What do we want to know?
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Evolution of CGGBP1
The human CGGBP1 has a unique evolutionary status: it is conserved in homeotherms. The last CGGBP1 that evolved cladistically is found in amniotes, including reptiles, but not in the amphibians. Recent works have shown that the CGG-binding protein present in fishes and invertebrates are not homologous to the homeothermic CGGBP1. The evolution of tetrapods, adaptation to tthe stresses of the terrestrial habitats and concomitant changes in the genome composition suggest a crucial role of CGGBP1 in cellular homeostasis. We aim to understand why the metazoan eukaryotic cells depend on CGGBP1 and why it evolved independently multiple times. We are using functional evolutionary genomics to answer these questions.
Molecular functions of CGGBP1
Our group is identifying novel non-oncogene addiction mechanisms. Our recent work has established the human factor CGGBP1 and interacting proteins as a paradigm to study non-canonical cell survival mechanisms that are advantageous for normal cell survival but required for cancer cell proliferation. We employ a combination of multiple approaches; epigenomic, genomic, transcriptomic and cDNA library-based studies in conjunction with cellular phenotyping. By enhancing our understanding of cell survival biology, our work potentially adds to the development of novel therapeutic modalities against survival vulnerabilities of cancer cells.
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Describing the changes in the genome caused by depletion of CGGBP1
Some of these changes include
somatic chromosomal fusions
somatic allelic recombinations
Regulation of secondary structures R-loops & G4 quadruplexes
Allelic imbalances in cytosine methylation in normal cells (Patel et al., BMC Genetics, 2020)
Characterising how the epigenomic landscape depends on CGGBP1
Studying cytosine methylation at a base-level resolution genome-wide
stochastic methylation changes using MeDIP-seq
CTCF occupancy using ChIP-seq.
Histone modifications using ChIP-seq
Patel and Patel et al., Epigenetics & Chromatin, 2019
CGGBP1 on DNA versus CGGBP1 in the chromatin
Generating and studying mutant forms of CGGBP1
Abnormal nuclear localization and retention
CGGBP1-repetitive DNA interactions, ChIP-seq
In vitro assays on recombinant and immunoprecipitated protein
Unpublished Observations [HoMeCell Lab, 2021].