The mouse Ulnaless mutation deregulates posterior HoxD gene expression and alters appendicular patterning

Essay the (unusual) heuristic value of Hox gene clusters; a matter of time?

Ever since their first report in 1984, Antennapedia-type homeobox (Hox) genes have been involved in such a series of interesting observations, in particular due to their conserved clustered organization between vertebrates and arthropods, that one may legitimately wonder about the origin of this heuristic value. In this essay, I first consider different examples where Hox gene clusters have been instrumental in providing conceptual advances, taken from various fields of research and mostly involving vertebrate embryos. These examples touch upon our understanding of genomic evolution, the revisiting of 19th century views on the relationships between development and evolution and the building of a new framework to understand long-range and pleiotropic gene regulation during development. I then discuss whether the high value of the Hox gene family, when considered as an epistemic object, is related to its clustered structure (and the absence thereof in some animal species) and, if so, what is it in such particular genetic oddities that made them so generous in providing the scientific community with interesting information.

(Non)Parallel developmental mechanisms in vertebrate appendage reduction and loss

Appendages have been reduced or lost hundreds of times during vertebrate evolution. This phenotypic convergence may be underlain by shared or different molecular mechanisms in distantly related vertebrate clades. To investigate, we reviewed the developmental and evolutionary literature of appendage reduction and loss in more than a dozen vertebrate genera from fish to mammals. We found that appendage reduction and loss was nearly always driven by modified gene expression as opposed to changes in coding sequences. Moreover, expression of the same genes was repeatedly modified across vertebrate taxa. However, the specific mechanisms by which expression was modified were rarely shared. The multiple routes to appendage reduction and loss suggest that adaptive loss of function phenotypes might arise routinely through changes in expression of key developmental genes.

Mesomelic dysplasias associated with the HOXD locus are caused by regulatory reallocations

Human families with chromosomal rearrangements at 2q31, where the human HOXD locus maps, display mesomelic dysplasia, a severe shortening and bending of the limb. In mice, the dominant Ulnaless inversion of the HoxD cluster produces a similar phenotype suggesting the same origin for these malformations in humans and mice. Here we engineer 1 Mb inversion including the HoxD gene cluster, which positioned Hoxd13 close to proximal limb enhancers. Using this model, we show that these enhancers contact and activate Hoxd13 in proximal cells, inducing the formation of mesomelic dysplasia. We show that a secondary Hoxd13 null mutation in-cis with the inversion completely rescues the alterations, demonstrating that ectopic HOXD13 is directly responsible for this bone anomaly. Single-cell expression analysis and evaluation of HOXD13 binding sites suggests that the phenotype arises primarily by acting through genes normally controlled by HOXD13 in distal limb cells. Altogether, these results provide a conceptual and mechanistic framework to understand and unify the molecular origins of human mesomelic dysplasia associated with 2q31.

Vertebrate Chromosome Evolution

The study of chromosome evolution is undergoing a resurgence of interest owing to advances in DNA sequencing technology that facilitate the production of chromosome-scale whole-genome assemblies de novo. This review focuses on the history, methods, discoveries, and current challenges facing the field, with an emphasis on vertebrate genomes. A detailed examination of the literature on the biology of chromosome rearrangements is presented, specifically the relationship between chromosome rearrangements and phenotypic evolution, adaptation, and speciation. A critical review of the methods for identifying, characterizing, and visualizing chromosome rearrangements and computationally reconstructing ancestral karyotypes is presented. We conclude by looking to the future, identifying the enormous technical and scientific challenges presented by the accumulation of hundreds and eventually thousands of chromosome-scale assemblies.

HOX13-dependent chromatin accessibility underlies the transition towards the digit development program

Hox genes encode transcription factors (TFs) that establish morphological diversity in the developing embryo. The similar DNA-binding motifs of the various HOX TFs contrast with the wide-range of HOX-dependent genetic programs. The influence of the chromatin context on HOX binding specificity remains elusive. Here, we used the developing limb as a model system to compare the binding specificity of HOXA13 and HOXD13 (HOX13 hereafter), which are required for digit formation, and HOXA11, involved in forearm/leg development. We find that upon ectopic expression in distal limb buds, HOXA11 binds sites normally HOX13-specific. Importantly, these sites are loci whose chromatin accessibility relies on HOX13. Moreover, we show that chromatin accessibility specific to the distal limb requires HOX13 function. Based on these results, we propose that HOX13 TFs pioneer the distal limb-specific chromatin accessibility landscape for the proper implementation of the distal limb developmental program.

Pioneer factors direct cell fate through switching inaccessible chromatin to an accessible state at specific target enhancers. Here the authors show that HOX13 transcription factors have a pioneer activity which is required for the proper implementation of the distal limb developmental program.

