{"id":83240,"date":"2016-06-13T14:02:39","date_gmt":"2016-06-13T14:02:39","guid":{"rendered":"http:\/\/healthmedicinet.com\/i\/evolutionary-origin-and-functional-divergence-of-totipotent-cell-homeobox-genes-in-eutherian-mammals\/"},"modified":"2016-06-13T14:02:39","modified_gmt":"2016-06-13T14:02:39","slug":"evolutionary-origin-and-functional-divergence-of-totipotent-cell-homeobox-genes-in-eutherian-mammals","status":"publish","type":"post","link":"http:\/\/healthmedicinet.com\/i\/evolutionary-origin-and-functional-divergence-of-totipotent-cell-homeobox-genes-in-eutherian-mammals\/","title":{"rendered":"Evolutionary origin and functional divergence of totipotent cell homeobox genes in eutherian mammals"},"content":{"rendered":"

A defining feature of therian mammals (marsupials and placentals) is internal retention of the developing embryo, involving implantation, protection and active nourishment through specialised extra-embryonic tissues. Monotremes, birds and reptiles also have extra-embryonic tissues but generally do not face the same challenges of prolonged maternal retention and implantation. Extra-embryonic membranes are especially sophisticated in placental mammals which retain the developing embryo for longer than do marsupials. Key to the development of extra-embryonic membranes are the very earliest cell fate decisions made in development [34<\/a><\/span>]. After fertilization, a series of cell divisions produces a ball of identical cells, the morula. The end of the morula stage is marked by cellular compaction and the first cell fate decisions as a hollow blastocyst is generated, comprising an outer cell layer fated to become extraembryonic trophectoderm (which forms the majority of the foetal contribution to the placenta) around a multicellular inner cell mass. The inner cell mass rapidly undergoes a further cell fate decision to specify a second extraembryonic layer of cells (parietal endoderm which contributes to yolk sac) around the true embryonic cells or epiblast. The ETCHbox genes we analyse in this study, or at least their human and bovine orthologues, are expressed just prior to (and to a lesser extent during) these cell fate decisions that establish the critical distinctions between embryonic and extra-embryonic tissues of the mammalian embryo. This precise temporal pattern of gene expression suggests they are likely to have roles in the totipotent morula stage, when the necessary cellular conditions are established for cell fate specification, and subsequent mammalian development and pregnancy. The collective name we propose, ETCHbox genes, reflects their expression and evolutionary origin.<\/p>\n

In seeking to determine the precise molecular roles of these genes, the biggest challenges are practical and ethical issues concerning experimental manipulation of the earliest developmental stages of mammals, particularly humans. Mice cannot be used as straightforward models since, as we demonstrate, murid rodents have lost Argfx<\/em>, Dprx<\/em>, Leutx<\/em> and Pargfx<\/em>, and have undergone duplication and further radical sequence divergence of Tprx<\/em> genes. Lack of expression after blastocyst stage also precludes loss-of-function experiments in adult human cells. We therefore designed a gain-of-function approach, using transfection into primary fibroblast cells that do not normally express these genes. By using ectopic expression of ETCHbox genes in fibroblasts followed by high-throughput RNA-seq, we uncovered dramatic transcriptional changes driven by these genes. Most strikingly, many of the ETCHbox downstream genes that changed in expression (up or down) belong to a particular set of genes with a shared temporal profile in the human embryo, characterised by a sharp \u2018pulse\u2019 of high expression at the 8-cell to morula stages. This is precisely the stage of development when the ETCHbox genes themselves are expressed. This finding suggests that the ectopic expression experiment has most likely recapitulated some aspects of in vivo biological roles and allows us to gain insights into the functions of these newly evolved homeobox genes.<\/p>\n

We extract two main biological conclusions from the up- and down-regulated gene sets. First, we find that ARGFX<\/em> is acting antagonistically to LEUTX<\/em> and TPRX1<\/em> genes; together, these genes may shape the rapid on\/rapid off temporal profile of target genes, peaking just before the first cell fate decisions. The deployment of antagonistic regulators to effect precise modulation is a common feature of biological systems. Second, we identify putative downstream effectors, which may include direct and indirect transcriptional targets involved in developmental processes in humans. These include the gene encoding histone H2 variant HIST1H2BD<\/em> and the RELB<\/em> gene encoding a transcription factor in the NFkB pathway. Other developmentally-relevant genes up-regulated by ARGFX<\/em> and down-regulated by either LEUTX<\/em> or TPRX1<\/em> include the TGF?-responsive RHOB<\/em> gene and a gene encoding a signalling molecule HBEGF<\/em>. Expression profiles of several of these genes differ between human, cow and mouse, suggesting some target genes may differ across mammals (data not shown). Nonetheless, even though the kinetics of early development and genome activation differ between mammalian species, we detect a strong signal of conservation of downstream activity in cow, with 58\u00a0% of comparable bovine genes (19\/33) having similar expression profiles to human.<\/p>\n

