Chromosomal control of nuclear composition in maize

Transcribing the enigma: the B chromosome as a territory of uncharted RNAs

B chromosomes are supernumerary elements found in several groups of eukaryotes, including fungi, plants, and animals. Typically, these chromosomes either originate from their hosts through errors in meiosis or interspecifically through horizontal transfer. While many B chromosomes are primarily heterochromatic and possess a low number of coding genes, these additional elements are still capable of transcribing sequences and exerting influence on the expression of host genes. How B chromosomes escape elimination and which impacts can be promoted in the cell always intrigued the cytogeneticists. In pursuit of understanding the behavior and functional impacts of these extra elements, cytogenetic studies meet the advances of molecular biology, incorporating various techniques into investigating B chromosomes from a functional perspective. In this review, we present a timeline of studies investigating B chromosomes and RNAs, highlighting the advances and key findings throughout their history. Additionally, we identified which RNA classes are reported in the B chromosomes and emphasized the necessity for further investigation into new perspectives on the B chromosome functions. In this context, we present a phylogenetic tree that illustrates which branches either report B chromosome presence or have functional RNA studies related to B chromosomes. We propose investigating other unexplored RNA classes and conducting functional analysis in conjunction with cytogenetic studies to enhance our understanding of the B chromosome from an RNA perspective.

Genomic imbalance determines positive and negative modulation of gene expression in diploid maize

Genomic imbalance caused by changing the dosage of individual chromosomes (aneuploidy) has a more detrimental effect than varying the dosage of complete sets of chromosomes (ploidy). We examined the impact of both increased and decreased dosage of 15 distal and 1 interstitial chromosomal regions via RNA-seq of maize (Zea mays) mature leaf tissue to reveal new aspects of genomic imbalance. The results indicate that significant changes in gene expression in aneuploids occur both on the varied chromosome (cis) and the remainder of the genome (trans), with a wider spread of modulation compared with the whole-ploidy series of haploid to tetraploid. In general, cis genes in aneuploids range from a gene-dosage effect to dosage compensation, whereas for trans genes the most common effect is an inverse correlation in that expression is modulated toward the opposite direction of the varied chromosomal dosage, although positive modulations also occur. Furthermore, this analysis revealed the existence of increased and decreased effects in which the expression of many genes under genome imbalance are modulated toward the same direction regardless of increased or decreased chromosomal dosage, which is predicted from kinetic considerations of multicomponent molecular interactions. The findings provide novel insights into understanding mechanistic aspects of gene regulation.

Gene dosage compensation of rRNA transcript levels in Arabidopsis thaliana lines with reduced ribosomal gene copy number

The 45S rRNA genes (rDNA) are among the largest repetitive elements in eukaryotic genomes. rDNA consists of tandem arrays of rRNA genes, many of which are transcriptionally silenced. Silent rDNA repeats may act as 'back-up' copies for ribosome biogenesis and have nuclear organization roles. Through Cas9-mediated genome editing in the Arabidopsis thaliana female gametophyte, we reduced 45S rDNA copy number (CN) to a plateau of ∼10%. Two independent lines had rDNA CNs reduced by up to 90% at the T7 generation, named low copy number (LCN) lines. Despite drastic reduction of rDNA copies, rRNA transcriptional rates, and steady-state levels remained the same as wild-type plants. Gene dosage compensation of rRNA transcript levels was associated with reduction of silencing histone marks at rDNA loci and altered Nucleolar Organiser Region 2 organization. Although overall genome integrity of LCN lines appears unaffected, a chromosome segmental duplication occurred in one of the lines. Transcriptome analysis of LCN seedlings identified several shared dysregulated genes and pathways in both independent lines. Cas9 genome editing of rRNA repeats to generate LCN lines provides a powerful technique to elucidate rDNA dosage compensation mechanisms and impacts of low rDNA CN on genome stability, development, and cellular processes.

