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Heterochromatin Is No Longer the Dark Side of the Genome:...
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Heterochromatin Is No Longer the Dark Side of the Genome: A Themed Issue in Honor of Prof. Sergio Pimpinelli

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cell Nuclei: Function, Transport and Receptors".

Deadline for manuscript submissions: closed (15 November 2022) | Viewed by 34786

Special Issue Editors

Prof. Dr. Laura Fanti

E-Mail Website
Guest Editor
Department of Biology and Biotechnology “Charles Darwin”, Laboratory of Epigenetics, “Sapienza” University of Rome, Rome, Italy
Interests: transposable elements; epigenetics; chromosome organization; genome evolution
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Patrizio Dimitri

E-Mail Website
Guest Editor
Department of Biology and Biotechnology “Charles Darwin”, Laboratory of Epigenetics, “Sapienza” University of Rome, Rome, Italy
Interests: chromosome biology; genome evolution; heterochromatin; epigenetics; chromatin remodeling; cytokinesis; drosophila
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Heterochromatin has long been considered the inert portion of the genome devoid of biological significance. However, during the last few decades, important advances have been achieved toward understanding of its apparently elusive nature. Sergio Pimpinelli is a well-known scientist for his studies on two interconnected research fields concerning heterochromatin: (i) the biology of the chromosome, with particular regard to the cytological and molecular organization of constitutive heterochromatin and telomeres, and (ii) the genomic organization of transposons and the regulation of their activity. Sergio Pimpinelli showed for the first time that constitutive heterochromatin, instead of being a homogeneous material as previously thought, is composed of regions with different cytochemical characteristics (Nature, 1974). The considerable interest aroused by these seminal studies triggered an international line of research that led to the discovery of significant roles of heterochromatin contributing to the functions and evolution of genomes. Heterochromatin was indeed found to carry functional genes and to play important roles in ensuring chromosomal and genome integrity and in the regulation of gene expression. Heterochromatin is also involved in several biological processes, such as that development and differentiation, and aging and its epigenetic perturbations, can cause human diseases including cancer. The development of third-generation sequencing and other technologies will allow new discoveries about heterochromatin in the future. The aim of this Special Issue is to present a collection of papers reporting the latest research advances on the biology of this peculiar genomic component.

Prof. Laura Fanti
Prof. Dimitri Patrizio
Guest Editors

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Keywords

  • heterochromatin
  • repetitive DNA
  • transposable elements
  • centromere
  • telomere
  • genome instability
  • epigenetics
  • position effects
  • aging and disease
  • chromosome evolution

Published Papers (13 papers)

