Darío G. Lupiáñez

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

Mammalian genomes are organized into megabase-scale topologically associated domains (TADs). We demonstrate that disruption of TADs can rewire long-range regulatory architecture and result in pathogenic phenotypes. We show that distinct human limb malformations are caused by deletions, inversions, or duplications altering the structure of the TAD-spanning WNT6/IHH/EPHA4/PAX3 locus. Using CRISPR/Cas genome editing, we generated mice with corresponding rearrangements. Both in mouse limb tissue and patient-derived fibroblasts, disease-relevant structural changes cause ectopic interactions between promoters and non-coding DNA, and a cluster of limb enhancers normally associated with Epha4 is misplaced relative to TAD boundaries and drives ectopic limb expression of another gene in the locus. This rewiring occurred only if the variant disrupted a CTCF-associated boundary domain. Our results demonstrate the functional importance of TADs for orchestrating gene expression via genome architecture and indicate criteria for predicting the pathogenicity of human structural variants, particularly in non-coding regions of the human genome.

Breaking TADs: How Alterations of Chromatin Domains Result in Disease

Spatial organization is an inherent property of the vertebrate genome to accommodate the roughly 2m of DNA in the nucleus of a cell. In this nonrandom organization, topologically associating domains (TADs) emerge as a fundamental structural unit that is thought to guide regulatory elements to their cognate promoters. In this review we summarize the most recent findings about TADs and the boundary regions separating them. We discuss how the disruption of these structures by genomic rearrangements can result in gene misexpression and disease.

A MicroRNA (mmu-miR-124) Prevents Sox9 Expression in Developing Mouse Ovarian Cells

ABSTRACT In mammals, sex differentiation depends on gonad development, which is controlled by two groups of sex-determining genes that promote one gonadal sex and antagonize the opposite one. SOX9 plays a key role during testis development in all studied vertebrates, whereas it is kept inactive in the XX gonad at the critical time of sex determination, otherwise, ovary-to-testis gonadal sex reversal occurs. However, molecular mechanisms underlying repression of Sox9 at the beginning of ovarian development, as well as other important aspects of gonad organogenesis, remain largely unknown. Because there is indirect evidence that micro-RNAs (miRNA) are necessary for testicular function, the possible involvement of miRNAs in mammalian sex determination deserved further research. Using microarray technology, we have identified 22 miRNAs showing sex-specific expression in the developing gonads during the critical period of sex determination. Bioinformatics analyses led to the identification of miR-124 as the candidate gene for ovarian development. We knocked down or overexpressed miR-124 in primary gonadal cell cultures and observed that miR-124 is sufficient to induce the repression of both SOX9 translation and transcription in ovarian cells. Our results provide the first evidence of the involvement of a miRNA in the regulation of the gene controlling gonad development and sex determination. The miRNA microarray data reported here will help promote further research in this field, to unravel the role of other miRNAs in the genetic control of mammalian sex determination.

Identification of Live Germ-Cell Desquamation as a Major Mechanism of Seasonal Testis Regression in Mammals: A Study in the Iberian Mole (Talpa occidentalis)

ABSTRACT In males of seasonally breeding species, testes undergo a severe involution at the end of the breeding season, with a major volume decrease due to massive germ-cell depletion associated with photoperiod-dependent reduced levels of testosterone and gonadotropins. Although it has been repeatedly suggested that apoptosis is the principal effector of testicular regression in vertebrates, recent studies do not support this hypothesis in some mammals. The purpose of our work is to discover alternative mechanisms of testis regression in these species. In this paper, we have performed a morphological, hormonal, ultrastructural, molecular, and functional study of the mechanism of testicular regression and the role that cell junctions play in the cell-content dynamics of the testis of the Iberian mole, Talpa occidentalis, throughout the seasonal breeding cycle. Desquamation of live, nonapoptotic germ cells has been identified here as a new mechanism for seasonal testis involution in mammals, indicating that testis regression is regulated by modulating the expression and distribution of the cell-adhesion molecules in the seminiferous epithelium. During this process, which is mediated by low intratesticular testosterone levels, Sertoli cells lose their nursing and supporting function, as well as the impermeability of the blood-testis barrier. Our results contradict the current paradigm that apoptosis is the major testis regression effector in vertebrates, as it is clearly not true in all mammals. The new testis regression mechanism described here for the mole could then be generalized to other mammalian species. Available data from some previously studied mammals should be reevaluated.

Exome sequencing and CRISPR/Cas genome editing identify mutations of ZAK as a cause of limb defects in humans and mice

The CRISPR/Cas technology enables targeted genome editing and the rapid generation of transgenic animal models for the study of human genetic disorders. Here we describe an autosomal recessive human disease in two unrelated families characterized by a split-foot defect, nail abnormalities of the hands, and hearing loss, due to mutations disrupting the SAM domain of the protein kinase ZAK. ZAK is a member of the MAPKKK family with no known role in limb development. We show that Zak is expressed in the developing limbs and that a CRISPR/Cas-mediated knockout of the two Zak isoforms is embryonically lethal in mice. In contrast, a deletion of the SAM domain induces a complex hindlimb defect associated with down-regulation of Trp63, a known split-hand/split-foot malformation disease gene. Our results identify ZAK as a key player in mammalian limb patterning and demonstrate the rapid utility of CRISPR/Cas genome editing to assign causality to human mutations in the mouse in <10 wk.