The tissues and regulatory pattern of limb chondrogenesis

Initial limb chondrogenesis offers the first differentiated tissues that resemble the mature skeletal anatomy. It is a developmental progression of three tissues. The limb begins with undifferentiated mesenchyme-1, some of which differentiates into condensations-2, and this tissue then transforms into cartilage-3. Each tissue is identified by physical characteristics of cell density, shape, and extracellular matrix composition. Tissue specific regimes of gene regulation underlie the diagnostic physical and chemical properties of these three tissues. These three tissue based regimes co-exist amid a background of other gene regulatory regimes within the same tissues and time-frame of limb development. The bio-molecular indicators of gene regulation reveal six identifiable patterns. Three of these patterns describe the unique bio-molecular indicators of each of the three tissues. A fourth pattern shares bio-molecular indicators between condensation and cartilage. Finally, a fifth pattern is composed of bio-molecular indicators that are found in undifferentiated mesenchyme prior to any condensation differentiation, then these bio-molecular indicators are upregulated in condensations and downregulated in undifferentiated mesenchyme. The undifferentiated mesenchyme that remains in between the condensations and cartilage, the interdigit, contains a unique set of bio-molecular indicators that exhibit dynamic behaviour during chondrogenesis and therefore argue for its own inclusion as a tissue in its own right and for more study into this process of differentiation.

Hoxa13 regulates expression of common Hox target genes involved in cartilage development to coordinate the expansion of the autopodal anlage

To elucidate the role of Hox genes in limb cartilage development, we identified the target genes of HOXA11 and HOXA13 by ChIP‐Seq. The ChIP DNA fragment contained evolutionarily conserved sequences and multiple highly conserved HOX binding sites. A substantial portion of the HOXA11 ChIP fragment overlapped with the HOXA13 ChIP fragment indicating that both factors share common targets. Deletion of the target regions neighboring Bmp2 or Tshz2 reduced their expression in the autopod suggesting that they function as the limb bud‐specific enhancers. We identified the Hox downstream genes as exhibiting expression changes in the Hoxa13 knock out (KO) and Hoxd11‐13 deletion double mutant (Hox13 dKO) autopod by Genechip analysis. The Hox downstream genes neighboring the ChIP fragment were defined as the direct targets of Hox. We analyzed the spatial expression pattern of the Hox target genes that encode two different categories of transcription factors during autopod development and Hox13dKO limb bud. (a) Bcl11a, encoding a repressor of cartilage differentiation, was expressed in the E11.5 autopod and was substantially reduced in the Hox13dKO. (b) The transcription factors Aff3, Bnc2, Nfib and Runx1t1 were expressed in the zeugopodal cartilage but not in the autopod due to the repressive or relatively weak transcriptional activity of Hox13 at E11.5. Interestingly, the expression of these genes was later observed in the autopodal cartilage at E12.5. These results indicate that Hox13 transiently suspends the cartilage differentiation in the autopodal anlage via multiple pathways until establishing the paddle‐shaped structure required to generate five digits.

Distal Limb Patterning Requires Modulation of cis-Regulatory Activities by HOX13

The combinatorial expression of Hox genes along the body axes is a major determinant of cell fate and plays a pivotal role in generating the animal body plan. Loss of HOXA13 and HOXD13 transcription factors (HOX13) leads to digit agenesis in mice, but how HOX13 proteins regulate transcriptional outcomes and confer identity to the distal-most limb cells has remained elusive. Here, we report on the genome-wide profiling of HOXA13 and HOXD13 in vivo binding and changes of the transcriptome and chromatin state in the transition from the early to the late-distal limb developmental program, as well as in Hoxa13^−/−; Hoxd13^−/−limbs. Our results show that proper termination of the early limb transcriptional program and activation of the late-distal limb program are coordinated by the dual action of HOX13 on cis-regulatory modules.

Cerebral laterality for language is related to adult salivary testosterone levels but not digit ratio (2D:4D) in men: A functional transcranial Doppler ultrasound study

The adequacy of three competing theories of hormonal effects on cerebral laterality are compared using functional transcranial Doppler sonography (fTCD). Thirty-three adult males participated in the study (21 left-handers). Cerebral lateralization was measured by fTCD using an extensively validated word generation task. Adult salivary testosterone (T) and cortisol (C) concentrations were measured by luminescence immunoassay and prenatal T exposure was indirectly estimated by the somatic marker of 2nd to 4th digit length ratio (2D:4D). A significant quadratic relationship between degree of cerebral laterality for language and adult T concentrations was observed, with enhanced T levels for strong left hemisphere dominance and strong right hemisphere dominance. No systematic effects on laterality were found for cortisol or 2D:4D. Findings suggest that higher levels of T are associated with a relatively attenuated degree of interhemispheric sharing of linguistic information, providing support for the callosal and the sexual differentiation hypotheses rather than the Geschwind, Behan and Galaburda (GBG) hypothesis.

Assessment of the 2D:4D ratio in aggression-related injuries in children attending a paediatric emergency department

BACKGROUND

The 2D:4D ratio is a sexually dimorphic trait. A lower ratio is correlated with sporting prowess, successful financial trading, risk taking behaviour, aggression, and aggression-related injuries, such as the fifth metacarpal fractures.

AIMS

We aimed to assess if the ratio correlates to skeletally immature patient aggression.

