scholarly journals Three-dimensional organization of Drosophila melanogaster interphase nuclei. II. Chromosome spatial organization and gene regulation.

1987 ◽  
Vol 104 (6) ◽  
pp. 1471-1483 ◽  
Author(s):  
M Hochstrasser ◽  
J W Sedat
Keyword(s):  
Gene Regulation ◽  
Drosophila Melanogaster ◽  
Nuclear Envelope ◽  
Spatial Organization ◽  
Polytene Chromosomes ◽  
Three Dimensional ◽  
Nucleolar Organizer ◽  
Cell Types ◽  
Functional Changes ◽  
Specific Subset

In the preceding article we compared the general organization of polytene chromosomes in four different Drosophila melanogaster cell types. Here we describe experiments aimed at testing for a potential role of three-dimensional chromosome folding and positioning in modulating gene expression and examining specific chromosome interactions with different nuclear structures. By charting the configurations of salivary gland chromosomes as the cells undergo functional changes, it is shown that loci are not repositioned within the nucleus when the pattern of transcription changes. Heterologous loci show no evidence of specific physical interactions with one another in any of the cell types. However, a specific subset of chromosomal loci is attached to the nuclear envelope, and this subset is extremely similar in at least two tissues. In contrast, no specific interactions between any locus and the nucleolus are found, but the base of the X chromosome, containing the nucleolar organizer, is closely linked to this organelle. These results are used to evaluate models of gene regulation that involve the specific intranuclear positioning of gene sequences. Finally, data are presented on an unusual class of nuclear envelope structures, filled with large, electron-dense particles, that are usually associated with chromosomes.

scholarly journals Spatial organization of chromosomes in the salivary gland nuclei of Drosophila melanogaster.

1986 ◽  
Vol 102 (1) ◽  
pp. 112-123 ◽  
Author(s):  
M Hochstrasser ◽  
D Mathog ◽  
Y Gruenbaum ◽  
H Saumweber ◽  
J W Sedat
Keyword(s):  
Drosophila Melanogaster ◽  
Salivary Gland ◽  
Nuclear Envelope ◽  
Spatial Organization ◽  
Model Building ◽  
Three Dimensional ◽  
Structural Features ◽  
Chromosome Domains ◽  
Relative Placement ◽  
Three Dimensional Models

Using a computer-based system for model building and analysis, three-dimensional models of 24 Drosophila melanogaster salivary gland nuclei have been constructed from optically or physically sectioned glands, allowing several generalizations about chromosome folding and packaging in these nuclei. First and most surprising, the prominent coiling of the chromosomes is strongly chiral, with right-handed gyres predominating. Second, high frequency appositions between certain loci and the nuclear envelope appear almost exclusively at positions of intercalary heterochromatin; in addition, the chromocenter is always apposed to the envelope. Third, chromosomes are invariably separated into mutually exclusive spatial domains while usually extending across the nucleus in a polarized (Rabl) orientation. Fourth, the arms of each autosome are almost always juxtaposed, but no other relative arm positions are strongly favored. Finally, despite these nonrandom structural features, each chromosome is found to fold into a wide variety of different configurations. In addition, a set of nuclei has been analyzed in which the normally aggregrated centromeric regions of the chromosomes are located far apart from one another. These nuclei have the same architectural motifs seen in normal nuclei. This implies that such characteristics as separate chromosome domains and specific chromosome-nuclear envelope contacts are largely independent of the relative placement of the different chromosomes within the nucleus.

The spatial organization of epidermal structures: hairy establishes the geometrical pattern of Drosophila leg bristles by delimiting the domains of achaete expression

Development ◽  
1993 ◽  
Vol 118 (1) ◽  
pp. 9-20 ◽  
Author(s):  
T.V. Orenic ◽  
L.I. Held ◽  
S.W. Paddock ◽  
S.B. Carroll
Keyword(s):  
Drosophila Melanogaster ◽  
Spatial Organization ◽  
Expression Patterns ◽  
Cell Types ◽  
Precursor Cells ◽  
Geometrical Pattern ◽  
Leg Development ◽  
Puparium Formation ◽  
Late Expression ◽  
Bristle Pattern

