Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity
- University of Queensland, Australia
Figures
Figure 1 with 4 supplements
Chromatin states in Amphimedon.
(A) Schematic representation of Amphimedon life cycle. Larvae (oval shaped, 300–500 µm long) emerge from maternal brood chambers and then swim in the water column before they develop competence to …
-
Figure 1—source data 1
Histone H3 covalent post-translation modifications and RNA Polymerase II investigated in this study and their typical genomic localization relative to coding genes and regulatory regions in bilaterian model organisms.
- https://doi.org/10.7554/eLife.22194.004
-
Figure 1—source data 2
Histone H3 sequences used to generate Figure 1—figure supplement 1.
- https://doi.org/10.7554/eLife.22194.005
-
Figure 1—source data 3
BLASTp search outcome of the relevant histone methyltransferases and acetyltransferases against Amphimedon queenslandica proteins (NCBI nr database; E-value <1e-09).
- https://doi.org/10.7554/eLife.22194.006
-
Figure 1—source data 4
Summary statistics and quality metrics of the ChIP-seq datasets used in this study.
See also Materials and methods for preprocessing of ChIP-seq datasets procedure.
- https://doi.org/10.7554/eLife.22194.007
-
Figure 1—source data 5
Validation of the ChIP-seq results by ChIP-quantitative PCRs (ChIP-qPCRs).
- https://doi.org/10.7554/eLife.22194.008
Figure 1—figure supplement 1
Multiple sequence alignment of various eukaryotic histone H3 proteins (1–136 amino acids), produced by using ClustalO (RRID:SCR_001591) (Sievers et al., 2011).
Note that the entire amino acid sequence of histone H3 is highly conserved across eukaryotes. Sponge sequence is highlighted. The amino acid sequences used to generate the alignment are also …
Figure 1—figure supplement 2
Assessment of reproducibility for biological replicates between histone modifications andRNA Polymerase II.
(A) Pearson correlation coefficients between histone modifications and RNA Polymerase II (RNAPII). Adult experiments (combined biological replicates) are shown. Underlying colors indicate the …
Figure 1—figure supplement 3
Neighborhood positional enrichment plots of adult chromatin states around transcription start site (TSS) and transcription end site (TES) of proteins-coding genes, produced by ChromHMM (Ernst and Kellis, 2012).
For the definition of adult chromatin states see Figure 1A. (A) Positional enrichments in 100 bp genomic bins around the TSS and TES (±1 kb) of expressed protein-coding genes in adult Amphimedon. (B)…
Figure 1—figure supplement 4
Chromatin states in Amphimedonlarva.
(A) Definition and enrichments for a 9-state Hidden Markov Model based on four histone PTMs (H3K4me3, H3K27ac, H3K4me1, H3K27me3) in Amphimedon larva. From left to right: chromatin state …
Figure 2 with 4 supplements
Histone PTMs are correlated with gene expression variations during development.
(A) TSS-centred average input DNA normalised read coverage plot of H3K4me3 across Amphimedon protein-coding genes. The x-axis spans ± 3 kb around TSSs and represents the position within the gene …
-
Figure 2—source data 1
GO biological process term enrichment outcome for the high-variance and low-variance gene sets (Hypergeometric test, FDR<0.01).
- https://doi.org/10.7554/eLife.22194.014
-
Figure 2—source data 2
KEGG pathways significantly enriched in low-variance and high-variance genes.
- https://doi.org/10.7554/eLife.22194.015
Figure 2—figure supplement 1
TSS-centred average input DNA normalised read coverage plots and heatmaps of RNAPII, H3K27ac, H3K36me3, H3K4me1 and H3K27me3 across Amphimedon protein-coding genes.
The x-axis spans ± 3 kb around TSSs and represents the position within the gene relative to TSS. The y-axis represents the input DNA normalised enrichment for ChIP-seq reads in adult. The shaded …
Figure 2—figure supplement 2
Histone PTMs and gene expression variations during development.
(A) TSS-centred average input DNA normalised read coverage plot of H3K4me3 across Amphimedon protein-coding genes. The x-axis spans ± 3 kb around TSSs and represents the position within the gene …
Figure 2—figure supplement 3
H3K4me3 enrichment at genes with head-to-head orientation and alternative TSSs.
(A) Example of coding genes with alternative TSSs (Aqu2.1.39785_001 and Aqu2.1.396786_001) marked by successive H3K4me3 peaks. The genomic window shows input DNA-normalized H3K4me3 coverage and …
Figure 2—figure supplement 4
ChIP-seq profiles of H3K4me3 and total histone H3 across high-variance and low-variance genes.
(A) Developmental expression profile, from early cleavage to adult, of the highly expressed high-variance genes (n = 1066). Expression levels were measured by CEL-seq and rescaled by row. Red …
Figure 3 with 1 supplement
Expression without H3K4me3 in strongly developmentally regulated genes.
(A) TSS-centred average input DNA normalised read coverage plot of H3K4me3 across ‘regulated’ and ‘stable’ protein-coding genes during Amphimedon development. The x-axis spans ± 3 kb around TSSs and …
Figure 3—figure supplement 1
ChIP-seq profiles of RNAPII, total histone H3, H3K36me3 and H3K27me3 across regulated and stable genes.
(A) Developmental expression profile, from early cleavage to adult, of the regulated and stable protein-coding genes (see main text and Materials and methods for details). Expression levels were …
Figure 4 with 1 supplement
DNA motifs overrepresented in H3K27me3 transcriptionally silenced regions.
