Academic Profile

Academic Profile

Asst Prof Amartya Sanyal

Nanyang Assistant Professor, School of Biological Sciences

Asst Prof Amartya Sanyal

Dr. Amartya Sanyal obtained his Bachelor’s and Master’s degree in India from University of Calcutta and Banaras Hindu University respectively. He then pursued his Ph.D. from Indian Institute of Science, Bangalore during which he worked on human germ cell gene expression and their regulation during spermatogenesis. He then moved to University of Massachusetts Medical School, Worcester, MA, USA for his postdoctoral training under the supervision of Dr. Job Dekker who pioneered the Chromosome Conformation Capture (3C) technique. During his postdoctoral tenure, Dr. Sanyal was actively involved in the NHGRI funded ENCODE (ENCyclopedia Of DNA Elements) consortium projects. He successfully generated high-resolution 3D chromatin architecture map and comprehensively annotated long-range chromatin interactions in 1% of human genome using high throughput 3C-based method combined with next-generation sequencing (NGS). Dr. Sanyal’s work has been published in leading research journals and is highly cited. He worked in close collaboration with several reputed laboratories at Stanford University, University of Washington, Emory University, Harvard Medical School, etc. His research has made significant impact in the understanding of genome organization and chromatin looping interactions. In August 2014, Dr. Sanyal joined NTU as Nanyang Assistant Professor in School of Biological Sciences (SBS) and Lee Kong Chian School of Medicine (LKCMedicine) - a joint medical school by Imperial College London and NTU.

Awards and achievements:
1. Nanyang Assistant Professorship 2014 (Nanyang Technological University, Singapore)
2. Selected for the prestigious Wellcome Trust/DBT India Alliance Intermediate Fellowship in 2014 (not availed)
3. Junior Research Fellowship and eligibility for Lectureship through Joint CSIR-UGC National Eligibility Test (NET, December 2001) in Life sciences conducted by Council for Scientific and Industrial Research and University Grants Commission, Govt. of India
4. Lectureship in Life Sciences through State Level Eligibility Test (SLET) 2002 accredited by University Grants Commission, Govt. of India and conducted by the West Bengal College Service Commission, Kolkata, India
5. Qualified Graduate Aptitude Test in Engineering (GATE) in Life Sciences (All India rank- 22)
Research Interests
The main focus of our research is to understand 3D genome organization inside the nucleus and its impact on transcriptional regulatory code during mammalian development, differentiation and disease. Please visit Sanyal Lab webpage (

Human genome is organized in highly complex conformations inside the nucleus. How this three-dimensional organization of chromatin affects gene regulation is largely unknown. Genome-wide annotations of genes and functional regulatory elements do not give an insight into which regulatory elements control any given gene. Long-range looping interactions between gene promoters and distal genomic elements such as enhancers are known to be important for regulation of transcription. The advent of Chromosome Conformation Capture (3C)-based techniques and its high-throughput adaptations has made it possible to detect spatial proximity and high-resolution chromatin interactions between genomic elements.

We are particularly interested in understanding how non-coding sequence variants identified by genome-wide association studies (GWAS) contribute to human disease risk and pathogenesis. In the past decade, genome-wide scans of SNPs (single nucleotide polymorphisms) in populations have identified many genomic loci associated with the predisposition to disease. The observed associations are possibly driven by linkage disequilibrium with the disease-associated region in vicinity. However, >90% GWAS SNPs do not map to coding regions suggesting these variants may, in fact, affect gene regulatory mechanism and involved in controlling the expression of distal target genes, the identity of which remain unknown. Connecting the GWAS SNPs to their target genes would aid in understanding genotype-phenotype relationships in disease and in designing effective treatment and therapeutics.

In our lab, we intend using high-throughput genomic methods, genome-editing and imaging techniques in combination with bioinformatics and computational approaches to understand structure-function relationship of chromatin. Overall, we are trying to decipher the regulatory mechanisms of cell- and tissue-specific gene expression in relation to 3D chromatin architecture, epigenetic mechanisms (chromatin modifications) and binding of trans-acting factors to understand various biological processes in normal and disease conditions.
Current Projects
  • Deciphering the interplay between genetics and epigenetics in mammalian hybrids
  • Identifying disease-associated gene from non-coding geneticvariants using chromatin interaction map
Selected Publications
  • Phillips-Cremins JE et. al. (2013). Architectural protein subclasses shape 3-D organization of genomes during lineage commitment. Cell, 153(6), 1281-95.
  • Sanyal A, Lajoie BR, Jain G, Dekker J. (2012). The long-range interaction landscape of gene promoters. Nature, 489(7414), 109-13.
  • Sanyal A, Baù D, Martí-Renom MA, Dekker J. (2011). Chromatin globules: a common motif of higher order chromosome structure?. Current Opinion in Cell Biology, 23(3), 325-31.
  • Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA, Chang HY. (2011). A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature, 472(7341), 120-4.
  • Baù D, Sanyal A, Lajoie BR (2011). The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules. Nature Structural and Molecular Biology, 18(1), 107-14.

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