Dr Partha Pratim Das, Group Leader
Dr Partha Pratim Das
T: 61 3 9902 4009
Our laboratory research interest focuses on how transcription factors (TFs) and epigenetic regulators, along with small RNAs and long non-coding RNAs (lncRNAs), regulate gene expression programs in embryonic stem cells (ESCs), neural stem cells and differentiated cells under normal and pathological conditions, such as cancers and neurodegenerative diseases. We use various experimental approaches and cutting edge technologies including- Cell and Molecular Biology, Biochemistry, CRISPRs, CRISPR screens (using sgRNAs to target all the genes in the genome, epigenetic regulators and regulatory elements), ChIPs, ChIP-sequencing, RNA-seq, WGS, ATAC-seq, RRBS, ChIA-PET, 3C, 4C, Hi-C, proteomics, bioinformatics and computational biology to understand the gene regulation under physiological condition and diseases.
- Dr Pratibha Tripathi
Senior Research Assistant Position Available
PhD Positions Available
Multiple PhD positions in the field of Stem cells, Epigenetics, Gene regulation and Computational Biology at Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia - click here for more information.
1. Dissect the role of histone demethylases (HDMs) in transcriptional regulatory network in mouse ESCs
ESC identity is established through interconnected regulatory networks of TFs, and these TF networks are intimately linked with epigenetic regulators to control chromatin organization and gene expression. However, the role of epigenetic regulators in the networks that establish ESC identity is poorly understood. Our recent studies have demonstrated that the two closely related HDMs, KDM4B and KDM4C- individually and combinatorially regulate mESC identity through different ESC regulatory modules/networks (Das et al, Molecular Cell, 2014). These findings led us to hypothesize that other HDMs play a similarly important role in ESC regulatory networks to establish and/or maintain ESC identity. The objective of our present research is to understand the detailed molecular mechanisms by which HDMs are involved in ESC regulatory networks for gene regulation that ultimately control the ESC state. We anticipate proposed studies on the role of HDMs in regulatory networks will improve our understanding of HDMs in gene regulation of ESC biology.
2. Investigating substrate specificity and redundancy of HDMs and their role in controlling gene expression programs in mouse ESCs and development
HDM sub-family members demethylate the same histone marks, suggesting that HDM sub-family members share enzymatic and/or substrate specificities and may have redundant functions. We are aiming to examine this issue focusing on KDM4/5/6 sub-family members to figure out the molecular details how substrate specificity and redundant functions of HDMs control gene regulation for ESC identity.
We also have generated "conditional" Kdm4b and Kdm4c KO mice. These mice will be crossed with different tissue-specific Cre-recombinases of interest, and further genetic, biochemical and genomics analyses will be performed to discover the mechanism by which KDM4B and KDM4C control substrate specificity and transcriptional output to regulate the identity of different cell types. These studies will not only provide a comprehensive understanding of HDM substrate specificity and its function in regulating gene expression in mESCs but will also explore the roles of HDMs in vivo.
3. Examining the functions of Enhancer and Super-enhancer regulatory elements in ESCs
Enhancers (ENs) and super-enhancers (SEs) are cis-acting regulatory DNA elements that significantly "enhance" the expression of target genes and independent of location or orientation with respect to their target genes. In mouse embryonic stem cells (mESCs), several putative ENs (8563) and SEs (231) have been identified. However, little is known about the "functions" of these ENs and SEs in mESC identity. We took a high-throughput clustered regularly interspaced palindromic repeat (CRISPR)-Cas9 mediated gene editing functional genomics approach by using "saturating mutagenesis CRISPR-Cas9 pool library" to target all known putative EN and SE regulatory elements in mESCs. We anticipate, this high-resolution, high-throughput screen will not only reveal the underlying minimal critical regulatory sequences, but also discover the functional significance of the several regulatory elements in mESCs for its identity.
4. Investigating the roles of regulatory elements in human medullobalstoma, a paediatric brain cancer
Medulloblastoma (MB) is the most common malignant pediatric brain tumor. Recent whole genome (WGS) and whole exome sequencing (WES) has identified only ~12 genes that are recurrently mutated in a sub-group specific manner, suggesting that prominent "driver genes" for MB are limited. As "driver genes" are limited for MB pathogenesis, it is likely that recurrent mutations exist outside of the coding regions, particularly at enhancer/super-enhancer regulatory elements. The role of regulatory elements in MB has not been explored to date. Our goal is to identify regulatory elements that harbor somatic mutations as well as MB-associated SNPs and study detail roles of these regulatory elements in MB pathogenesis.