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Research

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20 pages, 4097 KiB  
Article
WiFi Related Radiofrequency Electromagnetic Fields Promote Transposable Element Dysregulation and Genomic Instability in Drosophila melanogaster
by Ugo Cappucci, Assunta Maria Casale, Mirena Proietti, Fiorenzo Marinelli, Livio Giuliani and Lucia Piacentini
Cells 2022, 11(24), 4036; https://0-doi-org.brum.beds.ac.uk/10.3390/cells11244036 - 13 Dec 2022
Cited by 2 | Viewed by 5704
Abstract
Exposure to artificial radio frequency electromagnetic fields (RF-EMFs) has greatly increased in recent years, thus promoting a growing scientific and social interest in deepening the biological impact of EMFs on living organisms. The current legislation governing the exposure to RF-EMFs is based exclusively [...] Read more.
Exposure to artificial radio frequency electromagnetic fields (RF-EMFs) has greatly increased in recent years, thus promoting a growing scientific and social interest in deepening the biological impact of EMFs on living organisms. The current legislation governing the exposure to RF-EMFs is based exclusively on their thermal effects, without considering the possible non-thermal adverse health effects from long term exposure to EMFs. In this study we investigated the biological non-thermal effects of low-level indoor exposure to RF-EMFs produced by WiFi wireless technologies, using Drosophila melanogaster as the model system. Flies were exposed to 2.4 GHz radiofrequency in a Transverse Electromagnetic (TEM) cell device to ensure homogenous controlled fields. Signals were continuously monitored during the experiments and regulated at non thermal levels. The results of this study demonstrate that WiFi electromagnetic radiation causes extensive heterochromatin decondensation and thus a general loss of transposable elements epigenetic silencing in both germinal and neural tissues. Moreover, our findings provide evidence that WiFi related radiofrequency electromagnetic fields can induce reactive oxygen species (ROS) accumulation, genomic instability, and behavioural abnormalities. Finally, we demonstrate that WiFi radiation can synergize with RasV12 to drive tumor progression and invasion. All together, these data indicate that radiofrequency radiation emitted from WiFi devices could exert genotoxic effects in Drosophila and set the stage to further explore the biological effects of WiFi electromagnetic radiation on living organisms. Full article
(This article belongs to the Special Issue Heterochromatin Is No Longer the Dark Side of the Genome: A Themed Issue in Honor of Prof. Sergio Pimpinelli)
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22 pages, 4325 KiB  
Article
A Spontaneous Inversion of the X Chromosome Heterochromatin Provides a Tool for Studying the Structure and Activity of the Nucleolus in Drosophila melanogaster
by Tatyana D. Kolesnikova, Mikhail S. Klenov, Alina R. Nokhova, Sergey A. Lavrov, Galina V. Pokholkova, Veit Schubert, Svetlana V. Maltseva, Kevin R. Cook, Michael J. Dixon and Igor F. Zhimulev
Cells 2022, 11(23), 3872; https://0-doi-org.brum.beds.ac.uk/10.3390/cells11233872 - 01 Dec 2022
Viewed by 1790
Abstract
The pericentromeric heterochromatin is largely composed of repetitive sequences, making it difficult to analyze with standard molecular biological methods. At the same time, it carries many functional elements with poorly understood mechanisms of action. The search for new experimental models for the analysis [...] Read more.
The pericentromeric heterochromatin is largely composed of repetitive sequences, making it difficult to analyze with standard molecular biological methods. At the same time, it carries many functional elements with poorly understood mechanisms of action. The search for new experimental models for the analysis of heterochromatin is an urgent task. In this work, we used the Rif1 mutation, which suppresses the underreplication of all types of repeated sequences, to analyze heterochromatin regions in polytene chromosomes of Drosophila melanogaster. In the Rif1 background, we discovered and described in detail a new inversion, In(1)19EHet, which arose on a chromosome already carrying the In(1)sc8 inversion and transferred a large part of X chromosome heterochromatin, including the nucleolar organizer to a new euchromatic environment. Using nanopore sequencing and FISH, we have identified the eu- and heterochromatin breakpoints of In(1)19EHet. The combination of the new inversion and the Rif1 mutation provides a promising tool for studies of X chromosome heterochromatin structure, nucleolar organization, and the nucleolar dominance phenomenon. In particular, we found that, with the complete polytenization of rDNA repeats, the nucleolus consists of a cloud-like structure corresponding to the classical nucleolus of polytene chromosomes, as well as an unusual intrachromosomal structure containing alternating transcriptionally active and inactive regions. Full article
(This article belongs to the Special Issue Heterochromatin Is No Longer the Dark Side of the Genome: A Themed Issue in Honor of Prof. Sergio Pimpinelli)
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18 pages, 3603 KiB  
Article
The Drosophila simulans Genome Lacks the crystal-Stellate System
by Anna De Grassi, Patrizia Tritto, Valeria Palumbo, Maria Pia Bozzetti and Maria Francesca Berloco
Cells 2022, 11(23), 3725; https://0-doi-org.brum.beds.ac.uk/10.3390/cells11233725 - 22 Nov 2022
Viewed by 1170
Abstract
The cry-Ste system is a genetic interaction system between heterochromatin and euchromatin in Drosophila melanogaster, regulated via the piRNA pathway. Deregulation of this system leads to meiotic defects and male sterility. Although the cry-Ste system is peculiar to D. melanogaster, ancestors [...] Read more.
