Question

Retinitis pigmentosa is a genetic disease that causes the breakdown and loss of retinal cells. Retinitis pigmentosa often starts with decreased night vision and will progress to blindness as retinal cells die.

Several genes have been linked to Retinitis pigmentosa, one of which is GADD. Mice lacking GADD (these mice were experimentally created so that the GADD region of the genome was deleted) have increased expression of non-retinal genes in retinal cells. In other words, in these mutant mice, genes that are not normally expressed in the retina are expressed.  

Crx is a key retinal transcription factor. Crx binds regulatory elements called CBRs (Crx-binding regions). GADD has two CBRs, one immediately proximal to the transcription start site (TSS), and one a few hundred base pairs downstream of the TSS.

You have received DNA from three patients with Retinitis pigmentosa. From the DNA, you sequence the GADD gene and its proximal/core promoter region.   

None of the patients have mutations in the coding region of GADD. All of the mutations you find are in the CBRs. Your findings are below:

• Patient 1 – Mutation in CBR1
• Patient 2 – Mutation in CBR2
• Patient 3 – Mutation in CBR1 and CBR2

How can mutations in non-coding regions cause a change in phenotype (in this case leading to retinitis pigmentosa)? Note: you do not have to give all possible reasons, explanations of one or two ways mutations in non-coding regions can have phenotypic effects is sufficient.

Answer 1

Retinitis pigmentosa: It is a group of eye problem that affects the retina. This condition changes the response of retina to light and make it hard to see. People with this problem lose their vision in due course of time slowly. It is a genetic condition which is passed down from generations in families and their rate of vision loss and its type varies from person to person.

A homozygous RHO mutation c.448G > A, p.E150K was found in two affected siblings, while no coding SAMD7 mutations were identified. Interestingly, four non-coding homozygous variants were found in two SAMD7 genomic regions relevant for binding of the retinal transcription factor CRX (CRX-bound regions, CBRs) in these affected siblings. Samd7 is a recently identified as Crx-regulated transcriptional repressor in retina, is hypothesized that these SAMD7 variants might contribute to the retinal phenotype. Three variants are located in a promoter CBR termed CBR1, while the fourth is located more downstream in CBR2. The combined CBR2/CBR1 variant construct showed a significantly decreased SAMD7 reporter activity when compared to the wild-type sequence suggested a cis-regulatory effect on SAMD7 expression.