayan Roy, Pratap Chandra, Kusum K Singh "Proteomic Analysis of CRISPR/Cas9-mediated UPF3B-Knockout HEK293 Cells", 11th RNA Group Meeting. Vol., , P.P - , (2022)

4. Priyanka Yadav, Kusum K Singh "MicroRNA-mediated regulation of UPF3 for the development of novel therapeutics.", 11th RNA Group Meeting. Vol., , P.P - , (2022)

5. Priyanka Yadav, Kusum K Singh "MicroRNA-mediated regulation of UPF3B for the development of novel therapeutics.", Functional nucleic acids: Recent landscapes and therapeutic applications (ielc22-095). Vol., , P.P - , (2022)

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