S1 | Trans-factors and trinucleotide repeat instability

Trans-factor (human protein/
function)

Studied in…*

Repeat length

Replication direction

Comments/implications

Ref

Rad27 (FEN1/
recognizes 5
flap structures in DNA repair and Okazaki processing)

Yeast

Yes

-

­­­ CTG expansions and ­­ breakage (rad27D), ­­ CTG expansions and ­ breakage (rad27-G240D no endonuclease activity), ­ CTG expansions and (breakage (rad27-G67S moderate endonuclease activity)

1

 

Yeast

Yes

-

­­ CTG instability (rad27D)

2

 

Yeast

-

-

­­ CAG contractions (rad27D) (contraction assay)

3

 

Yeast

Yes

Yes

­ CGG instability (rad27D)

4

 

Yeast

Yes

Yes

­­ CTG/CAG instability (rad27D)

5,6

 

Yeast

-

Yes

­­­ CTG/­­ CAG expansions (rad27D) (expansion assay)

7

 

Yeast

Yes

-

­­­ CAG breakage and ­­­ CAG expansions/­ contractions (rad27D)

8

 

Yeast

-

Yes

­­ CTG/CAG expansions (5 polarity bias), ­­­ CTG/­­ CAG contractions (no polarity bias) (rad27D)

9

 

Mouse

-

-

hHD(+/–) FEN1(+/–) ­ CAG contractions (transmission), no effect on somatic CAG instability

10

 

hcell extract

-

-

­ CAG contractions and ­ genomic instability (D181A — nuclease deficient FEN1)

10

 

hprotein

Yes

-

Cleaves 5 GAA flaps, inhibited by structures in flap (oligo assay)

11

 

hprotein

Yes

Yes

Inhibited by long >(CNG)11 5 flap (CTG more than CAG) (oligo assay)

12

 

hprotein

Yes

-

Inhibited by 5 CTG flaps (oligo assay)

13

 

hprotein

Yes

-

Reduced cleavage activity allows more unprocessed 5 CTG flap for ligation leading to expansions (G66S, G242D endo/exonuclease defects), endonuclease activity resolves bubble structures by processing 5’ flaps (oligo assay)

14

 

yprotein

Yes

-

Stimulated by DNA2 only on CTG flaps with 5 T‑tails (oligo assay)

15

 

Human

-

-

Huntington disease patients lack polymorphisms/mutations in FEN1

16

Pola (DNA polymerase‑a/DNA replication and repair)

Yeast

-

Yes

­­ CAG instability, ­ CTG instability (pol1-1 primase interaction mutation), no effect on CTG/CAG instability (pol1-17 polymerization mutation)

5

Pold (DNA polymerase‑d/DNA replication and repair)

Yeast

Yes

No

­­ CAG/CTG instability (pol3-14 mutation), no effect on CTG/CAG instability (pol3-01 proofreading mutation)

5

 

Yeast

-

-

­­ CTG expansions (pol32D) (expansion assay)

17

 

Yeast

Yes

-

­ CAG contractions (pol3‑t mutant)

8

Pole (DNA polymerase‑e/DNA repair and chromosomal replication)

Yeast

-

-

No effect on CTG/CAG (pol2-18 & pol2-4 mutants)

5

 

 Yeast

-

-

No effect on CTG/CAG instability

46

Polg (DNA polymerase‑g/replication of mitochondrial DNA)

Yeast

-

-

No effect on CTG instability (expansion assay)

18

Polz (DNA polymerase-z/bypass)

Yeast

-

-

No effect on CTG/CAG instability

46

RF‑C complex (Replication factor C/DNA replication)

Yeast

-

-

­­ CGG expansions (rfc1-1 mutation) (expansion assay)

18

Pol30 (PCNA/
associates with DNA polymerase during replication and repair)

Yeast

Yes

Yes

­­­ CAG/­­ CTG instability (pol30-52, pol30-79 & pol30-90 mutants)

5

RNAseH (RNaseH/
involved in DNA replication and associates with FEN1 in repair)

Yeast

-

-

No effect on CAG instability (rnh1D, rnh35D)

19

 

Yeast

Yes

-

­­ CAG155 breakage, no effect on CAG instability (rnh35D)

8

Dna2 (Dna2/unwinds duplex DNA during replication)

Yeast

-

-

No effect on CAG instability (dna2-1 mutant)

19

 

Yeast

Yes

-

­ CAG155 breakage, no effect on CAG instability (dna2-1 mutant)

8

 

yprotein

Yes

-

Inhibited by CTG flaps, cleaves if 5 T‑tail present

15

Cdc9 (DNA ligase I)

Yeast

Yes

-

­­ CAG155 breakage and ­ CAG expansions (cdc9-2 mutant)

8

 

Yeast

-

Yes

­ CAG instability (mostly expansions) & ­ CTG expansions (cdc9-1 & cdc9-2 mutants)

19

 

Yeast

-

Yes

­ CAG  expansions & ­ CTG contractions (Overexpression of CDC9 wt, binds PCNA way form Rad27/Fen1)

