Polymorphic inactivation of human TIMP1

My first paper examined the expression of genes on the X chromosome.  The paper is OA through PubMedCentral and you can read it here

[learn_more caption=”Journal Abstract”]X inactivation silences most but not all of the genes on one of the two X chromosomes in mammalian females. The human X chromosome preserves its activation status when isolated in rodent/human somatic-cell hybrids, and hybrids retaining either the active or inactive X chromosome have been used to assess the inactivation status of many X-linked genes. Surprisingly, the X-linked gene for human tissue inhibitor of metalloproteinases (TIMP1) is expressed in some but not all inactive X-containing somatic-cell hybrids, suggesting that this gene is either prone to reactivation or variable in its inactivation. Since many genes that escape X inactivation are clustered, we examined the expression of four genes (ARAF1, ELK1, ZNF41, and ZNF157) within approximately 100 kb of TIMP1. All four genes were expressed only from the active X chromosome, demonstrating that the factors allowing TIMP1 expression from the inactive X chromosome are specific to the TIMP1 gene. To determine if this variable inactivation of TIMP1 is a function of the hybrid-cell environment or also is observed in human cells, we developed an allele-specific assay to assess TIMP1 expression in human females. Expression of two alleles was detected in some female cells with previously demonstrated extreme skewing of X inactivation, indicating TIMP1 expression from the inactive chromosome. However, in other cells, no expression of TIMP1 was observed from the inactive X chromosome, suggesting that TIMP1 inactivation is polymorphic in human females.[/learn_more]

Language for non-expert

(I hope – this was done quickly)

Background

Women have two X chromosomes and men have one X chromosome (and a Y). The X chromosome has many genes that aren’t found on the Y chromosome. To prevent an imbalance in gene product amounts between males and females, one of the two X chromosomes is shut off in women, leading to one functional X chromosome as seen in men. This process is called X inactivation. [should be knowledge from high school but refreshers are nice]

Some genes escape X inactivation and both copies are active. Some of these escaping genes are found on the Y chromosome so having two copies expressed is similar to the situation in men.

To study X inactivation, human chromosomes can be put into mouse cell lines. The X chromosome keeps its original state of gene expression (silenced or active) and the two X chromosomes separated into different cell lines for easy comparison.

This paper

When examining inactive X chromosomes in culture, the TIMP1 gene was inconsistently expressed. In some cell lines, it was on (escape inactivation) and in others, it was off (subject to inactivation). This was odd because all X-linked genes had been consistent – escape in all situations or silenced in all.

We examined the inactivation pattern in human female cells and saw the same inconsistencies. Therefore, the variable inactivation is not a function of being in culture, but a inherent feature of this gene on the X chromosome.