[Analysis of the length variation in the human Y chromosome by aids of the quinacrine fluorochrome method]

Specific functions for Mediator complex subunits from different modules in the transcriptional response of Arabidopsis thaliana to abiotic stress

Adverse environmental conditions are detrimental to plant growth and development. Acclimation to abiotic stress conditions involves activation of signaling pathways which often results in changes in gene expression via networks of transcription factors (TFs). Mediator is a highly conserved co-regulator complex and an essential component of the transcriptional machinery in eukaryotes. Some Mediator subunits have been implicated in stress-responsive signaling pathways; however, much remains unknown regarding the role of plant Mediator in abiotic stress responses. Here, we use RNA-seq to analyze the transcriptional response of Arabidopsis thaliana to heat, cold and salt stress conditions. We identify a set of common abiotic stress regulons and describe the sequential and combinatorial nature of TFs involved in their transcriptional regulation. Furthermore, we identify stress-specific roles for the Mediator subunits MED9, MED16, MED18 and CDK8, and putative TFs connecting them to different stress signaling pathways. Our data also indicate different modes of action for subunits or modules of Mediator at the same gene loci, including a co-repressor function for MED16 prior to stress. These results illuminate a poorly understood but important player in the transcriptional response of plants to abiotic stress and identify target genes and mechanisms as a prelude to further biochemical characterization.

Sex, rebellion and decadence: the scandalous evolutionary history of the human Y chromosome

It can be argued that the Y chromosome brings some of the spirit of rock&roll to our genome. Equal parts degenerate and sex-driven, the Y has boldly rebelled against sexual recombination, one of the sacred pillars of evolution. In evolutionary terms this chromosome also seems to have adopted another of rock&roll's mottos: living fast. Yet, it appears to have refused to die young. In this manuscript the Y chromosome will be analyzed from the intersection between structural, evolutionary and functional biology. Such integrative approach will present the Y as a highly specialized product of a series of remarkable evolutionary processes. These led to the establishment of a sex-specific genomic niche that is maintained by a complex balance between selective pressure and the genetic diversity introduced by intrachromosomal recombination. Central to this equilibrium is the "polish or perish" dilemma faced by the male-specific Y genes: either they are polished by the acquisition of male-related functions or they perish via the accumulation of inactivating mutations. Thus, understanding to what extent the idiosyncrasies of Y recombination may impact this chromosome's role in sex determination and male germline functions should be regarded as essential for added clinical insight into several male infertility phenotypes. This article is part of a Special Issue entitled: Molecular Genetics of Human Reproductive Failure.

High mutation rates have driven extensive structural polymorphism among human Y chromosomes

Although much structural polymorphism in the human genome has been catalogued, the kinetics of underlying change remain largely unexplored. Because human Y chromosomes are clonally inherited, it has been possible to capture their detailed relationships in a robust, worldwide genealogical tree. Examination of structural variation across this tree opens avenues for investigating rates of underlying mutations. We selected one Y chromosome from each of 47 branches of this tree and searched for large-scale variation. Four chromosomal regions showed extensive variation resulting from numerous large-scale mutations. Within the tree encompassed by the studied chromosomes, the distal-Yq heterochromatin changed length > or = 12 times, the TSPY gene array changed length > or = 23 times, the 3.6-Mb IR3/IR3 region changed orientation > or = 12 times and the AZFc region was rearranged > or = 20 times. After determining the total time spanned by all branches of this tree (approximately 1.3 million years or 52,000 generations), we converted these mutation counts to lower bounds on rates: > or = 2.3 x 10(-4), > or = 4.4 x 10(-4), > or = 2.3 x 10(-4) and > or = 3.8 x 10(-4) large-scale mutations per father-to-son Y transmission, respectively. Thus, high mutation rates have driven extensive structural polymorphism among human Y chromosomes. At the same time, we found limited variation in the copy number of Y-linked genes, which raises the possibility of selective constraints.