Cell and Molecular Biology of Nucleolar Assembly and Disassembly

Nucleoli disassemble in prophase of the metazoan mitotic cycle, and they begin their reassembly (nucleologenesis) in late anaphase?early telophase. Nucleolar disassembly and reassembly were obvious to the early cytologists of the eighteenth and nineteenth centuries, and although this has lead to a plethora of literature describing these events, our understanding of the molecular mechanisms regulating nucleolar assembly and disassembly has expanded immensely just within the last 10-15 years. We briefly survey the findings of nineteenth-century cytologists on nucleolar assembly and disassembly, followed by the work of Heitz and McClintock on nucleolar organizers. A primer review of nucleolar structure and functions precedes detailed descriptions of modern molecular and microscopic studies of nucleolar assembly and disassembly. Nucleologenesis is concurrent with the reinitiation of rDNA transcription in telophase. The perichromosomal sheath, prenucleolar bodies, and nucleolar-derived foci serve as repositories for nucleolar processing components used in the previous interphase. Disassembly of the perichromosomal sheath along with the dynamic movements and compositional changes of the prenucleolar bodies and nucleolus-derived foci coincide with reactivation of rDNA synthesis within the chromosomal nucleolar organizers during telophase. Nucleologenesis is considered in various model organisms to provide breadth to our understanding. Nucleolar disassembly occurs at the onset of mitosis primarily as a result of the mitosis-specific phosphorylation of Pol I transcription factors and processing components. Although we have learned much regarding nucleolar assembly and disassembly, many questions still remain, and these questions are as vibrant for us today as early questions were for nineteenth- and early twentieth-century cytologists.

A correlated light and electron microscope study of the nucleolar material during mitosis in Vicia faba

Root meristematic cells of Vicia faba were examined, with both light and electron microscopes, in order to study the behaviour of the nucleolar material during the mitotic process. Under light microscopy, the preprophase nucleolus is seen to consist of a densely stained material in which are embedded several unstained vacuole-like structures of varying size. The electron microscope reveals that the dense nucleolar material is formed of two structurally distinct components, each segregated into irregularly shaped zones blending with one another. One of these components is represented by 150 A granules which, in places, are arranged into thread-like structures approximately 0.1 µ in diameter; the other component apparently consists of fibrils 60 to 100 A in diameter. The large and medium sized intranucleolar vacuoles contain loosely scattered granules and fibrils similar to those just described. The granular and fibrillar components of the denser portion of the nucleolus persist as such during prophase and disperse throughout the nuclear cavity at the time of nucleolar disintegration. After nuclear membrane breakdown, these granules and fibrils, as well as those of the nucleoplasm, mix freely with similar elements already present within the forming spindle. No evidence has been obtained that, during or after nucleolar disintegration, the structural components of the nucleolus become associated as such with the chromosomes to form an external or internal matrix. Our observations suggest the existence, of a matrix substance within late prophase, metaphase, and anaphase chromosomes, the fine structure of which bears strong resemblance to that of their constituent coiled chromonemata. Data are presented, moreover, that indicate that part of this matrix substance, presumably formed at some time during prophase, is released from the chromosomes during their anaphasic movement. A number of observations indicate that the main bulk of the next nucleolus is derived from a prenucleolar fibrillogranular material, arranged into thread-like structures some 0.1 µ in diameter, which collect in the interchromosomal spaces during early and midtelophase. Finally, our data would seem to favour the view that most of this prenucleolar material results from a resumption of the synthetic activity of the early and midtelophase chromosomes rather than from a mere shedding of a preexisting matrix substance.

Quantitative relationships between deoxyribonucleic and ribonucleic acid in isolated plant nuclei

Nuclei were isolated from the roots of different species of higher plants and the amounts of both deoxyribonucleic acid ( DNA ) and ribonucleic acid ( RNA ) in these nuclei were determined by a modification of the Schmidt-Thannhauser procedure. A new method of isolation was used which involved fixing the roots for a short time in ice-cold 2% (w/v) formaldehyde, and then crushing them in a press. Between 25 and 50% of the nuclei known to be present in the roots could be recovered. It was shown by interferometry, microphotometry and autoradiography, as well as by an examination of all the solutions used, that there was no significant loss of nucleic acids from the nuclei during the isolation procedure. Nuclei from root apices of diploid, tetraploid and hexaploid Allium species, from diploid and tetraploid forms of Tradescantia ohioensis and from Vicia faba , Pisum sativum and Zea mays showed large differences in DNA content. However, these were not accompanied by corresponding differences in RNA content; the DNA ; RNA ratio varied from about unity to more than ten irrespective of the relative amounts of meristematic and differentiating tissue present in the roots. In the nuclei of four of these species, the DNA ; RNA ratio increased as the temperature at which the plants were grown was raised from 4 to 25°C. The results of all these experiments showed the absence of any correlation between the amount of DNA and the total amount of nuclear RNA ; but the possible existence of a correlation between DNA and chromosomal RNA was not excluded.

