Supplementary Information for GC-content elevates mutation and recombination rates in the yeast Saccharomyces cerevisiae. Authors: Denis A. Kiktev1, Ziwei Sheng 2, Kirill S. Lobachev2, and Thomas D. Petes1 Corresponding author: Thomas D. Petes E-mail:
[email protected] This PDF file includes: Figs. S1 to S3 Tables S1 and S2 Captions for Datasets S1 to S8 References for SI reference citations Other supplementary materials for this manuscript include the following: Datasets: 8 Excel file with Datasets S1 to S8
1 www.pnas.org/cgi/doi/10.1073/pnas.1807334115
WT GC
ATGTCGAAAGCTACATATAAGGAACGTGCTGCTACTCATCCTAGTCCTGTTGCTGCCAAGCTATTTAATATCATGCACGAAAAGCAAACAAACTTGTGTGCTTCATTGGATGTTCGTACC ATGTCGAAGGCCACCTATAAGGAGCGTGCGGCCACCCACCCCAGCCCGGTCGCGGCCAAGCTATTCAACATCATGCACGAGAAGCAAACCAACCTGTGCGCCTCCTTGGACGTGCGTACC ******** ** ** ******** ***** ** ** ** ** ** ** ** ** *********** ** *********** ******** *** **** ** ** ***** ** ******
WT GC
ACCAAGGAATTACTGGAGTTAGTTGAAGCATTAGGTCCCAAAATTTGTTTACTAAAAACACATGTGGATATCTTGACTGATTTTTCCATGGAGGGCACAGTTAAGCCGCTAAAGGCATTA ACCAAGGAGCTGCTGGAGTTGGTCGAGGCCCTGGGCCCCAAGATCTGCTTGCTAAAGACCCACGTGGACATCCTGACGGACTTCTCCATGGAGGGCACCGTGAAGCCGCTAAAGGCGTTG ******** * ******** ** ** ** * ** ***** ** ** ** ***** ** ** ***** *** **** ** ** ************** ** ************** **
WT GC
TCCGCCAAGTACAATTTTTTACTCTTCGAAGACAGAAAATTTGCTGACATTGGTAATACAGTCAAATTGCAGTACTCTGCGGGTGTATACAGAATAGCAGAATGGGCAGACATTACGAAT TCCGCCAAGTACAACTTCCTGCTCTTCGAGGACAGGAAGTTCGCGGACATCGGCAACACCGTCAAGTTGCAGTACTCCGCGGGCGTCTACAGGATCGCCGAGTGGGCGGACATCACGAAC ************** ** ********** ***** ** ** ** ***** ** ** ** ***** *********** ***** ** ***** ** ** ** ***** ***** *****
WT GC
GCACACGGTGTGGTGGGCCCAGGTATTGTTAGCGGTTTGAAGCAGGCGGCGGAAGAAGTAACAAAGGAACCTAGAGGCCTTTTGATGTTAGCAGAATTGTCATGCAAGGGCTCCCTAGCT GCCCACGGCGTGGTGGGCCCGGGCATCGTCAGCGGCCTGAAGCAGGCGGCGGAGGAAGTGACCAAGGAGCCCAGGGGCCTTTTGATGCTGGCGGAGTTGTCCTGCAAGGGCTCCCTAGCC ** ***** *********** ** ** ** ***** ***************** **** ** ***** ** ** ************ * ** ** ***** *****************
WT GC
ACTGGAGAATATACTAAGGGTACTGTTGACATTGCGAAGAGCGACAAAGATTTTGTTATCGGCTTTATTGCTCAAAGAGACATGGGTGGAAGAGATGAAGGTTACGATTGGTTGATTATG ACCGGCGAGTACACGAAGGGCACCGTGGACATCGCGAAGAGCGACAAGGACTTCGTCATCGGCTTCATCGCCCAAAGGGACATGGGCGGGAGGGACGAGGGCTACGACTGGCTGATCATG ** ** ** ** ** ***** ** ** ***** ************** ** ** ** ******** ** ** ***** ******** ** ** ** ** ** ***** *** **** ***
WT GC
ACACCCGGTGTGGGTTTAGATGACAAGGGAGACGCATTGGGTCAACAGTATAGAACCGTGGATGATGTGGTCTCTACAGGATCTGACATTATTATTGTTGGAAGAGGACTATTTGCAAAG ACCCCCGGCGTGGGCTTGGACGACAAGGGCGACGCCCTGGGCCAACAGTACAGGACCGTGGACGATGTGGTCTCCACCGGGTCCGACATCATTATCGTGGGCAGGGGGCTATTCGCGAAG ** ***** ***** ** ** ******** ***** **** ******** ** ******** *********** ** ** ** ***** ***** ** ** ** ** ***** ** ***
WT GC
GGAAGGGATGCTAAGGTAGAGGGTGAACGTTACAGAAAAGCAGGCTGGGAAGCATATTTGAGAAGATGCGGCCAGCAAAACTAA GGCAGGGACGCGAAGGTCGAGGGCGAGCGTTACAGGAAGGCCGGCTGGGAGGCGTACTTGAGGAGGTGCGGCCAGCAAAACTAA ** ***** ** ***** ***** ** ******** ** ** ******** ** ** ***** ** ******************
Figure S1. URA3-GC allele. The sequences of both URA3-WT (wild-type allele) and URA3-GC (GCRich allele) are shown with asterisks indicating identical bases.