The spatial organization of Drosophila melanogaster epidermal structures in embryos and adults constitutes a classic model system for understanding how the two dimensional arrangement of particular cell types is generated. For example, the legs of the Drosophila melanogaster adult are covered with bristles, which in most segments are arranged in longitudinal rows. Here we elucidate the key roles of two regulatory genes, hairy and achaete, in setting up this periodic bristle pattern. We show that achaete is expressed during pupal leg development in a dynamic pattern which changes, by approximately 6 hours after puparium formation, into narrow longitudinal stripes of 3–4 cells in width, each of which represents a field of cells (proneural field) from which bristle precursor cells are selected. This pattern of gene expression foreshadows the adult bristle pattern and is established in part through the function of the hairy gene, which also functions in patterning other adult sense organs. In pupal legs, hairy is expressed in four longitudinal stripes, located between every other pair of achaete stripes. We show that in the absence of hairy function achaete expression expands into the interstripe regions that normally express hairy, fusing the two achaete stripes and resulting in extra-wide stripes of achaete expression. This misexpression of achaete, in turn, alters the fields of potential bristle precursor cells which leads to the misalignment of bristle rows in the adult. This function of hairy in patterning achaete expression is distinct from that in the wing in which hairy suppresses late expression of achaete but has no effect on the initial patterning of achaete expression. Thus, the leg bristle pattern is apparently regulated at two levels: a global regulation of the hairy and achaete expression patterns which partitions the leg epidermis into striped zones (this study) and a local regulation (inferred from other studies on the selection of neural precursor cells) that involves refinement steps which may control the alignment and spacing of bristle cells within these zones.

scholarly journals ECOA-5. Integrative 3D spatial characterization of genomic and epigenomic intratumoral heterogeneity in glioblastoma

2021 ◽  
Vol 3 (Supplement_2) ◽  
pp. ii2-ii2
Author(s):  
Radhika Mathur ◽  
Qixuan Wang ◽  
Patrick Schupp ◽  
Stephanie Hilz ◽  
Chibo Hong ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Spatial Organization ◽  
Three Dimensional ◽  
Spatial Location ◽  
Cell Types ◽  
Intratumoral Heterogeneity ◽  
Tumor Evolution ◽  
Open Chromatin ◽  
Spatial Characterization

Abstract Treatment failure in glioblastoma is often attributed to intratumoral heterogeneity (ITH), which fosters tumor evolution and selection of therapy-resistant clones. While genomic alterations are known contributors to ITH, emerging studies highlight functional roles for epigenomic ITH which integrates differentiation status, stochastic events, and microenvironmental inputs. Here, we have established a novel platform for integrative characterization of genomic and epigenomic ITH of glioblastoma in three-dimensional (3-D) space. In collaboration with neurosurgeons and biomedical imaging experts, we utilize 3-D surgical neuro-navigation to safely acquire ~10 tumor samples per patient representing maximal anatomical diversity. We conduct whole-exome sequencing, RNA sequencing, and assay for transposase-accessible chromatin using sequencing (ATAC-Seq) on each sample. The spatial location of each sample is mapped by its 3-D coordinates, allowing 360-degree visualization of genomic and epigenomic ITH for each patient. We demonstrate this approach on 8 patients with primary IDH-WT glioblastoma (83 spatially mapped samples), providing unprecedented insight into their spatial organization at the genomic and epigenomic levels. We link genetically defined tumor subclones to patterns of open chromatin and gene regulation, revealing underlying transcription factor binding at active promoters and enhancers. We also identify ITH in whole-genome doubling and focal oncogene amplification events in multiple patients, which we then link with epigenomic ITH. Further, to study microenvironmental inputs and their contribution to epigenomic ITH, we conduct deconvolution of RNA sequencing and ATAC-Seq data by analyzing feature co-variation. We resolve the 3-D spatial organization of immune, neural, and other nontumor cell types present in glioblastoma, characterizing their functional states and interactions with tumor cells. This work provides the most comprehensive spatial characterization of genomic and epigenomic ITH to date in glioblastoma. As a resource for further investigation, we have developed an interactive data sharing platform – The 3D Glioma Atlas – that enables 360-degree visualization of both genomic and epigenomic ITH.

scholarly journals Physicochemical characteristics of the Dombrovska pit lake (Ukraine) formed in an opencast potassium salt mine and the genome response of Chironomus salinarius Kieffer (Chironomidae, Diptera) to these conditions

2020 ◽  
Vol 28 (1) ◽  
pp. 446-458
Author(s):  
Paraskeva Michailova ◽  
Ewa Szarek-Gwiazda ◽  
Andrzej Kownacki
Keyword(s):  
Potassium Salt ◽  
Major Ions ◽  
Genome Instability ◽  
Polytene Chromosomes ◽  
Benthic Fauna ◽  
Nucleolar Organizer ◽  
Salt Mine ◽  
Pit Lake ◽  
Functional Changes ◽  
Chironomus Salinarius

