Table S. All regions of WCC enrichment at p<. and z score >3.9 N. crassa contig start nt # of reads z score promoter coding region intergenic chrvii_contig7. 776 738 5.66 frq chrvi_contig7. 696.93 vvd chri_contig7. 985 657. cry chrii_contig7.57 6 5.68 bli- chrii_contig7.57 65 5.68 bli- chri_contig7.9 875 387.87 os-/ncu37 chrvii_contig7. 75 378.8 frq AS/NCU6 chriv_contig7.3 9 353.5.69 none chrv_contig7.3 558 3 9.8 sah- chrv_contig7.8 936 3 8.58 NCU63 chrvi_contig7. 636 98 7.9 NCU chrii_contig7.3 375 67 5.7 NCU58/NCU55 chrii_contig7.3 38 67 5.7 NCU58/NCU55 chrvi_contig7. 973 6.75 NCU559 chri_contig7.7 78 53.7 NCU8/NCU8 chri_contig7.7 785 53.7 NCU8/NCU8 chrvii_contig7. 65 5 3.65 wc- chrv_contig7.3 575 36 3.6 NCU95 chriii_contig7.5 385 35 3. NCU75 chri_contig7. 9665 3.67 al- chrvi_contig7. 65 6. NCU3968 chrvii_contig7. 65.37 NCU3/NCU67 chrii_contig7.8 666 3.9 NCU965 chri_contig7. 3595.7 al-/ncu58 chriii_contig7. 9785 96.5.5 NCU57 chriii_contig7.7 577 95. NCU9 chrii_contig7.8 769 89. NCU353 chri_contig7.9 95 87.5 9.9 tca- chri_contig7.6 875 86 9.8 NCU75 chri_contig7.59 7 8 9.56 nit- chri_contig7.9 5885 7 9. NCU35/ chrvi_contig7. 3365 7 8.8 NCU596 chrii_contig7.7 5 7.5 8.8 NCU9335 chri_contig7.3 576 7 8.78 NCU997/ prr-5 chrv_contig7.88 33 7 8.78 NCU989 chrvii_contig7.3 378 65 8.5 NCU695 chrvi_contig7. 5 65 8.5 NCU3865 chriv_contig7. 395 6 8.39 NCU5 chrvii_contig7.66 388 63 8.3 NCU395 chrv_contig7. 6535 63 8.3 NCU568 chrv_contig7.5 936 6 8.7 NCU/NCU3 chrii_contig7.3 585 6 8.9 NCU53/NCU5338 chriv_contig7.6 3535 58 8. crf5-/ncu637 chri_contig7.3 665 58 8. NCU87 chriii_contig7. 7655 56 7.87 nst-5/ncu chriii_contig7. 7985 5 7.7 cdc-7/ncu6 chrii_contig7.5 7 5 7.8 hsf- chrv_contig7.3 37 9 7. tre- chrvi_contig7. 95 7 7.8 NCU3967/vvd chri_contig7.7 799 5 7.5 NCU89 chrii_contig7.5 95755 6.83 NCU8 chriv_contig7.8 5875 37 6.63 NCU655/NCU6553 chrvi_contig7. 57 3 6. NCU3866 chriii_contig7.5 369 3 6. NCU75
chri_contig7.38 7555 3 6.3 msh- chriv_contig7.53 665 3 6.3 mus-5 chrv_contig7.88 338 3 6. NCU983 chrii_contig7.8 355 3 6.8 NCU333 chrii_contig7.8 36 3 6.8 NCU333 chrvi_contig7.6 3 8 6.5 NCU78 chriv_contig7.6 36 6 5.89 rhp-55 chri_contig7.3 5 5.85 NCU9 chri_contig7.58 5 5.85 NCU866 chrvi_contig7. 575 5 5.8 prk-7/ylo- chri_contig7.6 95 5.79 csp- chrv_contig7.3 55955 5.79 sah- chrii_contig7.5 58 3 5.69 rpn- chriv_contig7.6 55 5.66 cre- chriv_contig7.7 385 5.66 NCU773 chrvi_contig7. 685 5.59 NCU53 chrv_contig7.37 335 5.59 NCU76/spr-7 chrvi_contig7. 85 5.59 NCU3968/NCU3969 chrvi_contig7. 855 5.59 NCU3968/NCU3969 chriii_contig7. 375 9 5.6 NCU359/NCU36 chri_contig7. 5785 8 5. NCU939 chrv_contig7. 8 8 5. NCU953/NCU9535 chrii_contig7.3 95 6 5.7 NCU5373/NCU5375 chri_contig7.58 655 5.5 5. phr chri_contig7.38 95 5 5. adv- chriii_contig7. 