The germline is a tissue that is known as immunologically privileged, because normally it is kept isolated from the cells of our immune system. This means that our immune system never learns that the cells of immunologically privileged sites are a normal part of our body. If proteins from the germline are switched on in adult muscle cells, the immune system may respond as if they are foreign organisms and attack the cells that express these previously unencountered elements.
So FSHD provides us with an example of the importance of junk DNA in disease. A genetic defect changes the amount of junk DNA. As a consequence of this, a junk element is expressed and modified by the addition of a junk sequence. But there is yet more to the picture. The FSHD retrogene only becomes stably expressed in the presence of a particular pattern of epigenetic modifications.
In normal cells, the FSHD repeats are usually expressed when the cells are in a pluripotent state, such as embryonic stem cells. At this stage, the FSHD repeats are covered with activating epigenetic modifications. But as the cells differentiate, the activating modifications are replaced by repressive ones, and the region is silenced. But if pluripotent cells are created from FSHD patients, the activating modifications aren’t replaced as the cells differentiate, and the repeats remain switched on.
Another aspect of the picture is the overall control of the FSHD genetic domain. There is an insulator region between the repeated region and the rest of chromosome 4. The protein 11-FINGERS (see page 178) binds to this region and ensures that different patterns of epigenetic modifications are maintained in the FSHD domain compared with the adjacent areas of the chromosome.
On top of all these features, the three-dimensional structure of the relevant regions of chromosome 4 also plays a role in the expression of the FSHD retrogene. It’s almost certainly the combination of all these factors that results in the restricted pattern of muscle wasting that we see in patients with FSHD. All of these aspects have to be right (or perhaps wrong) for the symptoms to develop.
The mechanism by which a change in a junk region leads to disease in FSHD is a stunning example of the complex and multilayered ways in which the different elements of our genome work together. It also demonstrates how we need to think not in terms of linear pathways when we consider what is happening in our cells, but in terms of complex interlocking processes. Figure 20.1 demonstrates this graphically. It exemplifies why the arguments about which is the most important feature of our genome are ultimately sterile. If we disrupt any aspect there will be consequences. Some will be bigger than others, but all work together.
Of course, this doesn’t mean that every single one of our billions of base pairs has a function. Some may truly just be genomic garbage, with no utility, whereas other regions are junk in the sense that they could have been discarded but instead have been turned into something useful.{413}
There is still a lot we don’t know, including some questions that we might think are very straightforward. We haven’t even got a definitive answer for how many functional regions of junk DNA exist in a cell. That might seem easy to answer but have a quick look at Figure 20.2 and then answer the following question. How many squares are there on a chessboard?
Figure 20.1 Just some of the interacting factors that have to work together to create the great organism that is you.
The instant instinctive response is always 64. But the actual answer is 204, because we can draw bigger squares of various sizes around the more obvious single black and white ones. Our genome is like that. One stretch of DNA can include a protein-coding gene, long non-coding RNAs, smallRNAs, antisense RNAs, splice signal sites, untranslated regions, promoters and enhancers. Layer on to this the effects of variations in DNA sequence between individuals, directed and random epigenetic modifications, changeable three-dimensional interactions, plus binding to other RNAs and proteins; then add in the effects of our constantly altering environment.
Figure 20.2 Quickly now, how many squares are on a chessboard?
When we really think about the complexity of our genomes, it isn’t surprising that we can’t understand everything yet. The astonishing triumph is that we understand any of it. There is always something new to be learnt, out there in the dark.
Appendix
List of Human Diseases cited in the main text, in which Junk DNA Has Been Implicated
Alzheimer’s disease May involve over-expression of an antisense RNA that binds to and stabilises the critical BACE1 mRNA.
Angelman syndrome A condition caused by abnormal imprinting. Junk DNA is vital in control of imprinting, including the involvement of imprinting control regions, promoters, long non-coding RNAs and cross-talk with the epigenetic systems.
Aplastic anaemia Around 5 per cent of cases are caused by mutations in some of the critical genes that maintain the lengths of telomeres, the junk regions at the ends of chromosomes.
Basal cell carcinoma A small number of cases are caused by mutations in the non-protein-coding region at the beginning of a gene, which result in decreased expression of the RNA from that gene.
Beckwith-Wiedemann syndrome A condition caused by abnormal imprinting. Junk DNA is vital in control of imprinting, including the involvement of imprinting control regions, promoters, long non-coding RNAs and cross-talk with the epigenetic systems.
Burkitt’s lymphoma Caused when the Myc oncogene from chromosome 8 gets translocated to chromosome 14 and placed under the control of the immunoglobulin promoter.
Cancer Junk DNA has been implicated at a number of levels in cancer, such as over-expression of certain long non-coding RNAs in specific cancer types. In most cases, the evidence isn’t yet strong enough to determine how significant a role these play in human pathology. However, over-expression of the proteins that maintain the lengths of telomeres, the junk regions at the ends of chromosomes, are now generally accepted as having a causal role in the progression of some tumours. Mis-targeting of epigenetic enzymes to the wrong genes because of abnormal expression of long non-coding RNAs is also under active investigation as another method by which cancer cells proliferate abnormally.
Cartilage-hair hypoplasia Caused by mutations which affect smallRNAs embedded within long non-coding RNAs.
Congenital diarrhoea disorder Caused by a mutation in a splicing signal in a gene.
Cornelia de Lange syndrome Caused by defects in a protein required for the junk-mediated higher-order structuring of DNA.
Down’s syndrome Caused by uneven distribution of chromosome 21 to developing gametes, a process dependent on a junk region called the centromere.
Duchenne muscular dystrophy Some cases are caused by mutations which result in abnormal splicing of the dystrophin RNA molecule.
Dyskeratosis congenita Can be caused by mutations in a number of different genes, each of which is involved in maintaining the lengths of telomeres, the junk regions at the ends of chromosomes.