Dynamics of Cardiomyocyte Transcriptome and Chromatin Landscape Demarcates Key Events of Heart Development

Abstract

29The development of an organ involves dynamic regulation of gene transcription and complex multi-30 pathway interactions. To better understand transcriptional regulatory mechanism driving heart 31 development and the consequences of its disruption, we isolated cardiomyocytes (CMs) from wild-32 type zebrafish embryos at 24, 48 and 72 hours post fertilization corresponding to heart looping, 33 chamber formation and heart maturation, and from mutant lines carrying loss-of-function mutations in 34 gata5, tbx5a and hand2, transcription factors (TFs) required for proper heart development. The 35 integration of CM transcriptomics (RNA-seq) and genome-wide chromatin accessibility maps 36 (ATAC-seq) unravelled dynamic regulatory networks driving crucial events of heart development. 37These networks contained key cardiac TFs including Gata5/6, Nkx2.5, Tbx5/20, and Hand2, and are 38 associated with open chromatin regions enriched for DNA sequence motifs belonging to the family of 39 the corresponding TFs. These networks were disrupted in cardiac TF mutants, indicating their 40 importance in proper heart development. The most prominent gene expression changes, which 41 correlated with chromatin accessibility modifications within their proximal promoter regions, 42 occurred between heart looping and chamber formation, and were associated with metabolic and 43 hematopoietic/cardiac switch during CM maturation. Furthermore, loss of function of cardiac TFs 44 Gata5, Tbx5a, and Hand2 affected the cardiac regulatory networks and caused global changes in 45 chromatin accessibility profile. Among regions with differential chromatin accessibility in mutants 46were highly conserved non-coding elements which represent putative cis regulatory elements with 47 65 CMs are specified early during embryogenesis and undergo various cellular processes of proliferation, 66 migration, and differentiation which collectively give rise to a fully formed and functioning heart. 67Crucial to regulating each step of heart morphogenesis are cardiac transcription factors (TFs) which 68 include Nkx2.5, Gata5, Tbx5, and Hand2 (Clark et al. 2006;Nemer 2008). These TFs are known to 69 play a role in establishing the CM identity of mesodermal progenitor cells, regulating the formation 70 and looping of the heart tube, as well as the specification of atrial and ventricular CMs. Specification 71 and differentiation of the cardiac progenitors are regulated by the interactions between several key 72 TFs -Nkx2.5, Gata5, Tbx5, and Hand2. Members of the GATA family of TFs, Gata4, Gata5, and 73Gata6, are responsible for the earliest step of cardiac progenitor specification (Jiang and Evans 1996; 74 Jiang et al. 1998;Reiter et al. 1999;Singh et al. 2010;Lou et al. 2011;Turbendian et al. 2013). Gata 75 factors activate the expression of nkx2.5, another early marker of CMs (Chen and Fishman 1996; Lien 76 et al. 1999). Although not essential for specification of CMs, Nkx2.5 plays an important role in 77 initiating the expression of many cardiac genes in mouse ...

Semaphorin3f as a cardiomyocyte derived regulator of heart chamber development

“…1). These data indicate that mRNA for a secreted Sema is expressed by cardiomyocytes at the time they undergo differentiation, and agree with reported RNAseq analysis of FACs-isolated zebrafish cardiomyocytes, where sema3fb mRNA is enriched in the heart over the rest of the embryo [47].…”

The tissue-specific chromatin accessibility landscape of Papaver somniferum

“…ATAC-seq method, which uses a hyperactive Tn5 transposase that is preloaded with sequencing adapters as a probe for chromatin accessibility, provides a valuable technique for investigating the chromatin accessibility in the scope of the genome (Buenrostro et al ., 2015). ATAC-seq has been successfully applied in mammals, certain plants, and fungi (Lu et al ., 2017, Maher et al ., 2018, Sijacic et al ., 2018, Klemm et al ., 2019, Pawlak et al ., 2019, Chen et al ., 2021).…”

“…ATAC-seq has been successfully applied in mammals, certain plants, and fungi (Lu et al, 2017, Maher et al, 2018, Sijacic et al, 2018, Klemm et al, 2019, Pawlak et al, 2019.…”

“…At present, the assay for transposase accessible chromatin sequencing (ATAC-seq) is being developed as an alternative approach for detecting the highly ACRs and then identifying TF-binding sites within these regions. ATAC-seq has been widely employed in recent years for large-scale identification of open chromatin in mammals, fungi and plants as a quicker and more efficient approach (Lu et al, 2017, Maher et al, 2018, Sijacic et al, 2018, Klemm et al, 2019, Pawlak et al, 2019, however, there has been no report regarding P. somniferum.…”

“…At present, the assay for transposase accessible chromatin sequencing (ATAC-seq) is being developed as an alternative approach for detecting the highly ACRs and then identifying TF-binding sites within these regions. ATAC-seq has been widely employed in recent years for large-scale identification of open chromatin in mammals, fungi and plants as a quicker and more efficient approach (Lu et al ., 2017, Maher et al ., 2018, Sijacic et al ., 2018, Klemm et al ., 2019, Pawlak et al ., 2019, Chen et al ., 2021), however, there has been no report regarding P. somniferum . Herein, we conducted comprehensive tissue-specific assay for ATAC-seq and transcriptome sequencing (RNA-seq) analysis of six different tissues in opium poppy to dissect the epigenetic and transcriptional regulation mechanisms for plant development and secondary metabolism.…”