Organization of DYZ2 repetitive DNA on the human Y chromosome

The location of the human Y-specific repetitive DNA sequence DYZ2 with HaeIII cleavage sites spaced at 2.1 kb was reexamined. Previous reports had mapped the 2000 DYZ2 copies to the very distal end of the heterochromatic Yq12 band. In the present study, a cloned DYZ2 fragment (pHY2.1) was used for Southern and slot blot analyses of male DNA as well as for nonradioactive in situ hybridization to chromosomes. DNA and metaphase preparations from 79 individuals with polymorphic or aberrant Y chromosomes were examined. DYZ2 repeats are not confined to the distal tip of Yq12, but extend through the entire heterochromatin of Yq12. In the naturally occurring length polymorphisms of Yq, the amount of DYZ2 sequence varies in proportion to the measured sizes of band Yq12. Explanations are presented for the fact that previous studies restricted the location of DYZ2 to the telomeric end of Yq12.

Variability of euchromatic and heterochromatic segment of the Y chromosome in men with malignant tumors and in a control group

In this study, Y chromosome variability was analyzed in 58 male patients with malignant tumors and 55 healthy male controls. No difference in the size of Y chromosome was established between the two groups studied, but a statistically significant difference in the length of euchromatic and heterochromatic segments was found. A significantly greater length of heterochromatic segments was established in the patients compared with the control group (p less than 0.02). The length of the euchromatic segment was shorter in the patients than in the controls (p less than 0.02).

Racial variation of a non-fluorescent segment of the Y chromosome in East Indians

Seventy normal male East Indians were selected to study the length of the fluorescent (f), non-fluorescent (nf), and total length of the Y chromosome by the QFQ technique. The length of the Y chromosome was classified into five groups using subjectively defined criteria, namely, very small, small, average, large, and very large. The frequencies of Y/F indices for these groups were 0.0%, 1.42%, 15.71%, 58.57%, and 24.28%, respectively. The variation in the total length of the Y chromosome was accounted for by variations in the length of the nf as well as the f segments. The mean Y/F, f/F, and nf/F indices for East Indians were 1.20, 0.47, and 0.73, respectively. A longer Y was noted in East Indians primarily owing to an increase in size of the nf segment in comparison to normal black and Caucasian populations. Furthermore, it is emphasised that the definition of 'average' or 'large' Y varies from race to race.

Relationship between Y-chromosome length and first-trimester spontaneous abortions

The hypothesis that variation in Y-chromosome length is associated with repetitive fetal wastage was tested. Chromosome lengths were objectively quantitated by scanning photographic negatives of metaphases with a computer programmed to (1) select boundary thresholds and (2) construct and measure centerlines with a cubic spline-fitting algorithm. Variation in Y length among cells of different individuals was standardized by use of the ratio of the length of the Y to the average of the lengths of the No. 20s (20) in the same cell. Three groups were studied: (1) men whose wives had three or more spontaneous abortions and no live-born infants, (2) men whose wives had both abortions and normal live-born infants, and (3) control men whose wives had normal live-born infants only. Although central tendencies were similar in the three groups, the distributions of Y lengths among the three groups were significantly different (chi 2(6) = 15.33, 0.025 greater than p greater than 0.010). This difference was primarily because more of the subjects with only repetitive loss had Y lengths in the "tails" of the distribution rather than in the center. Our observations suggest the existence of an optimal Y length with respect to reproductive performance.

Human chromosomal heteromorphisms in American blacks. VI. Higher incidence of longer Y owing to non-fluorescent (nf) segment

Sixty normal male American blacks were selected to study the length of fluorescent (f), non-fluorescent (nf), and total length of the Y chromosome by the QFQ technique. The length of the Y chromosome was classified into five groups: very small, small, average, large, and very large. The frequencies of Y/F indices for these groups were 0.0, 3.33, 56.67, 30.00, and 10.00%, respectively. The variation in the total length of the Y chromosome was accounted for by variations in the length of the nf as well as the f segment. A longer Y was noted in blacks owing to an increase in size of the nf segment in comparison with a normal Caucasian population. Forty percent of American blacks had large or very large Y chromosomes, while this class comprised only 18.3% of Caucasians, which is significantly different (p less than 0.05). Furthermore, the length of the Y chromosome was normally distributed among Caucasians, while among blacks the distribution was skewed to the left. The mean Y/F, f/F, and nf/F indices were 1.09 +/- 0.10, 0.42 +/- 0.09, and 0.67 +/- 0.04, respectively.

