Meaning of Chromatin state

Question

[Prakki Rama]

Hi all,

Could someone explain me the meaning of Chromatin state or point me to a simple definition? Some where I came across this sentence that "One of the data types that has now been published is about the chromatin state dynamics that were determined using ChIP-Seq technologies". May I know what are other technologies that can determine chromatin state.

Thanks in advance.

[Alastair Kerr]

Have a look at https://en.wikipedia.org/wiki/Chromatin_remodeling and http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001046

Answer 1

[Ryan Dale]

I've seen the term used in different ways. In the more general sense, the "chromatin state" of a genomic region can refer to the set of chromatin-associated proteins and histone modifications in that region. These are most often assayed by ChIP-seq, but also ATAC-seq, DNase-seq, ChIP-exo, and other methods.

"Chromatin state" can also mean a descriptive classification of chromatin, like "enhancer" or "promoter-like" or "repressed". These are often interpreted from chromatin segmentation tools like ChromHMM, Segway, or HiHMM. The input to these algorithms are the same kinds of assays as above, and, being HMM-based, they output "states" of chromatin. Keep in mind that there is quite a bit of interpretation needed to go from the mathematically-defined probabilities output from those tools to a meaningful human-language description like "enhancer".

[Fidel]

Regarding to the definition of chromatin state based on the partition of the genome I suggest you to take a look at this seminal publication: http://www.sciencedirect.com/science/article/pii/S0092867410010573 The abstract and graphical abstract offer a very good summary. They define 5 states, although other publications usually infer more states that distinguish enhancers, promoters etc. Such chromatin states are combination of histone marks and DNA binding proteins that are uncovered by machine-learning approaches like HMM. It is known that such 'chromatin states' change between different cell types and also for disease cells that express different sets of genes. That's why it is dynamic.

[Prakki Rama]

Thank you Ryan Dale. It is more clear.

Answer 2

[Benn]

It has to do with modification of histone tails, mostly methylation and acetylation.

Some specific modifications on particular histone (at specific lysine residues), are used as mark for chromatin state (such as repressed or activated).

Read more about it in literature I would say.

[Prakki Rama]

can you elaborate a bit more?

[Benn]

Start with wikipedia and the references therein:

https://en.wikipedia.org/wiki/Histone_code