48

 

hprotein

Yes

-

Ligates 5 CTG flaps (oligo assay)

20

Pri2 (DNA Primase/ initiation of replication and Okazaki synthesis)

Yeast

Yes

-

­­­ CAG155 breakage, ­ CAG instability (pri2-1 mutant)

8

 

Yeast

-

No

­ CTG/CAG instability (pri2-1 mutant)

19

Mrc1 (claspin/ replication checkpoint)

Yeast

Yes

-

­­­ CAG breakage, ­ CAG instability (mrc1-1 mutant)

21

Wrn (Wrn/
maintenance of genome stability)

Mouse

-

-

No effect on CGG/CCG instabilit

22

TP53 (p53/DNA repair)

Mouse

-

-

No effect on CGG/CCG instability

22

SSB (Replication factor A/DNA replication and repair)

Bacteria

Yes

-

­ CAG contractions (ssb-1 mutant)

23

MSH2 (MSH2/mismatch repair)

Yeast

-

-

No effect on CGG instabilit

4

 

Yeast

Yes

No

­­ CAG/CTG instability (msh2 mutant)

24

 

Yeast

-

-

No effect on CTG instability (msh2 mutant) (expansion assay)

25

 

Yeast

Yes

-

­ CAG contractions (msh2D) (contraction assay)

3

 

Yeast

-

-

No effect on CTG/CAG instability (msh2 mutant) (expansion assay)

26

 

Yeast

No

Yes

­ CTG/CAG expansions and ­­­ CTG/­­ CAG contractions (msh2D)

9

 

Mouse

-

-

­­­ Contractions in Msh2(-/-) DM CTG mice

27

 

Mouse

-

-

­­ Premeiotic contractions in gametes of Msh2(-/-) DM CTG mice

28

 

Mouse

-

-

Paternal expansion, ­ paternal contractions, no effect on maternal transmission

29

 

Mouse

-

-

Striatal instability in HdhQ111/+ msh2(-/-)

29

 

Mouse

-

-

Somatic heterogeneity in Msh2(-/-) HD CAG mice

30

 

Mouse

-

-

Somatic and sperm heterogeneity in Msh2(-/-) HD CAG mice

31

 

hprotein

Yes

-

Binds preferentially to CAG loop-out structure

32

 

hcell extract

-

-

No effect on processing of CTG/CAG slipouts

47

MSH6 (MSH6/
mismatch repair)

Yeast

-

-

No effect on CGG instability

4

 

Yeast

-

-

­ CTG expansions (msh6 mutant) (expansion assay)

25

 

Mouse

Yes

-

­ CTG somatic instability in Msh6 (‑/-) DM1 knock-in mouse

33

MSH3 (MSH3/
mismatch repair)

Yeast

-

-

No effect on CGG instability

4

 

Yeast

-

-

­ CTG expansions (msh3 mutant) (expansion assay)

25

 

Mouse

Yes

-

CTG somatic instability in Msh3 (‑/-) DM1 knock-in mouse

33

 

hcell extract

-

-

No effect on processing of CTG/CAG slipouts

47

yPMS1 (PMS1,PMS2/mismatch repair)

Yeast

Yes

Yes

­­ CAG instability, no effect on CTG instability (pms1 mutant)

34

 

Yeast

-

-

No effect on CAG contractions (pms1D) (contraction assay)

3

 

Yeast

-

-

No effect on CTG instability (pms1 mutant) (expansion assay)

25

 

Mouse

 

 

CTG expansions in PMS2(-/-) Dmt‑D mouse

34

MLH1 (MLH1/
mismatch repair)

Yeast

-

-

No effect on CGG instability

4

 

Yeast

-

-

No effect on CAG contractions (mlh1D) (contraction assay

3

 

hcell extract

-

-

No effect on processing of CTG/CAG slipout

47

MRE11 (MRE11/
involved in double-strand break repair and meiotic recombination

Yeast

-

-

CAG contractions (mre11D) (DSB assay)

35

 

Bacteria

Yes

Yes

CTG contractions, CAG contractions (sbcC mutant) (contraction assay)

36

RAD50 (RAD50/double-strand break repair)

Yeast

-

-

No effect on CAG instability (rad50D) (DSB assay)

35

 

Yeast

Yes

-

CTG breakage (rad50D)

2

RAD1 (RAD1/
exonuclease activity on 3
ends of dsDNA)

Yeast

Yes

-

CTG breakage (rad1D)

2

RAD52 (RAD52/double-strand break repair and recombination)

Yeast

-

-

No effect on CTG/CAG instability (rad52D)

5

 

Yeast

-

-

No effect on CAG instability (rad52D) (expansion assay)

26

 

Yeast

Yes

-

CTG breakage (rad52D)

2

 

Yeast

-

-

No effect on CTG instability (expansion assay) (rad52 mutant)

17

 

Mouse

-

-

No effect on CTG instability in Rad52(-/-) DM CTG mice ( in mean size of expansion)

27

RAD53 (Chk2/DNA damage response)