Human chromosomal polymorphism. I. Chromosomal Q polymorphism in Mongoloid populations of Central Asia

A comparative study of frequencies and types of Q-polymorphic variants in seven autosome pairs (3, 4, 13-15, 21, and 22) was performed in three steppe Mongoloid populations of Central Asia (Kazakhs, Dunghans, Mongolians) and three highland Kirghiz populations of Pamir and Tien-Shan. The three steppe Mongoloid populations showed statistically significant homogeneity both in the frequency of Q-polymorphic variants and the distribution of homo- and heteromorphs, with complete agreement of observed frequencies with those theoretically predicted by the law of Hardy-Weinberg. Similar homogeneity was revealed in the three highland Kirghiz populations of Pamir and Tien-Shan. However, comparative analysis of highland and steppe Mongoloids revealed significant differences in the following variables: (1) mean number of Q variants per individual, 2.50 and 3.49 in the highland and steppe populations, respectively; (2) frequency of Q variants in 7 of the 12 autosomes studied; and (3) distribution of homo- and heteromorphs in four autosomal pairs (13-15, 21), with a preponderance of individuals with increased hemomorph (-/-) frequency in highlanders. The following questions are discussed: (1) the possible selective value of chromosomal Q-heterochromatin material in the adaptation of human populations to extreme environmental factors, in particular to the high-altitude environment of Pamir and Tien-Shan; (2) the existence of intraracial heterogeneity in Mongoloids living in different ecological zones; and (3) the possible taxonomic value of Q-variant inversion in chromosome 3.

Size variability of the Y chromosome distal C-band in Brazilian Indians and Caucasoids

Densitometric measurements of the Y chromosome distal heterochromatin were performed on 183 Indians and 21 Caucasoids living in Brazil. No significant intratribal intervillage variation was observed, but the tribal averages were different, ranging from 0.81 to 1.32 mu. The Caucasoid mean presented an intermediate value. Wide intrapopulation variability occurs, as well as a suggestion of bimodality in the measurements obtained among the Indians of the Amazon region. Surprisingly a positive correlation was found between this variable and the C-band size of chromosome 16, as well as between it and the heteromorphism index of chromosome 1.

[Etiology of mongolism]

Beside the rare cares of translocation mongolism, Down syndrome is caused by meiotic malsegregation of chromosomes, No. 21. The meiotic error can take place in both sexes and was found twice as frequently in the female as in the male. The same 2:1 ratio was found concerning nondisjunction in the first and in the second meiotic division. The rate of meiotic errors, which occur at random, is largely dependent on age; this tendency is more pronounced in oogenesis than in spermatogenesis. The results of prenatal chromosomal diagnosis indicate that the recurrence risk of trisomy 21 is not above the age-dependent average.

Frequencies of centromeric heteromorphisms of human chromosomes 3 and 4 as detected by QFQ technique: can they be identified by RFA technique?

One hundred normal Caucasians were studied by sequential QFQ and RFA banding techniques in order to estimate the type and frequency of heteromorphisms in the centromeric regions of chromosome 3 and 4. Intensity variants were classified into 1 of 5 levels of QFQ banding. QFQ intensity heteromorphisms (greater than or equal to level 3) for chromosomes 3 and 4 were 62 and 15 percent respectively. The interrelationship between QFQ and RFA variants were also examined. When the centromere was brilliant by QFQ, it was found that it was deep red by RFA; when it was pale by QFQ, it was light red by RFA. Neverthless, a blind coded study could not pick up these color variants by RFA. QFQ banding showed variations of the centromeric regions of chromosomes 3 and 4 while RFA banding failed to demonstrate it. It was concluded that QFQ is the most useful technique in detecting the different intensity levels in the centromeric regions of chromsomes 3 and 4.

Human Y chromosome variation in normal and abnormal babies and their fathers

C-banded chromosome preparations were obtained from cord blood from normal newborns and venous blood from abnormal newborns and the corresponding fathers. There is significant heterogeneity between individuals in euchromatin and especially heterochromatin lengths of the Y chromosome. The average dimensions of the Y of fathers of normal and abnormal babies do not differ. Y chromosomes from cord blood appear more condensed than from venous blood and the consequences are not removed by the use of the Y/F index. Such differences have not been considered in reported apparent variation in the size of the Y chromsome in relation to criminality.

