scholarly journals Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0/G1 interphase nucleus.

1995 ◽  
Vol 130 (6) ◽  
pp. 1239-1249 ◽  
Author(s):  
H Yokota ◽  
G van den Engh ◽  
J E Hearst ◽  
R K Sachs ◽  
B J Trask
Keyword(s):  
Random Walk ◽  
Dna Sequences ◽  
Large Scale ◽  
Loop Model ◽  
Interphase Nuclei ◽  
Attachment Sites ◽  
The Relationship ◽  
Made In ◽  
Random Walk Path

We determined the folding of chromosomes in interphase nuclei by measuring the distance between points on the same chromosome. Over 25,000 measurements were made in G0/G1 nuclei between DNA sequences separated by 0.15-190 megabase pairs (Mbp) on three human chromosomes. The DNA sequences were specifically labeled by fluorescence in situ hybridization. The relationship between mean-square interphase distance and genomic separation has two linear phases, with a transition at approximately 2 Mbp. This biphasic relationship indicates the existence of two organizational levels at scales > 100 kbp. On one level, chromatin appears to be arranged in large loops several Mbp in size. Within each loop, chromatin is randomly folded. On the second level, specific loop-attachment sites are arranged to form a supple, backbonelike structure, which also shows characteristic random walk behavior. This random walk/giant loop model is the simplest model that fully describes the observed large-scale spatial relationships. Additional evidence for large loops comes from measurements among probes in Xq28, where interphase distance increases and then locally decreases with increasing genomic separation.

Genomic organization and dynamics of repetitive DNA sequences in representatives of three Fagaceae genera

Genome ◽  
2012 ◽  
Vol 55 (5) ◽  
pp. 348-359 ◽  
Author(s):  
Sofia Alves ◽  
Teresa Ribeiro ◽  
Vera Inácio ◽  
Margarida Rocheta ◽  
Leonor Morais-Cecílio
Keyword(s):  
Dna Sequences ◽  
Genome Organization ◽  
Genomic Organization ◽  
Fish Analysis ◽  
Genome Composition ◽  
Interphase Nuclei ◽  
Specific Primers ◽  
Important Species ◽  
The Relationship ◽  
Quercus Rotundifolia

Oaks, chestnuts, and beeches are economically important species of the Fagaceae. To understand the relationship between these members of this family, a deep knowledge of their genome composition and organization is needed. In this work, we have isolated and characterized several AFLP fragments obtained from Quercus rotundifolia Lam. through homology searches in available databases. Genomic polymorphisms involving some of these sequences were evaluated in two species of Quercus , one of Castanea , and one of Fagus with specific primers. Comparative FISH analysis with generated sequences was performed in interphase nuclei of the four species, and the co-immunolocalization of 5-methylcytosine was also studied. Some of the sequences isolated proved to be genus-specific, while others were present in all the genera. Retroelements, either gypsy-like of the Tat/Athila clade or copia-like, are well represented, and most are dispersed in euchromatic regions of these species with no DNA methylation associated, pointing to an interspersed arrangement of these retroelements with potential gene-rich regions. A particular gypsy-sequence is dispersed in oaks and chestnut nuclei, but its confinement to chromocenters in beech evidences genome restructuring events during evolution of Fagaceae. Several sequences generated in this study proved to be good tools to comparatively study Fagaceae genome organization.

Use of fluorescence in situ hybridization to study the arrangement of DNA sequences in normal and disease-related chromosomes

1995 ◽  
Vol 53 ◽  
pp. 748-749
Author(s):  
Barbara J. F. Trask ◽  
Hillary Massa ◽  
Cynthia Friedman ◽  
Richard Esposito ◽  
Ger van den Engh ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Dna Sequences ◽  
Single Copy ◽  
Two Dimensions ◽  
Genetic Maps ◽  
Epifluorescence Microscopy ◽  
Metaphase Chromosomes ◽  
Interphase Nuclei

The sites of specific DNA sequences can be fluorescently tagged by fluorescence in situ hybridization (FISH). Different sequences can be labeled with different fluorochromes so that their arrangement can be studied using epifluorescence microscopy. The distances between points on the same or different chromosomes can be determined easily in a large number of interphase nuclei or metaphase chromosomes. A variety of probe types, ranging from single-copy sequences to highly repeated sequences can be employed. Our work has focussed on the analysis of hybridization patterns in two dimensions using conventional fluorescence microscopy.We have used FISH to study various aspects of genome organization that are difficult to study using other techniques. Examples of these applications will be presented.FISH is now the method of choice for determining the chromosomal location of DNA sequences. DNA sequences can be positioned in the genome with <1:1000 accuracy (to a 3-Mbp region within a 3000-Mbp genome). Through FISH, the cytogenetic, physical and genetic maps of chromosomes can be linked.

