This is an excellent genetics question!

First, to address the comments above, the basic premise of epigenetics involves changes in gene expression that are inherited but do not involve changes in DNA sequence structure. So epigenetics would not be an answer to this question.

Also, it can be noted that DNA based alterations in the genome can affect the transcriptome.

So my answer comes from two good examples of somatic genome rearrangements:

1) By "jumping" from one site to another in the genome, Transposons change the DNA's structure and sequence. They can also change the expression of genes during development. Although they are mostly known from causing mutations, much evidence indicates that rather than acting as parasites such as viruses, they are more likely essential parts of the genome that are intimately involved with genome structure and development. See for example: http://www.nature.com/scitable/topicpage/transposons-or-jumping-genes-not-junk-dna-1211 and http://hmg.oxfordjournals.org/content/16/R2/R159.fullResearch connecting their function in development is ongoing. In 1983, Barbara McClintock received the Nobel Prize in Physiology or Medicine for her discovery of mobile genetic elements (transposons).

2) An even better example of a DNA based change that occurs during differentiation establishes the genetic origin of antibody diversity (somatic recombination). B and T cells differentiate by deleting relatively large DNA segments to establish specialized antibody producing genes. This is also called V-D-J recombination (for Variable, Diverse, and Joining gene segments of vertebrates). In 1987, Susumu Tonegawa received the Nobel Prize in Physiology or Medicine for his discovery of the genetic principle behind generating antibody diversity. See http://www.nature.com/nri/journal/v4/n7/fig_tab/nri1395_F1.html

Study epigenetics!

Are you talking about genomic (DNA based) or transcriptomic changes? Each is different.

DNA based changes

This is an excellent genetics question!

First, to address the comments above, the basic premise of epigenetics involves changes in gene expression that are inherited but do not involve changes in DNA sequence structure. So epigenetics would not be an answer to this question.

Also, it can be noted that DNA based alterations in the genome can affect the transcriptome.

So my answer comes from two good examples of somatic genome rearrangements:

1) By "jumping" from one site to another in the genome, Transposons change the DNA's structure and sequence. They can also change the expression of genes during development. Although they are mostly known from causing mutations, much evidence indicates that rather than acting as parasites such as viruses, they are more likely essential parts of the genome that are intimately involved with genome structure and development. See for example: http://www.nature.com/scitable/topicpage/transposons-or-jumping-genes-not-junk-dna-1211 and http://hmg.oxfordjournals.org/content/16/R2/R159.fullResearch connecting their function in development is ongoing. In 1983, Barbara McClintock received the Nobel Prize in Physiology or Medicine for her discovery of mobile genetic elements (transposons).

2) An even better example of a DNA based change that occurs during differentiation establishes the genetic origin of antibody diversity (somatic recombination). B and T cells differentiate by deleting relatively large DNA segments to establish specialized antibody producing genes. This is also called V-D-J recombination (for Variable, Diverse, and Joining gene segments of vertebrates). In 1987, Susumu Tonegawa received the Nobel Prize in Physiology or Medicine for his discovery of the genetic principle behind generating antibody diversity. See http://www.nature.com/nri/journal/v4/n7/fig_tab/nri1395_F1.html

Thanks Christian : )

Differential methylation of cytosine bases in CpG doublets is responsible for origin of different cell types. Such epigenetic changes in DNA are involved in differentiation process.

Dear it all due to switch on and switch off mechanism,

The epigenetic term" Methylation is found in one of the building blocks of DNA, is remembered by a cell when it divides, and often is associated with turning off genes. Below link reported the varing pattern of DNA methylation during differentiation http://www.sciencedaily.com/releases/2010/08/100816122200.htm..... Also R. Keith Slotkin et al 2007 Nat. Rev. Gen...Abstract.... Overlapping epigenetic mechanisms have evolved in eukaryotic cells to silence the expression and mobility of transposable elements (TEs). Owing to their ability to recruit the silencing machinery, TEs have served as building blocks for epigenetic phenomena, both at the level of single genes and across larger chromosomal regions. Important progress has been made recently in understanding these silencing mechanisms. In addition, new insights have been gained into how this silencing has been co-opted to serve essential functions in 'host' cells, highlighting the importance of TEs in the epigenetic regulation of the genome. http://www.nature.com/nrg/journal/v8/n4/abs/nrg2072.htm.

I agree with Muhammad Abid Khan.