Vani Brahmachari


Epigenetics lab

Dr. Vani Brahmachari did her Ph.D. from Indian Institute of Science, Bangalore. Her research interest is in the area human molecular epigenetics and genetics. She has worked at the National Cancer Centre, Tokyo, Wister Institute for Biology, Philadelphia, USA and Medical Research Council (MRC), London.

Areas of research interest:
  1. 1. Mining and characterisation of novel trans and cis acting elements for maintenance of developmental memory.

  2. 2. Epigenetic mechanisms of incomplete penetrance and variable expressivity: role of microRNA

  3. 3. Nucleosome organization as a part of the epigenetic architecture of the genome.

  4. 4. Mechanism of genomic imprinting: the mealybug as a model system.

One of the major focus is to utilize the complete genome sequence of mouse and human to discover novel genes thatgenes that could be are part of global regulation and are important for maintaining developmental memory. The lab combines in silico analysis and validatation by in vitro and in vivo experiments. Dr. Vani and her groupidentified a dual activity of chromatin remodeling protein, INO80. These proteins are important in maintaining developmental memory and they act through consensus sequences on DNA. The focus of Dr. Vani Brahmachari’s is the detection of both trans and cis-acting factors contributing to this memory. They have identified a few such sequences, PRE/TRE(polycomb/trithorax responsive elements) in the human genome. Her group has discovered a putative signature peptide for SNF2 family members that are also global regulators.

In the area of epigenetics she and her group have contributed in the discovery of unique DNA interacting activity in chromatin remodeling protein, INO80. . Their work on transgenic mouse models has led to the identification of nucleosome organisation as a modifier of repeat instability in the human genome leading to fragile X syndrome and demonstrated that repeat expansion is a post-zygotic event which is independent of parental-origin-effect in mice.

In the area of incomplete penetrance and variable expressivity, they we have proposed a novel mechanism mediated by microRNA.

Ongoing Projects:
  1. 1. Understanding the dual function of chromatin remodeling protein INO80 in Drosophila development(DBT-2012-15)

  2. 2. Dissecting the novel dual function of a chromatin remodeling protein human INO80 to understand its context dependent function.(DU-DST-PURSE Grant: 2011-13).

  3. 3. Genome-wide mapping of interaction sites of hINO80, a dual function chromatin remodeling protein on the human genome and analysis of its effect on target gene regulation (CSIR-Univ. Interaction: 2012-15)

Selected Recent Publications:
  1. 1. Proximity of H2A.Z containing nucleosome to the transcription start site influences gene expression levels in the mammalian liver and brain. Bargaje R, Alam P, Patowary A, Sarkar M, Ali T, Gupta S, Garg M, Singh M, Purkanti R, Scaria V, Sivasubbu S, Brahmachari V, Pillai B. Nucleic Acids Res.(2012) doi: 10.1093/nar/gks665.

  2. 2. Modeling SNP mediated differential targeting of homologous 3'UTR by MicroRNA. Ahluwalia JK, Soni K, Sivasubbu S, Brahmachari V. RNA Biol. 2012 Mar 1; 9(3).

  3. 3. Nucleosomal occupancy and CGG repeat expansion: a comparative analysis of triplet repeat region from mouse and human fragile X mental retardation gene 1.Datta S, Alam MP, Majumdar SS, Mehta AK, Maiti S, Wadhwa N, Brahmachari V.(2011) Chromosome Res. Volume 19, Issue 4, 445-455.

  4. 4. Single nucleotide polymorphism in the genes of mce1 and mce4 operons of Mycobacterium tuberculosis: analysis of clinical isolates and standard reference strains. Pasricha R, Chandolia A, Ponnan P, Saini N.K., Sharma S, Chopra M, Basil M.V., Brahmachari V and Bose M. (2011) BMC Microbiology 2011, 11:41.

  5. 5. Differential serum cytokine levels are associated with cytokine gene polymorphisms in north Indians with active pulmonary tuberculosis. Abhimanyu, Mangangcha IR, Jha P, Arora K, Mukerji M, Banavaliker JN, Indian Genome Variation Consortium, Brahmachari V, Bose M. Infect Genet Evol. 2011 Jul;11(5):1015-22. Epub 2011 Apr 1.