3895 5 5. bek- chrii_contig7.7 935 5 5. NCU935/NCU935 chriii_contig7.7 95 5. NCU68/NCU69 chri_contig7.9 738 5. cr-/ncu7378 chri_contig7.9 7385 5. cr-/ncu7378 chrv_contig7. 35 3 5.7 NCU7/7 chriii_contig7.7 75.5 5. NCU68/NCU69 chri_contig7.7 755 5. dtn- chrv_contig7.3 956 5. NCU76 PP chrv_contig7.6 665 5. NCU779 PP chrii_contig7. 785 5. NCU83 chrvii_contig7. 85.5.98 NCU9 chriv_contig7. 8.9 NCU9/NCU9 chriii_contig7. 655.88 NCU6/NCU6 chri_contig7.7 7.88 NCU933/con-8 chrv_contig7.6 575 9.8 ccg-3 chri_contig7.56 55 9.8 NCU89/3 chri_contig7. 8653 8.75 NCU7/ (PP/CH) chri_contig7.3 385 8.75 NCU86 chrvi_contig7. 5795 8.75 NCU59 chriii_contig7.7 739 8.75 NCU6 chri_contig7.6 588 7.5.7 NCU69 chrii_contig7.8 37 7.5.7 NCU3388 chriv_contig7.9 33 7.69 erg- chri_contig7.38 79 7.69 gh38- chriv_contig7.7 9 7.69 NCU775 chrvii_contig7.5 83 7.69 NCU867 chrvii_contig7.5 8 7.69 NCU867 chriv_contig7.35 956 7.69 os- chri_contig7.3 5355 6.6 NCU9 chrv_contig7.6 38 6.6 NCU8883 PP chrvi_contig7. 8875 6.6 ubi chriv_contig7.36 75 5.5.59 NCU736
chri_contig7.9 7898 5.56 gh5-/ncu397 chriv_contig7.9 3365 5.56 NCU59 PP chrvi_contig7. 369 5.56 NCU557 PP chriv_contig7.6 55.9 bdp- chrvi_contig7. 697.9 NCU56 chrv_contig7.5 65 3.3 NCU6/gh7-3 chri_contig7.7 95885 3.3 NCU77/NCU77 chrii_contig7.3 985 3.3 NCU539/NCU5395 chrvii_contig7.3 695 3.3 NCU687 chriv_contig7.6 95 3.3 NCU885 PP chrv_contig7.3 585 3.3 nup-/ncu87 chriv_contig7.9 565 3.3 NCU53 chrii_contig7.3 5 3.3 NCU537/NCU5373 chriii_contig7.5 5685 3.3 NCU755 chriv_contig7.8 6365.36 NCU983 contig7.5 67.36 none contig7.5 735.36 none chrii_contig7.5 5.36 NCU536 chrii_contig7.5 855.36 NCU/NCU63 chriii_contig7. 55.3 csb/pan-3 chriii_contig7. 5.3 csb/pan-3 chrv_contig7. 38595.3 gt- chri_contig7. 88655.3 NCU76 PP chrii_contig7.5 865.3 NCU788 chriv_contig7.8 335.3 NCU66 CH chriv_contig7.8 583.5.6 NCU97 chri_contig7.3 5.3 NCU97/NCU97 (CH/CH) chriv_contig7.35 8.3 NCU7 chriii_contig7. 7.3 NCU69 chrii_contig7. 3.3 NCU8/NCU83 chriii_contig7. 987 99.7 NCU chri_contig7.9 8 99.7 NCU3/NCU33 chrv_contig7.37 895 99.7 NCU793 chriv_contig7.8 765 99.7 NCU3 chri_contig7.3 9865 99.7 NCU9 chrv_contig7.8 98.5.3 NCU77 chri_contig7.9 57 98. NCU369 chrvi_contig7. 995 98. NCU559 chrv_contig7.3 35 98. NCU6655 chrv_contig7.6 686 98. NCU775 PP chrv_contig7. 55 98. NCU6 contig7.5 6 98. none chri_contig7.3 836 98. NCU8/NCU8 chrvi_contig7.6 375 98. mus-5/ncu73 chri_contig7.3 95 97.5.7 NCU/NCU3 chriv_contig7. 76 97. NCU5 chrv_contig7.88 385 97. NCU983 contig7. 9 97. none chrv_contig7.8 65 97. NCU8956 chrii_contig7.5 67 97. NCU87 chrvii_contig7.3 5 96 3.97 NCU6888 PP chriv_contig7.9 35 96 3.97 NCU PP chrv_contig7.5 3995 96 3.97 sub- chri_contig7.6 683 96 3.97 NCU59 chrvii_contig7.76 5 96 3.97 NCU9 chri_contig7.9 39735 95.5 3.9 NCU33/NCU3 chrvii_contig7.3 3835 95 3.9 NCU5897 chrvii_contig7.3 38 95 3.9 NCU5897
