Agarwal, Manu

Bi, Liu

Chen, Xuemei

Ding, Shou-Wei

Li, Shengben

Meyers, Blake C.

Vaucheret, Hervé

Wu, Qingfa

Yu, Bin

Zhai, Jixian

English

UNL | Libraries

University of Nebraska - Lincoln 
DigitalCommons@University of Nebraska - Lincoln 
Bin Yu Publications Papers in the Biological Sciences 
2010 
siRNAs compete with miRNAs for methylation by HEN1 in 
Arabidopsis (Supplementary Material) 
Bin Yu 
University of Nebraska-Lincoln, byu3@unl.edu 
Liu Bi 
University of California - Riverside 
Jixian Zhai 
University of Delaware 
Manu Agarwal 
University of California - Riverside 
Shengben Li 
University of California - Riverside 
See next page for additional authors 
Follow this and additional works at: https://digitalcommons.unl.edu/bioscibinyu 
Yu, Bin; Bi, Liu; Zhai, Jixian; Agarwal, Manu; Li, Shengben; Wu, Qingfa; Ding, Shou-Wei; Meyers, Blake C.; 
Vaucheret, Hervé; and Chen, Xuemei, "siRNAs compete with miRNAs for methylation by HEN1 in 
Arabidopsis (Supplementary Material)" (2010). Bin Yu Publications. 5. 
https://digitalcommons.unl.edu/bioscibinyu/5 
This Article is brought to you for free and open access by the Papers in the Biological Sciences at 
DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Bin Yu Publications by an 
authorized administrator of DigitalCommons@University of Nebraska - Lincoln. 
Authors 
Bin Yu, Liu Bi, Jixian Zhai, Manu Agarwal, Shengben Li, Qingfa Wu, Shou-Wei Ding, Blake C. Meyers, Hervé 
Vaucheret, and Xuemei Chen 
This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/
bioscibinyu/5 
 1 
Supplementary Material for Yu et al. 
 
Legends of supplemental figures 
 
Figure S1. Characterization of nrpd1 and nrpd2 alleles. (A) Expressing NRPD1 and 
NRPD2 in nrpd1-8 hen1-2 and nrpd2-16 hen1-2, respectively, restores the levels of 
miRNAs to those in hen1-2. (B) AtSN1 and cluster 2 siRNAs are absent in nrpd1 hen1-2 
and nrpd2 hen1-2. Ler, the wild-type control for hen1-2; nrpd1 hen1-2, nrpd1-8 hen1-2; 
nrpd2 hen1-2, nrpd2-16 hen1-2; nrpd1 hen1-2+NRPD1, an nrpd1-8 hen1-2 mutant 
harboring NRDP1 genomic DNA. nrpd2 hen1-2 +NRPD2, a nrpd2-16 hen1-2 mutant 
harboring NRPD2 genomic DNA. RNAs were extracted from inflorescences, separated 
on a 15% polyacrylamide gel and probed for miR167 and miR173. The ethidium-
bromide stained tRNA region of the gel is shown below to indicate the amount of RNAs 
used. 
 
Figure S2. Characterization of the L1-derived hen1-8 allele. The L1 line carries a tandem 
repeat of a 35S-GUS transgene silenced by PTGS. Screening the L1 mutagenized library 
for plants exhibiting high GUS activity allowed the identification of PTGS-deficient 
mutants, including hen1-4. Rescreening the L1 mutagenized library for plants exhibiting 
miRNA-related developmental phenotypes allowed the identification of mutants that 
support GUS silencing but have defects in the miRNA pathway, including hen1-8. (A) 
hen1-8 exhibits similar miRNA impairment as the strong hen1 alleles hen1-4 and hen1-5 
in Col. Filter hybridization shows that miRNAs accumulate at similarly low levels in 
Yu, Bi, Zhai, Agarwal, Li, Wu, Ding, Meyers, Vaucheret & Chen. siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis. 
Nucleic Acids Research (2010) 38(17): 5,844-5,850. DOI: 10.1093/nar/gkq348.
 2 
hen1-4, hen1-5 and hen1-8 relative to L1. (B) hen1-8 does not efficiently suppress PTGS 
of the L1 locus. Filter hybridization shows that GUS mRNAs accumulate at similarly low 
levels in L1 and hen1-8 whereas they accumulate at high levels in hen1-4. GUS activities, 
as measured from plant extracts, correlate with GUS mRNA levels. (C) hen1-8 does not 
affect PTGS triggered by the cucumber mosaic virus (CMV). Hypersusceptibility to 
CMV infection is a hallmark of PTGS-deficient mutants and correlates with increased 
accumulation of viral RNA due to the impairment of the PTGS antiviral defense, which 
leads to the eventual death of the infected plant. Consistent with its ability to undergo 
transgene PTGS, hen1-8 mutants exhibit CMV tolerance, whereas hen1-4 exhibits CMV 
hypersusceptibility. 
 