METHODS

Radiology reports were searched for the terms "5th metacarpal" or "boxer". Of 537 X-rays, 142 had fractures. The mechanism of injury was recorded in 102 patients, differentiating aggressive and non-aggressive injury groups. Bone age and chronological age were recorded.

RESULTS

A clear male preponderance for aggression was identified with only 60% of non-aggressive injuries occurring in males compared to 95% in the aggression group (p < 0.001). Patients with aggression injuries were older chronologically (14.6 vs 12.7, p < 0.001) and by bone age (14.5 vs 13.0, p < 0.001). For male patients, there was no difference in the 2D:4D ratio (p = 0.94); however, for females, the difference was significant (p = 0.04).

CONCLUSIONS

Aggression injuries occur at an older age and are more common in males. In the female cohort, there was a distinct difference in digit ratio.

The Genetic Basis of Baculum Size and Shape Variation in Mice

The rapid divergence of male genitalia is a preeminent evolutionary pattern. This rapid divergence is especially striking in the baculum, a bone that occurs in the penis of many mammalian species. Closely related species often display diverse baculum morphology where no other morphological differences can be discerned. While this fundamental pattern of evolution has been appreciated at the level of gross morphology, nearly nothing is known about the genetic basis of size and shape divergence. Quantifying the genetic basis of baculum size and shape variation has been difficult because these structures generally lack obvious landmarks, so comparing them in three dimensions is not straightforward. Here, we develop a novel morphometric approach to quantify size and shape variation from three-dimensional micro-CT scans taken from 369 bacula, representing 75 distinct strains of the BXD family of mice. We identify two quantitative trait loci (QTL) that explain ∼50% of the variance in baculum size, and a third QTL that explains more than 20% of the variance in shape. Together, our study demonstrates that baculum morphology may diverge relatively easily, with mutations at a few loci of large effect that independently modulate size and shape. Based on a combination of bioinformatic investigations and new data on RNA expression, we prioritized these QTL to 16 candidate genes, which have hypothesized roles in bone morphogenesis and may enable future genetic manipulation of baculum morphology.

Does human ejaculate quality relate to phenotypic traits?

A given man's phenotype embodies cues of his ancestral ability to effectively defend himself and his kin from harm, to survive adverse conditions, and to acquire status and mating opportunities. In this review, we explore the hypothesis that a man's phenotype also embodies cues to fertility or the probability that an ejaculate will fertilize ova. Female mate choice depends on the ability to discern the quality of a male reproductive partner through his phenotype, and male fertility may be among the traits that females have evolved to detect. A female who selects as mates males that deliver higher quality ejaculates will, on average, be more fecund than her competitors. Data on several non-human species demonstrate correlations between ejaculate quality and secondary sexual characteristics that inform female mate choice, suggesting that females may select mates in part on the basis of fertility. While the non-human literature on this topic has advanced, the human literature remains limited in scope and there is no clear consensus on appropriate methodologies or theoretical positions. We provide a comprehensive review and meta-analysis of this literature, and conclude by proposing solutions to the many issues that impede progress in the field. In the process, we hope to encourage interest and insight from investigators in other areas of human mating and reproductive biology. Am. J. Hum. Biol. 28:318-329, 2016. © 2015 Wiley Periodicals, Inc.

Sexual dimorphism in finger length ratios and sex determination - A study in Indo-Mauritian population

Many studies have shown that the finger length ratios might be characteristic for sexual dimorphism. The aim of the study was to determine sexual dimorphism in finger length ratios among the representatives of the Indo-Mauritian population. The study group comprised of 200 healthy Indo-Mauritian people (100 male and 100 female) of the age ranged from 19 to 25 years. The lengths of second (2D), third (3D), forth (4D) and fifth (5D) finger of both hands were measured by using a vernier caliper. Our results indicate that all finger length ratios have significant sex differences (p-value < 0.05) except 2D:5D and 3D:5D. To conclude, 2D:4D ratio is the most decisive ratio (predictive accuracy = 0.61) which can demarcate between male and female.

Structure, function and evolution of topologically associating domains (TADs) at HOX loci

Hox genes encode transcription factors necessary for patterning the major developing anterior to posterior embryonic axis. In addition, during vertebrate evolution, various subsets of this gene family were co-opted along with the emergence of novel body structures, such as the limbs or the external genitalia. The morphogenesis of these axial structures thus relies in part upon the precisely controlled transcription of specific Hox genes, a mechanism involving multiple long-range enhancers. Recently, it was reported that such regulatory mechanisms were largely shared between different developing tissues, though with some specificities, suggesting the recruitment of ancestral regulatory modalities from one tissue to another. The analysis of chromatin architectures at HoxD and HoxA loci revealed the existence of two flanking topologically associating domains (TADs), precisely encompassing the adjacent regulatory landscapes. Here, we discuss the function of these TADs in the control of Hox gene regulation and we speculate about their capacity to serve as structural frameworks for the emergence of novel enhancers. In this view, TADs may have been used as genomic niches to evolve pleiotropic regulations found at many developmental loci.

