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Rapid evolution of the embryonically-expressed homeobox gene LEUTX within primates

ABSTRACT: Rapid evolution of the embryonically-expressed homeobox gene LEUTX within primates

PROVIDER: PRJNA930750 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23319473_1.fastq.gz	Fastqsanger.gz
	SRR23319473_2.fastq.gz	Fastqsanger.gz
	SRR23319474_1.fastq.gz	Fastqsanger.gz
	SRR23319474_2.fastq.gz	Fastqsanger.gz
	SRR23319475_1.fastq.gz	Fastqsanger.gz

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Rapid evolution of the embryonically-expressed homeobox gene LEUTX within primates

Project description:LEUTX is a homeodomain transcription factor expressed in the very early embryo with a function around embryonic genome activation. The LEUTX gene is found only in eutherian mammals, including humans, but unlike the majority of homeobox genes, the encoded amino acid sequence is very different between divergent mammalian species. However, whether dynamic evolution has also occurred between closely related mammalian species remains unclear. In this work, we perform a comparative genomics study of LEUTX within the primates, revealing dramatic evolutionary sequence change between closely related species. Positive selection has acted on sites in the LEUTX protein, including six sites within the homeodomain; this suggests that selection may have driven changes in the set of downstream targets. Transfection into cell culture followed by transcriptomic analysis reveals small functional differences between human and marmoset LEUTX, suggesting rapid sequence evolution has fine-tuned the role of this homeodomain protein within the primates.

2023-02-06 | GSE224384 | GEO

Rapid Evolution of the Embryonically Expressed Homeobox Gene LEUTX within Primates.

Project description:LEUTX is a homeodomain transcription factor expressed in the very early embryo with a function around embryonic genome activation. The LEUTX gene is found only in eutherian mammals including humans but, unlike the majority of homeobox genes, the encoded amino acid sequence is very different between divergent mammalian species. However, whether dynamic evolution has also occurred between closely related mammalian species remains unclear. In this work, we perform a comparative genomics study of LEUTX within the primates, revealing dramatic evolutionary sequence change between closely related species. Positive selection has acted on sites in the LEUTX protein, including six sites within the homeodomain; this suggests that selection has driven changes in the set of downstream targets. Transfection into cell culture followed by transcriptomic analysis reveals small functional differences between human and marmoset LEUTX, suggesting rapid sequence evolution has fine-tuned the role of this homeodomain protein within the primates.

| S-EPMC10246821 | biostudies-literature

Rapid evolution of mammalian X-linked testis-expressed homeobox genes.

Project description:Homeobox genes encode transcription factors that function in various developmental processes and are usually evolutionarily conserved in their sequences. However, two X-chromosome-linked testis-expressed homeobox genes, one from rodents and the other from fruit flies, are known to evolve rapidly under positive Darwinian selection. Here we report yet another case, from primates. TGIFLX is an X-linked homeobox gene that originated by retroposition of the autosomal gene TGIF2, most likely in a common ancestor of rodents and primates. While TGIF2 is ubiquitously expressed, TGIFLX is exclusively expressed in adult testis. A comparison of the TGIFLX sequences among 16 anthropoid primates revealed a significantly higher rate of nonsynonymous nucleotide substitution (d(N)) than synonymous substitution (d(S)), strongly suggesting the action of positive selection. Although the high d(N)/d(S) ratio is most evident outside the homeobox, the homeobox has a d(N)/d(S) of approximately 0.89 and includes two codons that are likely under selection. Furthermore, the rate of radical amino acid substitutions that alter amino acid charge is significantly greater than that of conservative substitutions, suggesting that the selection promotes diversity of the protein charge profile. More interestingly, an analysis of 64 orthologous homeobox genes from humans and mice shows substantially higher rates of amino acid substitution in X-linked testis-expressed genes than in other genes. These results suggest a general pattern of rapid evolution of mammalian X-linked testis-expressed homeobox genes. Although the physiological function of and the exact selective agent on TGIFLX and other rapidly evolving homeobox genes are unclear, the common expression pattern of these transcription factor genes led us to conjecture that the selection is related to one or more aspects of male reproduction and may contribute to speciation.

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Primates

Project description:Primates

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Meis homeobox genes control cell competence within the eye-specified neuroepithelium (RNA-seq)

Project description:Meis homeobox genes control cell competence within the eye-specified neuroepithelium (RNA-seq)

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Meis homeobox genes control cell competence within the eye-specified neuroepithelium (ChIP-seq)

Project description:Meis homeobox genes control cell competence within the eye-specified neuroepithelium (ChIP-seq)

| PRJEB43136 | ENA

Primates

Project description:Primates Raw sequence reads