(A) Diagram representing the composition of Drosophila PRC2 complex and its four core components: the catalytic subunit of the complex E(z), the zinc finger protein SU(z)12, the WD-repeat protein …
-
Figure 4—source data 1
Putative orthologs of Drosophila PcG components and associated factors in yeast, Capsaspora, sponge, nematode, and human genome.
Table of PcG proteins is adapted from (http://www.igh.cnrs.fr/equip/cavalli/link.PolycombTeaching.html).
- https://doi.org/10.7554/eLife.22194.023
Figure 4—figure supplement 1
Matching sequence logos of the DNA motifs determined by MEME-ChIP analysis to be significantly enriched in the transcriptionally silenced regions marked by H3K27me3 in both adult and larva.
The E-value (log likelihood ratio of each motif) and the number of sites contributing to the construction of the motif are shown, respectively.
Figure 5 with 1 supplement
Amphimedon lincRNA populations defined by histone PTM signatures.
(A) Heatmap showing the average read normalised coverage of H3K4me1, H3K4me3 and their ratio in adult Amphimedon across a 4 kb interval centred on TSSs of lincRNAs. Each line of the heatmaps …
-
Figure 5—source data 1
Annotation of putative elincRNAs and plincRNAs.
- https://doi.org/10.7554/eLife.22194.026
Figure 5—figure supplement 1
Additional examples of plincRNAs and elincRNAs.
(A) Example of a lincRNA with promoter-like chromatin signature (plincRNA). For the definition of adult chromatin states see Figure 1A. Promoter-like lincRNA (blue) is shown, along with input …
Figure 6 with 5 supplements
Distal enhancer regulation at the dawn of animals.
(A) Overview of the computational filtering pipeline adopted to predict the putative Amphimedon activated enhancer-like elements. See main text and Materials and methods for details. (B) Heatmap …
-
Figure 6—source data 1
Genomic location of all the predicted activated enhancer-like elements and their distance to the closest TSS.
- https://doi.org/10.7554/eLife.22194.029
-
Figure 6—source data 2
Functional annotation of nearest neighbors genes of the adult predicted activated enhancer-like elements.
- https://doi.org/10.7554/eLife.22194.030
-
Figure 6—source data 3
Functional annotation of nearest neighbors genes of the larva predicted activated enhancer-like elements.
- https://doi.org/10.7554/eLife.22194.031
-
Figure 6—source data 4
GO term enrichment outcome for the nearest neighbors genes of the adult predicted activated enhancer-like elements (Hypergeometric test, FDR<0.01).
- https://doi.org/10.7554/eLife.22194.032
-
Figure 6—source data 5
GO term enrichment outcome for the nearest neighbors genes of the larva predicted activated enhancer-like elements (Hypergeometric test, FDR<0.01).
- https://doi.org/10.7554/eLife.22194.033
Figure 6—figure supplement 1
Activated enhancer-like elements have higher H3K4me1 than H3K4me3 levels.
(A) Enrichment of H3K4me1 (red) and H3K4me3 (blue) (ChIP versus input) at predicted activated enhancer-like elements (left) and TSSs (right), showing that activated enhancer-like elements have …
Figure 6—figure supplement 2
Examples of CEL-seq or RNA-seq expression detected at putative activated enhancer-like sites, suggesting that 1D eRNAs, which are generally polyadenylated (Natoli and Andrau, 2012; Li et al., 2016), might be transcribed from these regions.
Protein-coding genes (purple) are shown, along with input DNA-normalized coverage tracks of different histone modifications. Regions of enrichments (high confidence peaks, representing reproducible …
Figure 6—figure supplement 3
Additional sequence logos of the DNA motifs determined by MEME-ChIP analysis to be significantly enriched in the adult predicted activated enhancer-like sequences.
The E-value (log likelihood ratio of each motif) and the number of sites contributing to the construction of the motif are shown, respectively. The matched motif is shown on the top and the query …
Figure 6—figure supplement 4
Matching sequence logos of the DNA motifs determined by MEME-ChIP analysis to be significantly enriched in the predicted activated enhancer-like sequences in both adult and larva.
The E-value (log likelihood ratio of each motif) and the number of sites contributing to the construction of the motif are shown, respectively.
Figure 6—figure supplement 5
Examples of predicted enhancer-like elements in proximity of well-known developmental and transcription factor genes.
Protein-coding genes (purple) are shown, along with input DNA-normalized coverage of different histone modifications and RNA-seq expression. Regions of enrichments (high confidence peaks, …
Figure 7 with 1 supplement
Amphimedon enhancer-like elements are enriched in metazoan-specific microsyntenic units.
(A) Putative adult and larva enhancer-like signatures identified in the 60 metazoan-specific microsyntenic pairs investigated. (B) The cladogram represents known phylogenetic distribution of the Isl2…
-
Figure 7—source data 1
60 microsyntenic units representing functional gene linkages and presence-absence of chromatin states containing typical eumetazoan enhancer histone PTM patterns (‘EnhP’,’ EnhWk’,’ TxEnhA’) (adult only) and/or in silico predicted enhancer-like elements (both larva and adult).
- https://doi.org/10.7554/eLife.22194.040
Figure 7—figure supplement 1
Additional examples of predicted enhancer-like elements in conserved microsyntenic units.
Protein-coding genes (purple) are shown, along with input DNA-normalized coverage of different histone modifications and RNA-seq/CEL-seq expression. Regions of enrichments (high confidence peaks, …
Figure 8
Origin of animal cis-regulatory complexity.
The phylogenetic relationship of representative animal lineages and unicellular holozoans is shown here. Highlighted are the major genomic innovations that correlate with the emergence and early …
Additional files
-
Supplementary File 1
Primer sequences.
- https://doi.org/10.7554/eLife.22194.043