Evaluating the relationship between SIF and GPP under climate extremes

2021 ◽  
Author(s):  
Sebastian Wieneke ◽  
Ana Bastos ◽  
Manuela Balzarolo ◽  
José Miguel Barrios ◽  
Ivan Janssens
Keyword(s):  
Large Scale ◽  
Gross Primary Production ◽  
Vegetation Indices ◽  
Climate Extremes ◽  
Vegetation Stress ◽  
Linear Relationships ◽  
Forest Sites ◽  
Good Proxy ◽  
The Relationship

&lt;p&gt;Sun Induced Chlorophyll Fluorescence (SIF) is considered as a good proxy for photosynthesis given its closer link to the photosynthetic light reactions compared to remote sensing vegetation indices typically used for ecosystem productivity modelling (eg. NDVI). Satellite-based SIF shows significant linear relationships with gross primary production (GPP) from in-situ measurements across sites, biomes and seasons. While SIF can be considered a good proxy for large scale spatial and seasonal variability in GPP, much of the SIF-GPP co-variance can be explained by their common dependence on the absorbed photosynthetically active radiation. Whether SIF can be an equally good proxy for interannual variability in GPP especially during periods of vegetation stress (drought/heat) is, so far, not clear.&lt;/p&gt;&lt;p&gt;In this study, we evaluate the relationship between satellite-based SIF and in-situ GPP measurements during vegetation stress periods (drought/heat), compared to non-stress periods. GPP is obtained from eddy-covariance measurements from a set of forest sites pre-filtered to ensure homonegeous footprints. SIF is obtained from GOME-2 covering the period 2007-2018. Because of scale mismatch between each site&amp;#8217;s footprint (in the order of hundred meters) and the spatial resolution of GOME-2 (ca. 50km), we additionally use SIF from the downscale product from Duveiller et al. 2020 (ca. 5km) and the more recent dataset from TROPOMI (ca. 7 x 3.5 km), covering only the last year of the study period.&lt;/p&gt;&lt;p&gt;We develop a classification of stress periods that is based on both the occurrence of drought/heat extreme events and the presence of photosynthetic downregulation. We then evaluate the relationship between SIF and GPP and their yields, for different plant functional types and at site-level. We evaluate how these relationships vary depending on environmental conditions and in particular for &amp;#8220;stress&amp;#8221; versus &amp;#8220;non-stress&amp;#8221; days.&lt;/p&gt;&lt;p&gt;Duveiller, G., Filipponi, F., Walther, S., K&amp;#246;hler, P., Frankenberg, C., Guanter, L., and Cescatti, A.: A spatially downscaled sun-induced fluorescence global product for enhanced monitoring of vegetation productivity, Earth Syst. Sci. Data, 12, 1101&amp;#8211;1116, https://doi.org/10.5194/essd-12-1101-2020, 2020.&lt;/p&gt;

Differential dissociation of chromatin digests: a novel approach revealing a hierarchy of DNA-protein interactions within chromatin domains

1991 ◽  
Vol 99 (3) ◽  
pp. 503-513
Author(s):  
A.V. Lichtenstein ◽  
M.M. Zaboikin ◽  
N.I. Sjakste ◽  
R.P. Alechina
Keyword(s):  
Protein Interactions ◽  
Dna Sequences ◽  
Attachment Site ◽  
Chromatin Domain ◽  
Dna Fragments ◽  
S1 Nuclease ◽  
Novel Approach ◽  
Attachment Sites ◽  
Dna Protein Interactions

We describe here a novel approach to the dissection of chromatin structure by extracting DNA fragments from digested nuclei irreversibly immobilized (via proteins) on Celite columns. Three successive gradients (NaCl, LiCl-urea, temperature) are used to release three families of DNA fragments: namely, the ‘DNA adherence’ classes DNA-0, DNA-I and DNA-II, respectively. This ‘protein image’ DNA chromatography separates DNA fragments in accordance with the tightness of their bonds with proteins in situ. There are at least two DNA-skeleton attachment sites differing from each other by their resistance to the dissociating agents used as well as their susceptibility to DNAase I and S1 nuclease treatments, DNA cross-linking and single-stranded breaks. Several lines of evidence show a specific, topological rather than chemical, DNA-protein linkage at the tight attachment site. A hierarchy of chromatin loops demarcated by these attachment sites was determined. The technique described is generally applicable and can be used both to probe DNA-protein interactions and to map specific DNA sequences within the chromatin domain.

