http://orcid.org/0000-0001-5111-8816 http://orcid.org/0000-0001-5111-8816
Figures & data
Figure 1. Early evolution of animal long non-coding RNAs: Insights from the sponge Amphimedon queenslandica. (A) Despite a growing number of lncRNAs having been identified in bilaterian animals, the systematic investigation of lncRNAs in non-bilaterian animals has been lagging behind and, thus, we lack an understanding of their origin and early evolution. Yellow background highlights the animal kingdom. (B) and (C) Identification of Amphimedon lncRNAs. (B) Schematic representation of the Amphimedon queenslandica life cycle. Larvae emerge from maternal brood chambers and then swim in the water column as precompetent larvae before they develop competence to settle and initiate metamorphosis. Upon settling, the larva adopts a flattened morphology as it metamorphoses into a juvenile, which displays the hallmarks of the adult body plan. This juvenile will grow and mature into a benthic adult [Citation121]. Adapted from [Citation23]. (C) Developmental expression profiles of Amphimedon lncRNAs. Expression profiles of the top 50 differentially expressed lncRNAs during the transition from pelagic swimming competent larva to benthic juvenile. Each row represents data for one lncRNA. Pelagic stages include precompetent (P) and competent (C) larva; benthic stages include juvenile (J) and adult (A). Red indicates high expression level, light blue low expression. Adapted from [Citation23].
![Figure 1. Early evolution of animal long non-coding RNAs: Insights from the sponge Amphimedon queenslandica. (A) Despite a growing number of lncRNAs having been identified in bilaterian animals, the systematic investigation of lncRNAs in non-bilaterian animals has been lagging behind and, thus, we lack an understanding of their origin and early evolution. Yellow background highlights the animal kingdom. (B) and (C) Identification of Amphimedon lncRNAs. (B) Schematic representation of the Amphimedon queenslandica life cycle. Larvae emerge from maternal brood chambers and then swim in the water column as precompetent larvae before they develop competence to settle and initiate metamorphosis. Upon settling, the larva adopts a flattened morphology as it metamorphoses into a juvenile, which displays the hallmarks of the adult body plan. This juvenile will grow and mature into a benthic adult [Citation121]. Adapted from [Citation23]. (C) Developmental expression profiles of Amphimedon lncRNAs. Expression profiles of the top 50 differentially expressed lncRNAs during the transition from pelagic swimming competent larva to benthic juvenile. Each row represents data for one lncRNA. Pelagic stages include precompetent (P) and competent (C) larva; benthic stages include juvenile (J) and adult (A). Red indicates high expression level, light blue low expression. Adapted from [Citation23].](/cms/asset/ee44679a-e724-415b-bac0-a1b40f5d0dce/krnb_a_1460166_f0001_oc.jpg)
Figure 2. Long non-coding RNAs are defined by specific chromatin signatures. (A) Recent analyses [Citation94,Citation96,Citation101] of non-coding regulatory DNA and histone marks have revealed that some cis-regulatory mechanisms, such as those associated with proximal promoters, are present in non-metazoan holozoans (right panel) while others appear to be metazoan innovations, most notably distal enhancer regulation (left panel). Shown is a schematic representation of the presence or absence of the typical chromatin signatures associated with animal distal enhancer elements [the transcriptional cofactor p300, histone 3 lysine 4 monomethylation (H3K4me1), histone 3 lysine 27 acetylation (H3K27ac), and ATAC site]. Adapted from [Citation122]. (B) LincRNAs can be separated in two distinct populations of polyadenylated transcripts based on the chromatin status at their transcription-start sites. Shown is the enrichment of H3K4me1 (left) and H3K4me3 (right) (ChIP versus input) at enhancer-associated and promoter-like lincRNAs, respectively.
![Figure 2. Long non-coding RNAs are defined by specific chromatin signatures. (A) Recent analyses [Citation94,Citation96,Citation101] of non-coding regulatory DNA and histone marks have revealed that some cis-regulatory mechanisms, such as those associated with proximal promoters, are present in non-metazoan holozoans (right panel) while others appear to be metazoan innovations, most notably distal enhancer regulation (left panel). Shown is a schematic representation of the presence or absence of the typical chromatin signatures associated with animal distal enhancer elements [the transcriptional cofactor p300, histone 3 lysine 4 monomethylation (H3K4me1), histone 3 lysine 27 acetylation (H3K27ac), and ATAC site]. Adapted from [Citation122]. (B) LincRNAs can be separated in two distinct populations of polyadenylated transcripts based on the chromatin status at their transcription-start sites. Shown is the enrichment of H3K4me1 (left) and H3K4me3 (right) (ChIP versus input) at enhancer-associated and promoter-like lincRNAs, respectively.](/cms/asset/9d4416d3-fe8e-425b-b8dc-b6e5a595401c/krnb_a_1460166_f0002_oc.jpg)