chrv_contig7.37 8 95 3.9 NCU7 chriii_contig7.7 365 95 3.9 NCU996 chri_contig7.9 8535 95 3.9 NCU6 chri_contig7.6 639 95 3.9 NCU593/NCU59 chri_contig7.7 8365 95 3.9 hda-/ncu897 chriv_contig7.36 6595 95 3.9 NCU776/NCU777 chrv_contig7.37 65 95 3.9 NCU76 chrvi_contig7.6 5 9.5 3.87 mrp-7 contig7.7 9.5 3.87 none chriv_contig7.6 933 9.5 3.87 trm- chrv_contig7. 55 9.5 3.87 NCU36/NCU36 chrii_contig7.33 65 9.5 3.87 chrii_contig7.5 5 9 3.8 hda-/gpd- (ccg-7) chriii_contig7. 8885 9 3.8 NCU36 chrii_contig7.5 685 9 3.8 NCU76/NCU78 chri_contig7.6 59585 9 3.8 NCU66 chri_contig7.9 57 9 3.8 NCU336/nca- chrv_contig7. 638 9 3.8 NCU376 chrv_contig7. 566 9 3.8 NCU37/NCU37 chrvi_contig7. 5 9 3.8 NCU3865 chrv_contig7.3 75975 9 3.8 NCU8 chrv_contig7. 7865 9 3.8 NCU639 PP chrvi_contig7.6 3389 9 3.8 NCU765 PP chrvi_contig7.6 6535 9 3.8 NCU8 CH chriv_contig7.3 3665 9 3.8 NCU76 PP chriii_contig7. 5 9 3.8 NCU783 chriii_contig7. 85 9 3.8 NCU7869 chriii_contig7.7 83 9 3.8 NCU8797 PP chriii_contig7.7 6 9 3.8 NCU959/NCU95 chrv_contig7. 65 9 3.8 NCU6/NCU376 chrv_contig7.5 37595 9 3.8 NCU56/sub- chri_contig7.39 357 9 3.8 NCU77/NCU78 chriv_contig7.36 8895 93.5 3.8 asn- chrvi_contig7.6 798 93.5 3.8 NCU78 chriv_contig7.8 5375 93.5 3.8 NCU969 chrvi_contig7. 5 93 3.78 NCU387 chrvi_contig7. 7385 93 3.78 NCU55/NCU56 PPs chriv_contig7.9 55 93 3.78 NCU539/NCU53 chriv_contig7.6 955 93 3.78 trm- chri_contig7. 895 93 3.78 NCU59 chri_contig7.7 65 93 3.78 NCU33/msp- chrii_contig7.8 793 93 3.78 un- chrv_contig7. 965 93 3.78 NCU389 chrv_contig7. 97 93 3.78 NCU389 chrv_contig7.37 9785 93 3.78 NCU79/NCU79 chrv_contig7.6 965 93 3.78 NCU7786/ccg- chrii_contig7.68 3385 9.5 3.7 none chrv_contig7. 359 9 3.7 NCU3586 chrvi_contig7. 58 9 3.7 NCU59 chriii_contig7.5 375 9 3.7 NCU683 chriv_contig7.8 9 3.7 NCU653/NCU6536 chri_contig7.9 9 3.7 NCU99 PP contig7.5 63 9 3.7 none contig7.5 635 9 3.7 none chrvi_contig7. 3955 9 3.7 NCU598/NCU599 chrv_contig7. 895 9 3.7 mbf-/ncu chrvi_contig7.6 993 9 3.7 nuo.6/ilv-6 chrv_contig7. 735 9 3.7 NCU8
chrii_contig7.33 6955 9 3.7 NCU6785 chrii_contig7.8 65565 9.5 3.68 NCU355 chri_contig7. 9535 9 3.65 cea- chri_contig7. 675 9 3.65 ck- chrv_contig7. 9365 9 3.65 gh63- chri_contig7.6 95 9 3.65 msr-7/ad-5 chri_contig7.7 586 9 3.65 NCU9 PP chrvi_contig7. 587 9 3.65 NCU55 chri_contig7.38 65 9 3.65 NCU75 chriv_contig7.3 9335 9 3.65 NCU7635 PP chrvii_contig7.66 935 9 3.65 NCU936/7 contig7. 39 9 3.65 none chrii_contig7.8 85 9 3.65 vph- chrii_contig7.8 855 9 3.65 vph- chri_contig7. 55 9 3.65 hom- chri_contig7.7 65 9 3.65 NCU979 chrii_contig7.8 895 9 3.65 NCU3375 chriii_contig7.7 3695 9 3.65 NCU667/NCU668 chrii_contig7.33 95 9 3.65 NCU678/mrp-9 chriv_contig7.35 85 9 3.65 NCU7/NCU7 chri_contig7.39 69 9 3.65 prm-/chi-3 chri_contig7.39 695 9 3.65 prm-/chi-3 contig7.6 865 9 3.65 NCU576 chrvi_contig7.6 5 9.5 3.6 sah- chriii_contig7. 