AbstractThis study focuses on the Dombrovska pit lake, near the city of Kalush in Ukraine, which is a former potassium salt mine filled with brine and freshwater. The water level is still increasing and as a result the salinity is decreasing. We analyzed the benthic fauna communities and the genome instability by assessing the rearrangements in the polytene chromosomes of Chironomus salinarius and the physicochemical parameters of the near-bottom water (pH, conductivity, mineralization, major ions, NO3−, NH4+, metals Cd, Pb, Cu, Mn, and Fe) and sediment (pH, organic matter and metals Cd, Pb, Cu, Zn, Mn, and Fe) at four sites. The water mineralization ranged from 17.3 to 26.2 g dm−3 which are classified as mesohaline and polyhaline waters, respectively. The biodiversity of the benthic fauna was low, and the dominant species was C. salinarius. The density of C. salinarius varied spatially and changed from 637 ind./m2 at a depth of 5 m to 8167 ind./m2 at a depth of 2.5 m. The genome instability was analyzed by examining the structural and functional changes in the salivary gland chromosomes of C. salinarius. The exposure of C. salinarius damaged the chromosomes and the activities of key structures, such as the Balbiani ring and nucleolar organizer, were partially or completely suppressed.

scholarly journals Specific interactions of chromatin with the nuclear envelope: positional determination within the nucleus in Drosophila melanogaster.

1996 ◽  
Vol 7 (5) ◽  
pp. 825-842 ◽  
Author(s):  
W F Marshall ◽  
A F Dernburg ◽  
B Harmon ◽  
D A Agard ◽  
J W Sedat
Keyword(s):  
Drosophila Melanogaster ◽  
Nuclear Envelope ◽  
Three Dimensional ◽  
Specific Interactions ◽  
Early Embryos ◽  
Chromatin Proteins ◽  
Discrete Site ◽  
Large Stretch ◽  
Drosophila Embryos

Specific interactions of chromatin with the nuclear envelope (NE) in early embryos of Drosophila melanogaster have been mapped and analyzed. Using fluorescence in situ hybridization, the three-dimensional positions of 42 DNA probes, primarily to chromosome 2L, have been mapped in nuclei of intact Drosophila embryos, revealing five euchromatic and two heterochromatic regions associated with the NE. These results predict that there are approximately 15 NE contacts per chromosome arm, which delimit large chromatin loops of approximately 1-2 Mb. These NE association sites do not strictly correlate with scaffold-attachment regions, heterochromatin, or binding sites of known chromatin proteins. Pairs of neighboring probes surrounding one NE association site were used to delimit the NE association site more precisely, suggesting that peripheral localization of a large stretch of chromatin is likely to result from NE association at a single discrete site. These NE interactions are not established until after telophase, by which time the nuclear envelope has reassembled around the chromosomes, and they are thus unlikely to be involved in binding of NE vesicles to chromosomes following mitosis. Analysis of positions of these probes also reveals that the interphase nucleus is strongly polarized in a Rabl configuration which, together with specific targeting to the NE or to the nuclear interior, results in each locus occupying a highly determined position within the nucleus.

Genetic and molecular analysis of the X chromosomal region 14B17-14C4 in Drosophila melanogaster: loss of function in NONA, a nuclear protein common to many cell types, results in specific physiological and behavioral defects.

Genetics ◽  
1993 ◽  
Vol 135 (2) ◽  
pp. 419-442
Author(s):  
R Stanewsky ◽  
K G Rendahl ◽  
M Dill ◽  
H Saumweber
Keyword(s):  
Drosophila Melanogaster ◽  
Nuclear Protein ◽  
Rna Binding ◽  
Sequence Data ◽  
Polytene Chromosomes ◽  
Cell Types ◽  
Nucleic Acid Binding ◽  
Loss Of Function ◽  
Nucleic Acid Binding Proteins ◽  
Hypomorphic Alleles

