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Critical Reviews™ in Eukaryotic Gene Expression

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ISSN Druckformat: 1045-4403

ISSN Online: 2162-6502

The Impact Factor measures the average number of citations received in a particular year by papers published in the journal during the two preceding years. 2017 Journal Citation Reports (Clarivate Analytics, 2018) IF: 1.6 To calculate the five year Impact Factor, citations are counted in 2017 to the previous five years and divided by the source items published in the previous five years. 2017 Journal Citation Reports (Clarivate Analytics, 2018) 5-Year IF: 2.2 The Immediacy Index is the average number of times an article is cited in the year it is published. The journal Immediacy Index indicates how quickly articles in a journal are cited. Immediacy Index: 0.3 The Eigenfactor score, developed by Jevin West and Carl Bergstrom at the University of Washington, is a rating of the total importance of a scientific journal. Journals are rated according to the number of incoming citations, with citations from highly ranked journals weighted to make a larger contribution to the eigenfactor than those from poorly ranked journals. Eigenfactor: 0.00058 The Journal Citation Indicator (JCI) is a single measurement of the field-normalized citation impact of journals in the Web of Science Core Collection across disciplines. The key words here are that the metric is normalized and cross-disciplinary. JCI: 0.33 SJR: 0.345 SNIP: 0.46 CiteScore™:: 2.5 H-Index: 67

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Chromosome Territories, Interchromatin Domain Compartment, and Nuclear Matrix: An Integrated View of the Functional Nuclear Architecture

Volumen 10, Ausgabe 2, 2000, 38 pages
DOI: 10.1615/CritRevEukarGeneExpr.v10.i2.60
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ABSTRAKT

Advances in the specific fluorescent labeling of chromatin in fixed and living human cells in combination with three-dimensional (3D) and 4D (space plus time) fluorescence microscopy and image analysis have opened the way for detailed studies of the dynamic, higher-order architecture of chromatin in the human cell nucleus and its potential role in gene regulation. Several features of this architecture are now well established:

  1. Chromosomes occupy distinct territories in the cell nucleus with preferred nuclear locations, although there is no evidence of a rigid suprachromosomal order.
  2. Chromosome territories (CTs) in turn contain distinct chromosome arm domains and smaller chromatin foci or domains with diameters of some 300 to 800 nm and a DNA content in the order of 1 Mbp.
  3. Gene-dense, early-replicating and gene-poor, middle-to-late-replicating chromatin domains exhibit different higher-order nuclear patterns that persist through all stages of interphase. In mitotic chromosomes early replicating chromatin domains give rise to Giemsa light bands, whereas middle-to-late-replicating domains form Giemsa dark bands and C-bands.
In an attempt to integrate these experimental data into a unified view of the functional nuclear architecture, we present a model of a modular and dynamic chromosome territory (CT) organization. We propose that basically three nuclear compartments exist, an "open" higher-order chromatin compartment with chromatin domains containing active genes, a "closed" chromatin compartment comprising inactive genes, and an interchromatin domain (ICD) compartment (Cremer et al., 1993; Zirbel et al., 1993) that contains macromolecular complexes for transcription, splicing, DNA replication, and repair. Genes in "open," but not in "closed" higher-order chromatin compartments have access to transcription and splicing complexes located in the ICD compartment. Chromatin domains that build the "open" chromatin compartment are organized in a way that allows the direct contact of genes and nascent RNA to transcription and splicing complexes, respectively, preformed in the ICD compartment. In contrast, chromatin domains that belong to the "closed" compartment are topologically arranged and compacted in a way that precludes the accessibility of genes to transcription complexes. We argue that the content of the ICD compartment is highly enriched in DNA depleted biochemical matrix preparations. The ICD compartment may be considered as the structural and functional equivalent of the in vivo nuclear matrix. A matrix in this functional sense is compatible with but does not necessitate the concept of a 3D nuclear skeleton existing of long, extensively arborized filaments. In the absence of unequivocal evidence for such a structural matrix in the nucleus of living cells we keep an agnostic attitude about its existence and possible properties in maintaining the higher-order nuclear architecture. Quantitative modeling of the 3D and 4D human genome architecture in situ shows that such an assumption is not necessary to explain presently known aspects of the higher-order nuclear architecture. We expect that the interplay of quantitative modeling and experimental tests will result in a better understanding of the compartmentalized nuclear architecture and its functional consequences.

