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X chromosome inactivation silences one X chromosome in female mammals. However, this silencing is incomplete, and some genes escape X inactivation. We describe methods to determine the chromosome-wide X inactivation status of genes in tissues or cell lines derived from mice using a combination of skewing of X inactivation and allele-specific analyses of gene expression based on RNA-seq.

Culturing and subcultivation of normal human diploid fibroblasts have advanced our understanding of the molecular events involved in aging. This progress is leading to the development of therapies that slow or ablate the adverse physiological and pathological changes associated with aging. It has been established that normal human diploid fibroblasts can proliferate in culture for only finite periods of time. Hayflick and Moorhead and others have described numerous types of cells, ranging from fetal to adult, that were incapable of indefinite proliferation. There are many ways to study aging in vitro, and this chapter summarizes some laboratory procedures.

Epigenetic alterations of DNA play key roles in determining gene structure and expression. Methylation of the 5-position of cytosine is thought to be the most common modification of the genome in mammals. Studies have generally shown that hypermethylation in gene regulatory regions is associated with inactivation and reduced transcription and that alteration in established methylation patterns during development can affect embryonic viability. Changes in methylation have also been associated with aging and cellular senescence as well as tumorogenesis. DNA methyltransferase 1 (DNMT1) is thought to play an important role in maintaining already established methylation patterns during DNA replication and catalyzes the transfer of a methyl moiety from S-adenosyl-L-methionine (SAM) to the 5-position of cytosines in the CpG dinucleotide. Several studies illustrate changes in activity and transcription of DNMT1 during aging and here we show a comprehensive method of detection of DNMT1 mRNA transcription from senescing cells in culture.

The methylation of CpG dinucleotides located in key protein binding sites within gene regulatory regions often leads to gene silencing. A mechanism of aging is proposed whereby an accumulation of methylation at gene regulatory sites contributes to cellular senescence. DNA methyltransferases (DNMTs) are enzymes that catalyze the transfer of a methyl moiety from S-adenosyl-L-methionine (SAM) to the cytosine of a CpG dinucleotide and are responsible for establishing and maintaining methylation patterns in the genome. It is important to study not only transcription of the DNMTs, but also their protein expression because studies illustrate that it is possible for the enzymes to undergo posttranslational physical changes in response to stimulation even though gene transcription remains unchanged. Here, we discuss an in vitro method to study protein expression of DNMTs in aging systems.