Probing and rearranging the transcription factor network controlling the C. elegans endoderm

Abstract

The ELT-2 GATA factor is the predominant transcription factor regulating gene expression in the C. elegans intestine, following endoderm specification. We comment on our previous study (Wiesenfahrt et al., 2016) that investigated how the elt-2 gene is controlled by END-1, END-3 and ELT-7, the 3 endoderm specific GATA factors that lie upstream in the regulatory hierarchy. We also discuss the unexpected result that ELT-2, if expressed sufficiently early and at sufficiently high levels, can specify the C. elegans endoderm, replacing the normal functions of END-1 and END-3.

Keywords: C. elegans; ELT-2; ELT-7; END-1; END-3; GATA factor; gene regulation; intestine; transcription.

Figure 1.

The regulatory network that specifies and differentiates the C. elegans endoderm consists of a cascade of 4 GATA-type transcription factors: END-3, END-1, ELT-7 and ELT-2 in order of appearance. The time scale of early C. elegans embryogenesis is shown at left (minutes at 20°C after the first cell division). In the center are shown 3 differential interference contrast images of early C. elegans embryos, at the 1E, 2E and 4E cell stage from top to bottom; E cell nuclei are marked with white dots. Arrows indicate both proposed and established regulatory relations between the 4 GATA factors, as well as between the 4 GATA factors and genes expressed in the differentiated intestine. (From Wiesenfahrt et al.⁴).

Figure 2.

Features of the C. elegans elt-2 promoter. Dot matrix comparisons (EMBOSS dotmatcher) between 6 kb upstream of the C. elegans elt-2 ATG initiation codon and the corresponding 6 kb upstream of the elt-2 homologs in C. briggsae (upper), C. remanei (middle) and C. japonicum (lower). The dot matrix diagonals observed in the C. briggsae and C. remanei comparisons indicate 3 conserved regions (CR I, CR II and CR III); in the (reduced stringency) comparison with the more distantly related C. japonicum, CR III appears the most highly conserved region. The dot matrix plots are aligned with the genomic region containing the C. elegans elt-2 gene, showing the upstream elt-4 gene, the uncharacterized ORF C39B10.7 that appears to overlap with CR III, 2 genomic deletions (ca16 and gk153) that have no obvious effects on elt-2 expression, the elt-2 transcription start site (TSS) and the elt-2 coding region itself. TGATAA sites are indicated by black triangles, WGATAR sites that are not TGATAA sites are indicated by open circles and the unique TGATAA “A” site identified by Du et al. is indicated by an asterisk. ELT-2 ChIP-seq reveals 3 regions of high ELT-2 occupancy that align with the 3 conserved regions: solid bars represent peaks called as significant, defined in .

Figure 3.

Schematic alignment between the ELT-2 protein and the END-1 and END-3 proteins. The highest degree of conservation (52–56% identical residues) is found in the zinc finger DNA binding domain (dark gray). The adjacent 25 amino acid basic region (light gray) shows lower levels of conservation (24% identical residues). Remaining regions of the proteins (unshaded) show low levels of conservation. The number of amino acid residues in each protein is shown beside their respective C-termini.