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  114. Hübner Barbara, Cremer Thomas, Neumann Jürgen, Correlative Microscopy of Individual Cells: Sequential Application of Microscopic Systems with Increasing Resolution to Study the Nuclear Landscape, in Imaging Gene Expression, 1042, 2013. Crossref

  115. Abel Steven, Le Roch Karine G, The role of epigenetics and chromatin structure in transcriptional regulation in malaria parasites, Briefings in Functional Genomics, 18, 5, 2019. Crossref

  116. Zhou Harry Yu, Mitchell Jennifer A., Genome Organization in Cancer Cells, in Systems Analysis of Chromatin-Related Protein Complexes in Cancer, 2014. Crossref

  117. Mantovani Monique, dos Luciano Douglas, Abel Santos, Moreira-Filho Orlando, Conserved 5S and variable 45S rDNA chromosomal localisation revealed by FISH in Astyanax scabripinnis (Pisces, Characidae), Genetica, 123, 3, 2005. Crossref

  118. Cornforth Michael N., Perspectives on the formation of radiation-induced exchange aberrations, DNA Repair, 5, 9-10, 2006. Crossref

  119. Jakob B., Scholz M., Taucher-Scholz G., Biological Imaging of Heavy Charged-Particle Tracks, Radiation Research, 159, 5, 2003. Crossref

  120. Wasserman Wyeth W., Krivan William, In silico identification of metazoan transcriptional regulatory regions, Naturwissenschaften, 90, 4, 2003. Crossref

  121. Moraes Alberto S, Mondin Mateus, Beletti Marcelo E, Aguiar‑Perecin Margarida LR, Guaraldo Ana MA, Mello Maria Luiza S, Age-related association of rDNA and telomeres with the nuclear matrix in mouse hepatocytes, Cell Biology International, 34, 9, 2010. Crossref

  122. Imperador Carlos Henrique L., Bardella Vanessa B., dos Anjos Eli Heber M., Rodrigues Vera L.C.C., Cabral-de-Mello Diogo C., Mello Maria Luiza S., Spatial Distribution of Heterochromatin Bodies in the Nuclei of Triatoma infestans (Klug), Microscopy and Microanalysis, 26, 3, 2020. Crossref

  123. Cremer Thomas, Cremer Marion, Hübner Barbara, Silahtaroglu Asli, Hendzel Michael, Lanctôt Christian, Strickfaden Hilmar, Cremer Christoph, The Interchromatin Compartment Participates in the Structural and Functional Organization of the Cell Nucleus, BioEssays, 42, 2, 2020. Crossref

  124. George Phillip, Kinney Nicholas A., Liang Jiangtao, Onufriev Alexey V., Sharakhov Igor V., Three-dimensional Organization of Polytene Chromosomes in Somatic and Germline Tissues of Malaria Mosquitoes, Cells, 9, 2, 2020. Crossref

  125. Beklemisheva Violetta R., Perelman Polina L., Lemskaya Natalya A., Proskuryakova Anastasia A., Serdyukova Natalya A., Burkanov Vladimir N., Gorshunov Maksim B., Ryder Oliver, Thompson Mary, Lento Gina, O’Brien Stephen J., Graphodatsky Alexander S., Karyotype Evolution in 10 Pinniped Species: Variability of Heterochromatin versus High Conservatism of Euchromatin as Revealed by Comparative Molecular Cytogenetics, Genes, 11, 12, 2020. Crossref

  126. Park Tae Lim, Lee YigJi, Cho Won-Ki, Visualization of chromatin higher-order structures and dynamics in live cells, BMB Reports, 54, 10, 2021. Crossref

  127. Lam Eric, Kato Naohiro, Watanabe Koichi, VISUALIZING CHROMOSOME STRUCTURE/ORGANIZATION, Annual Review of Plant Biology, 55, 1, 2004. Crossref

  128. Wong Xianrong, Cutler Jevon A, Hoskins Victoria E, Gordon Molly, Madugundu Anil K, Pandey Akhilesh, Reddy Karen L, Mapping the micro-proteome of the nuclear lamina and lamina-associated domains, Life Science Alliance, 4, 5, 2021. Crossref

  129. Gil Laura, Niño Sandra A., Guerrero Carmen, Jiménez-Capdeville María E., Phospho-Tau and Chromatin Landscapes in Early and Late Alzheimer’s Disease, International Journal of Molecular Sciences, 22, 19, 2021. Crossref