Abstract We have performed a genetic analysis of the 14C region of the X chromosome of Drosophila melanogaster to isolate loss of function alleles of no-on-transient A (nonA; 14C1-2; 1-52.3). NONA is a nuclear protein common to many cell types, which is present in many puffs on polytene chromosomes. Sequence data suggest that the protein contains a pair of RNA binding motifs (RRM) found in many single-strand nucleic acid binding proteins. Hypomorphic alleles of this gene, which lead to aberrant visual and courtship song behavior, still contain normally distributed nonA RNA and NONA protein in embryos, and in all available alleles NONA protein is present in puffs of third instar larval polytene chromosomes. We find that complete loss of this general nuclear protein is semilethal in hemizygous males and homozygous cell lethal in the female germline. Surviving males show more extreme defects in nervous system function than have been described for the hypomorphic alleles. Five other essential genes that reside within this region have been partially characterized.

scholarly journals Quantification of the Spatial Organization of the Nuclear Lamina as a Tool for Cell Classification

2013 ◽  
Vol 2013 ◽  
pp. 1-6
Author(s):  
Christiaan H. Righolt ◽  
Diana A. Zatreanu ◽  
Vered Raz
Keyword(s):  
Nuclear Envelope ◽  
Spatial Organization ◽  
Structural Changes ◽  
Structural Integrity ◽  
Quantitative Description ◽  
Three Dimensional ◽  
Nuclear Lamina ◽  
Cellular Functions ◽  
Cell Classification ◽  
Nuclear Stability

The nuclear lamina is the structural scaffold of the nuclear envelope that plays multiple regulatory roles in chromatin organization and gene expression as well as a structural role in nuclear stability. The lamina proteins, also referred to as lamins, determine nuclear lamina organization and define the nuclear shape and the structural integrity of the cell nucleus. In addition, lamins are connected with both nuclear and cytoplasmic structures forming a dynamic cellular structure whose shape changes upon external and internal signals. When bound to the nuclear lamina, the lamins are mobile, have an impact on the nuclear envelop structure, and may induce changes in their regulatory functions. Changes in the nuclear lamina shape cause changes in cellular functions. A quantitative description of these structural changes could provide an unbiased description of changes in cellular function. In this review, we describe how changes in the nuclear lamina can be measured from three-dimensional images of lamins at the nuclear envelope, and we discuss how structural changes of the nuclear lamina can be used for cell classification.

Interpretation of the three-dimensional structure of living nuclei by specimen tilt

1975 ◽  
Vol 19 (1) ◽  
pp. 1-10
Author(s):  
R.J. Skaer ◽  
S. Whytock
Keyword(s):  
Nuclear Envelope ◽  
Polytene Chromosomes ◽  
Three Dimensional ◽  
Optical Microscope ◽  
Dimensional Structure ◽  
Optical Sectioning ◽  
Three Dimensional Structure

A mechanism is described that enables a specimen to be tilted through a known angle and continuously observed under the highest power of the optical microscope. Objects can thus be localized accurately in space. This facility in conjunction with serial optical sectioning by Nomarski optics has been used to construct models of the arrangement of polytene chromosomes in nuclei of Drosophila, Simulium and Chironomus. Telomeres and chromocentre lie on the nuclear envelope. In Simulium they lie close to an equator of the nucleus. Despite these constraints, different nuclei in the same gland do not resemble each other closely.

scholarly journals Three-dimensional reconstructions of haustoria in two parasitic plant species in the Orobanchaceae

2021 ◽  
Author(s):  
Natsumi Masumoto ◽  
Yuki Suzuki ◽  
Songkui Cui ◽  
Mayumi Wakazaki ◽  
Mayuko Sato ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Three Dimensional ◽  
Parasitic Plants ◽  
Cell Types ◽  
Striga Hermonthica ◽  
Microscopy Observation ◽  
Internal Structures ◽  
Facultative Parasite ◽  
Multiple Cell ◽  
Structural Insights

Abstract Parasitic plants infect other plants by forming haustoria, specialized multicellular organs consisting of several cell types, each of which has unique morphological features and physiological roles associated with parasitism. Understanding the spatial organization of cell types is, therefore, of great importance in elucidating the functions of haustoria. Here, we report a three-dimensional (3-D) reconstruction of haustoria from two Orobanchaceae species, the obligate parasite Striga hermonthica infecting rice (Oryza sativa) and the facultative parasite Phtheirospermum japonicum infecting Arabidopsis (Arabidopsis thaliana). In addition, field-emission scanning electron microscopy observation revealed the presence of various cell types in haustoria. Our images reveal the spatial arrangements of multiple cell types inside haustoria and their interaction with host roots. The 3-D internal structures of haustoria highlight differences between the two parasites, particularly at the xylem connection site with the host. Our study provides cellular and structural insights into haustoria of S. hermonthica and P. japonicum and lays the foundation for understanding haustorium function.

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