A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes

Despite the well-documented role of remote enhancers in controlling developmental gene expression, the mechanisms that allocate enhancers to genes are poorly characterized. Here, we investigate the cis-regulatory organization of the locus containing the Tfap2c and Bmp7 genes in vivo, using a series of engineered chromosomal rearrangements. While these genes lie adjacent to one another, we demonstrate that they are independently regulated by distinct sets of enhancers, which in turn define non-overlapping regulatory domains. Chromosome conformation capture experiments reveal a corresponding partition of the locus in two distinct structural entities, demarcated by a discrete transition zone. The impact of engineered chromosomal rearrangements on the topology of the locus and the resultant gene expression changes indicate that this transition zone functionally organizes the structural partition of the locus, thereby defining enhancer-target gene allocation. This partition is, however, not absolute: we show that it allows competing interactions across it that may be non-productive for the competing gene, but modulate expression of the competed one. Altogether, these data highlight the prime role of the topological organization of the genome in long-distance regulation of gene expression.

The specificity of enhancer-gene interactions is fundamental to the execution of gene regulatory programs underpinning embryonic development and cell differentiation. However, our understanding of the mechanisms conferring specificity to enhancers and target gene interactions is limited. In this study, we characterize the cis-regulatory organization of a large genomic locus consisting of two developmental genes, Tfap2c and Bmp7. We show that this locus is structurally partitioned into two distinct domains by the constitutive action of a discrete transition zone located between the two genes. This separation restricts selectively the functional action of enhancers to the genes present within the same domain. Interestingly, the effects of this region as a boundary are relative, as it allows some competing interactions to take place across domains. We show that these interactions modulate the functional output of a brain enhancer on its primary target gene resulting in the spatial restriction of its expression domain. These results support a functional link between topological chromatin domains and allocation of enhancers to genes. They further show that a precise adjustment of chromatin interaction levels fine-tunes gene regulation by long-range enhancers.

Second to fourth digit ratio: a predictor of adult testicular volume

It has been suggested that second to fourth digit ratio (digit ratio) may correlate with male reproductive system function or disorders. This hypothesis is based on finding that the Hox genes control finger development and differentiation of the genital bud during embryogenesis. Thus, we investigated the association between digit ratio and adult testicular volume. A total of 172 Korean men (aged 20-69 years) hospitalized for urological surgery were prospectively enrolled. Patients with conditions known to strongly influence testicular volume were excluded. Before determining testicular volume, the lengths of the second and fourth digits of the right hand were measured by a single investigator using a digital vernier calliper. Using orchidometry, the testes were measured by an experienced urologist who had no information about the patient's digit ratio. To identify the independent predictive factors influencing testicular volume, univariate and multivariate analyses were performed using linear regression models. Age, height, serum testosterone and free testosterone level were not correlated with testicular volume. Digit ratio, along with weight, was significantly correlated with testicular volume (right testicular volume: r = -0.185, p = 0.015; left testicular volume: r = -0.193, p = 0.011; total testicular volume: r = -0.198, p = 0.009). Multivariate analysis using linear regression models showed that only digit ratio was the independent factor to predict all (right, left and total) testicular volumes (right testicular volume: β = -0.174, p = 0.023; left testicular volume: β = -0.181, p = 0.017; total testicular volume: β = -0.185, p = 0.014). Our findings demonstrated that digit ratio is negatively associated with adult testicular volume. This means that men with a higher digit ratio may be more likely to have smaller testis compared to those with a lower digit ratio.

Second to fourth digit ratio confirms aggressive tendencies in patients with boxers fractures

BACKGROUND

Upper limb second to fourth digit ratio (2D:4D) has been shown to be dependent on prenatal androgen exposure. A longer relative fourth digit to second digit is indicative of increased intrauterine testosterone exposure prenatally and the converse is also true for oestrogen exposure. The 2D:4D ratio has implications in the sporting, academic, financial and sexual arenas. The purpose of this study was to examine the association between smaller finger length ratios (2D:4D) and boxers fractures, in both men and women, by comparing the 2D:4D ratios in 150 boxers fractures and comparing them to matched controls. Boxers fractures are an injury classically incurred during acts of aggression and we postulated that this cohort of patients would have a smaller 2D:4D ratio in comparison to the normal population mean ratio.

METHODS

One hundred and fifty radiographs from patients with boxers fractures secondary to aggressive actions were analysed and the 2D:4D ratio was calculated. A further 150 X-rays from patients not involved in aggressive activities were used as a control group and the 2D:4D ratio was calculated in the same manner. We then performed statistical analysis to compare the 2D:4D ratios between our two groups.

RESULTS

As predicted, the 2D:4D in males was smaller than females in all of the groups. However, our results showed that those presenting with a boxers fracture due to an aggression related injury had a statistically significant smaller 2D:4D ratio when compared to the normal population.

CONCLUSION

Boxers fractures are injuries that typically occur from an aggressive act. It is well documented that a low 2D:4D ratio is reflective of an increased prenatal exposure to androgens, particularly testosterone. We have shown that boxers fractures are associated with a smaller 2D:4D ratio than the normal population, thus suggesting that persons exposed to high levels of prenatal androgens are more likely to exhibit aggressive tendencies in adulthood. Our results suggest that smaller digit ratios may predict a predisposition to acts of aggression, and as such result in an increased likelihood of sustaining an injury such as a boxers fracture. This relationship seems to be present independently of gender.

