Abstract
Chromatin is a dynamic structure comprising of DNA and proteins. Its unique nature not only help to pack the DNA tightly within the cell but also is pivotal in regulating gene expression DNA replication. Furthermore it also protects the DNA from being damaged. Various proteins are involved in making a specific complex within a chromatin and the knowledge about these interacting partners is helpful to enhance our understanding about the pathophysiology of various chromatin associated diseases. Moreover, it could also help us to identify new drug targets and design more effective remedies. Due to the existence of chromatin in different forms under various physiological conditions it is hard to develop a single strategy to study chromatin associated proteins under all conditions. In our current review, we tried to provide an overview and comparative analysis of the strategies currently adopted to capture the DNA bounded protein complexes and their mass spectrometric identification and quantification. Precise information about the protein partners and their function in the DNA-protein complexes is crucial to design new and more effective therapeutic molecules against chromatin associated diseases.
Highlights
Chromatin is a unique structure made up of proteins and nucleic acid which helps to tightly pack the nucleic acid within the eukaryotic nucleus
A number of cellular process, such as DNA packaging, transcriptional regulation, and DNA repair during cell divisions, are regulated by the chromatin. It exists in two predominant forms named as heterochromatin and euchromatin, respectively, by which it regulates the access of nucleic acid to various regulatory proteins and, its cellular functions
QTIP approach can be useful to investigate the disease models, such as cancer and could help to design targeted therapy to treat telomere associated fatal diseases. Another approach is “Proteomics of isolated chromatin segments (PICh)” which is used to identify proteins associated with specific genomic loci of repetitive chromatin, such as telomeres
Summary
Chromatin is a unique structure made up of proteins and nucleic acid which helps to tightly pack the nucleic acid within the eukaryotic nucleus. A number of cellular process, such as DNA packaging, transcriptional regulation, and DNA repair during cell divisions, are regulated by the chromatin It exists in two predominant forms named as heterochromatin (condensed) and euchromatin (extended), respectively, by which it regulates the access of nucleic acid to various regulatory proteins and, its cellular functions. Chromatin-associated proteins play a crucial role in accomplishing all these cellular activities [1] To study these proteins is not trivial due to their low abundance in isolated chromatin complexes [2]. Isolating chromatin complex itself is a laborious, time consuming, and expensive multistep process which is prone to yield inconsistent results These protocols are mostly developed for the chromatin-based study of higher eukaryotic cells and are not suitable for eukaryotic cells such as yeast [3]. We discussed various analytical strategies and highlight their importance in unravienlifnogrmthaetioinnfroergmaardtiionng rcehgraormdaintign cahssroomciaatteind pasrosoteciinastefdorpbreottteeirnusnfodrerbsetattnedriungndoefrtshteainrdrionlge ionf vthaeriirouroslceeilnluvlaarrifouunscctieolnlusl.ar functions
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