Yeast

Yes

-

­­ CAG breakage, ­­ CAG contractions (rad53-21 mutant)

37

 

Yeast

Yes

-

­­­ CAG breakage (rad53-21 mutant)

21

RAD54 (RAD54/recombination and repair)

Mouse

-

-

No effect on CTG instability in Rad54(-/-) DM CTG mice

27

Mec1 (ATM/ DNA damage response)

Yeast

Yes

-

­­ CAG breakage, ­ CAG contractions (mec1D)

37

Rad17(Rad17/checkpoint signalling)

Yeast

Yes

-

­ CAG breakage, ­­ CAG contractions (rad17D)

37

Rad9 (Rad9/DNA damage response)

Yeast

Yes

-

­­ CAG breakage, less in larger repeat, No effect on CAG instability (rad9D)

37

Rad24 (Rad24/DNA damage checkpoint)

Yeast

Yes

-

No effect on CAG breakage, ­ CAG contractions (rad24D)

37

Ddc2(ATRIP/
DNA excision)

Yeast

Yes

-

­ CAG breakage for larger repeat, ­­ CAG contractions (dcd2D)

37

DNA-PKcs (DNA-dependant protein kinases/DNA repair)

Mouse

-

-

No effect on CTG instability in DNA-PKcs (‑/-) DM CTG mice

27

Sgs1 (similar to BLM & WRN/helicase)

Yeast

-

-

CGG contractions (sgs1D)

4

Srs2 (RecQ family member/DNA helicase)

Yeast

Yes

Yes

­­ CTG expansions, ­­ CGG expansions (expansion assay) (srs2 mutant)

17

Din7 (XPG family/DNA repair and replication)

Yeast

-

-

No effect on CGG instability

4

XPF (nucleotide excision repair endonuclease)

hcell extract

-

-

No effect on processing of CTG/CAG slipouts

47

XPG (nucleotide excision repair endonuclease)

hcell extract

-

-

No effect on processing of CTG/CAG slipouts

47

Exo1 (Exonuclease 1/DNA replication, repair and recombination)

Yeast

-

-

No effect on CGG instability

4

RecA (RAD51/homologous recombination)

Yeast

-

-

No effect on CTG instability

17

 

Bacteria

Yes

Yes

­­ CTG/CAG contractions (recA-)

38

 

Bacteria

Yes

Yes

CTG (lagging strand) instability and CAG (lagging strand) instability (recA56 mutant) (deletion assay)

39

 

Bacteria

-

-

No effect on CTG and CGG instability (recA-)

40

RecBC (bacterial double-strand break repair)

Bacteria

Yes

Yes

­ CTG/CAG contractions (recBC-)

38

DNA polymerase III

Bacteria

Yes

No

­ CGG contractions (mutD5 & dnaQ49ts), ­ CTG/CAG contractions (dnaQ49ts destabilizes the replication fork/proofreading)

41

 

 

-

-

­ CTG/CAG expansions (mutD5 impairs exonuclease activity)

41

Spo11 (Spo11/meiotic early recombination)

Yeast

-

-

Meiotic CAG instability (spo11D)

42

Spo 13 (yeast meiosis regulator)

Yeast

-

-

No effect on CAG meiotic instability (spo13D)

42

MutS (bacterial mismatch repair)

Bacteria

Yes

Yes

­­ CAG (lagging strand) instability, no effect on CTG (lagging strand) instability (mutS mutant) (deletion assay)

39

 

Bacteria

Yes

-

Large CAG contractions, ­ small CAG contractions (mutS mutant)

43

 

Bacteria

-

Yes

CAG instability, magnitude of CTG contractions (mutS mutant)

40

MutL (bacterial mismatch repair)

Bacteria

-

Yes

CAG instability, magnitude of CTG contractions (mutL mutant)

40

MutH (bacterial mismatch repair)

Bacteria

-

Yes

CAG instability, magnitude of CTG contractions (mutH mutant)

40

Mus81 (Mus81, structure specific endonuclease)

Yeast

-

-

No effect on CAG/CTG instability (mus81D) (recombination assay)

44

UvrA (bacterial nucleotide excision repair)

Bacteria

Yes

Yes

­ CTG contractions, no effect on CAG, CGG or GAA instability (uvrA mutant)

45

 

Bacteria

Yes

Yes

CTG contractions, CAG contractions (uvrA6 mutant) (contraction assay)

36

UvrB (bacterial nucleotide excision repair)

Bacteria

Yes

Yes

CTG instability, no effect on CAG, CGG or GAA instability (uvrB mutant)

45

 

Bacteria

Yes

Yes

CAG contractions (contraction assay) (uvrB5 mutant)

36

Rtg2 (yeast metabolic regulation)

Yeast

-

-

No effect on (CTG)25 (rtg2D) (expansion assay)

17

-, Not applicable;­, increased; , decreased (number of arrows indicate relative extent of change within, not between, reference; that is, >); instability, both expansions and contractions; xprotein, yeast or human purified protein. Wherever possible the lagging template strand repeat sequence is noted.

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