Length heteromorphisms of fluorescent (f) and non-fluorescent (nf) segments of human Y chromosome: classification, frequencies, and incidence in normal Caucasians

Sixty normal male Caucasians were selected to study the length of the Y chromosome. QFQ banding was performed. Chromosomes 19 and 20 (F) and Y were measured directly from the film. Y/F, f/F, and nf/F indices (f = fluorescent; nf = non-fluorescent segment) were determined. The length of the Y chromosome was classified into 5 groups; very small, small, average, large, and very large with Y/F indices of less than 0.8, 0.81--0.94, 0.95--1.09, 1.1--1.23, and greater than 1.23, respectively. The frequencies of Y/F indices for these groups were 0 (0%), 9 (15.0%), 40 (66.7%), 8 (13.3%), and 3 (5.0%), respectively. The most frequent class was 0.95--1.09 and was defined as the 'average' Y/F index for the human Y chromosome. The variation in the total length of the Y chromosome was accounted for by variations in the length of the non-fluorescent as well as the fluorescent segments. No relation between f and nf segments was observed. The mean Y/F, f/F, and nf/F indices were 1.022, 0.441, and 0.574, respectively.

DIPI and DAPI: fluorescence banding with only negliglible fading

DIPI and DAPI produce distinct fluorescent bands in human chromosomes similar to quinacrine banding patterns. Additionally, the AT rich secondary constrictions in the chromosomes Nos. 1, 9 and 16 are brightly fluorescent. On the other hand the brilliantly fluorescent regions after staining with quinacrine mustard in the chromosomes Nos. 3 and 4, satellites and some other regions in the acrocentric chromosomes are less striking. The distal part of the Y, however, is clearly discernible. Thus DIPI and DAPI seem to be strictly AT specific fluorochromes like Hoechst 33258. In interphase nuclei the Y chromosome can be identified. However, quinacrines are superior for Y-body analysis in buccal, hair cell and sperm smears. BrdU labeled chromatids show reduced fluorescence intensity. The difference, however, is less apparent than after staining with Hoechst 33 258. DAPI and especially DIPI are highly resistant to UV-irradiation; there is almost no fading within 30 min when using DIPI. Moreover, fluorescence intensity is stronger than in quinicrines. When photographing, exposure times may be reduced to about one quarter compared to quinacrine mustard.

Localization of factors controlling spermatogenesis in the nonfluorescent portion of the human Y chromosome long arm

A deletion of the Y chromosome at the distal portion of band q11 was found in 6 men with normal male habitus but with azoospermia. Five of them were found during a survey of 1170 subfertile males while the sixth was karyotyped because of slight bone abnormalities. These findings, together with a review of the literature, suggest that on the distal portion of the nonfluoresecent segment of the long arm of the Y, factors are located controlling spermatogenesis.

Origin of the extra chromosome no. 21 in Down's syndrome

Eighteen of 38 examined families with children with Down's syndrome showed polymorphisms of chromosome 21 elucidating the origin of the extra chromosome 21. Maternal origin was found in 10 cases and paternal origin in 8 cases. In both sexes errors occurred both in the first and in the second meiotic division.

Chromosome analysis on 930 consecutive newborn children using quinacrine fluorescent banding technique

Chromosome analysing using quinacrine fluorescence was performed on 930 consecutive newborn infants. The total incidence of major chromosome aberrations including numerical changes of the sex chromosomes, and structural changes of autosomes, was 0.54%. Incidence of XYY (0.4%) and XXY (0.2%) were relatively higher as compared to other studies. About 0.75% of the newborn infants were found to have a variable bright fluorescent band located on the proximal area of the short arm (p11) rather than on the proximal long arm (q11) of chromosome No. 3. Attempts were also made to record the variable fluorescent regions on 7 autosomes and the Y chromosome.

Morphological variability of the human chromosomes in two Indian populations - Rajputs and Punjabis

Karotypic evaluation of 100 Rajputs and 100 Punjabis revealed different frequencies of Y chromosome polymorphism and minor chromosome variants. Long Y chromosome were observed 5% of the Rajputs and 3% of the Punjabis. The Y indices of Rajputs were consistently higher than those of Punjabis. Significant differences were noted between Rajputs and Punjabis with respect to the 5 Y indices. Significant differences were also found when those 2 populations were compared with different populations of the world. Minor chromosome variants were observed in 18% of the Rajputs and 19% of the Punjabis.

The use of new staining techniques for human chromosome identification

Images