  6. 6. Chromatin remodeling protein INO80 has a role in regulation of homeotic gene expression in Drosophila. Shipra Bhatia, Hema Pawar, Vasanthi Dasari, Rakesh K. Mishra, Shanti Chandrashekaran and Vani Brahmachari (2010), Genes to Cells, 15,725-735.

  7. 7. Comparative analysis of DNA methylation in transgenic mice with unstable CGG repeats from FMR1 gene. Mohammad Parwez Alam, Sonal Datta, Subeer Majumdar, Abhishek K Mehta, Sujatha Baskaran ,Neerja Gulati and Vani Brahmachari (2010) Epigenetics 5:3, 241-248

  8. 8. Functional analysis of an intergenic non-coding sequence within mce1 operon of M.tuberculosis. Monika Joon, Shipra Bhatia, Rashmi Pasricha, Mridula Bose , Vani Brahmachari (2010) BMC Microbiology,10:128.

  9. 9. An analysis of histone modifications in relation to sex specific chromatin organization in the mealybug Maconellicoccus hirsutus. V. Mathur, G. Mendiratta, M. Ganapathi, P. K. Kennady, B. S. Dwarkanath, G. Pande and V. Brahmachari (2010) Cytogen. and Genomics. Cytogenet Genome Res. 2010;129:323-331(DOI:10.1159/00031589.

  10. 10. Incomplete penetrance and variable expressivity: is there a micro RNA connection? Ahluwalia, J., Hariharan M., Bargaje R., Pillai B., Brahmachari V., (2009) BioEssays:31, 981-992.

  11. 11. Application of SNaPshot technique for analysis of thiopurine methyltransferase gene polymorphism .Gauri Kapoor , Arindam Maitra, Somlata and Vani Brahmachari. IJMR (2009) IJMR, 129; 500-505 (Commentary by Sonja Pavlovic IJMR, 129,478-480).

  12. 12. Genomic analysis of local isolate of Mycobacterium avium subspecies Paratuberculosis. Jagdeep Singh Sohal , Neelam Sheoran , Krishnamoorthy Narayanasamy ,Vani Brahmachari , Shoorvir Singh, Swati Subodh. Veterinary Microbiology 2009 Mar 2; 134 (3-4):375-82.

  13. 13. Epigenetic regulation of cytomegalovirus major immediate-early promoter activity in transgenic mice Abhishek Kumar Mehta , Subeer S. Majumdar , Parwez Alam , Neerja Gulati , Vani Brahmachari. Gene 428 (2009) 20–24.

  14. 14. Characterization of Mce4A protein of Mycobacterium tuberculosis:role in invasion and survival. Neeraj Kumar Saini, Monika Sharma, Amita Chandolia, Rashmi Pasricha, Vani Brahmachari and Mridula Bose. BMC Microbiology 2008, 8: 200 doi:10.1186/1471-2180-8-200

  15. 15. Detection of altered global methylation in coronary artery disease patients. Sharma P, Kumar J, Garg G, Kumar A, Patowary A, Karthikeyan G, Ramakrishnan L, Brahmachari V, Sengupta S. DNA and Cell Biology, 2008: 27:357-365.

  16. 16. Loss of kinase activity in Mycobacterium tuberculosis multidomain protein Rv1364c. Preeti Sachdeva, Azeet Narayan, Richa Misra, Vani Brahmachari and Yogendra Singh. FEBS J. 2008,275(24):6295-308.

  17. 17. Mining of Putative cis-acting Elements for Chromatin Mediated Regulation of Hox Genes in Mammals by in-silico Analysis. Bengani H, Ganapathi M, Singh G.P. And Brahmachari V. J of Expt. Zool. (Mol Devel & Evol.) (2007), 308: 1-12.

  18. 18. A whole genome analysis of 5’ regulatory regions of human genes for putative cis-acting modulators of nucleosome positioning. Ganapathi M, Singh G.P, Sandhu K.S., Brahmachari S.K., Brahmachari V. Gene (2007), 391, 242-251.