655 9 3.58 gh6-5 chrv_contig7. 77 9 3.58 NCU9/NCU9 chri_contig7.6 355 9 3.58 NCU665 chriv_contig7.8 665 9 3.58 NCU98 chriii_contig7. 7585 9 3.58 NCU5688 PP chrvii_contig7.3 77 9 3.58 NCU585 CH/NCU5855 chri_contig7.9 765 9 3.58 NCU838 chriii_contig7.69 39 9 3.58 NCU956 chrii_contig7.7 656 9 3.58 nmt- contig7.6 53 9 3.58 none chriv_contig7.7 5 9 3.58 sre chriv_contig7.7 55 9 3.58 sre chri_contig7.6 5775 9 3.58 arg- chri_contig7.9 65 9 3.58 gh7- chriv_contig7.9 5675 9 3.58 NCU536/gh8-6 chriii_contig7. 75365 89.5 3.55 NCU chriii_contig7. 7537 89.5 3.55 NCU chrv_contig7.5 59 89 3.5 NCU78 chrv_contig7.5 595 89 3.5 NCU78 chriv_contig7.9 385 89 3.5 NCU567 chriii_contig7.5 383 89 3.5 NCU6 chrv_contig7.3 565 89 3.5 NCU669 PP chriii_contig7. 73 89 3.5 NCU786 chriii_contig7.7 9 89 3.5 NCU8533 PP chri_contig7.9 695 89 3.5 NCU9 chri_contig7.65 585 89 3.5 NCU9 chrv_contig7.3 5378 89 3.5 prk- chriv_contig7.53 7335 89 3.5 pyr-3/ncu883 chriv_contig7.53 735 89 3.5 pyr-3/ncu883 chri_contig7.9 3375 89 3.5 trm- chriii_contig7. 788 89 3.5 mrp-35 chri_contig7. 355 89 3.5 NCU596 chri_contig7. 67975 89 3.5 NCU687/8 chri_contig7. 6798 89 3.5 NCU687/8
chrii_contig7.5 36 89 3.5 NCU598/NCU599 chrv_contig7. 335 89 3.5 NCU59/3678 chrv_contig7.3 65 89 3.5 NCU6 chriii_contig7.7 87 89 3.5 ptr-/ncu8 chriii_contig7.7 875 89 3.5 ptr-/ncu8 chriii_contig7.5 89 3.5 NCU63/ chriv_contig7.36 95 89 3.5 NCU738 chriv_contig7.5 73 89 3.5 NCU7995 chri_contig7.56 965 89 3.5 cyt-/gh6- chrvii_contig7.66 65 89 3.5 NCU93 chrii_contig7.3 3535 88.5 3.8 none contig7.5 5 88.5 3.8 none chriii_contig7. 5755 88 3.5 NCU39 chri_contig7. 59685 88 3.5 NCU667/NCU668 chrvi_contig7. 9835 88 3.5 NCU5/NCU53 chriv_contig7.8 773 88 3.5 NCU659 chriv_contig7.8 995 88 3.5 NCU6597 PP chri_contig7.9 779 88 3.5 NCU936 CH chri_contig7.6 957 88 3.5 NCU7/NCU73 chri_contig7.7 5 88 3.5 NCU33/msp- chri_contig7.9 875 88 3.5 NCU386/NCU6 chri_contig7.9 37 88 3.5 NCU839/NCU839 chri_contig7.7 38 88 3.5 NCU93/NCU933 chriii_contig7.95 5 88 3.5 NCU566 contig7.98 385 88 3.5 NCU999 chrii_contig7.5 85 87 3.39 eas chrvi_contig7.3 835 87 3.39 gh7-5 chriii_contig7. 39 87 3.39 NCU75/mip- chri_contig7. 98 87 3.39 NCU857/NCU859 chriv_contig7.9 8 87 3.39 NCU796 chrv_contig7.63 5 87 3.39 NCU887 PP chrv_contig7. 535 87 3.39 NCU95 CH chrv_contig7.8 6 87 3.39 NCU9678/NCU9679 chrii_contig7.7 67 87 3.39 nup-3 chriii_contig7. 3 87 3.39 NCU3 chrv_contig7. 3965 87 3.39 NCU3689/NCU369 chrv_contig7.3 785 87 3.39 NCU3/NCU3 chriv_contig7.6 85 87 3.39 NCU638/NCU639 chriv_contig7.35 5 87 3.39 NCU698/NCU698 chriv_contig7.5 33 87 3.39 vsp-/ncu8 chriv_contig7.5 335 87 3.39 vsp-/ncu8 chrii_contig7.68 7575 87 3.39 NCU538 chriv_contig7.8 6355 86.5 3.35 NCU983 chriv_contig7.6 37935 86.5 3.35 NCU698 chri_contig7. 