The origin of the tetrapod limb: from expeditions to enhancers

More than three centuries ago natural philosophers, and later anatomists, recognized a fundamental organization to the skeleton of tetrapod limbs. Composed of three segments, stylopod, zeugopod, and autopod, this pattern has served as the basis for a remarkably broad adaptive radiation from wings and flippers to hands and digging organs. A central area of inquiry has been tracing the origins of the elements of this Bauplan in the fins of diverse fish. Can equivalents of the three segments, and the developmental processes that pattern them, be seen in fish fins? In addition, if so, how do these data inform theories of the transformation of fins into limbs? Answers to these questions come from linking discoveries in paleontology with those of developmental biology and genetics. Burgeoning discoveries in the regulatory biology of developmental genes and in the genomics of diverse species offer novel data to investigate these classical questions.

The Ratio of Second to Fourth Digit Length in Azoospermic Males Undergoing Surgical Sperm Retrieval: Predictive Value for Sperm Retrieval and on Subsequent Fertilization and Pregnancy Rates in IVF/ICSI Cycles

The differentiation of the urogenital system and the appendicular skeleton in vertebrates is under the control of Homeobox (Hox) genes. It has been shown that this common control of digit and gonad differentiation has connected the pattern of digit formation to spermatogenesis and prenatal hormone concentrations in males. We wished to establish whether digit patterns, particularly the ratio between the lengths of the second and fourth digit in males (2D : 4D), was related to spermatogenesis and, more specifically, the presence of spermatozoa in testicular biopsies from azoospermic men undergoing surgical sperm retrieval. Forty-four men were recruited, of whom 16 were diagnosed with nonobstructive azoospermia and 4 with congenital bilateral absence of the vas deferens, and 24 previously fertile men were azoospermic after previous vasectomy. Our results show that men with previous fertility or of an acquired form of azoospermia had significantly lower 2D : 4D ratios than men with nonobstructive azoospermia. In nonobstructive azoospermia, there was a significantly lower 2D : 4D ratio on the left side in men who had successful retrieval than those with unsuccessful retrieval. For these men who had a successful retrieval, none had a 2D : 4D ratio more than 1 on the left side, whereas 4 of 7 men in whom sperm was not found had a 2D : 4D ratio greater than 1. On successful sperm retrieval, subsequent fertilization and clinical pregnancy rates were unaffected by 2D : 4D ratios.

Correlations between digit ratio and infertility in Chinese men

BACKGROUND

Digit ratio, especially second to fourth digit ratio (2D:4D) is lower in men than in women. The ratios of digit may be established in utero and is negatively correlated with sperm counts and testosterone in men and positively correlated with estrogen in men and women.

AIM

To study whether the digit ratio (especially 2D:4D) are associated with the a+b ratio of sperm number in Chinese populations.

METHODS

Photocopies of the two hands of 268 men (controls: 72; patients: 196) and seminal parameters of masturbatory semen samples were collected.

RESULTS

The mean values of digit ratio of the controls and the patients all presented a trend as 2D:3D<2D:4D<3D:4D<2D:5D<4D:5D<3D:5D; the patients have higher mean values than controls; significant variances of 2D:3D, 3D:4D (left: P<0.05; right: P ≤ 0.05) and 2D:4D (left: P<0.001; right: P<0.01) were found between two groups; there was a higher percentage of 2D>4D in the patients; the relationship between 2D:4D and a+b ratio of sperm number in the patients was significant (P<0.001).

CONCLUSION

Digit ratio, especially 2D:4D in the left hand maybe one of the important markers of infertility in men for early diagnosis.

Aggression, digit ratio, and variation in the androgen receptor, serotonin transporter, and dopamine D4 receptor genes in African foragers: the Hadza

The role of genes in the expression of aggression and masculinity traits in humans has been a focus of recent behavioral genetic studies. This is the first study on the variation in aggression, the digit ratio (the ratio between the second and the fourth digits, 2D:4D), the directional asymmetry in 2D:4D (D(R-L)) and polymorphisms of the AR, DRD4, and 5-HTTL genes in simple hunter-gatherers, namely the Hadza of Tanzania (142 adult men). The distribution of AR, DRD4E3, and 5-HTTLPR genotypes and allele frequencies in Hadza was compared to other African populations on which the data were available. Hadza and Ariaal differed significantly in the distributions of frequencies of AR alleles with different numbers of CAG repeats. Hadza population was similar to other African populations in the distribution of allelic frequencies of the DRD4E3 locus, and to Afro-Americans in the distribution of allelic types of the 5-HTTLPR locus. We found no influence of AR gene on the right hand 2D:4D ratio, D(R-L), and any of aggression subscales of the Buss-Perry Aggression Questionnaire (AQ). Although, a weak positive correlation between CAG repeats and the left hand 2D:4D was found. The multiple regression analysis with digit ratios, D(R-L) and aggression subscales of AQ as dependent variables and the three gene candidates (AR, DRD4E3, and 5-HTTLPR) as independent variables revealed the following: men with lower number of CAG repeats had significantly lower left hand 2D:4D ratio; men with higher numbers of 48-bp unit copies in exon 3 of a VNTR polymorphism in the DRD4 gene had significantly lower digit ratios on both hands; no effect of the 5-HTTLPR gene on either the digit ratio or aggressive behavior. These findings demonstrate the complexity of gene effects on digit ratios and aggression and call for simultaneous analysis of more candidate genes. It is noteworthy that these results were obtained for a human population that is still practicing foraging and has been subjected to a high selective pressure due to harsh environments and practically has no access to modern medical care. Hadza are highly egalitarian, and their culture does not favor persons with a dominant or aggressive behavior. It is still to be found to what extent the relationships observed in this study are similar to those in other human populations.

