Stress Conditions Modulate the Chromatin Interactions Network in Arabidopsis

Stresses have been known to cause various responses like cellular physiology, gene regulation, and genome remodeling in the organism to cope and survive. Here, we assessed the impact of stress conditions on the chromatin-interactome network of Arabidopsis thaliana. We identified thousands of chromatin interactions in native as well as in salicylic acid treatment and high temperature conditions in a genome-wide fashion. Our analysis revealed the definite pattern of chromatin interactions and stress conditions could modulate the dynamics of chromatin interactions. We found the heterochromatic region of the genome actively involved in the chromatin interactions. We further observed that the establishment or loss of interactions in response to stress does not result in the global change in the expression profile of interacting genes; however, interacting regions (genes) containing motifs for known TFs showed either lower expression or no difference than non-interacting genes. The present study also revealed that interactions preferred among the same epigenetic state (ES) suggest interactions clustered the same ES together in the 3D space of the nucleus. Our analysis showed that stress conditions affect the dynamics of chromatin interactions among the chromatin loci and these interaction networks govern the folding principle of chromatin by bringing together similar epigenetic marks.

Cytogenetical analysis of Clitoria ternatea

Clitoria ternatea L. of the family Fabaceae is an economical, ornamental as well as medicinal important species. Chromosome characterization of C. ternatea, encompassing karyomorphological as well as fluorochrome binding was carried out in the present investigation. Karyomorphological studies showed the presence of 2n = 16 somatic chromosome number with three pairs of metacentric chromosomes and five pairs of submedian chromosomes. The analysis also revealed the present of one pair of nucleolar organizing region or satellite. Fluorochrome binding using chromomycin A3 (CMA) and 4-6-diamidino-2-phenylindole (DAPI) showed the presence of GC- and AT- rich heterochromatic region. Further analysis revealed the percentage of GC-rich was comparatively higher than AT-rich heterochromatic region. This is the first report on heterochromatin characterization in C. ternatea.

Comparative cytogenetic of six species of Amazonian Peacock bass (Cichla, Cichlinae): intrachromosomal variations and genetic introgression among sympatric species

Cytogenetic data for the genus Cichla Bloch et Schneider, 1801 are still very limited, with only four karyotype descriptions to date. The sum of the available cytogenetic information for Cichla species, points to a maintenance of the diploid number of 48 acrocentric chromosomes, considered a typical ancestral feature in cichlids. In the current study, we performed molecular and classical cytogenetic analyses of the karyotype organization of six species of Cichla, the earliest-diverging genus of Neotropical cichlids. We cytogenetically analysed Cichla kelberi Kullander et Ferreira, 2006, Cichla monoculus Agassiz, 1831, Cichla piquiti Kullander et Ferreira, 2006, Cichla temensis Humboldt, 1821, Cichla vazzoleri Kullander et Ferreira, 2006 and Cichla pinima Kullander et Ferreira, 2006, including three individuals that showed mixed morphological characteristics, likely from different species, suggesting they were hybrid individuals. All individuals analysed showed 2n = 48 acrocentric chromosomes, with centromeric heterochromatic blocks on all chromosomes and a terminal heterochromatic region on the q arm of the 2nd pair. Mapping 18S rDNA gave hybridization signals, correlated with the nucleolus organizer regions, on the 2nd pair for all analyzed individuals. However, we found distinct patterns for 5S rDNA: interstitially at the proximal position on 6th pair of four species (C. kelberi, C. pinima, C. piquiti and C. vazzoleri), and on the distal of the 4th pair in two (C. monoculus and C. temensis). Accordingly, we present here new data for the genus and discuss the evolutionary trends in the karyotype of this group of fish. In addition, we provide data that supports the occurrence of hybrid individuals in the Uatumã River region, mainly based on 5S rDNA mapping.

High-quality chromosome-level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes

BackgroundTilapias are one of the most farmed fishes that are coined as ‘aquatic chicken’ by the food industry. Like many other teleosts, Nile tilapia and blue tilapia exhibit very recent transition of sex chromosome systems since their divergence about 5 million years ago, making them a great model for elucidating the molecular and evolutionary mechanisms of sex chromosome turnovers. Studies into their sex-determining pathways are also critical for developing genetic sex control in aquaculture.ResultsWe report here the newly produced genomes of Nile tilapia and blue tilapia that integrate long-read sequencing and chromatin conformation data. The two nearly complete genomes have anchored over 97% of the sequences into linkage groups (LGs), and assembled majorities of complex repetitive regions including telomeres, centromeres and rDNA clusters. In particular, we inferred two episodes of repeat expansion at LG3 respectively in the ancestor of cichlids and that of tilapias. The consequential large heterochromatic region concentrated at one end of LG3 comprises tandem arrays of mRNA and small RNA genes, among which we have identified a candidate female determining gene Paics in blue tilapia. Paics show female-specific patterns of single-nucleotide variants, copy numbers and expression patterns in gonads during early gonadogenesis.ConclusionsOur work provide a very important genomic resource for functional studies of cichlids, and suggested that unequal distribution of repeat content that impacts the local recombination rate might make some chromosomes more likely to become sex chromosomes.

