Genome-Wide Nucleosome Occupancy and Organization Modulates the Plasticity of Gene

Genome-wide nucleosome occupancy and organization modulates the plasticity of gene transcriptional statusin 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. China

2These authors contributed equally to this work.

* Corresponding author

E-mail: (JL)

Tel: 86-10-62731405

Running title: The effect of nucleosomes on gene transcription

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 genesfor 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.

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 inshoot.

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

SupplementalTable 2: Comparison of expression levels of six homologous maize genes of Arabidopsis histone H1.

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.

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.

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

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.

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.

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.

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.

Supplemental Figure 8: Average nucleosome occupancy patterns near the TSSs and TTSs of genesfor 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.

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.

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 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 dataof shoot and endosperm generated with 2 U and 1 U of MNase, respectively, was used.

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.

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.

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).

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 inshoot.

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

Sequencing
type / Sample / Raw reads / Mapped
reads / Mapped
effect (%) / Unique
mapped reads / Uniquemapped
effect (%) / Effective
coverage#
MNase-seq / 14 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) * 200bp/Assembly genome size.

SupplementalTable 2: Comparison of expression levels of six homologous maize genes of Arabidopsis histone H1.

Gene ID / Shoot(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