Copy-number variations, noncoding sequences, and human phenotypes

Whereas single-nucleotide polymorphisms and their role in predisposition to disease have been studied extensively, the analysis of structural variants--genomic changes such as insertions, deletions, inversions, duplications, and translocations--is still in its infancy. Changes in copy number, also known as copy-number variations (CNVs), constitute one such group of these structural variants. CNVs are structural genomic variants that arise from deletions (loss) or duplications (gain), and as a consequence result in a copy-number change of the respective genomic region. CNVs may include entire genes or regions of transcribed sequence, or, indeed, comprise only nontranscribed sequences. Whereas the duplication or deletion of a gene can be expected to have an effect on gene dosage, the consequences of CNVs in nontranscribed sequences are less obvious. Here we review CNVs that involve regulatory nontranscribed regions of the genome, describe the associated human phenotypes, and discuss possible disease mechanisms.

Digit ratios and relation to myocardial infarction in Greek men and women

BACKGROUND

Digit ratios, such as the second to fourth digit ratio (2D:4D), are biometric markers that are influenced by estrogen and testosterone concentrations in utero and are determined genetically by HOX genes (homeodomain-containing homeotic genes). Sex steroids also play a crucial role in the occurrence of myocardial infarction (MI), which is considered to be gender dependent and related to testosterone. Additionally, first-trimester exposure to excess levels of estrogens and progesterone has been linked to cardiovascular anomalies.

OBJECTIVE

The aim of this work was to study digit ratios in a Greek population and assess their clinical importance as markers of predisposition to MI.

METHODS

Two samples were used: a group of Greek men and women hospitalized with MI, and a control group of healthy Greek men and women of the same age. Finger lengths were measured twice for both hands using electronic calipers. In the results, digits were designated as 2D (second digit), 3D (third digit), 4D (fourth digit), and 5D (fifth digit).

RESULTS

A total of 50 Greek men and 50 Greek women with MI were recruited (mean [SD] age, 69.3 [11.2] years for men; 69.7 [11.0] years for women). The control group consisted of 40 healthy Greek men and 40 healthy Greek women (mean age, 68.0 [11.8] years for men; 66.8 [10.7] years for women). In the control group, 2D:4D, 2D:3D, and 2D:5D ratios were significantly higher in women than in men (2D:4D: right hand, P < 0.001; left hand, P = 0.002; 2D:3D: right hand, P < 0.001; left hand, P = 0.003; 2D:5D: right hand, P < 0.001; left hand, P < 0.05). The mean values of 2D:4D ratios appeared to increase in the following order: healthy men < men with MI < healthy women < women with MI, although this difference was not statistically significant. In men with MI, 2D:4D and 3D:4D ratios were significantly higher than the respective ratios in healthy men (2D:4D: right hand, P = 0.001; left hand, P < 0.05; 3D:4D: right hand, P < 0.05; left hand, P = 0.001), but no significant differences were observed in the ratios between women with MI and healthy women.

CONCLUSIONS

Digit ratios that include ring-finger length (ie, 4D) may be useful biomarkers for predisposition to MI in Greek men, but not in Greek women. Sexual dimorphism of digit ratios was present in both groups and was independent of the individuals' health status.

Functional analysis of CTCF during mammalian limb development

CCCTC-binding factor (CTCF) is a nuclear zinc-finger protein that displays insulating activity in a variety of biological assays. For example, CTCF-binding sites have been suggested to isolate Hox gene clusters from neighboring transcriptional interference. We investigated this issue during limb development, where Hoxd genes must remain isolated from long-range effects to allow essential regulation within independent sub-groups. We used conditional Ctcf inactivation in incipient forelimbs and show that the overall pattern of Hoxd gene expression remains unchanged. Transcriptome analysis using tiling arrays covering chromosomes 2 and X confirmed the weak effect of CTCF depletion on global gene regulation. However, Ctcf deletion caused massive apoptosis, leading to a nearly complete loss of limb structure at a later stage. We conclude that, at least in this physiological context, rather than being an insulator, CTCF is required for cell survival via the direct transcriptional regulation of target genes critical for cellular homeostasis.