Interferometric studies of endothelial cells in primary culture

A population of endothelial cells grown from Xenopus laevis tadpole hearts was investigated by microinterferometry. The resulting interferograms were evaluated by an automatic image analyzer. The mean values of dry mass were 778 +/- 340 pg (10(-15) g) for whole cells, 648 +/- 309 pg for cytoplasm, 116 +/- 45 pg for nuclei, and 19 +/- 10 pg for nucleoli. Two subpopulations of cells were identified, an actively growing one and a less active one. The density (dry mass per microm2) of the nuclei and nucleoli of less active cells was greater than that of the nuclei and nucleoli of actively growing cells. In addition, the inactive cells were always large and possessed a considerable amount of cytoplasm. The entrance of cells into S-phase could not be detected by microinterferometry; and no differences were apparent between cells possessing one nucleolus and those containing two nucleoli. The values obtained in these amphibian cells were compared with those derived from mammalian cells.

A chromosome rearrangement of Neurospora that produces viable progeny containing two nucleolus organizers

In rearrangement T(VL leads to IVL)AR33 the segment of chromosome 2 bearing the nucleolus organizer is translocated to the end of chromosome 4. When AR33 is crossed by Normal sequence (N), one third of the viable progeny contain a stable nontandem duplication with two organizers per nucleus. The organizer-deficient complementary products are inviable. Chromosomes and nucleoli have been examined during meiosis and postmeiotic nuclear divisions in the ascus, comparing heterozygous AT33 X N crosses with N X N and with crosses heterozygous for other interchanges. When AR33 is heterozygous, asci are of three types having the nucleolus organizer dupliciated in 0, 1 or 2 of the meiotic products. Frequencies of the ascus types are as expected from the known positions of rearrangement break points. Nucleoli formed by two organizers frequently fuse. Deficiency nuclei that contain no nucleolus organizer may form one or more small nucleolus-like bodies.

Nucleolar relationships in some Australian chironomus species

Members of a group of Australian Chironomus species in the pseudothummi complex show wide variation in number and location of nucleolar organizing regions (NORs). The structure of these regions has been examined by phase contrast microscopy and silver banding of salivary gland polytene chromosomes. Presence of nucleoli was also checked on other types of chromosomes in some species. The contribution of the silver banding technique to nucleolar studies in these chironomid chromosomes is discussed. Nucleoli often seem to emerge from groups of (up to 9) bands. Further studies are necessary to confirm the presence of rRNA cistrons in all of these bands. Banding differences, in particular absence of bands from homologous regions of some species which have smaller nucleoli or lack particular nucleoli, have been found. In the case of Ch. tepperi, however, little banding difference is apparent in the 16B region between the N(IV)+ and N(IV)- chromosomes, although in situ hybridization (Eigenbrod 1978) shows a deletion of rRNA cistrons in the N(IV)- stock. Differences in heterochromatin amount have also been observed at different NORs. A scheme for the evolution of nucleolar-producing regions in this Chironomus group in terms of these and other known chromosomal changes is presented and discussed.

An analysis of heterochromatin in maize root tips

The B chromosomes of maize are condensed in appearance during interphase and are relatively inert genetically; therefore they fulfill the definition of heterochromatin. This heterochromatin was studied in root meristem cells by radioautography following administration of tritiated thymidine and cytidine, and was found to behave in a characteristic way, i.e. it showed asynchronous DNA synthesis and very low, if any, RNA synthesis. A cytochemical comparison of normal maize nuclei with nuclei from isogenic maize stock containing approximately 15-20 B-chromosomes in addition to the normal complement has revealed the following: (a) the DNA and histone contents are greater in nuclei with B chromosomes; (b) the proportion of DNA to histone is identical with that of nuclei containing only normal chromosomes; (c) the amount of nonhistone protein in proportion to DNA in interphase is less in nuclei with B chromosomes than in normal nuclei. In condensed B chromosomes the ratio of nonhistone protein to DNA is similar to that in other condensed chromatin, such as metaphase chromosomes and degenerating nuclei. The B chromosomes appear to have no effect on nucleolar RNA and protein. Replication of B chromosomes is precisely controlled and is comparable to that of the ordinary chromosomes not only in synthesis for mitosis but also in formation of polyploid nuclei of root cap and protoxylem cells.