Research Article

Acoel genome reveals the regulatory landscape of whole-body regeneration

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Science  15 Mar 2019:
Vol. 363, Issue 6432, eaau6173
DOI: 10.1126/science.aau6173

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Acoel-regeneration regulatory landscapes

Some animals, including some types of worms, can undergo whole-body regeneration and replace virtually any missing cell type. Gehrke et al. sequenced and assembled the genome of Hofstenia miamia, a regenerative acoel worm species (see the Perspective by Alonge and Schatz). They identified a variable motif corresponding to regulation of the early growth response (egr) gene that was involved in regeneration. RNA interference experiments and validation in a second species showed that the protein Egr is a pioneer factor that stimulates regeneration.

Science, this issue p. eaau6173; see also p. 1152

Structured Abstract

INTRODUCTION

Although all animals can heal wounds, some are capable of reconstructing their entire bodies from small fragments of the original organism. Whole-body regeneration requires the interplay of wound signaling, stem cell dynamics, and positional identity, all of which have been investigated at the protein-coding level of the genome. Little is known about how the noncoding portion of the genome responds to wounding to control gene expression and to launch the process of whole-body regeneration. Understanding how these control points (regulatory regions) are activated and then operate during regeneration would uncover how genes connect into networks, ultimately restructuring entire body axes. Networks of transcriptional regulatory genes can reveal important mechanisms for how animals can grow new skin, muscles, or even entire brains.

RATIONALE

To identify regulatory regions involved in whole-body regeneration, we sequenced the genome of the highly regenerative acoel Hofstenia miamia, commonly known as the three-banded panther worm. Equipped with this genome, we reasoned that applying the assay for transposase-accessible chromatin using sequencing (ATAC-seq) would identify regulatory regions that change in response to amputation and during whole-body regeneration. Further, by analyzing the sequence motifs contained within these regulatory regions, we sought to predict which transcription factors (TFs) control regeneration gene networks.

RESULTS

The Hofstenia genome assembly totals 950 megabases of sequence, with sufficient contiguity for functional genomics. ATAC-seq data revealed thousands of chromatin regions that respond dynamically during regeneration. A genome-wide scan for TF binding motifs in these regions identified the EGR (early growth response) motif as the most dynamic. By combining RNA interference (RNAi) and RNA-seq, we predicted a set of Egr target genes in Hofstenia. We found that most of these target genes contained EGR binding motifs in neighboring regions of regeneration-responsive chromatin, which failed to respond under egr-RNAi. This functional validation allowed us to build a gene regulatory network (GRN) with Egr as a direct master regulator of downstream regeneration genes. Lastly, by quantifying the binding probabilities of TFs at individual motifs, we identified targets of TFs further downstream of Egr, extending the regeneration GRN.

CONCLUSION

Using our regulatory data, we inferred a GRN for launching whole-body regeneration in the acoel H. miamia, where the master regulator Egr acts as a putative pioneer factor to directly activate wound-induced genes. This network includes homologs of genes that are involved in regeneration in other species, suggesting that it can serve as a template for direct comparisons of regeneration pathways across distantly related animals. Our approach of combining genome-wide assays for chromatin accessibility with functional studies can be applied to extend the network further in time in Hofstenia regeneration and to construct GRNs for regeneration in other systems.

The regulatory landscape of whole-body regeneration.

Hofstenia represents the sister-lineage of other bilaterians and regenerates extensively. We sequenced the genome of H. miamia and used ATAC-seq to identify thousands of regeneration-responsive regions of chromatin. Combining motif analysis, ATAC-seq, and RNAi, we identified Egr as a master regulator of regeneration in Hofstenia and inferred an Egr-controlled GRN for regeneration.

Abstract

Whole-body regeneration is accompanied by complex transcriptomic changes, yet the chromatin regulatory landscapes that mediate this dynamic response remain unexplored. To decipher the regulatory logic that orchestrates regeneration, we sequenced the genome of the acoel worm Hofstenia miamia, a highly regenerative member of the sister lineage of other bilaterians. Epigenomic profiling revealed thousands of regeneration-responsive chromatin regions and identified dynamically bound transcription factor motifs, with the early growth response (EGR) binding site as the most variably accessible during Hofstenia regeneration. Combining egr inhibition with chromatin profiling suggests that Egr functions as a pioneer factor to directly regulate early wound-induced genes. The genetic connections inferred by this approach allowed the construction of a gene regulatory network for whole-body regeneration, enabling genomics-based comparisons of regeneration across species.

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