5. Examining the role of genetic and epigenetic regulation in neural stem cells, brain development and neurodegenerative diseases
Recent discoveries massively ignited the potential importance of epigenetic mechanism in brain development and neurological diseases. Our lab is currently focuses on the following -i) understanding the role of epigenetic regulators in neural stem cells ii) investigating the role of regulatory elements in mouse and human brain development and iii) modeling neurodegenerative diseases using induced pluripotent stem cell (iPSCs) from healthy individuals and patients.
-Xie H, Peng C, Huang J, Li BE, Kim W, Smith EC, Fujiwara Y, Qi J, Cheloni G, Das PP, Nguyen M, Li S, Bradner JE, Orkin SH. Chronic myelogenous leukemia initiating cells require Polycomb group protein EZH2. Cancer Discovery (2016 Sep 14. pii: CD-15-1439 2016)
-Das PP, Hendrix DA, Apostolou E, Buchner AH, Canver MC, Beyaz S, Ljuboja D, Kuintzle R, Kim W, Karnik R, Shao Z, Xie H, Xu J, De Los Angeles A, Zhang Y, Choe J, Jun DL, Shen X, Gregory RI, Daley GQ, Meissner A, Kellis M, Hochedlinger K, Kim J, Orkin SH. PRC2 is required to maintain expression of the maternal Gtl2-Rian-Mirg locus by preventing de novo DNA methylation in mouse embryonic stem cells. Cell Reports (2015 Sep 1;12(9):1456-70)
-Kim PG, Das PP, Rowe RG, Nakano H, Chou SS, Ross SJ, Chen MJ, Sakamoto KM, Zon LI, Nakano A, Orkin SH, Daley GQ. Flow-induced Protein Kinase A/ CREB pathway acts via BMP signaling to promote AGM hematopoiesis. J Exp Med (2015 May 4;212(5):633-48)
-Das PP, Shao Z, Beyaz S, Apostolou E, Pinello L, Los Angeles AD, O'Brien K, Atsma JM, Fujiwara Y, Nguyen M, Ljuboja D, Guo G, Woo A, Yuan GC, Onder T, Daley GQ, Hochedlinger K, Kim J, Orkin SH. Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cells identity. Molecular Cell (2014 Jan 9; 53(1): 32-48)
-Guo G, Luc S, Marco E, Lin TW, Peng C, Kerenyi MA, Beyaz S, Kim W, Xu J, Das PP, Neff T, Zou K, Yuan GC, Orkin SH. Mapping the hematopoietic hierarchy by single cell analysis of the cell surface repertoire. Cell Stem Cell (2013 Oct 3; 13(4): 492-505)
-Das PP, Bagijn MP, Goldstein LD, Woolford JR, Lehrbach NJ, Sapetschnig A, Buhecha HR, Gilchrist MJ, Howe KL, Stark R, Matthews N, Berezikov E, Ketting RF, Tavare S, Miska EA. Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Molecular Cell (2008 Jul 11; 31(1): 79-90)
-O'carroll D, Mecklenbrauker I, Das PP, Santana A, Koenig U, Enright AJ, Miska EA, Tarakhovsky. A Slicer-independent role for Argonaute 2 in hematopoiesis and the microRNA pathway. Genes & Development (2007 Aug 15; 21(16): 1999-2004)
-Rodriguez A, Vigorito E, Clare S, Warren MV, Couttet P, Soond DR, van Dongen S, Grocock RJ, Das PP, Miska EA, Vetrie D, Okkenhaug K, Enright AJ, Dougan G, Turner M, Bradley. A Requirement of bic/microRNA-155 for normal immune function. Science (2007 Apr 27; 316(5824): 608-11)
Research related images
|Heat map of genome-wide mapping of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mESCs by ChIP-Seq (Das et al., Molecular Cell, 2014)|
|Differential expression of miRNAs (chromosome wise) from Ezh2-/-, Eed-/- and Jarid2-/- mESCs of PRC2 complex (small RNA-seq) (Das et al., Cell Reports, 2015)|
|Designing of tiled sgRNAs prior to NGG-protospacer adjacent motif (PAM) at the enhancer regulatory element of Nanog locus (Unpublished)|
|Histone Demethylome regulatory map (Unpublished)|