76 86 3.3 crf9- chrv_contig7. 69 86 3.3 mrp-33/ad-6 chri_contig7.3 7 86 3.3 NCU889/NCU89 PPs chrvi_contig7.6 59685 86 3.3 NCU83 chriv_contig7.8 65 86 3.3 NCU983 chrvi_contig7. 675 86 3.3 NCU53 PP chrvi_contig7. 86 3.3 NCU599 chrv_contig7.6 6555 86 3.3 NCU7778 chrv_contig7.6 656 86 3.3 NCU7778 chrv_contig7.8 577 86 3.3 NCU9685 CH chriv_contig7.83 885 86 3.3 NCU977 contig7.9 3935 86 3.3 NCU988/NCU988 chriii_contig7. 57 86 3.3 NCU387 chrii_contig7.68 9 86 3.3 none
chri_contig7.6 75 86 3.3 rpn-5 chri_contig7.3 995 86 3.3 vad-/ncu95 chriii_contig7. 78 86 3.3 NCU5 chri_contig7. 68 86 3.3 NCU688 chrii_contig7.5 9698 86 3.3 NCU8 chrii_contig7.5 96985 86 3.3 NCU8 chrvi_contig7. 88 86 3.3 nuo3./ncu75 chrv_contig7. 355 86 3.3 NCU65/NCU653 chriii_contig7.7 595 86 3.3 NCU63/NCU6 chriv_contig7.53 98 86 3.3 NCU83/NCU835 chrvi_contig7.6 3669 85.5 3.9 NCU77 chrii_contig7.3 78 85.5 3.9 NCU5388 PP chri_contig7.9 975 85.5 3.9 NCU838/NCU838 chri_contig7.9 37 85 3.6 efr-3 chriii_contig7. 5555 85 3.6 NCU CH chri_contig7. 535 85 3.6 NCU786/NCU787 chrii_contig7.5 533 85 3.6 NCU653/NCU65 chri_contig7.7 89 85 3.6 NCU33 chri_contig7.7 776 85 3.6 NCU335 chri_contig7.9 757 85 3.6 NCU373/NCU37 chrv_contig7.3 3855 85 3.6 NCU9 CH chrvi_contig7. 35 85 3.6 NCU5563 PP chriii_contig7. 5 85 3.6 NCU5737 chri_contig7.38 635 85 3.6 NCU7359 CH chriv_contig7.53 7 85 3.6 NCU83 PP chrv_contig7.8 65 85 3.6 NCU8966 PP chrvi_contig7. 955 85 3.6 NCU78 PP chriii_contig7. 95 85 3.6 NCU878 chri_contig7. 5968 85 3.6 vma-/ncu668 chriii_contig7. 78765 85 3.6 NCU/mrp-35 chriii_contig7. 5765 85 3.6 NCU6 chri_contig7. 675 85 3.6 nuo9.5 chrvi_contig7. 68 85 3.6 gh7-/ncu69 chri_contig7.9 57 85 3.6 NCU355 chrvii_contig7. 535 85 3.6 NCU33 chriv_contig7.9 75 85 3.6 NCU53/NCU533 chriii_contig7.5 59 85 3.6 NCU68/NCU69 chrv_contig7. 377 85 3.6 NCU65/NCU66 chrv_contig7. 3775 85 3.6 NCU65/NCU66 chriii_contig7.5 3 85 3.6 NCU753 chrii_contig7.5 95 85 3.6 NCU89/NCU89 chri_contig7.9 985 8.5 3. NCU38 chrvii_contig7.55 3695 8.5 3. none chri_contig7.7 8876 8.5 3. NCU79 chri_contig7.3 9995 8 3.9 gh7-7 chri_contig7.6 595 8 3.9 NCU79 chri_contig7.9 75 8 3.9 NCU3 chrii_contig7.8 635 8 3.9 NCU358 chrv_contig7. 635 8 3.9 NCU375 ccg- chrvi_contig7. 3 8 3.9 NCU389/NCU385 chriii_contig7.7 365 8 3.9 NCU635/NCU636 chriii_contig7.7 3 8 3.9 NCU683 chri_contig7.38 98 8 3.9 NCU7353 PP chriv_contig7.5 997 8 3.9 NCU8 chrii_contig7.5 789 8 3.9 NCU859 PP chriii_contig7.7 565 8 3.9 NCU8779 chri_contig7.59 83 8 3.9 NCU978 chrii_contig7.5 588 8 3.9 NCU5
