Senior Principal Investigator - Systems Biology
Neerja Karnani received her PhD (2002) from School of Life Sciences, Jawaharlal Nehru University in India, where she worked on multidrug resistance in pathogenic yeast, Candida albicans. During her graduate studies, she was a recipient of the C. R. Krishna Murti Memorial Young Scientist Award. In 2003 she joined Prof. Anindya Dutta’s laboratory at University of Virginia for her postdoctoral studies. In his lab she headed the ENCODE (Encyclopedia of DNA Elements) project. This project was initiated by NHGRI (National Human Genome Research Institute) to identify various functional elements in the human genome sequence (Science. 2004, 306: 636-640). Her work in association with ENCODE identifiedi)DNA replication elements, ii) chromatin domains (Nature 2007, 447:799-816 andGenome Res, 2007, 17:865-876), and iii) sites of DNA damage induced by replication inhibitors (Genes & Dev., 2011, 25:621-3).She joined SICS in 2013 as Principal Investigator.
In utero growth of fetus is the most active period of cell proliferation and copying of genetic information. This is also the phase of laying down the epigenetic framework. Though genetic information is relatively stable, epigenetic marks are more dynamic and constantly edited during the fetal growth, and post-birth. Hergroupis interested in understanding the epigenetic modulations during early development, and its role in establishment of complex diseases later in life. Their approach is to perform a comprehensive genome based evaluation of different epigenetic regulatory networks (DNA methylation, post-translational modification of histones, and non-coding RNAs) in patient populations. All these studies are currently being conductedon clinical subjects,as well as model organisms, in collaboration with the clinicians and research groups at SICS. The genomics data generated on multiple epigenetic platforms is being analyzed and integrated for biomarker discovery and pharmacological intervention.
In addition, they are also interested in identifying the sites of somatic instability in utero. During pregnancy, the expecting moms can undergo nutritional deficiency and metabolic disorders that can put the genome integrity of the growing fetus at a risk. Some of these lesions can skip DNA damage repair and be propagated in dividing fetal cells. They are interested in investigating the genotype data from offspring-parent trioto identifythe somatic hotspotsof chromosome fragility,triplet expansion and copy number variations (CNVs).
Zhang Y, Subbaiah VK, Rajagopalan D, Tham CY, Abdullah LN, Toh TB, Gong M, Tan TZ, Jadhav SP, Pandey AK, Karnani N, Chow EK, Thiery JP, Jha S. ''TIP60 inhibits metastasis by ablating DNMT1-SNAIL2-driven epithelial-mesenchymal transition program''. J Mol Cell Biol. 20 Sep 2016. 8(5):1-16. doi: 10.1093/jmcb/mjw038.
Kim SY, Sim CK, Zhang Q, Tang H, Brunmeir R, Pan H, Karnani N, Han W, Zhang K, Xu F. ''An Alternative Strategy for Pan-acetyl-lysine Antibody Generation''. PLoS One. 08 Sep 2016. 11(9):e0162528. doi: 10.1371/journal.pone.0162528.
Pan H, Holbrook JD, Karnani N, Kwoh CK. ''Gene, Environment and Methylation (GEM): a tool suite to efficiently navigate large scale epigenome wide association studies and integrate genotype and interaction between genotype and environment''. BMC Bioinformatics. 02 Aug 2016. 17:299. doi: 10.1186/s12859-016-1161-z.
Teh AL, Pan H, Lin X, Lim YI, Patro CP, Cheong CY, Gong M, MacIsaac JL, Kwoh CK, Meaney MJ, Kobor MS, Chong YS, Gluckman PD, Holbrook JD, Karnani N. ''Comparison of Methyl-capture Sequencing vs. Infinium 450K methylation array for methylome analysis in clinical samples''. Epigenetics. 19 Jan 2016. 11(1):36-48. doi: 10.1080/15592294.2015.1132136.
Tsotsi S, Abdulla N, Li C, Chong YS, Richmond J, Saw SM, Kwek K, Gluckman P, Meaney MJ, Holbrook JD, Karnani N, Rifkin-Graboi A. ''Fetal DNA methylation of cortisol-related genes and infant neurobehavior at 6 months: The role of antenatal maternal anxiety''. Psychoneuroendocrinology. 08 Aug 2015. 61:35. doi: 101016/jpsyneuen201507484.
Pan H, Lin X, Wu Y, Chen L, Teh AL, Soh SE, Lee YS, Tint MT, MacIsaac JL, Morin AM, Tan KH, Yap F, Saw SM, Kobor MS, Meaney MJ, Godfrey KM, Chong YS, Gluckman P, Karnani N, Holbrook JD. ''HIF3A association with adiposity: the story begins before birth''. Epigenomics. 26 May 2015. 7(6):937-50. doi: 102217/epi1545.
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