Figure S3. Levels of HEN1 protein do not differ between Ler and Col backgrounds. 
Total proteins from Ler and Col inflorescences were resolved by SDA-PAGE and 
transferred to a nitrocellulose membrane. The top and bottom halves of the membrane 
were probed with anti-HEN1 and anti-Hsp73 (mouse monoclonal antibody) antibodies, 
respectively. The anti-Hsp73 antibody detects Arabidopsis Hsp70 proteins, which serve 
as a loading control. A portion of the stained protein gel is shown at the bottom. 
 
 
 3 
Table S1. The relative abundance of rare miRNAs in rdr2-1 and WT 
 
 rdr2-1a WTa Fold changeb 
miR771 5.2E-05 1.0E-04 0.5 
miR773 1.6E-05 1.3E-05 1.2 
miR774 3.2E-06 N/Ac  
miR775 7.5E-04 1.9E-04 4 
miR776 4.3E-06 N/A  
miR777 5.0E-05 N/A  
miR778 5.3E-06 N/A  
miR779 1.1E-06 N/A  
miR780 2.2E-03 3.4E-04 6.4 
miR781 2.0E-05 N/A  
miR822 1.1E-05 6.3E-06 1.7 
miR823 1.4E-05 6.3E-06 2.2 
miR824 1.4E-03 8.2E-05 17.4 
miR825 5.4E-05 3.1E-05 1.7 
miR826 5.4E-06 N/A  
miR827 5.5E-05 1.7E-04 0.3 
miR829 2.0E-03 1.1E-03 1.7 
miR830 2.0E-05 N/A  
miR832 2.1E-06 N/A  
miR835 3.2E-06 N/A  
miR837 1.1E-06 N/A  
miR838 1.2E-05 N/A  
miR839 9.6E-06 7.0E-05 0.1 
miR840 1.9E-05 6.3E-06 3.0 
miR844 2.1E-05 6.3E-06 3.4 
miR845a 1.7E-04 1.3E-05 13.1 
miR845b 1.8E-05 N/A  
miR848 2.8E-04 1.3E-05 21.3 
miR851 4.8E-05 1.9E-05 2.5 
miR852 6.2E-05 6.3E-06 9.7 
miR853 1.1E-06 N/A  
miR856 N/A 6.5E-06  
miR858 6.7E-05 7.0E-05 1.0 
miR860 5.1E-05 1.9E-05 2.7 
miR861 7.4E-06 N/A  
miR862 1.1E-05 6.3E-06 1.7 
miR864 6.5E-05 1.9E-05 3.4 
miR865 1.1E-06 N/A  
miR866 1.2E-04 3.2E-05 3.8 
miR867 2.6E-04 6.3E-06 41.0 
miR869 2.1E-04 3.8E-05 5.6 
 
 4 
a: The relative abundance was calculated as: individual miRNA count/total miRNA count 
b: Fold change was calculated as: relative miRNA abundance of rdr2-1/relative miRNA 
abundance of wt 
c: N/A, undetected.  
 
 
 
 5 
 
 6 
 
 7 
 


siRNAs compete with miRNAs for methylation by HEN1 in \u3ci\u3eArabidopsis\u3c/i\u3e (Supplementary Material)