It is striking that the evolutionary origin of most, and possibly all, ETCHbox genes dates precisely to the stem lineage of eutherian mammals. This date is inferred from finding orthologues of Argfx<\/em>, Dprx<\/em>, Leutx<\/em>, Tprx1<\/em> and Tprx2<\/em> in both the Atlantogenata and Boreoeutheria clades, and a Pargfx<\/em> gene or pseudogene in Boreoeutheria (Euarchontoglires and Laurasiatheria). None are found in monotremes or marsupials. The origin of the genes represents a particularly clear example of \u2018asymmetric\u2019 evolution, whereby after tandem gene duplication, one gene diverges little in sequence and retains the original role, while daughter genes diverge in sequence and function [14<\/a><\/span>]. In this case, the progenitor gene is Crx<\/em>, which retained its retinal function in mammals and changed little in amino acid sequence from Crx<\/em> of other vertebrates; the daughter genes, Argfx<\/em>, Dprx<\/em>, Leutx<\/em>, Tprx<\/em> and Pargfx<\/em>, diverged greatly in sequence and were recruited for novel early embryonic roles. The Crx<\/em> gene in non-mammalian species, notably Xenopus<\/em> and dogfish, is expressed in the early embryo in addition to the developing eye [35<\/a><\/span>\u201337<\/a><\/span>]. It is possible, therefore, that early embryonic expression was shared by the Crx<\/em> gene early in mammalian evolution when its tandem duplicates were formed, facilitating recruitment of the tandem duplicates to early embryonic expression. Asymmetric evolution is not seen in all cases of homeobox gene duplication, with many examples known of subtle evolutionary changes to daughter genes after a duplication events [3<\/a><\/span>, 38<\/a><\/span>, 39<\/a><\/span>]. It will be interesting to clarify the situations under which symmetric versus asymmetric evolution of transcription factor genes is favoured.<\/p>\n

It would be wrong, however, to characterise the origin of ETCHbox genes as a simple case of tandem duplication and divergence. Our comparative analyses of the genomic regions around these genes reveals a far more dynamic picture. Many mammals have lost genes, including the human lineage, which lost Pargfx<\/em>. Elephant, guinea pig, horse, bat, cow and pig have duplicated ETCHbox genes further, with murid rodents having an extreme combination of gene loss and additional duplication. In addition, we detect evidence for ghost ETCHbox loci, inferred from the presence of characteristic CNEs without associated genes. Furthermore, in at least two cases, the parental Crx<\/em> gene has continued to spawn duplicates, with recent pseudogenes found in tenrecs and murid rodents. Also nearby are other multigene families, including the extensive leukocyte receptor complex, a dynamic cluster of immunoglobulin-like receptor genes with copy number variation in humans [22<\/a><\/span>], and large arrays of C2H2 zinc finger genes [40<\/a><\/span>]. The different gene components between species may seem in conflict with proposed critical roles in early developmental events; this may be reconciled by the partial redundancy we detect between LEUTX<\/em> and TPRX1<\/em> in humans, and the observation that all placental mammals analysed retain at least one Tprx<\/em> gene copy.<\/p>\n

Taken together, these data paint a picture of a complex and unstable chromosomal region that has been expanding and contracting extensively since the origin of placental mammals, spawning and deleting genes in its wake. The mechanism is unknown, but may be related to the low density of recombination hotspots in this region (the long arm of human chromosome 19), which may facilitate unequal cross-over [10<\/a><\/span>, 41<\/a><\/span>], together with a high density of long interspersed nuclear elements that could promote tandem gene duplication [40<\/a><\/span>, 42<\/a><\/span>]. Human chromosome 19 also has an elevated GC content [40<\/a><\/span>, 43<\/a><\/span>]. Whatever the mechanisms, we propose that this chromosomal region has been a hotspot for tandem gene duplication and gene loss for over 70 million years. We liken this unusual genomic region to a site of tectonic activity, where geologically unstable regions spawn or swallow the earth\u2019s crust. One important result of \u2018genomic volcanism\u2019 was the birth of the ETCHbox genes, which were recruited for novel roles in mammalian embryogenesis, facilitating the formation of sophisticated extra-embryonic membranes necessary for internal development in placental mammals.<\/p>\n","protected":false},"excerpt":{"rendered":"

A defining feature of therian mammals (marsupials and placentals) is internal retention of the developing embryo, involving implantation, protection and active nourishment through specialised extra-embryonic tissues. Monotremes, birds and reptiles also have extra-embryonic tissues but generally do not face the same challenges of prolonged maternal retention and implantation. Extra-embryonic membranes are especially sophisticated in placental Read More<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[],"tags":[],"class_list":["post-83240","post","type-post","status-publish","format-standard","hentry"],"_links":{"self":[{"href":"http:\/\/healthmedicinet.com\/i\/wp-json\/wp\/v2\/posts\/83240","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/healthmedicinet.com\/i\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/healthmedicinet.com\/i\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/healthmedicinet.com\/i\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/healthmedicinet.com\/i\/wp-json\/wp\/v2\/comments?post=83240"}],"version-history":[{"count":0,"href":"http:\/\/healthmedicinet.com\/i\/wp-json\/wp\/v2\/posts\/83240\/revisions"}],"wp:attachment":[{"href":"http:\/\/healthmedicinet.com\/i\/wp-json\/wp\/v2\/media?parent=83240"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/healthmedicinet.com\/i\/wp-json\/wp\/v2\/categories?post=83240"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/healthmedicinet.com\/i\/wp-json\/wp\/v2\/tags?post=83240"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}