chrvi_contig7.6 683 8 3.9 phy- chriii_contig7. 55 8 3.9 NCU5 chriii_contig7. 59 8 3.9 NCU/NCU86 chrii_contig7.5 6 8 3.9 hh- chrii_contig7.5 5375 8 3.9 NCU66/NCU66 chri_contig7.6 6895 8 3.9 NCU598/NCU597 chri_contig7.7 5697 8 3.9 NCU869 chri_contig7.9 7595 8 3.9 NCU36 chrv_contig7. 55 8 3.9 NCU36/NCU365 chrv_contig7. 6 8 3.9 NCU36/NCU365 chrv_contig7.5 3355 8 3.9 NCU76/fpp chriii_contig7.7 35 8 3.9 NCU687/crf3- chrii_contig7.33 5 8 3.9 NCU6775 chrii_contig7.33 875 8 3.9 NCU683 chriv_contig7.7 735 8 3.9 trm-9/ncu77 chri_contig7.58 5 5.53 contig7.6 63 8 3.9 NCU573 chrii_contig7.77 3 8 3.9 NCU989/NCU99 chri_contig7.39 56 83.5 3.6 NCU775 PP chrv_contig7.3 6855 83.5 3.6 NCU3/hsp-8 chrvii_contig7.3 3935 83.5 3.6 NCU5793/NCU579 chrii_contig7.5 55 83.5 3.6 crp-/ncu85 chriv_contig7.9 66 83 3.3 cys- chriii_contig7. 85 83 3.3 NCU/NCU chriii_contig7. 85 83 3.3 NCU/NCU chrv_contig7.5 535 83 3.3 NCU7 chri_contig7.7 953 83 3.3 NCU773/NCU77 PPs chri_contig7.7 895 83 3.3 NCU79 CH chri_contig7.9 965 83 3.3 NCU36/NCU365 chri_contig7.9 9655 83 3.3 NCU36/NCU365 chrii_contig7.8 58 83 3.3 NCU36/NCU38 PPs chriv_contig7. 39 83 3.3 NCU79/NCU8 chrvi_contig7.6 55 83 3.3 NCU8 PP chrvi_contig7. 955 83 3.3 NCU58 PP chriii_contig7. 383 83 3.3 NCU573 PP chrvii_contig7. 67 83 3.3 NCU695 chriii_contig7.5 7 83 3.3 NCU63 chriii_contig7.5 9835 83 3.3 NCU63 chriv_contig7.6 8 83 3.3 NCU6375 chriv_contig7.9 5 83 3.3 NCU789 chrii_contig7.57 73 83 3.3 NCU878/NCU879 chri_contig7.7 65 83 3.3 NCU93 chriv_contig7.79 35 83 3.3 NCU9657 chriv_contig7.79 3 83 3.3 NCU9657 contig7.93 3 83 3.3 NCU996 chrv_contig7. 6855 83 3.3 NCU57 PP chriv_contig7.83 5 83 3.3 xdh- chri_contig7. 565 83 3.3 NCU3/NCU68 chri_contig7.3 9 83 3.3 NCU88 chrvi_contig7. 975 83 3.3 coq-3/ncu598 chrvi_contig7. 5875 83 3.3 NCU5978 chrii_contig7.5 535 83 3.3 NCU557 chrii_contig7.5 675 83 3.3 NCU633 chrv_contig7. 37 83 3.3 tah-3 chrvi_contig7. 3657 83 3.3 NCU399 chrv_contig7.3 5 83 3.3 apr-6 chriii_contig7.7 585 83 3.3 cat- chrvii_contig7. 355 83 3.3 NCU63
chrii_contig7.33 665 83 3.3 NCU675 chrii_contig7.33 775 83 3.3 NCU6769 chriii_contig7.69 93 83 3.3 cyp5- chriv_contig7.83 7 83 3.3 NCU979/NCU973 chriv_contig7.8 575 8.5 3.9 gh6- chrv_contig7. 5 8.5 3.9 NCU chrii_contig7.33 75 8.5 3.9 NCU675 chri_contig7.39 3 8.5 3.9 NCU75 chrvii_contig7.5 665 8.5 3.9 NCU859 chrii_contig7.7 335 8.5 3.9 NCU9336 chri_contig7.9 3963 8.5 3.9 NCU33/NCU3 chriii_contig7. 83 8.5 3.9 ncw-3 contig7.6 566 8.5 3.9 NCU57 See Experimental Procedures for details. PP denotes predicted protein, CH denotes conserved hypothetical protein. Promoter denotes WC- binding sites close to known or predicted transcriptional start sites, coding region denotes peaks found only in coding regions of genes but not also in the promoter, and intergenic denotes peaks that are in gene-poor non-coding regions. A z score of 3.9 or greater means significance at p<..