A regulatory 'landscape effect' over the HoxD cluster

Faithful expression of Hox genes in both time and space is essential for proper patterning of the primary body axis. Transgenic approaches in vertebrates have suggested that this collinear activation process is regulated in a largely gene cluster-autonomous manner. In contrast, more recently co-opted expression specificities, required in other embryonic structures, depend upon long-range enhancer sequences acting from outside the gene clusters. This regulatory dichotomy was recently questioned, since gene activation along the trunk seems to be partially regulated by signals located outside of the cluster. We investigated these alternative regulatory strategies by engineering a large inversion that precisely separates the murine HoxD complex from its centromeric neighborhood. Mutant animals displayed posterior transformations along with subtle deregulations of Hoxd genes, indicating an impact of the centromeric landscape on the fine-tuning of Hoxd gene expression. Proximal limbs were also affected, suggesting that this 'landscape effect' is generic and impacts upon regulatory mechanisms of various qualities and evolutionary origins.

Comparative analyses of vertebrate posterior HoxD clusters reveal atypical cluster architecture in the caecilian Typhlonectes natans

BACKGROUND

The posterior genes of the HoxD cluster play a crucial role in the patterning of the tetrapod limb. This region is under the control of a global, long-range enhancer that is present in all vertebrates. Variation in limb types, as is the case in amphibians, can probably not only be attributed to variation in Hox genes, but is likely to be the product of differences in gene regulation. With a collection of vertebrate genome sequences available today, we used a comparative genomics approach to study the posterior HoxD cluster of amphibians. A frog and a caecilian were included in the study to compare coding sequences as well as to determine the gain and loss of putative regulatory sequences.

RESULTS

We sequenced the posterior end of the HoxD cluster of a caecilian and performed comparative analyses of this region using HoxD clusters of other vertebrates. We determined the presence of conserved non-coding sequences and traced gains and losses of these footprints during vertebrate evolution, with particular focus on amphibians. We found that the caecilian HoxD cluster is almost three times larger than its mammalian counterpart. This enlargement is accompanied with the loss of one gene and the accumulation of repeats in that area. A similar phenomenon was observed in the coelacanth, where a different gene was lost and expansion of the area where the gene was lost has occurred. At least one phylogenetic footprint present in all vertebrates was lost in amphibians. This conserved region is a known regulatory element and functions as a boundary element in neural tissue to prevent expression of Hoxd genes.

CONCLUSION

The posterior part of the HoxD cluster of Typhlonectes natans is among the largest known today. The loss of Hoxd-12 and the expansion of the intergenic region may exert an influence on the limb enhancer, by having to bypass a distance seven times that of regular HoxD clusters. Whether or not there is a correlation with the loss of limbs remains to be investigated. These results, together with data on other vertebrates show that the tetrapod Hox clusters are more variable than previously thought.

Mesomelic dysplasia Kantaputra type is associated with duplications of the HOXD locus on chromosome 2q

Mesomelic dysplasia Kantaputra type (MDK) is characterized by marked mesomelic shortening of the upper and lower limbs originally described in a Thai family. To identify the cause of MDK, we performed array CGH and identified two microduplications on chromosome 2 (2q31.1-q31.2) encompassing ∼481 and 507 kb, separated by a segment of normal copy number. The more centromeric duplication encompasses the entire HOXD cluster, as well as the neighboring genes EVX2 and MTX2. The breakpoints of the duplication localize to the same region as the previously identified inversion of the mouse mutant ulnaless (Ul), which has a similar phenotype as MDK. We propose that MDK is caused by duplications that modify the topography of the locus and as such result in deregulation of HOXD gene expression.

Generation and expression of a Hoxa11eGFP targeted allele in mice

Hox genes are crucial for body axis specification during embryonic development. Hoxa11 plays a role in anteroposterior patterning of the axial skeleton, development of the urogenital tract of both sexes, and proximodistal patterning of the limbs. Hoxa11 expression is also observed in the neural tube. Herein, we report the generation of a Hoxa11eGFP targeted knock-in allele in mice in which eGFP replaces the first coding exon of Hoxa11 as an in-frame fusion. This allele closely recapitulates the reported mRNA expression patterns for Hoxa11. Hoxa11eGFP can be visualized in the tail, neural tube, limbs, kidneys, and reproductive tract of both sexes. Additionally, homozygous mutants recapitulate reported phenotypes for Hoxa11 loss of function mice, exhibiting loss of fertility in both males and females. This targeted mouse line will prove useful as a vital marker for Hoxa11 protein localization during control (heterozygous) or mutant organogenesis.

Global control regions and regulatory landscapes in vertebrate development and evolution

During the course of evolution, many genes that control the development of metazoan body plans were co-opted to exert novel functions, along with the emergence or modification of structures. Gene amplification and/or changes in the cis-regulatory modules responsible for the transcriptional activity of these genes have certainly contributed in a major way to evolution of gene functions. In some cases, these processes led to the formation of groups of adjacent genes that appear to be controlled by both global and shared mechanisms.

