Vani Brahmachari


Epigenetics and Developmental Regulation

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.

Our research interest is in the area of epigenetic regulation in development and disease. We mine the human genome sequence to identify novel putative genes coding for the components of epigenetic regulatory complex. This led to identify the human homologue of the chromatin remodeling protein hINO80 (OMIM *610169). We have successfully demonstrated the role of this protein in epigenetic regulation as a ETP protein (Enhancer of Polycomb and Trithorax proteins), having the dual role in repression as well as activation of developmental genes like the homoetic genes. In the light of the direct interaction of INO80 with DNA through a consensus motif, we are exploring the diversity of interaction of INO80 to form novel protein complexes to mediate multiple functions, through proteome analysis.

We have also identified novel cis-regulatory element(s) from the human genome, where the epigenetic complexes bind, namely a novel PRE/TRE element (Polycomb/Trithorax Responsive Element) mapping in the PIK3C2B gene. Having identified the long-range interaction of this PRE/TRE through 4C approach, we are investigating its role in coordinated transcription regulation of the genes within these interacting loops.

We have completed the whole genome sequencing and de novo assembly of the genome of a unique model for epigenetic regulation, the mealybugs that exhibit the phenomenon of Genomic Imprinting. We are engaged in identifying the epigenetic gene repertoire including non-coding RNA in this system and the differential expression of this epigenetic tool-kit in the males and females of this insect which exhibit differential regulation of chromosome-cycle in spite of identical chromosomal constitution.

In collaboration with other groups, we are investigating the genetic plasticity of M.tuberculosis clinical isolates and its possible functional implications.

Ongoing Projects:
  1. 1. Epigenetics in Health and Disease - (EpiHeD): Work package: Molecular basis of genomic imprinting in mealybugs (CSIR, 2012-17) Network Project.

  2. 2. Delineating the mechanism of transcriptional regulation by chromatin remodelling protein, IN080; Identification and characterisation of the protein complexes(DST 2016-19).

  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: 2013-16).

Selected Recent Publications:
  1. 1.Human PRE-PIK3C2B, an intronic cis-element with dual function of activation and repression. Maini J, Ghasemi M, Yandhuri D, Thakur SS, Brahmachari V. Biochim Biophys Acta. 2017 Feb;1860(2):196-204. doi: 10.1016/j.bbagrm.2016.12.003. Epub 2016 Dec 6

  2. 2.Interaction of the Chromatin Remodeling Protein hINO80 with DNA. Mendiratta S, Bhatia S, Jain S, Kaur T, Brahmachari V. PLoS One. 2016 Jul 18;11(7):e0159370. doi: 10.1371/journal.pone.0159370. eCollection 2016.

  3. 3.The functional diversity of Drosophila Ino80 in development. Ghasemi M, Pawar H, Mishra RK, Brahmachari V (2015) Mech. Dev. 138, 113-121.

  4. 4.Chandolia A, Rathor N, Sharma M, Saini NK, Sinha R, Malhotra P, Brahmachari V, Bose M (2014); Functional analysis of mce4A gene of Mycobacterium tuberculosis H37Rv using antisense approach. Microbiol Res., 169(2014): 780-787.

  5. 5.Sharma, P., Garg, G., Kumar, A., Mohammad, F., Kumar, S.R., Tanwar, V.S., Sati, S., Sharma, A., Karthikeyan, G., Brahmachari# V., Sengupta,# S. (2014); Genome wide DNA Methylation profiling for Epigenetic alteration in Coronary Artery Disease patients. Gene,10; 541(1):31-40.

  6. 6.Hemant Bengani, Shweta Mendiratta ,Jayant Maini, Dasari Vasanthi, Hina Sultana, Mohsen Ghasemi, JasmineAhluwalia, SowmyaRamachandran, Rakesh K Mishra and Vani Brahmachari (2013) Identification and validation of a putative polycomb responsive element in the human genome. PLoS One. 21;8(6):e67217.

  7. 7. 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.

  8. 8.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).

  9. 9.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.

  10. 10.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.

  11. 11.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.

  12. 12.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.

  13. 13.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

  14. 14.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.

  15. 15.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.