Centromere-proximal meiotic crossovers in Drosophila melanogaster are suppressed by both highly-repetitive heterochromatin and the centromere effect

Crossovers are essential in meiosis of most organisms to ensure the proper segregation of chromosomes. The lack or improper placement of crossovers can result in nondisjunction and aneuploidy in progeny. Crossovers near the centromere can cause nondisjunction; centromere-proximal crossovers are suppressed by what is termed the centromere effect, but the mechanism is unknown. Here, we investigate contributions to centromere-proximal crossover suppression in Drosophila melanogaster. We mapped a large number of centromere-proximal crossovers and find that crossovers are essentially absent from the highly-repetitive (HR)-heterochromatin surrounding the centromere but occur at a low frequency within the less-repetitive (LR)-heterochromatic region and adjacent euchromatin. Previous research suggested that flies that lack the Bloom syndrome helicase (Blm) lose meiotic of crossover patterning, including the centromere effect. Mapping of centromere-proximal crossovers in Blm mutants reveals that the suppression within the HR-heterochromatin is intact, but the centromere effect is lost. We conclude that centromere-proximal crossovers are suppressed by two separable mechanisms: the HR-heterochromatin effect, which completely suppresses crossovers in the HR-heterochromatin, and the centromere effect, which suppresses crossovers with a dissipating effect with distance from the centromere.

A Heterochromatin Domain Forms Gradually at a New Telomere and Is Dynamic at Stable Telomeres

ABSTRACTHeterochromatin domains play important roles in chromosome biology, organismal development, and aging, including centromere function, mammalian female X chromosome inactivation, and senescence-associated heterochromatin foci. In the fission yeastSchizosaccharomyces pombeand metazoans, heterochromatin contains histone H3 that is dimethylated at lysine 9. While factors required for heterochromatin have been identified, the dynamics of heterochromatin formation are poorly understood. Telomeres convert adjacent chromatin into heterochromatin. To form a new heterochromatic region inS. pombe, an inducible DNA double-strand break (DSB) was engineered next to 48 bp of telomere repeats in euchromatin, which caused formation of a new telomere and the establishment and gradual spreading of a new heterochromatin domain. However, spreading was dynamic even after the telomere had reached its stable length, with reporter genes within the heterochromatin domain showing variegated expression. The system also revealed the presence of repeats located near the boundaries of euchromatin and heterochromatin that are oriented to allow the efficient healing of a euchromatic DSB to cap the chromosome end with a new telomere. Telomere formation inS. pombetherefore reveals novel aspects of heterochromatin dynamics and fail-safe mechanisms to repair subtelomeric breaks, with implications for similar processes in metazoan genomes.

A heterochromatin domain forms gradually at a new telomere and is highly dynamic at stable telomeres

Heterochromatin domains play important roles in chromosome biology, organismal development and aging. In the fission yeast Schizosaccharomyces pombe and metazoans, heterochromatin is marked by histone H3 lysine 9 dimethylation. While factors required for heterochromatin have been identified, the dynamics of heterochromatin formation are poorly understood. Telomeres convert adjacent chromatin into heterochromatin. To form a new heterochromatic region in S. pombe, an inducible DNA double-strand break (DSB) was engineered next to 48 bp of telomere repeats in euchromatin, which caused formation of new telomere and gradual spreading of heterochromatin. However, spreading was highly dynamic even after the telomere had reached its stable length. The system also revealed the presence of repeats located at the boundaries of euchromatin and heterochromatin that are oriented to allow the efficient healing of a euchromatic DSB to cap the chromosome end with a new telomere. Telomere formation in S. pombe therefore reveals novel aspects of heterochromatin dynamics and the presence of failsafe mechanisms to repair subtelomeric breaks, with implications for similar processes in metazoan genomes.

Cytogenetics and Importance of Genetic Counselling in Recurrent Pregnancy Losses: Experience from Tertiary Care Laboratory

Loss of pregnancy either naturally or by medical termination is a destructive experience to the couple, especially those experiencing recurrent pregnancy losses (RPL). It is important to rule out the genetic aspect as the cause of pregnancy wastages. This retrospective study aimed to determine the frequency of chromosomal abnormalities and its various cytogenetic types in the samples received by Metropolis Healthcare laboratory, Mumbai. This study was conducted on the samples referred for chromosomal karyotyping with a history of Bad Obstetric History (BOH). The couples who had an experience of two or more pregnancy losses were included in this study. Out of the 2102 samples referred, chromosomal abnormality was recorded in 384 (18.27%) cases. Out of chromosomal abnormal cases, 126 (5.99%) patients had reciprocal translocations out of which 27 (21.43%) were Robertsonian translocations. Inversion of chromosome 9 was seen in 81 (21.09%) patients, while inversion Y in 28 (7.29%) patients, and polymorphic variation like increase in length of satellite or heterochromatic region recorded in almost 149 (38.30%) patients. Cytogenetic evaluation of couples with recurrent pregnancy losses (RPL) is very important as after knowing the parental chromosomal pattern appropriate counseling can be offered to know the risk of recurrence, option of prenatal diagnosis and also opens the option of reproduction in some cases. This will also help them to have a cytogenetically healthy baby. Since the cytogenetic abnormalities are usually familial, the close blood relatives may also be benefited once the abnormality is detected.

IDENTIFICATION OF CDNA FRAGMENT TIGHTLY LINKED TO NV AND TM-2 LOCI IN TOMATO

Tm-2 is a resistance gene in tomato to Tomato Mosaic Virus (ToMV), located in heterochromatic region of chromosome nine. Since map based cloning difficult to perform for identify the gene on that region, we apply differential display approach by using two near-isogenic tomato lines (NILs), one without Tm-2 and the other with Tm-2 to identify cDNAs of the transcripts from the region surrounding the Tm-2 locus. Among the 150 combinations of three anchor primers and fifty arbitrary primers, 10 combinations generated cDNA polymorphic bands. Out of them, only one combination of CA6, exhibited polymorphic band under southern blot analysis, subsequently a genetic experiment showed that the CA6 locus tightly linked to the Tm-2 locus. The CA6 fragment also hybridized to genomic DNA fragments from a tomato line carrying Tm-2a, a line of L. peruvianum from which Tm-2a originated, and a tomato line carrying another Tm-2-like gene. A northern hybridization blotting result suggested that the gene corresponding to CA6 fragment was constitutively transcribed.