Table S. Oligonucleotide primers. A. Primers used for ChIP-PCR. Name Sequence (5 to 3 ) expected size (bp) frq_plref GCAGAGGACCCTGAACTTTTC frq_plrer TCTCTTGCTCACTTTCCCACAG frq_dlref GGTCGGGTTGCCGTGACT frq_dlrer GTCATCGGTCTTGCAGCGG vvdf CGCACCCAAGATTACTGTTTCCACC vvdr TAGAGTCGAGGATGAGATGGAG 8 al-3f CTCAGCAGGCAAGCAGGGCAAATC al-3r CTAACCCCGTGCGTCGTCTGATCC 5 hh-f AACCACCGAAACCGTAGAGGGTAC hh-r ATCGCCGACACCGTGTGTTGTAAC B. Primers used for isolation of cdna. Name Sequence (5 to 3 ) act CTTGATGTCACGAACGATTTCG frq AAGACGAAATCCTCGTCATTC frq antisense GTATCTCAATCTGCTTTGTAACCTGGC C. Primers used for Taqman probe realtime PCR. Name Sequence (5 to 3 ) NCUf TCCGCACCGGTCAAGAAA NCUr GGAAGTGGGCGCATGAGAT NCUprobe CGACCAACGTATACCGCGACAACAAAGTC NCU73f TCCTGCAGCGAACATCCACTA NCU73r GTCATCACAGTCCTGCTCGAGAA NCU73probe ATGTCCTCCCGGAGCATCTTGCCA NCU87f CCACGACAACACAAGACCTTAACTT NCU87r CATCCATGACTTGAGACTGGAACA NCU87probe TCGAAGGCACAAATACCAACTCGCCA NCU3f CAATGCCGATGATGAGGAGAA NCU3r GGGAGAGGGACTGCGGAAT NCU3probe TCCAGACCCCCTCTGCGAACATCA NCU95f TCTTGTTGAGGCTCCCGAGTT NCU95r CGAGCCGCTCTGGAAGAAG NCU95probe CTCAGTCCAGCAGCGTTACCCGTTGA NCU3968f CATCTTTCCAAATCCGCTACCTACT NCU3968r CCCGTCAGCTGTGATTTACGA NCU3968probe TGGCGCCATCAACGATACCCTGTTT NCU58f CAGAGACCGTCAGAATGGAACTCT NCU58r GCGGAAAAGCTTGTCACCATAC NCU58probe TGGCGCGATTACATGAGGTTGTGTCA NCU37f TGCAGCATGAATGGATCATGA
NCU37r CGCCTTGACTCGTCGTTGA NCU37probe TCGAGC CTGCCACCCCTAGTAGCG NCU37f CGATGGTGGGTGACTCACAAG NCU37r AGCCGAGATGTGGTGTTTGG NCU37probe CAAGAGGATGAGAAAATGGTCGCGGC NCU67f AGCTATGGATCGAGGAGGGT NCU67r GTCCTCATTCATCTCGGGAA NCU67probe CGTCCAGACGTTTCCGGATTCG NCU7389f ACGTTCGCCAATTTCTTGAC NCU7389r GAGCACGTAATCTCGCATGA NCU7389probe CCAACACCGCCGTTCGAGCT NCU95f TTGATGCGCGTAAAGTCTTG NCU95r AGCTCTTGTCGTTTCTCCCA NCU95probe TCCATCTCCTCTTCGTATCTGCGCTC NCU37f CATCGATTTGCTTCCGTACA NCU37r AAACCCGTGAATGTGAATGG NCU37probe CGCTGCGCCATTCTTCACGA NCU8f CGATGCCTACAAGGAAGAGC NCU8r TTTCTGGGACATAGCGTTCC NCU8probe TCAGGCCAAGATGGCACAAACG NCU873f GAGTCTGTGGCAGTTCACGA NCU873r GATTGCGATTCGGAAGGTTA NCU873probe CGCCGAAACTGGCCTCACCT NCU6536f ACGAGACAGAATTGGGCAAG NCU6536r CTTGTACTTGCCATCGGGTT NCU6536probe TATGGCGCAGTCCGCAGCC NCU968f GCGGAATGGACGTTGATAGT NCU968r GTTGAAGGTGGGCATTGTTT NCU968probe CCCGCCAACTCGACAGGATCT NCU596f ATGCGCCATCAAATACACAA NCU596r CATCGTCGTGCTCGGTACTA NCU596probe CGTTTGCAAGCTTGTCGCTCCA NCU989f AAACAGACGTTGGATTTGGC NCU989r ACCGACAGGAAAGCAAACAC NCU989probe AGATCACCGCCAAGGCGTGC NCU97f CCAACACCAGCCCATATACC NCU97r GCCCATGACGGTGTTCTAGT NCU97probe CCCTCCTCACGGGTATCCTCAAGA NCU775f TGGACCTCTCCAACACTTCC NCU775r CGATAGTGGCTCCTCCATGT NCU775probe CAGGCGTACCAAACGTTGACACGA NCU653f GCTGATCCAGTCCTTGCTTC NCU653r GTAGCCATGCACGCTCACTA NCU653probe CGCATCCAAGGCCCTCACTGA Ncu778f AACCGTTGTTATTGCTTGCC Ncu778r CGCATTGCAAATGGTATGAC
Ncu778probe TTCGTCCCTTCGCCAGAGCG NCU75f CGACAATTTCATGGATGTGG NCU75r CTAGGCTTCGCTCGCATACT NCU75probe CGGGCACCTCTTCCGTATCCG NCU9f TATACCGAACCTTGGCCTTG NCU9r CCACCCATGGTAGTTGATCC NCU9probe CCGCCTCGAACGGATCCATC NCU599f AGGCACGCAACTCGTACTCT NCU599r GCGCTTTGAAAGGTTGAGTC NCU599probe CCGAGTCAGGCAACCCGCTG NCU373f AACGTCAACTGGTCCCAGAC NCU373r GGCTAGACTGTGCAGGAAGG NCU373probe CGCCCGACGAGAAGCGTCTC NCU38f TAGTCCTCCCATGTCTTCGG NCU38r AGTAGTTGGAGCTGCCCTGA NCU38probe TCGAGCAAGCCAGCAAGCCA NCU8f GTGGAAGCGTATCTGGTGGT NCU8r ATATGACAAGGTCGCCCAAG NCU8probe ACCGATCGACAGCTGTCGCG NCU859f TTTCCAATGGAGGAGACGAC NCU859r CAAGACCCGCTCTCTGTTTC NCU859probe CCCTCTGCCTTTCCCTCCACG NCU695f AGCACACCAGAGAGGAGGAA NCU695r GAGAAACCGTCAAACGAAGC NCU695probe CGATGCGCGTCCTCTTGTCG