Composition and dosage of a multipartite enhancer cluster control developmental expression of Ihh (Indian hedgehog)

Copy number variations (CNVs) often include noncoding sequences and putative enhancers, but how these rearrangements induce disease is poorly understood. Here we investigate CNVs involving the regulatory landscape of IHH (encoding Indian hedgehog), which cause multiple, highly localized phenotypes including craniosynostosis and synpolydactyly. We show through transgenic reporter and genome-editing studies in mice that Ihh is regulated by a constellation of at least nine enhancers with individual tissue specificities in the digit anlagen, growth plates, skull sutures and fingertips. Consecutive deletions, resulting in growth defects of the skull and long bones, showed that these enhancers function in an additive manner. Duplications, in contrast, caused not only dose-dependent upregulation but also misexpression of Ihh, leading to abnormal phalanges, fusion of sutures and syndactyly. Thus, precise spatiotemporal control of developmental gene expression is achieved by complex multipartite enhancer ensembles. Alterations in the composition of such clusters can result in gene misexpression and disease.

The spatio-temporal pattern of testis organogenesis in mammals - insights from the mole.

Some cellular events are crucial in testis organogenesis, including Sertoli and Leydig cell differentiation, mesonephric cell migration and testis cord formation. These processes are controlled by transcription factors, paracrine signalling and hormones. Using the mole species Talpa occidentalis as an alternative animal model, we report the expression patterns of nine genes during testis differentiation and analyse their implications in the above-mentioned cellular processes. We show that: 1) Sertoli cell differentiation occurs very early and precedes mesonephric cell migration, indicating that the latter is not needed for the endocrine cytodifferentiation of Sertoli cells; 2) the time of Leydig cell differentiation is consistent with the participation of PDGFR-alpha in promoting the migration and/or proliferation of Leydig cell precursors, and with that of WNT4 signalling in inhibiting Leydig cell differentiation and 3) the formation of the tunica albuginea involves intragonadal cell migration/movement. These results demonstrate that testicular organogenesis in the mole differs from that in the mouse in some particular aspects, thus providing evidence that the spatio-temporal pattern of testis development is not highly conserved during mammalian evolution.

Meiosis onset is postponed to postnatal stages during ovotestis development in female moles.

In mammals, germ cells are important both during development and for the function of female gonads, whereas male gonads may develop in the absence of germ cells. The gonads of female moles (genus Talpa) develop according to a testis-like pattern which results in the formation of ovotestes. In this paper, we studied the expression pattern of several pre-meiotic and meiotic germ cell markers, in order to establish the precise time of meiosis onset in the mole species T. occidentalis, and to investigate the location and possible role of germ cells in ovotestis organogenesis. Our results evidenced that: (1) the asymmetrical distribution of primordial germ cells, which concentrate in the cortex of the XX gonad, is brought about by germ cell depletion from the medulla between the s5a and s5b stages, (2) XX germ cells enter meiosis postnatally, which is quite exceptional among eutherian mammals, and (3) XX but not XY germ cells of moles express DMRT1 during premeiotic stages of development, an expression pattern not described previously in vertebrates.

SOX9 is not required for the cellular events of testicular organogenesis in XX mole ovotestes

Mammalian sex determination is the genetic process that commits the undifferentiated bipotential gonads to develop as either testes or ovaries. The differentiation of SOX9-expressing Sertoli cells is assumed to be necessary to initiate testis development. Insectivorous moles of the genus Talpa represent a unique case of generalized true hermaphroditism, as XX female moles constitutively develop two ovotestes instead of normal ovaries. In this work, we have investigated the expression patterns of a number of genes known to play key roles in gonad organogenesis, throughout the entire process of ovotestis development in female moles. Molecular and morphological evidence are provided that these ovotestes contain primary medullary testis-like cords, Leydig cells, peritubular myoid cells, and a testis-specific vasculature, but no Sertoli cells. Our results show for the first time that SOX9 is not required for the formation of the primary testis cords, but it is necessary for the maintenance and subsequent development of these cords. In addition, the expression pattern of WNT4 in male and female moles indicates that this gene inhibits Leydig cell differentiation and, contrary to the proposed scenario in the mouse, it is not required for the colonization and survival of primordial germ cells. According to our data, mole ovotestes result from a process of PDGFRalpha-mediated mesonephric cell migration, which occurs simultaneously in both sexes. The fact that FST remains inactive during the critical stages of female gonad development, explains the lack of migration inhibition, and may be a consequence of improper WNT4 signalling in the mole.

Expression of genes controlling testicular development in adult testis of the seasonally breeding iberian mole

Most testicular features undergo major circannual variation in seasonal breeding species. Although the ultimate cause of these variations is known to be the photoperiod in most cases, very little is known about the genetic mechanisms by which these changes are modulated in the testis. Many genes involved in testis development are known to be expressed in the adult testis as well. Since these genes encode genetic regulatory factors, it is reasonable to suspect that they could play some role in the control of the adult testis function. Using immunological detection techniques and RT-Q-PCR, we have studied the spatio-temporal expression pattern of WT1, SF1, SOX9, AMH, and DMRT1 in 4 representative stages of the circannual cycle of the testes of Talpa occidentalis, a mole species with strict seasonal reproduction. AMH is not expressed at any stage of the cycle, showing that inactive adult testes are functionally different from pre-pubertal, juvenile ones. The continuous presence of primary spermatocytes may explain the permanent repression of AMH in the mole testis. WT1 and SF1 are down-regulated and SOX9 is up-regulated in regressed mole testes, suggesting that the modulation of the expression of these genes may be involved in the control of circannual gonad variation. Furthermore, SOX9 and DMRT1 show clear spermatogenic stage-dependent expression patterns. Both genes are expressed more intensely during the proliferative stages of spermatogonia, although SOX9 expression is limited to Sertoli cells, whereas DMRT1 is expressed in both Sertoli and spermatogonial cells. Available data suggest that intratesticular levels of testosterone could regulate circannual spermatogenic variations of seasonal breeders by modulating the expression of DMRT1 to control spermatogonial proliferation.