Nuclear envelopes: Structure and biochemistry of the nuclear envelope

1974 ◽  
Vol 268 (891) ◽  
pp. 67-93 ◽  
Keyword(s):  
Nuclear Genome ◽  
Cell Types ◽  
Structure Lipid ◽  
Attachment Sites ◽  
Enzyme Pattern ◽  
The Stability ◽  
Pore Complexes ◽  
The Relationship ◽  
Kinetics Of

The ultrastructure of the nuclear evelope is described in various cell types with special emphasis on its pore complexes (p.c.). The architecture of the p.c. is defined against the properties of other membranous pore formations. Evidence is presented that the non-membranous p.c. components contain ribonucleoproteins but do not represent the attachment sites of nuclear chromatin. The possible dynamic nature of the p.c. material is discussed in relation to nucleocytoplasmic translocation processes. DNA of the nuclear genome is firmly attached to interporous sections of the inner nuclear membrane. The stability of this attachment is demonstrated, and chemical and conformational characteristics as well as periods and kinetics of replication are given for both isolated membrane DNA and the corresponding chromatin in situ . The membrane-associated chromatin is dominated by a heterochromatinous character; it does not represent a transitory membrane interaction of replicating DNA. It is hypothesized that membraneattachment of specific regions of the chromosomes are a means to their ordered arrangement during interphase and prophase. Structure, lipid, protein and enzyme pattern of the nuclear membranes, as well as the incorporation kinetics, underline the relationship to the endoplasmic reticulum.

scholarly journals Interphase and metaphase detection of the breakpoint of 14q32 translocations in B-cell malignancies by double-color fluorescence in situ hybridization

Blood ◽  
1995 ◽  
Vol 85 (11) ◽  
pp. 3223-3228 ◽  
Author(s):  
M Taniwaki ◽  
K Nishida ◽  
Y Ueda ◽  
S Misawa ◽  
M Nagai ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
B Cell ◽  
Fluorescence In Situ Hybridization ◽  
Cell Lines ◽  
Dna Sequences ◽  
Lymphoblastic Leukemia ◽  
Breakpoint Region ◽  
Interphase Nuclei ◽  
B Cell Malignancies

The breakpoint of 14q32 translocations found in B-cell malignancies was delineated specifically in both metaphase spreads and interphase nuclei by double-color fluorescence in situ hybridization (FISH) using bacteriophage clones containing the human immunoglobulin gamma chain gene locus (Ig gamma) and a cosmid clone, CY24–68, containing VH segments. CY24–68 is more telomeric than Ig gamma, separated by approximately 1 megabase (Mb). FISH studies were performed on four patients with non-Hodgkin's lymphoma (NHL), one with acute lymphoblastic leukemia (ALL), one with plasma cell leukemia (PCL), and three cell lines. In each patient with t(8;14), t(14;18), and t(3;14), the signal of Ig gamma gene was observed on der(14) and that of CY24–68 at respective partner sites of these translocations, 8q24.1, 18q21.3, and 3q27. Interphase nuclei with a signal of Ig gamma clearly separated from that of CY24–68 were more frequently encountered in all of the patients (45% to 74%) than those in normal controls (4% to 5%). Even in cases where only interphase nuclei were available for FISH studies, 14q32 translocations are detected as shown in two patients each with NHL and t(11;14)-carrying PCL. In two cell lines, HS-1 derived from ALL carrying t(8;14) and FR4 derived from a plasmacytoma carrying a complex form of t(8;14), the signal of Ig gamma was observed at the breakpoint region 8q24.1 of the der(8) in addition to the der(14), indicating that translocation event occurred within the Ig gamma locus. Intense Ig gamma signal was found at the breakpoint region on the der(14)t(11;14) in HBL-2 derived from NHL, indicating amplification of the Ig gamma gene, and presumably the resultant chimeric DNA between Ig gamma and DNA sequences at 11q13. The present approach allowed us to unequivocally detect tumor-specific breakpoints of 14q32 translocations. Furthermore, interphase FISH provides a rapid diagnostic procedure to detect 14q32 translocations in B-cell malignancies.

