Genome-wide nucleosome occupancy and organization modulates the plasticity

of gene transcriptional status in maize

Jian Chen1,2, En Li1,2, Xiangbo Zhang1, Xiaomei Dong1, Lei Lei1, Weibin Song1,

Haiming Zhao1, Jinsheng Lai1,*

1State Key Laboratory of Agrobiotechnology and National Maize Improvement

Center, Department of Plant Genetics and Breeding, China Agricultural University,

Beijing, 100193, P. R. China2These authors contributed equally to this work.

* Corresponding author

E-mail: jlai@cau.edu.cn (JL)

Tel: 86-10-62731405

Running title: The effect of nucleosomes on gene transcription

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SUPPLEMENTAL INFORMATION

Supplemental Figure 1: MNase-seq reveals the nucleosome-bound DNA in

genome.

Supplemental Figure 2: The genomic distributions of the paired reads with insert

sizes of 120-140 bp and 140-160 bp, respectively.

Supplemental Figure 3: Composite distribution of AA/AT/TA/TT and

CC/CG/GC/GG dinucleotides along the 147-bp axis of nucleosomal DNA.

Supplemental Figure 4: CG content affects dinucleotides composition of

nucleosome.

Supplemental Figure 5: Correlation between biological replicates of shoot (A)

and endosperm (B) for RNA-seq.

Supplemental Figure 6: Correlation between nucleosome organization and

expression levels of genes.

Supplemental Figure 7: Average nucleosome occupancy patterns near the TSSs

and the TTSs in shoot for genes with different expression levels based on analysis

of the paired reads with insert sizes of 120-140 bp (A) and 140-160 bp (B),

respectively.

Supplemental Figure 8: Average nucleosome occupancy patterns near the TSSs

and the TTSs of genes for the nucleosome occupancy data generated with light

concentration of MNase.

Supplemental Figure 9: Average nucleosome level in different genomic regions

for the nucleosome occupancy data generated with light concentration of MNase.

Supplemental Figure 10: Average nucleosome occupancy patterns near the TSSs

and TTSs for genes simultaneously expressed (A) or unexpressed (B) in shoot

and endosperm.

Supplemental Figure 11: Comparison of nucleosome level difference between

shoot and endosperm for genes expressed or unexpressed in both shoot and

endosperm, shoot-preferred genes, and endosperm-preferred genes.

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Supplemental Figure 12: Average nucleosome occupancy patterns near the TSSs

and TTSs in shoot (A) and endosperm (B) for constitutive, intermediate, and

tissue-specific genes.

Supplemental Figure 13: Average nucleosome occupancy patterns near the TSSs

and TTSs for the lowest-expressed constitutive genes and the highest-expressed

tissue-specific genes in shoot.

Supplemental Figure 14: Comparison of expression levels (A) and average

nucleosome occupancy patterns near the TSSs and TTSs (B) for the lowest-

expressed constitutive genes and the highest-expressed tissue-specific genes in

endosperm.

Supplemental Figure 15: Comparison of translational efficiencies of constitutive,

intermediate, and tissue-specific genes.

Supplemental Figure 16: Comparisons of nucleosome occupancy in exons and

introns for constitutive, intermediate, and tissue-specific genes.

Supplemental Figure 17: Comparisons of the 5′ UTRs lengths with the −1

nucleosome distances relative to the TTSs for constitutive, intermediate, and

tissue-specific genes in shoot.

Supplemental Table 1: Summary of the sequenced data used in this study.

Supplemental Table 2: Comparison of expression levels of six homologous maize

genes of Arabidopsis histone H1.

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Supplemental Figure 1: MNase-seq reveals the nucleosome-bound DNA in

genome.

(A) Schematic depiction of the MNase-seq experiment. (B) Agarose gels of

nucleosome-bound DNA in shoot and endosperm with treatment of different titration

levels of MNase. The appropriate levels of 2 U and 1 U of MNase were chosen for

shoot and endosperm samples, respectively. Bands isolated for sequencing were

marked by red rectangle. (C) Distribution of the insert size in MNase-seq data.

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Supplemental Figure 2: The genomic distributions of the paired reads with insert

sizes of 120-140 bp and 140-160 bp, respectively.

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Supplemental Figure 3: Composite distribution of AA/AT/TA/TT and

CC/CG/GC/GG dinucleotides along the 147-bp axis of nucleosomal DNA.

Upstream, upstream 2 kb of the TSSs. Downstream, downstream 2 kb of the TTSs.

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Supplemental Figure 4: CG content affects dinucleotides composition of

nucleosome.

(A) CG content of different genome regions. (B) Composite distribution of

AA/AT/TA/TT and CC/CG/GC/GG dinucleotides along the 147-bp axis of

nucleosomal DNA. Upstream, upstream 2 kb of TSSs. Downstream, downstream 2 kb

of TTSs.

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Supplemental Figure 5: Correlation between biological replicates of shoot (A)

and endosperm (B) for RNA-seq.

The normalized data of log2 (FPKM value + 1) was used to calculate the correlation

coefficient.

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Supplemental Figure 6: Correlation between nucleosome organization and

expression levels of genes.