  130. Fraser Peter, Engel James Douglas, Constricting restricted transcription: the (actively?) shrinking web, Genes & Development, 20, 11, 2006. Crossref

  131. Spector David L., The Dynamics of Chromosome Organization and Gene Regulation, Annual Review of Biochemistry, 72, 1, 2003. Crossref

  132. Morimoto Hiromu, Ueno Misuzu, Tanabe Hideyuki, Kono Tomohiro, Ogawa Hidehiko, Cui Wei, Progesterone depletion results in Lamin B1 loss and induction of cell death in mouse trophoblast giant cells, PLOS ONE, 16, 7, 2021. Crossref

  133. Lipps Hans J., Postberg Jan, Jackson Dean A., Postberg Jan, Lipps Hans J., Cremer Thomas, Evolutionary origin of the cell nucleus and its functional architecture, Essays in Biochemistry, 48, 2010. Crossref

  134. Smeets Daniel, Markaki Yolanda, Schmid Volker J, Kraus Felix, Tattermusch Anna, Cerase Andrea, Sterr Michael, Fiedler Susanne, Demmerle Justin, Popken Jens, Leonhardt Heinrich, Brockdorff Neil, Cremer Thomas, Schermelleh Lothar, Cremer Marion, Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci, Epigenetics & Chromatin, 7, 1, 2014. Crossref

  135. Thurman Robert E., Day Nathan, Noble William S., Stamatoyannopoulos John A., Identification of higher-order functional domains in the human ENCODE regions, Genome Research, 17, 6, 2007. Crossref

  136. Scherrer Klaus, Jost Jürgen, Gene and genon concept: coding versus regulation, Theory in Biosciences, 126, 2, 2007. Crossref

  137. Xu Qinghao, Li Mo, Adams Jessica, Cai Haini N., Nuclear location of a chromatin insulator in Drosophila melanogaster , Journal of Cell Science, 117, 7, 2004. Crossref

  138. Albiez Heiner, Cremer Marion, Tiberi Cinzia, Vecchio Lorella, Schermelleh Lothar, Dittrich Sandra, Küpper Katrin, Joffe Boris, Thormeyer Tobias, von Hase Johann, Yang Siwei, Rohr Karl, Leonhardt Heinrich, Solovei Irina, Cremer Christoph, Fakan Stanislav, Cremer Thomas, Chromatin domains and the interchromatin compartment form structurally defined and functionally interacting nuclear networks, Chromosome Research, 14, 7, 2006. Crossref

  139. Kirsch-Volders Micheline, Fenech Michael, Aneuploidy, inflammation and diseases, Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 824, 2022. Crossref

  140. Maldonado Rebecca J. Kaddis, Rice Breanna, Chen Eunice C., Tuffy Kevin M., Chiari Estelle F., Fahrbach Kelly M., Hope Thomas J., Parent Leslie J., Goff Stephen P., Visualizing Association of the Retroviral Gag Protein with Unspliced Viral RNA in the Nucleus, mBio, 11, 2, 2020. Crossref

  141. Vukojević Vladana, Papadopoulos Dimitrios K., Terenius Lars, Gehring Walter J., Rigler Rudolf, Quantitative study of synthetic Hox transcription factor–DNA interactions in live cells, Proceedings of the National Academy of Sciences, 107, 9, 2010. Crossref

  142. Ravi Maddaly, Ramanathan Srishti, Krishna Krupa, Factors, mechanisms and implications of chromatin condensation and chromosomal structural maintenance through the cell cycle, Journal of Cellular Physiology, 235, 2, 2020. Crossref

  143. Zhang Nianxiang, Kaur Ramandeep, Lu Xiaoyan, Shen Xi, Li Lei, Legerski Randy J., The Pso4 mRNA Splicing and DNA Repair Complex Interacts with WRN for Processing of DNA Interstrand Cross-links, Journal of Biological Chemistry, 280, 49, 2005. Crossref

  144. Scherrer Klaus, Primary transcripts: From the discovery of RNA processing to current concepts of gene expression ‐ Review, Experimental Cell Research, 373, 1-2, 2018. Crossref