2
WT AT
ATGTCGAAAGCTACATATAAGGAACGTGCTGCTACTCATCCTAGTCCTGTTGCTGCCAAGCTATTTAATATCATGCACGAAAAGCAAACAAACTTGTGTGCTTCATTGGATGTTCGTACC ATGTCAAAAGCTACATATAAAGAAAGAGCTGCTACTCATCCTAGTCCTGTTGCTGCTAAATTATTTAATATAATGCATGAAAAACAAACAAACTTATGTGCTTCATTAGATGTTAGAACC ***** ************** *** * ***************************** ** ********** ***** ***** *********** *********** ****** * ***
WT AT
ACCAAGGAATTACTGGAGTTAGTTGAAGCATTAGGTCCCAAAATTTGTTTACTAAAAACACATGTGGATATCTTGACTGATTTTTCCATGGAGGGCACAGTTAAGCCGCTAAAGGCATTA ACCAAAGAATTATTAGAATTAGTTGAAGCATTAGGTCCTAAAATTTGTTTATTAAAAACACATGTAGATATTTTAACTGATTTTTCTATGGAAGGTACAGTTAAACCATTAAAAGCATTA ***** ****** * ** ******************** ************ ************* ***** ** *********** ***** ** ******** ** **** ******
WT AT
TCCGCCAAGTACAATTTTTTACTCTTCGAAGACAGAAAATTTGCTGACATTGGTAATACAGTCAAATTGCAGTACTCTGCGGGTGTATACAGAATAGCAGAATGGGCAGACATTACGAAT TCTGCTAAATATAATTTTTTACTTTTTGAAGATAGAAAATTTGCTGATATTGGTAATACAGTTAAATTACAATATTCTGCAGGTGTATATAGAATAGCAGAATGGGCAGATATTACAAAT ** ** ** ** *********** ** ***** ************** ************** ***** ** ** ***** ******** ******************** ***** ***
WT AT
GCACACGGTGTGGTGGGCCCAGGTATTGTTAGCGGTTTGAAGCAGGCGGCGGAAGAAGTAACAAAGGAACCTAGAGGCCTTTTGATGTTAGCAGAATTGTCATGCAAGGGCTCCCTAGCT GCACATGGTGTAGTAGGTCCAGGTATTGTTAGTGGTTTAAAACAAGCAGCAGAAGAAGTAACAAAAGAACCTAGAGGTTTATTAATGTTAGCAGAATTATCATGTAAAGGTTCTTTAGCT ***** ***** ** ** ************** ***** ** ** ** ** ************** *********** * ** ************** ***** ** ** ** *****
WT AT
ACTGGAGAATATACTAAGGGTACTGTTGACATTGCGAAGAGCGACAAAGATTTTGTTATCGGCTTTATTGCTCAAAGAGACATGGGTGGAAGAGATGAAGGTTACGATTGGTTGATTATG ACTGGAGAATATACTAAAGGTACTGTTGATATTGCAAAAAGTGATAAAGATTTTGTTATAGGTTTTATTGCTCAAAGAGATATGGGTGGAAGAGATGAAGGTTATGATTGGTTAATTATG ***************** *********** ***** ** ** ** ************** ** ***************** *********************** ******** ******
WT AT
ACACCCGGTGTGGGTTTAGATGACAAGGGAGACGCATTGGGTCAACAGTATAGAACCGTGGATGATGTGGTCTCTACAGGATCTGACATTATTATTGTTGGAAGAGGACTATTTGCAAAG ACACCTGGTGTAGGTTTAGATGATAAAGGAGATGCATTAGGTCAACAATATAGAACTGTAGATGATGTAGTTTCTACAGGATCTGATATTATTATTGTTGGAAGAGGATTATTTGCAAAA ***** ***** *********** ** ***** ***** ******** ******** ** ******** ** ************** ********************* **********
WT AT
GGAAGGGATGCTAAGGTAGAGGGTGAACGTTACAGAAAAGCAGGCTGGGAAGCATATTTGAGAAGATGCGGCCAGCAAAACTAA GGAAGAGATGCTAAAGTAGAAGGTGAAAGATATAGAAAAGCAGGTTGGGAAGCATATTTAAGAAGATGTGGTCAACAAAATTAA ***** ******** ***** ****** * ** *********** ************** ******** ** ** ***** ***
Figure S2. URA3-AT allele. The sequences of the wild-type (URA3-WT) and AT-enriched (URA3-AT) alleles are shown with the identical bases indicated by asterisks.
3
5
OD595
4 3
URA3-WT URA3-GC
2
URA3-AT
1 0 0
2
4
6
8
10
12
14
Time (hrs)
Figure S3. Growth curves of strains with URA3-WT, URA3-GC and URA3-AT alleles
4
Table S1. Expected and observed sizes of deletions in URA3-GC
Repeat size (bp)
# of “unique” repeats1
Average distance between repeats (bp)2
11 10 9 8 7 6 5
1 3 4 9 33 83 271
285 369 300 264 260 293 262
285 394 124 111 89 97 93
4
1024
261
57
Observed median size of deletions (bp)
Number of deletions above/below median distance4
p value5
285 321 188 222 216 268 201
285 321 63 99 42 81 94
0 4/0 8/36 3/44 3/32 1/22 2/57
NR 0.14
