Figure 1.
Two round expansions and a fish specific duplication of HES/HEY in all the species.
The phylogenetic relationship of all the species investigated is in the left. The number of HES/HEY genes is in the right. Two round expansions and a fish specific duplication of HES/HEY are represented by arrows and bars.
Table 1.
Human 13 HES/HEY genes.
Figure 2.
Unrooted Neighbor-Joining and Bayesian phylogenetic tree of HES/HEY genes.
The trees were inferred by the Neighbor-Joining (NJ) with JTT model (A) and Bayesian (B) based on amino acid sequences of the bHLH and Orange domains. Colors denote different subgroups of HES/HEY, crimson: HEY1/2/L, dark green: V-DEC1/2, deep yellow: HESL, cyaneous: HES1/4, red: HES3, pink: HES6, prasinous: HES2, light blue: HES7, purple: HES5. Some species specific HES clusters including NvHES, DmHES, and BfHES were in black. Numbers in brackets refer to the numbers of the sequences in these species specific clusters. Nv, Dm and Bf are the abbreviations of Nematostella vectensis, Drosophila melanogaster and Branchiostoma floridae.
Figure 3.
Phylogenetic tree and gene structure of HES/HEY genes.
(A) Phylogenetic tree of HES/HEY genes were reconstructed by Mrbayes software. (B) The exon-intron structures of the HES/HEY genes in human, zebrafish, fruit fly, C. elegans, sea anemone and Sponge. Filled boxes: red for bHLH domain, orange for Orange domain, purple region with a star (*) on it represent the WRPW motif, blue region with an arrow (↓) on it represents YXXW motif; white boxes for other exon regions; and lines for introns. Numbers 0, 1, and 2: exon phases. The lengths of the boxes and lines are scaled based on the length of genes. The long introns, UTRs and exons were denoted by “//”. Numbers in the bracket of the compressed clades are the number of genes in those clades. Abbreviations of species names are in the following. Hs: Homo sapiens, Dr: Danio rerio, Dm: Drosophila melanogaster, Ce: Caenorhabditis elegans, Nv: Nematostella vectensis.
Figure 4.
The sequence logos of three conserved motifs in subgroups of HES/HEY genes.
The Motif 1 was created using an alignment of HEY1/2/L sequences near bHLH domain. The similar process was used to get Motif 2 (DEC1/2 sequence near Orange domain) and Motif 3 (DEC1 sequence in C-terminal). The overall height of each stack indicates the sequence conservation at that position, whereas the height of symbols within each stack reflects the relative frequency of the corresponding amino acid.
Figure 5.
Zebrafish HES/HEY gene loci and expression pattern.
(A) The gene loci of the zebrafish HES2, HES6, HES5 and HES7 genes. The arrows towards the right referred the gene on the positive-strand (+). The arrows towards the left referred the gene on the negative-strand (−). We cut short the Ensembl protein ID to reserve the last six digits in this diagram. For example, ENSDARP00000123627 is truncated as Dr123627. (B) Expression of HES7 genes in zebrafish. Transcripts of ENSDARP00000023627, ENSDARP00000006074, ENSDARP00000027076, ENSDARP00000017640 and β-actin were detected by RT-PCR. Lane 1 showed the molecular weight marker of 100 bp ladder. Gene expression patterns were obtained using total RNAs extracted from eye (lane 2), gill (lane 3), female ovary (lane 4), male testis (lanes 5), heart (lanes 6), and liver (lane 7). β-actin was performed to assess quantitative variations in mRNAs among all the samples.
Figure 6.
The alignment of the promoter, 5′ UTR and protein sequences in zebrafish HES5.
(A) Multiple sequence alignment of the promoter sequences of zebrafish HES5 genes using the ClustalX2. The TATA box was circled by purple box. (B) Alignment of 5′ UTR sequence of zebrafish HES5 genes. (C) Alignment of zebrafish HES5 protein sequences.
Figure 7.
A model for the evolutionary process of the HES/HEY gene family.
Filled boxes of the gene exon-intron structure: red represent bHLH domain, orange represent Orange domain, purple represent WRPW motif, blue represent YXXW motif; white boxes: other exon regions; lines: introns. Numbers 0, 1, and 2: exon phases. The length of the boxes and lines are scaled based on the length of genes. The transparent faint red boxes above exons or introns indicate the fused exons or lost exons.