  145. Almassalha Luay M., Bauer Greta M., Chandler John E., Gladstein Scott, Cherkezyan Lusik, Stypula-Cyrus Yolanda, Weinberg Samuel, Zhang Di, Thusgaard Ruhoff Peder, Roy Hemant K., Subramanian Hariharan, Chandel Navdeep S., Szleifer Igal, Backman Vadim, Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy, Proceedings of the National Academy of Sciences, 113, 42, 2016. Crossref

  146. Majumder Parimal, Cai Haini N., The functional analysis of insulator interactions in the Drosophila embryo , Proceedings of the National Academy of Sciences, 100, 9, 2003. Crossref

  147. Goo Young-Hwa, Sohn Young Chang, Kim Dae-Hwan, Kim Seung-Whan, Kang Min-Jung, Jung Dong-Ju, Kwak Eunyee, Barlev Nickolai A., Berger Shelley L., Chow Vincent T., Roeder Robert G., Azorsa David O., Meltzer Paul S., Suh Pan-Gil, Song Eun Joo, Lee Kong-Joo, Lee Young Chul, Lee Jae Woon, Activating Signal Cointegrator 2 Belongs to a Novel Steady-State Complex That Contains a Subset of Trithorax Group Proteins, Molecular and Cellular Biology, 23, 1, 2003. Crossref

  148. Mesner L. D., Hamlin J. L., Dijkwel P. A., The matrix attachment region in the Chinese hamster dihydrofolate reductase origin of replication may be required for local chromatid separation, Proceedings of the National Academy of Sciences, 100, 6, 2003. Crossref

  149. Dobi Albert, Szemes Marianna, Lee Cheol, Palkovits Miklos, Lim Francis, Gyorgy Andrea, Mahan Mark A., Agoston Denes V., AUF1 Is Expressed in the Developing Brain, Binds to AT-rich Double-stranded DNA, and Regulates Enkephalin Gene Expression, Journal of Biological Chemistry, 281, 39, 2006. Crossref

  150. Edelsbrunner Herbert, Iglesias-Ham Mabel, Multiple covers with balls I: Inclusion–exclusion, Computational Geometry, 68, 2018. Crossref

  151. Razin Sergey V., Ulianov Sergey V., Genome-Directed Cell Nucleus Assembly, Biology, 11, 5, 2022. Crossref

  152. Cremer Christoph, Birk Udo, Spatially modulated illumination microscopy: application perspectives in nuclear nanostructure analysis, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 380, 2220, 2022. Crossref

  153. Reis Bernardo Sgarbi, Jungbluth Achim A., Frosina Denise, Holz Megan, Ritter Erika, Nakayama Eiichi, Ishida Toshiaki, Obata Yuichi, Carver Brett, Scher Howard, Scardino Peter T., Slovin Susan, Subudhi Sumit K., Reuter Victor E., Savage Caroline, Allison James P., Melamed Jonathan, Jäger Elke, Ritter Gerd, Old Lloyd J., Gnjatic Sacha, Prostate Cancer Progression Correlates with Increased Humoral Immune Response to a Human Endogenous Retrovirus GAG Protein, Clinical Cancer Research, 19, 22, 2013. Crossref

  154. Hildenbrand Georg, Rapp Alexander, Spöri Udo, Wagner Christian, Cremer Christoph, Hausmann Michael, Nano-Sizing of Specific Gene Domains in Intact Human Cell Nuclei by Spatially Modulated Illumination Light Microscopy, Biophysical Journal, 88, 6, 2005. Crossref

  155. Elias M. Carolina Q. B., Faria Marcella, Mortara Renato A., Motta Maria Cristina M., de Souza Wanderley, Thiry Marc, Schenkman Sergio, Chromosome Localization Changes in the Trypanosoma cruzi Nucleus , Eukaryotic Cell, 1, 6, 2002. Crossref

  156. Banfalvi Gaspar, Macromolecular Structure of Linearly Arranged Eukaryotic Chromosomes, International Journal of Molecular Sciences, 23, 16, 2022. Crossref

  157. Wiech Thorsten, Timme Sylvia, Riede Florian, Stein Stefan, Schuricke Michael, Cremer Christoph, Werner Martin, Hausmann Michael, Walch Axel, Human archival tissues provide a valuable source for the analysis of spatial genome organization, Histochemistry and Cell Biology, 123, 3, 2005. Crossref

  158. Silahtaroglu Asli, Bridger Joanna M., Lei Elissa P., 3D genome organization, Scientific Reports, 12, 1, 2022. Crossref

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