Effect of

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 Hdh^Q111/+ 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 & dnaQ49^ts), CTG/CAG contractions (dnaQ49^ts 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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