Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory.

Alessandro Bertero,Charles E Murry,Lil Pabon,Vijay Ramani,William S Noble,Paul A Fields,Galip G Yardimci,Giancarlo Bonora,Jay Shendure,Hans Reinecke

doi:10.1038/s41467-019-09483-5

Alessandro Bertero, Charles E Murry + Show 8 more

Open Access

https://doi.org/10.1038/s41467-019-09483-5

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Abstract

Functional changes in spatial genome organization during human development are poorly understood. Here we report a comprehensive profile of nuclear dynamics during human cardiogenesis from pluripotent stem cells by integrating Hi-C, RNA-seq and ATAC-seq. While chromatin accessibility and gene expression show complex on/off dynamics, large-scale genome architecture changes are mostly unidirectional. Many large cardiac genes transition from a repressive to an active compartment during differentiation, coincident with upregulation. We identify a network of such gene loci that increase their association inter-chromosomally, and are targets of the muscle-specific splicing factor RBM20. Genome editing studies show that TTN pre-mRNA, the main RBM20-regulated transcript in the heart, nucleates RBM20 foci that drive spatial proximity between the TTN locus and other inter-chromosomal RBM20 targets such as CACNA1C and CAMK2D. This mechanism promotes RBM20-dependent alternative splicing of the resulting transcripts, indicating the existence of a cardiac-specific trans-interacting chromatin domain (TID) functioning as a splicing factory.

Highlights

Functional changes in spatial genome organization during human development are poorly understood
Further we find that genomic regions dynamically regulated during human pluripotent stem cells (hPSCs)-cardiomyocyte differentiation resolve to a state that closely resembles that of human fetal cardiomyocytes, indicating these dynamics likely reflect early steps in human cardiogenesis
This study provides a comprehensive integration of Hi-C, RNAseq, and ATAC-seq across a defined time course of human hPSC differentiation into cardiomyocytes, which demonstrates the dynamic interplay of local and global chromatin structure on gene regulation during cell fate transitions

Summary

Introduction

Functional changes in spatial genome organization during human development are poorly understood. Genome editing studies show that TTN pre-mRNA, the main RBM20-regulated transcript in the heart, nucleates RBM20 foci that drive spatial proximity between the TTN locus and other interchromosomal RBM20 targets such as CACNA1C and CAMK2D This mechanism promotes RBM20-dependent alternative splicing of the resulting transcripts, indicating the existence of a cardiac-specific trans-interacting chromatin domain (TID) functioning as a splicing factory. Chromosome conformation capture technologies such as Hi-C have identified complex three-dimensional dynamics during development, and abnormal chromosomal architecture has been implicated in a range of diseases, including cancer and limb malformations[4,5,6,7,8] While these studies have demonstrated regulated regions of chromosomes, how these transitions occur temporally across multiple stages of human lineage commitment remains to be addressed. This study demonstrates the dynamic interplay between global and local chromatin architecture during human development and exemplifies how this can influence gene expression patterns

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