Figure S. Validation of ChIP-seq libraries. After ChIP-seq library construction, PCR shows enrichment of four known WCC binding sites (frq plre and dlre, vvd and al-3) in the WC- library. Figure S. ChIP-seq reveals WCC regulation of TF genes. TFs with WCC peaks in their promoters and whose expression is: A. light induced and dependent on WC-, B. not light induced but dependent on WC-, and C. not light induced and independent of WC- (summarized in Table B; TF genes shown in Fig. are omitted). SOAP mapped sequence reads from the WC- ChIP library are plotted as a histogram of sequence coverage per base along fragments containing loci of interest. The y-axis has a maximum value of reads per base and regions with > reads are shown in black, others in grey. Gene annotations are based on known or predicted cdnas (UTRs are shown in light green, coding regions in dark green and introns are shown as thin lines). Quantitative RT-PCR was performed on RNA isolated from control (black bars) and Δwc- (white bars) strains grown in the dark (D) or following a 5-min light induction (L). Values shown are the average of two experiments (y-axis). Figure S3. Genes with WCC binding sites fall into diverse functional categories. The pie chart shows functional categories for all 58 regions. The tables show a comparison of the most significant 9 WC- binding sites (z-score >5, p<.9e-7) with all 58 regions (z-score 3.9, p<.). This comparison reveals enrichment for factors involved in cell cycle control, transcription, protein binding and interactions with the environment.
Smith et al., Figure S! WC- lib! Input DNA! hh! hh!
A! NCU95 TF! Smith et al., Figure S! 8 6 NCU965 TF! D D L L D D L! L! NCU596 TF! 8 6 NCU989 TF! NCU3 TF! NCU! NCU73 TF csp-! 6 8
A (continued)! Smith et al., Figure S (contʼd)! 6 NCU739 TF adv-! 8 6 NCU97 TF bek-! NCU775 TF! NCU5 TF sub-! 8 6 NCU73 TF sah-! NCU778 TF sre!
Smith et al., Figure S (contʼd)! A (continued)! NCU786 TF! NCU75 TF! NCU9 TF vad-! NCU95! NCU38 TF! NCU859 TF! 8 6 NCU695 TF ghh!
Smith et al., Figure S (contʼd)! B! NCU968 TF nit-! NCU653 TF! NCU6536! NCU8 TF!
Smith et al., Figure S (contʼd)! C! NCU886 rhp55! NCU887 cre-! NCU87 TF! NCU873! NCU599 TF! NCU373! NCU37!
Smith et al., Figure S3! All significant peaks (see above)! Functional category # % Metabolism 9 6% Energy 9 % Cell Cycle 7 5% Transcription 3 5% Protein Fate 3 5% Protein Binding % Transport % Cell Rescue % Environment 8 % Cellular Components % Unclassified 36 5% Not Near Gene 5 3% Cell Fate % Signal Transduction % Differentiation % Subcellular localization 3 % Protein Synthesis 7 % Regulation of Metabolism % Total 58 % Peaks with z score >5 (Fig. A)! Functional category # % Metabolism 8 7% Energy % Cell Cycle % Transcription 9 8% Protein fate 7 6% Protein Binding 7 6% Transport % Cell Rescue % Environment 3 3% Cellular Components 3 3% Unclassified 6 % Not Near Gene % Total 9 %