Which Proteins are responsible for protein-DNA compaction?

Dear Manoj Patel ,

Several proteins are responsible for DNA compaction inside the cytoplasm. These include histones, which form nucleosomes, and non-histone proteins such as HMG proteins. The specific proteins that go inside the Nuclear Pore Complex (NPC) pore and ensure that DNA remains in a compact form during transport into the nucleus are the importin and transportin proteins. These proteins bind specifically to the nuclear localization signals (NLS) present on the DNA-associated proteins and mediate their transport through the NPC pore.

The NPC is a large protein complex that spans the nuclear envelope and regulates the transport of macromolecules between the cytoplasm and the nucleus. The NPC is composed of multiple copies of several different types of proteins, including nucleoporins, which form the NPC pore. During transport, importin and transportin proteins bind to the NLS present on the DNA-associated proteins and mediate their transport through the NPC pore. As these proteins and DNA-associated proteins pass through the NPC, the nucleoporins form a tight pore around the transported molecules and help maintain the compact shape of the DNA. Additionally, it is thought that the energy from the hydrolysis of the GTPase Ran and its associated transportin may also help to maintain the compact shape of the DNA as it is transported through the NPC.

Sushanta Sethi

Nicolò M. Villa thanks for your quick response. Could you please provide references for the same? Secondly, how much role does the concentration of salt play in such cases?

Malcolm Nobre

Hello Manoj Patel and Sushanta Sethi

Please refer to the articles attached below. It may be helpful.

Article Cytoplasmic transport and nuclear import of plasmid DNA

Article Nuclear entry of nonviral vectors

Best.

Manoj Patel

Hi Nicolò M. Villa

Suggested articles waere really useful. However, papers doesn't discuss much about the histone binding to plasmid.

1) Does histone bind in form of nucleosome to plasmid? or they float in the cytoplasm as individual entity ?

2) does histone binding to plasmid occurs in non-specific non-sequential manner?

Nicolò M. Villa

Manoj Patel

1) Histones are primarily known for their role in packaging and arranging DNA into nucleosomes. However, there is evidence that histones can also be found outside the nucleus, including in the cytoplasm. In the cytoplasm, histones have been shown to bind to lipid droplets to fight intracellular bacteria. Additionally, histones can shuttle between the nucleus and cytoplasm. Karyopherins, which are nuclear import receptors, can interact with histones and function as chaperones, protecting histones from non-specific interactions in the cytoplasm. Furthermore, studies have suggested that karyopherins may participate in the deposition of histones into nucleosomes. Therefore, while histones are primarily associated with nucleosomes, they can also exist as individual entities in the cytoplasm and participate in cellular processes outside of chromosomal gene regulation.

Article Histones: The critical players in innate immunity

Article Nucleocytoplasmic Shuttling of the NAD+-dependent Histone De...

Article Nuclear import of histones

2) Histone binding to plasmids can occur in a non-specific and non-sequential manner. Nucleosome assembly on plasmids appears to be random rather than cooperative, with nucleosome formation equally likely to occur over all regions of the DNA molecule. This random assembly is supported by the observation that reconstituted plasmids lacking linker histones show no tendency towards precipitation or aggregation. Additionally, histones have been shown to bind bacterial plasmids with high affinity and form nucleosomes in vitro. The binding of histones to plasmids can limit the access of transcription factors to their recognition sites, affecting transgene expression. Therefore, histone binding to plasmids is not specific or sequential, and it can impact gene expression by modulating access to the DNA sequence.

Article Nucleosomes inhibit both transcriptional initiation and elon...

Article The histone deacetylase inhibitor Entinostat enhances polyme...

Article The location of the left-handedly curved DNA sequence affect...

Can anyone provide the Support vector regression code structure of LIBSVM MATLAB or python ?

Can anyone suggest me the best way for Regression analysis of Accidents?

Is there any solar electric power plant having the concentrated photovoltaic modules?

Use of Sine voltage source in Electrical circuit with frequency domain study in COMSOL?

No title

Low value of Cd for Flow Past a Square Cylinder Simulation?

Is there any specific software available for graphical presentation of signaling pathways/cycle in cells?

How can we count the number of edges in an edge detected image using canny/sobel algorithm in MATLAB?

Which are the vendors who sell commercial SWIR (NIR-II) dyes?

How to get doi of presentation ?

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

How do I determine the degree of polymerization of PEG 400 based on NMR integration?

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

Which cell line should we use to perform biological dosimetry experiments?

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

How vaccines of covid 19 work?

Problem with shRNA transfection. Why are only two plates getting contaminated instead of all?

What is the density for pva electrospining?

Genome-wide gene identification protocol ?

Any specific pipeline or parameter to analyse total transcriptomics study of brain tissue samples?