Junk DNA: A Journey Through the Dark Matter of the Genome

Примечания

1

The four classes are known as SINES (short interspersed repetitive repeats); LINEs (long interspersed elements); LTRs (elements with long terminal repeats); DNA transposons.

2

The gene is called Myc.

3

Yes, I do like Star Trek. Occasionally.

4

The gene was called Gcn5. It codes for a protein with a number of functions, one of which is to add a small molecular group called acetyl to the amino acid lysine in proteins.

5

The technical terms for this cell suicide are programmed cell death, or apoptosis.

6

The core enzyme is encoded by the TERT gene and the RNA template is encoded by the TR gene, also known as TERC.

7

The technical name for this population is the haematopoietic stem cell (HSC).

8

This gene is called Dyskeratosis congenita 1 (DKC1) or dyskerin.

9

Specifically, budding yeast such as Saccharomyces cerevisiae.

10

Caenorhabditis elegans.

11

This unit of 171 base pairs is called an alpha (α) satellite repeat.

12

These are called histone H3.

13

This gene is called SRY.

14

The name Xist is derived from X-inactive (Xi)-specific transcript.

15

Bases rather than base pairs, because RNA is single-stranded.

16

The gene is called MeCP2 and its role is to bind to epigenetically modified (methylated) DNA, where it interacts with other proteins and represses gene expression at the sites where it binds.

17

This is a famous thought experiment. No actual frogs were harmed in the creation of this anecdote.

18

They are known as linc RNAs, which stands for long intergenic non-coding RNAs.

19

The exceptions are the cells of the immune system that fight off specific infections. Unusually, these cells rearrange some of their genes to create different combinations of antibodies and receptors, able to respond to a vast range of foreign proteins.

20

The name for this major repressor enzyme is EZH2. It is responsible for adding three methyl molecules to an amino acid called lysine at position 27 on histone H3. The technical nomenclature for this modification is H3K27me3 and it is the best-characterised repressive mark in epigenetics outside of DNA methylation.

21

This complex is known as Polycomb Response Complex 2 or PRC2. The activity of PRC2 is closely coordinated with that of another repressive complex called PRC1. PRC2 usually establishes the first repressive modifications at a genomic region and PRC1 follows on with additional modifications that stabilise the repressive state.

22

The key proteins are called DNMT3A and DNMT3L, the de novo DNA methyltransferases.

23

This protein is called DNMT1 and it is known as a maintenance DNA methyltransferase.

24

This is known as a de novo mutation, meaning newly arising.

25

This is known as uniparental disomy, in this case maternal uniparental disomy.

26

This gene is called UBE3A. It adds a molecule called ubiquitin to other proteins, and this leads to degradation of those proteins.

27

The numbers here are random ones, just chosen to demonstrate the point.

28

The ones involved in the process described here are from a specific class called snoRNA C/D box.

29

The methyltransferase enzyme required for this process is called fibrillarin, which works in a complex with three other proteins and the snoRNA.

30

Mitochondria use lots of other proteins for their biochemical processes, but most of them they import from the cell cytoplasm. The ones that are uniquely encoded in the mitochondria are all involved in a process called the electron transport chain, which takes place within mitochondria themselves. This process is essential for life, as it is how we generate storable usable energy to power our cells.

31

The gene codes for a protein called MYC. MYC is also involved in a range of other cancers.

32

The modification is addition of a phosphate group (one phosphorus atom and four oxygen atoms) to a specific position on histone H3. This modification is usually associated with active genes.

33

The Mediator component is MED12.

34

These are known as induced pluripotent stem cells (iPS cells).

35

This additional complex is called Cohesin.

36

There are a couple of exceptions to this where genes are clustered in a way that reflects their expression patterns. The main ones are the HOX genes that control body patterning and the Ig genes that code for antibodies.

37

The formal name for this is CTCF.

38

This protein is known as SHOX or ‘short stature homeobox’.

39

These were typically accessibility to enzymes that can cut DNA molecules, which is a sign of an open structure that may be able to be copied into RNA.

40

The protein is called Sonic Hedgehog, symbol SHH. Researchers went through a phase of giving genes apparently comic names. This is now discouraged as it’s suddenly not so amusing if a genetic counsellor has to pass on a whimsical gene name to the parents of a child with a severe genetic condition.

41

The enhancer region is called ZRS and is found on the long arm of chromosome 7.

42

This transcription factor is called Six3.

43

This transcription factor is called GATA6.

44

This transcription factor is called PTF1A.

45

This variant base pair has the catchy name of rs12913932.

46

This gene is called OCA2.

47

This approach to finding disease/trait-associated genes and variants is known as GWAS — genome-wide association studies.

48

This gene is called FTO or ‘fat mass and obesity associated’.

49

This gene is called IRX3, or Iroquois homeobox protein 3.

50

Osteogenesis imperfecta type 5.

51

These are often referred to in the literature as UTRs, for untranslated regions. The one at the beginning of the messenger RNA is called the 5′UTR and the one at the end of the messenger RNA is called the 3′UTR.

52

The gene is called IFITM5.

53

This protein is called Muscleblind-like protein 1, or MBNL1.

54

This is known as a non-templated change because there is no underlying DNA template for these A bases in the genome.

55

IPEX stands for Immunodysregulation, Polyendocrinopathy, Enteropathy, X-linked.

56

FOXP3, a transcription factor.

57

Regulatory T cells.

58

The gene is called FUS — Fused in Sarcoma.

59

If you haven’t already, go and see The Lego Movie, it’s excellent.

60

As a reminder, the junk regions between amino acid-coding regions are known as introns. The amino acid-coding parts themselves are known as exons.

61

The type of smallRNA that triggers degradation is called microRNA, or miRNA. The type that triggers poor translation is called small interfering RNA, or siRNA. In order to avoid excessive technical language, the term smallRNA will be used to describe both of these.

62

These are known as satellite cells

63

This is a protein called BK, which is a potassium channel.

64

These are known as supratentorial neuroectodermal tumours.

65

The protein is called transthyretin.

66

The virus was cytomegalovirus (CMV).

67

The protein that is targeted is called apolipoprotein B100.

68

The drug is called Mipomersen, also known as Kynamro.

69

This particular retrogene is called DUX4.