Thalamic and Cortical Contributions to Neural Plasticity After Limb Amputation

2000 ◽  
Vol 83 (5) ◽  
pp. 3154-3159 ◽  
Author(s):  
S. L. Florence ◽  
T. A. Hackett ◽  
F. Strata
Keyword(s):  
Neural Plasticity ◽  
Large Scale ◽  
Receptive Fields ◽  
Cortical Reorganization ◽  
Limb Amputation ◽  
The Face ◽  
The Relationship ◽  
Area 3B ◽  
Made In ◽  
Stimulation Of

Little is known about the substrates for the large-scale shifts in the cortical representation produced by limb amputation. Subcortical changes likely contribute to the cortical remodeling, yet there is little data regarding the extent and pattern of reorganization in thalamus after such a massive deafferentation. Moreover, the relationship between changes in thalamus and in cortex after injuries of this nature is virtually unexplored. Multiunit microelectrode maps were made in the somatosensory thalamus and cortex of two monkeys that had long-standing, accidental forelimb amputations. In the deprived portion of the ventroposterior nucleus of the thalamus (VP), where stimulation to the hand would normally activate neurons, new receptive fields had emerged. At some recording sites within the deprived zone of VP, neurons responded to stimulation of the remaining stump of the arm and at other sites neurons responded to stimulation of both the stump and the face. This same overall pattern of reorganization was present in the deprived hand representation of cortical area 3b. Thus thalamic changes produced by limb amputation appear to be an important substrate of cortical reorganization. However, a decrease in the frequency of abnormal stump/face fields in area 3b compared with VP and a reduction in the size of the fields suggests that cortical mechanisms of plasticity may refine the information relayed from thalamus.

Scaffold attachments within the human genome

1997 ◽  
Vol 110 (21) ◽  
pp. 2673-2682 ◽  
Author(s):  
J.M. Craig ◽  
S. Boyle ◽  
P. Perry ◽  
W.A. Bickmore
Keyword(s):  
Dna Sequences ◽  
Constitutive Heterochromatin ◽  
In Situ Hybridisation ◽  
Fluorescence In Situ Hybridisation ◽  
Loop Size ◽  
Inactive X Chromosome ◽  
Attachment Sites ◽  
The Matrix ◽  
Eukaryotic Chromatin

It is generally agreed that, above the level of the 30 nm fibre, eukaryotic chromatin is constrained into loops, but there is disagreement about the nature of the substructure that serves to anchor loops and the DNA sequences that act as the attachment sites. This problem may stem from the very different methods that all purport to separate loop and attached DNAs. We have tested ideas about how the genome is arranged into loops by analysing the average loop size over different cytologically resolvable regions of human chromosomes using fluorescence in situ hybridisation with loop and attached DNA fractions. Variations in average loop size, along and between chromosomes, measurable at this level of resolution were small but significant and were dependent on the extraction method. This emphasises the fundamental differences between the nuclear substructure probed by different protocols. DNA attached to the nuclear ‘scaffold’ or ‘matrix’ hybridises preferentially to gene-poor regions of the genome (G-bands). Conversely, fractions attached to the nuclear ‘skeleton’ hybridise preferentially to gene-rich R-bands and sites of high levels of transcription. The inactive X chromosome has a deficit of associations with the nuclear skeleton but not with the matrix or scaffold. A large excess of attached sequences is found at some sites of constitutive heterochromatin, but not at centromeres.

Absence of Genomic Imprinting at the DiGeorge Locus

1996 ◽  
Vol 45 (1-2) ◽  
pp. 277-280
Author(s):  
D. Theophile ◽  
D. Bérubé ◽  
J. Augé ◽  
M. Vekemans
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Digeorge Syndrome ◽  
Replication Timing ◽  
Proximal Region ◽  
Chromosome 22 ◽  
Interphase Nuclei ◽  
Asynchronous Replication ◽  
Timing Pattern

Fluorescence in situ hybridization (FISH) has been used to visualize specific genomic DNA sequences in interphase nuclei. Timing of replication can be measured by FISH to interphase nuclei: nuclei with a sequence that has not replicated reveal two single signals (G1), whereas those in which the sequence has replicated show two signal doublets (G2). Asynchronous nuclei show a single signal on one allele and a double hybridization dot on the other homologue. In general, most sequences replicate synchronously on the two homologues, with only 10% of nuclei showing an asynchronous hybridization pattern. However, for the sequences known about to be imprinted, approximately 30% of nuclei reveal asynchronous replication. Little is known whether or not the proximal region of chromosome 22, involved in the DiGeorge syndrome [1], is imprinted. We have, therefore, examined the replication timing pattern of the DiGeorge critical region (DGCR).

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