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Blizard Institute - Barts and The London

Dr Pradeepa Madapura, PhD, MSc, BSc

Pradeepa

Lecturer

Centre: Centre for Genomics and Child Health

Email: p.m.madapura@qmul.ac.uk
Telephone: +44 (0)20 7882 2594
Twitter: @PradeepMadapura

Profile

Pradeepa Madapura did his Ph.D research (Bengaluru, India) on chromatin remodelling during spermatogenesis. Pradeep moved to Edinburgh, UK for postdoctoral research with Prof. Wendy Bickmore, a world leading scientist in epigenetics and chromatin field. In 2016 Pradeep started independent research as a University lecturer of genomics at the University of Essex, and is a fellow of higher education academy (FHEA). Pradeep’s lab is relocated to Blizard Institute in September 2018.

Pradeep’s lab is interested in studying the functional contribution of chromatin proteins, histone modifications and noncoding RNAs in the regulation of gene expression. His also actively collaborate with clinicians and genomics data scientists to use cutting-edge methods to investigate the contribution of sequence variation in noncoding regulatory elements in genetic disorders and cancer.

2018 –           Assistant professor (lecturer) at the Queen Mary University of London, UK
2016 – 2018 Assistant professor (lecturer) at the University of Essex, Colchester, UK
2009 – 2015 Postdoctoral Fellow in the laboratory of Prof Wendy Bickmore
2004 – 2009 PhD in Molecular biology and Genetics from JNCASR, Bangalore (Supervisor: MRS Rao)
2001­– 2003  MSc(Agri) Biochemistry, University of Agriculture Sciences, Bangalore
1997­– 2001  BSc(Agriculture), University of Agriculture Sciences, Bangalore

Website: /madapuralab.com
QMUL Epigenetics: /madapura
LinkedIn: /pradeepamm2207

Teaching

MBBS programme: PBL facilitator on three modules – Human Development 1, Human Development 2, and locomotor.

MEDPRO mentoring Scheme: I mentor 8 MBBS students.

BSc teaching: PBL tutor for Biomedical Science Case Approach to Problem Solving (BMD202)

PhD opportunities: 

Deciphering the mechanism through which mutations in BRD4 cause neurodevelopmental disorder

Research

Research Interests:

My research is focused on investigating the role of chromatin proteins, histone modifications in regulation of gene expression, splicing and DNA repair. We use genome-wide methodologies and single locus precision editing and gene engineering methods investigate how genome is regulated and factors contributing to function of gene regulatory elements. Highlight of my work includes identification of novel class of enhancer elements that lack acetylation of histone H3 at lysine 27 (H3K27ac), a widely used marker of active enhancers. We showed H3 globular acetylation at lysine 112 (H3K122ac) (Nature Genet 2016) and acetylation at H4 lysine 16 (H4K16ac) (Genome Res 2013) marks active enhancers. More importantly, we show that there are many enhancers in the genome that lack H3K27ac but are acetylated at H3K122 or H4K16 lysines. Our recently work demonstrated de novo mutations in a key transcriptional regulator BRD4 which is known to function at enhancers and promoters by binding to acetylated histones causes a neurodevelopmental disorder called Cornelia deLange Syndrome (CdLS) (Nature Genet 2018). Our ongoing work suggests that CdLS mutations in BRD4 leads to altered DNA damage response pathway (BioRxiv 2019).

Apart from my main focus on genome regulation, our lab is also interested in deciphering the role of chromatin proteins, homeobox (HOX) transcription factors and long noncoding RNA HOTTIP in cancer development and therapy resistance due to altered enhancer function. My lab is interested in deciphering the function of a very interesting multifunctional chromatin protein (PSIP1) implicated in HIV integration and Leukaemia. My work has demonstrated role of PSIP1 in coupling histone modification with RNA splicing (PLoS Genet 2012) and in regulation of HOX genes (Nucleic Acid Res 2014). Using cutting edge methods, we have demonstrated enhancer like function of a long noncoding RNA called HOTTIP (PLoS Genet 2017). Current and future projects include: 1) Improving our understanding of how pathogenic mutations in MOF/MSL3 impact normal development due to altered enhancer function; 2) Establish human embryonic stem cell (hPSC) to neuronal differentiation and brain organoid to study the effect of coding and noncoding mutations frequently found in neurodevelopmental disorder patients; 3) Development and use of highthroughput enhancer assays (STARRseq) to identify and further characterize enhancer elements.

Publications

Key Publications

Olley G, Ansari M, Bengani H, Grimes GR, Rhodes J, Kriegsheim AV, Blatnik A, Stewart F J, Ross A, Bickmore WA*, Pradeepa MM*, and FitzPatrick DR*. BRD4 interacts with NIPBL and is mutated in a Cornelia de Lange-like Syndrome. Nature Genet. 2018. doi:10.1038/s41588-018-0042-y

Pradeepa M M*, McKenna F, Taylor GCA, Bengani H, Grimes GR, Wood A, Bhatia S, and Bickmore W A*. (2017) Psip1/p52 regulates distal Hoxa genes through activation of lncRNA Hottip PloS Genet 13, e1006677 (2017). Perspective article highlighting this work is published in PLoS Genet 13(6): e1006797.

Pradeepa M M*, Grimes G, Kumar Y, Taylor G, Olley G, Schneider R and Bickmore W A* (2016) Histone H3 globular domain acetylation identifies a new class of enhancers. Nature Genet. 48, 681–686 doi:10.1038/ng.3550. Two recommendations by F1000 Prime.

Taylor G, Eskeland R. Balkan B H, Pradeepa M M* & Bickmore W A*. (2013) H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction. Genome Res. doi: 10.1101/gr.155028.113.

*corresponding author

All Publications

Supervision

Dr. Debosree Pal (PDRA)
Dr. Pankaj Dubey (PDRA)
Dr. Jayakumar Sundarraj (Marie Curie Fellow)
Dr. Ahmed Saleh Ali Saleh (M.B.B.Ch) (MD/PhD student)
Ms. Minal Patel (MRC PhD student)