Niraj Lodhi

Publications (14) View all

• Article: Effect of copy number and spacing of the ACGT and GTcis elements on transient expression of minimal promoter in plants

  Rajesh Mehrotra, Kanti Kiran, Chandra Prakash Chaturvedi, Suraiya Anjum Ansari, Niraj Lodhi, Samir Sawant, Rakesh Tuli
  Journal of Genetics 04/2012; 84(2):183-187. · 1.09 Impact Factor
• Article: Analysis of histones and histone variants in plants.

  Ila Trivedi, Krishan Mohan Rai, Sunil Kumar Singh, Verandra Kumar, Mala Singh, Amol Ranjan, Niraj Lodhi, Samir V Sawant
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  ABSTRACT: Histone proteins are the major protein components of chromatin - the physiologically relevant form of the genome (or epigenome) in all eukaryotic cells. For many years, histones were considered passive structural components of eukaryotic chromatin. In recent years, it has been demonstrated that dynamic association of histones and their variants to the genome plays a very important role in gene regulation. Histones are extensively modified during posttranslation viz. acetylation, methylation, phosphorylation, ubiquitylation, etc., and the identification of these covalent marks on canonical and variant histones is crucial for the understanding of their biological significance. Different biochemical techniques have been developed to purify and separate histone proteins; here, we describe techniques for analysis of histones from plant tissues.
  Methods in molecular biology (Clifton, N.J.) 01/2012; 833:225-36.
• Source

  Available from: Amol Ranjan

  Article: Analysis of chromatin structure in plant cells.

  Mala Singh, Amol Ranjan, Krishan Mohan Rai, Sunil Kumar Singh, Verandra Kumar, Ila Trivedi, Niraj Lodhi, Samir V Sawant
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  ABSTRACT: A vast body of evidence in the literature indicates that nucleosomes can act as barriers to transcriptional initiation. The nucleosome at the promoter inhibits association of transcription factors disallowing active transcription of the gene. We have found a nucleosome on tobacco pathogenesis-related gene-1a (PR-1a) core promoter and mapped its boundaries and extension to find its span. The nucleosome covers the TATA box and Inr region of the core promoter and gets disassembled upon induction. Prior to its removal, modifications (i.e., acetylation and methylation of histones) occur at the nucleosome, proving a role of epigenetic modifications in transcriptional regulation. We summarize here various methodologies to analyze promoter chromatin structure in plants using the PR-1a core promoter as an example.
  Methods in molecular biology (Clifton, N.J.) 01/2012; 833:201-23.
• Source

  Available from: Niraj Lodhi

  Article: Drosophila histone H2A variant (H2Av) controls poly(ADP-ribose) polymerase 1 (PARP1) activation in chromatin.

  Elena Kotova, Niraj Lodhi, Michael Jarnik, Aaron D Pinnola, Yingbiao Ji, Alexei V Tulin
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  ABSTRACT: According to the histone code hypothesis, histone variants and modified histones provide binding sites for proteins that change the chromatin state to either active or repressed. Here, we identify histone variants that regulate the targeting and enzymatic activity of poly(ADP-ribose) polymerase 1 (PARP1), a chromatin regulator in higher eukaryotes. We demonstrate that PARP1 is targeted to chromatin by association with the histone H2A variant (H2Av)--the Drosophila homolog of the mammalian histone H2A variants H2Az/H2Ax--and that subsequent phosphorylation of H2Av leads to PARP1 activation. This two-step mechanism of PARP1 activation controls transcription at specific loci in a signal-dependent manner. Our study establishes the mechanism through which histone variants and changes in the histone modification code control chromatin-directed PARP1 activity and the transcriptional activation of target genes.
  Proceedings of the National Academy of Sciences 03/2011; 108(15):6205-10. · 9.68 Impact Factor
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  Available from: Niraj Lodhi

  Article: PARP1 genomics: chromatin immunoprecipitation approach using anti-PARP1 antibody (ChIP and ChIP-seq).

  Niraj Lodhi, Alexei V Tulin
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  ABSTRACT: Poly(ADP-ribose) polymerase1 (PARP1) is a global regulator of different cellular mechanisms, ranging from DNA damage repair to control of gene expression. Since PARP1 protein and pADPr have been shown to persist in chromatin through cell cycle, they may both act as epigenetic markers. However, it is not known how many loci are occupied by PARP1 protein during mitosis genome-wide. To reveal the genome-wide PARP1 binding sites, we used the ChIP-seq approach, an emerging technique to study genome-wide PARP1 protein interaction with chromatin. Here, we describe how to perform ChIP-seq in the context of PARP1 binding sites identification in chromatin, using human embryonic kidney cell lines.
  Methods in molecular biology (Clifton, N.J.) 01/2011; 780:191-208.