(A, B) Average nucleosome occupancy patterns near the TSSs and TTSs for genes

classified by their expression levels. (C, D) The +1 (C) and −1 (D) nucleosomes

distance relative to the TSS and the TTS, respectively.

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Supplemental Figure 7: Average nucleosome occupancy patterns near the TSSs

and TTSs in shoot for genes with different expression levels based on analysis of

the paired reads with insert sizes of 120-140 bp (A) and 140-160 bp (B),

respectively.

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Supplemental Figure 8: Average nucleosome occupancy patterns near the TSSs

and TTSs of genes for the nucleosome occupancy data generated with light

concentration of MNase.

(A) Genes were classified by their expression levels in shoot. (B) Genes were

classified as constitutive, intermediate, and tissue-specific genes. All identified tissue-

specific genes were used for analysis. The nucleosome occupancy data of shoot was

used. 0.2 U MNase was used to generate mononucleosomes.

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Supplemental Figure 9: Average nucleosome level in different genomic regions

for the nucleosome occupancy data generated with light concentration of MNase.

Average nucleosome level of transposable element (TE), exon, intron, upstream 2 kb

of genes, downstream 2 kb of genes, and remained intergenic region was analyzed,

which were ordered by the priority. Average nucleosome level was normalized by the

average nucleosome level of whole genome. The nucleosome occupancy data of shoot

was used. 0.2 U MNase was used to generate mononucleosomes.

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Supplemental Figure 10: Average nucleosome occupancy patterns near the TSSs

and TTSs for genes simultaneously expressed (A) or unexpressed (B) in shoot

and endosperm.

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Supplemental Figure 11: Comparison of nucleosome level difference between

shoot and endosperm for genes expressed or unexpressed in both shoot and

endosperm, shoot-preferred genes, and endosperm-preferred genes.

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Supplemental Figure 12: Average nucleosome occupancy patterns near the TSSs

and TTSs in shoot (A) and endosperm (B) for constitutive, intermediate, and

tissue-specific genes.

The +1 and −1 nucleosomes and their distances relative to the TSSs and TTSs,

respectively, are shown in enlarged figures. All identified tissue-specific genes were

used for analysis. Nucleosome occupancy data of shoot and endosperm generated

with 2 U and 1 U of MNase, respectively, was used.

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Supplemental Figure 13: Average nucleosome occupancy patterns near the TSSs

and TTSs for the lowest-expressed constitutive genes and the highest-expressed

tissue-specific genes in shoot.

The +1 and −1 nucleosomes and their distances relative to the TSSs and TTSs,

respectively, are shown in enlarged figures.

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Supplemental Figure 14: Comparison of expression levels (A) and average

nucleosome occupancy patterns near the TSSs and TTSs (B) for the lowest-

expressed constitutive genes and the highest-expressed tissue-specific genes in

endosperm.

The +1 and −1 nucleosomes and their distances relative to the TSSs and TTSs,

respectively, are shown in enlarged figures.

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Supplemental Figure 15: Comparison of translational efficiencies of constitutive,

intermediate, and tissue-specific genes.

Fourteen days-after-pollination maize endosperm of reciprocal crosses of ‘B73’ and

‘Mo17’ inbred was used. Translational efficiency was calculated by FPKM(translational

level)/FPKM(transcript level). Only genes with FPKM > 1 at both transcriptional and

translational levels were used.

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Supplemental Figure 16: Comparisons of nucleosome occupancy in exons and

introns for constitutive, intermediate, and tissue-specific genes.

The nucleosome occupancy data of shoot was used. Asterisk, significant difference of

nucleosome occupancy (p-value < 0.01).

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Supplemental Figure 17: Comparisons of the 5′ UTRs lengths with the −1

nucleosome distances relative to the TTSs for constitutive, intermediate, and

tissue-specific genes in shoot.

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Supplemental Table 1: Summary of the sequenced data used in this study.

Sequencingtype

Sample Raw readsMapped

readsMapped

effect (%)Unique

mapped readsUnique mapped

effect (%)Effectivecoverage#

MNase-seq14 DAY Shoot 883,011,252 860,841,538 97.49 489,257,293 55.41 23.77 12 DAP Endosperm 950,186,078 924,542,555 97.30 521,966,560 54.93 25.36

RNA-seq

14 DAY Shoot Rep1 16,031,138 14,460,767 90.20 12,391,636 77.30 -14 DAY Shoot Rep2 15,805,238 14,166,210 89.63 12,140,801 76.82 -12 DAP Endosperm Rep1 20,958,352 14,440,820 68.90 13,736,978 65.54 -12 DAP Endosperm Rep2 18,449,352 13,030,221 70.63 12,395,149 67.18 -

#: Effective coverage = reads number (paired) * 200 bp / Assembly genome size.

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Supplemental Table 2: Comparison of expression levels of six homologous maize

genes of Arabidopsis histone H1.

Gene IDShoot

(FPKM)Endosperm

(FPKM)Shoot/endosperm

GRMZM2G164020 84.9 11.3 7.51

GRMZM2G003002 34.5 8.1 4.26

GRMZM2G121221 58.8 2.4 24.5

GRMZM2G080274 102.5 70.1 1.46

GRMZM2G069911 51.7 20.2 2.56

GRMZM2G401308 120.0 64.9 1.85

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