Behavioral Aggression Is Associated with the 2D:4D Ratio in Men but Not in Women

Abstract. Numerous studies have investigated the relationship between testosterone (T) and aggression but yielded inconsistent findings in healthy subjects. One possible reason for this might be the measurement of actual T-levels, ignoring that its role in neurodevelopment seems to be of predominant importance. The aim of our study was to further elucidate the effects of T availability during early phases of gestation, operationalized by the measurement of the 2nd to 4th digit ratio (2D:4D), on behavioral aggression in healthy volunteers. A low 2D:4D (indicating a long ring finger relative to the index finger) relates to high levels of prenatal T. A total number of 171 healthy subjects (98 men, 73 women) ranging in age from 20 to 30 years were tested. Participants were subjected to a modified version of a competitive reaction-time task, a commonly used and well-established tool to elicit and measure aggression (Taylor paradigm). They also completed self-report scales on trait aggression. Ventral surface scans of both hands were used to determine the 2D:4D ratio. As expected, the 2D:4D was lower in men as compared to women for both hands. Moreover, in contrast to questionnaire data, men reveal higher levels of aggression in the computer task compared to women. Finally, a negative correlation between 2D:4D and aggression was found in males but not in females. Results are discussed with respect to the usefulness of the 2D:4D construct as well as to sex differences in organizational effects of T.

Sexual dimorphism in the second-to-fourth digit length ratio in green anoles,Anolis carolinensis(Squamata: Polychrotidae), from the southeastern United States

Digit length ratios are organized during embryonic development and may show sexual dimorphism related to steroid exposure. The second-to-fourth digit length ratio (2D:4D) has received the most attention. In the present study, we measured 2D:4D of all four feet of adult male and female green anoles ( Anolis carolinensis Voigt, 1832) to determine whether it is sexually dimorphic and whether results are repeatable across laboratories. Lizards were housed at Michigan State University (MSU) and Oklahoma State University (OSU), and one investigator at each institution used digital calipers to measure the 2D:4D of each foot. At both MSU and OSU, we found that males had a significantly larger 2D:4D on the back right foot than females did, and that no sex difference existed in either the back left or the front right foot. Furthermore, although no sex difference in the front left foot was found at MSU, the 2D:4D on this foot was larger in females at OSU. Our results demonstrate both sexual dimorphism in 2D:4D and repeatability between laboratories, but they also suggest the importance of verifying such repeatability if 2D:4D or any other digit length ratio is used as a potential indicator of the early steroid environment.

A group 13 homeodomain is neither necessary nor sufficient for posterior prevalence in the mouse limb

Posterior prevalence is the general property attributed to HOX proteins describing the dominant effect of more posterior HOX proteins over the function of anterior orthologs in common areas of expression. To explore the HOX group 13 protein domains required for this property, we used the mouse Prx-1 promoter to drive transgenic expression of Hox constructs throughout the entire limb bud during development. This system allowed us to conclusively demonstrate a hierarchy of Hox function in developing limbs. Furthermore, by substituting the HOXD11 or HOXA9 homeodomain for that of HOXD13, we show that a HOXD13 homeodomain is not necessary for posterior prevalence. Proximal expression of these chimeric proteins unexpectedly caused defects consistent with wild-type HOXD13 mediated posterior prevalence. Moreover, group 13 non-homeodomain residues appear to confer the property as proximal expression of HOXA9 containing the HOXD13 homeodomain did not result in limb reductions characteristic of HOXD13. These data are most compatible with models of posterior prevalence based on protein-protein interactions and support examination of the N-terminal non-homeodomain regions of Hox group 13 proteins as necessary agents for posterior prevalence.

Finger-length ratios show evidence of prenatal hormone-transfer between opposite-sex twins

Finger-length ratio (second to fourth finger; 2D:4D) has been associated with various measures thought to be related to prenatal androgens. In addition, hormone-transfer theory posits that hormones can transfer between twins. We examined 2D:4D in same-sex (SS) and opposite-sex (OS) dizygotic twins to test both propositions. Results show that 2D:4D is masculinized in OS females compared to SS females. This provides strong evidence that 2D:4D is laid down prenatally, and that hormones (likely androgens) can transfer from male to female fetuses. Implications for developmental timeframes for both hormone-transfer and 2D:4D are discussed.

The ratio of the 2nd to 4th finger length predicts spatial ability in men but not women

On average men score higher on time-constrained tests of spatial ability than women. Both brain and behaviour are influenced by prenatal and adult exposure to gonadal steroid hormones. In humans the ratio of the 2nd to 4th finger length (2D:4D) is a sexually dimorphic character that is lower in men than women and negatively correlated with testosterone levels. We report three independent studies from Sweden/London, Hungary and Liverpool confirming that 2D:4D is generally larger in women than men, that men obtain higher MRT scores than women, and demonstrating that 2D:4D is negatively correlated with MRT score in men but not women. We argue that this negative correlation between 2D:4D and spatial ability reflects the association between 2D:4D and prenatal, rather than adult, exposure to testosterone and conclude that testosterone exposure influences brain development leading to better performance on male-favouring spatial tasks.