DigitalCommons@University of Nebraska

University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Bin Yu Publications Papers in the Biological Sciences 2010 siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis (Supplementary Material) Bin Yu University of Nebraska-Lincoln, byu3@unl.edu Liu Bi University of California - Riverside Jixian Zhai University of Delaware Manu Agarwal University of California - Riverside Shengben Li University of California - Riverside See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/bioscibinyu Yu, Bin; Bi, Liu; Zhai, Jixian; Agarwal, Manu; Li, Shengben; Wu, Qingfa; Ding, Shou-Wei; Meyers, Blake C.; Vaucheret, Hervé; and Chen, Xuemei, "siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis (Supplementary Material)" (2010). Bin Yu Publications. 5. https://digitalcommons.unl.edu/bioscibinyu/5 This Article is brought to you for free and open access by the Papers in the Biological Sciences at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Bin Yu Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Bin Yu, Liu Bi, Jixian Zhai, Manu Agarwal, Shengben Li, Qingfa Wu, Shou-Wei Ding, Blake C. Meyers, Hervé Vaucheret, and Xuemei Chen This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/bioscibinyu/5  1 Supplementary Material for Yu et al.  Legends of supplemental figures  Figure S1. Characterization of nrpd1 and nrpd2 alleles. (A) Expressing NRPD1 and NRPD2 in nrpd1-8 hen1-2 and nrpd2-16 hen1-2, respectively, restores the levels of miRNAs to those in hen1-2. (B) AtSN1 and cluster 2 siRNAs are absent in nrpd1 hen1-2 and nrpd2 hen1-2. Ler, the wild-type control for hen1-2; nrpd1 hen1-2, nrpd1-8 hen1-2; nrpd2 hen1-2, nrpd2-16 hen1-2; nrpd1 hen1-2+NRPD1, an nrpd1-8 hen1-2 mutant harboring NRDP1 genomic DNA. nrpd2 hen1-2 +NRPD2, a nrpd2-16 hen1-2 mutant harboring NRPD2 genomic DNA. RNAs were extracted from inflorescences, separated on a 15% polyacrylamide gel and probed for miR167 and miR173. The ethidium-bromide stained tRNA region of the gel is shown below to indicate the amount of RNAs used.  Figure S2. Characterization of the L1-derived hen1-8 allele. The L1 line carries a tandem repeat of a 35S-GUS transgene silenced by PTGS. Screening the L1 mutagenized library for plants exhibiting high GUS activity allowed the identification of PTGS-deficient mutants, including hen1-4. Rescreening the L1 mutagenized library for plants exhibiting miRNA-related developmental phenotypes allowed the identification of mutants that support GUS silencing but have defects in the miRNA pathway, including hen1-8. (A) hen1-8 exhibits similar miRNA impairment as the strong hen1 alleles hen1-4 and hen1-5 in Col. Filter hybridization shows that miRNAs accumulate at similarly low levels in Yu, Bi, Zhai, Agarwal, Li, Wu, Ding, Meyers, Vaucheret & Chen. siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis. Nucleic Acids Research (2010) 38(17): 5,844-5,850. DOI: 10.1093/nar/gkq348. 2 hen1-4, hen1-5 and hen1-8 relative to L1. (B) hen1-8 does not efficiently suppress PTGS of the L1 locus. Filter hybridization shows that GUS mRNAs accumulate at similarly low levels in L1 and hen1-8 whereas they accumulate at high levels in hen1-4. GUS activities, as measured from plant extracts, correlate with GUS mRNA levels. (C) hen1-8 does not affect PTGS triggered by the cucumber mosaic virus (CMV). Hypersusceptibility to CMV infection is a hallmark of PTGS-deficient mutants and correlates with increased accumulation of viral RNA due to the impairment of the PTGS antiviral defense, which leads to the eventual death of the infected plant. Consistent with its ability to undergo transgene PTGS, hen1-8 mutants exhibit CMV tolerance, whereas hen1-4 exhibits CMV hypersusceptibility.  Figure S3. Levels of HEN1 protein do not differ between Ler and Col backgrounds. Total proteins from Ler and Col inflorescences were resolved by SDA-PAGE and transferred to a nitrocellulose membrane. The top and bottom halves of the membrane were probed with anti-HEN1 and anti-Hsp73 (mouse monoclonal antibody) antibodies, respectively. The anti-Hsp73 antibody detects Arabidopsis Hsp70 proteins, which serve as a loading control. A portion of the stained protein gel is shown at the bottom.    3 Table S1. The relative abundance of rare miRNAs in rdr2-1 and WT   rdr2-1a WTa Fold changeb miR771 5.2E-05 1.0E-04 0.5 miR773 1.6E-05 1.3E-05 1.2 miR774 3.2E-06 N/Ac  miR775 7.5E-04 1.9E-04 4 miR776 4.3E-06 N/A  miR777 5.0E-05 N/A  miR778 5.3E-06 N/A  miR779 1.1E-06 N/A  miR780 2.2E-03 3.4E-04 6.4 miR781 2.0E-05 N/A  miR822 1.1E-05 6.3E-06 1.7 miR823 1.4E-05 6.3E-06 2.2 miR824 1.4E-03 8.2E-05 17.4 miR825 5.4E-05 3.1E-05 1.7 miR826 5.4E-06 N/A  miR827 5.5E-05 1.7E-04 0.3 miR829 2.0E-03 1.1E-03 1.7 miR830 2.0E-05 N/A  miR832 2.1E-06 N/A  miR835 3.2E-06 N/A  miR837 1.1E-06 N/A  miR838 1.2E-05 N/A  miR839 9.6E-06 7.0E-05 0.1 miR840 1.9E-05 6.3E-06 3.0 miR844 2.1E-05 6.3E-06 3.4 miR845a 1.7E-04 1.3E-05 13.1 miR845b 1.8E-05 N/A  miR848 2.8E-04 1.3E-05 21.3 miR851 4.8E-05 1.9E-05 2.5 miR852 6.2E-05 6.3E-06 9.7 miR853 1.1E-06 N/A  miR856 N/A 6.5E-06  miR858 6.7E-05 7.0E-05 1.0 miR860 5.1E-05 1.9E-05 2.7 miR861 7.4E-06 N/A  miR862 1.1E-05 6.3E-06 1.7 miR864 6.5E-05 1.9E-05 3.4 miR865 1.1E-06 N/A  miR866 1.2E-04 3.2E-05 3.8 miR867 2.6E-04 6.3E-06 41.0 miR869 2.1E-04 3.8E-05 5.6   4 a: The relative abundance was calculated as: individual miRNA count/total miRNA count b: Fold change was calculated as: relative miRNA abundance of rdr2-1/relative miRNA abundance of wt c: N/A, undetected.      5   6   7  

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siRNAs compete with miRNAs for methylation by HEN1 in \u3ci\u3eArabidopsis\u3c/i\u3e (Supplementary Material)

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