The cry-Ste system is a genetic interaction system between heterochromatin and euchromatin in Drosophila melanogaster, regulated via the piRNA pathway. Deregulation of this system leads to meiotic defects and male sterility. Although the cry-Ste system is peculiar to D. melanogaster, ancestors of Ste and Su(Ste) elements are present in the three closely related species, D. simulans, D. sechellia, and D. mauritiana. The birth, evolution, and maintenance of this genetic system in Drosophila melanogaster are of interest. We investigate the presence of sequences homologous to cry and Ste elements in the simulans complex and describe their chromosomal distribution. The organization and expression of cry- and Ste-like sequences were further characterized in the D. simulans genome. Our results allow us to conclude that the cry-Ste genetic interaction system is absent in the D. simulans genome. Full article
(This article belongs to the Special Issue Heterochromatin Is No Longer the Dark Side of the Genome: A Themed Issue in Honor of Prof. Sergio Pimpinelli)
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18 pages, 2901 KiB  
Article
Identification of the Telomere elongation Mutation in Drosophila
by Hemakumar M. Reddy, Thomas A. Randall, Francesca Cipressa, Antonella Porrazzo, Giovanni Cenci, Radmila Capkova Frydrychova and James M. Mason
Cells 2022, 11(21), 3484; https://0-doi-org.brum.beds.ac.uk/10.3390/cells11213484 - 03 Nov 2022
Viewed by 1994
Abstract
Telomeres in Drosophila melanogaster, which have inspired a large part of Sergio Pimpinelli work, are similar to those of other eukaryotes in terms of their function. Yet, their length maintenance relies on the transposition of the specialized retrotransposons Het-A, TART, [...] Read more.
Telomeres in Drosophila melanogaster, which have inspired a large part of Sergio Pimpinelli work, are similar to those of other eukaryotes in terms of their function. Yet, their length maintenance relies on the transposition of the specialized retrotransposons Het-A, TART, and TAHRE, rather than on the activity of the enzyme telomerase as it occurs in most other eukaryotic organisms. The length of the telomeres in Drosophila thus depends on the number of copies of these transposable elements. Our previous work has led to the isolation of a dominant mutation, Tel1, that caused a several-fold elongation of telomeres. In this study, we molecularly identified the Tel1 mutation by a combination of transposon-induced, site-specific recombination and next-generation sequencing. Recombination located Tel1 to a 15 kb region in 92A. Comparison of the DNA sequence in this region with the Drosophila Genetic Reference Panel of wild-type genomic sequences delimited Tel1 to a 3 bp deletion inside intron 8 of Ino80. Furthermore, CRISPR/Cas9-induced deletions surrounding the same region exhibited the Tel1 telomere phenotype, confirming a strict requirement of this intron 8 gene sequence for a proper regulation of Drosophila telomere length. Full article
(This article belongs to the Special Issue Heterochromatin Is No Longer the Dark Side of the Genome: A Themed Issue in Honor of Prof. Sergio Pimpinelli)
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21 pages, 2128 KiB  
Article
Characterization of Gfat1 (zeppelin) and Gfat2, Essential Paralogous Genes Which Encode the Enzymes That Catalyze the Rate-Limiting Step in the Hexosamine Biosynthetic Pathway in Drosophila melanogaster
by Shawn Cotsworth, Catherine J. Jackson, Graham Hallson, Kathleen A. Fitzpatrick, Monika Syrzycka, Alistair B. Coulthard, Amy Bejsovec, Marcella Marchetti, Sergio Pimpinelli, Simon J. H. Wang, Robert G. Camfield, Esther M. Verheyen, Donald A. Sinclair, Barry M. Honda and Arthur J. Hilliker
Cells 2022, 11(3), 448; https://0-doi-org.brum.beds.ac.uk/10.3390/cells11030448 - 27 Jan 2022
Cited by 3 | Viewed by 3524
Abstract
The zeppelin (zep) locus is known for its essential role in the development of the embryonic cuticle of Drosophila melanogaster. We show here that zep encodes Gfat1 (Glutamine: Fructose-6-Phosphate Aminotransferase 1; CG12449), the enzyme that catalyzes the [...] Read more.
The zeppelin (zep) locus is known for its essential role in the development of the embryonic cuticle of Drosophila melanogaster. We show here that zep encodes Gfat1 (Glutamine: Fructose-6-Phosphate Aminotransferase 1; CG12449), the enzyme that catalyzes the rate-limiting step in the hexosamine biosynthesis pathway (HBP). This conserved pathway diverts 2%–5% of cellular glucose from glycolysis and is a nexus of sugar (fructose-6-phosphate), amino acid (glutamine), fatty acid [acetyl-coenzymeA (CoA)], and nucleotide/energy (UDP) metabolism. We also describe the isolation and characterization of lethal mutants in the euchromatic paralog, Gfat2 (CG1345), and demonstrate that ubiquitous expression of Gfat1+ or Gfat2+ transgenes can rescue lethal mutations in either gene. Gfat1 and Gfat2 show differences in mRNA and protein expression during embryogenesis and in essential tissue-specific requirements for Gfat1 and Gfat2, suggesting a degree of functional evolutionary divergence. An evolutionary, cytogenetic analysis of the two genes in six Drosophila species revealed Gfat2 to be located within euchromatin in all six species. Gfat1 localizes to heterochromatin in three melanogaster-group species, and to euchromatin in the more distantly related species. We have also found that the pattern of flanking-gene microsynteny is highly conserved for Gfat1 and somewhat less conserved for Gfat2. Full article
(This article belongs to the Special Issue Heterochromatin Is No Longer the Dark Side of the Genome: A Themed Issue in Honor of Prof. Sergio Pimpinelli)
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17 pages, 1709 KiB  
Article
DNA Environment of Centromeres and Non-Homologous Chromosomes Interactions in Mouse
by Victor Spangenberg, Mikhail Losev, Ilya Volkhin, Svetlana Smirnova, Pavel Nikitin and Oxana Kolomiets
Cells 2021, 10(12), 3375; https://0-doi-org.brum.beds.ac.uk/10.3390/cells10123375 - 01 Dec 2021
Cited by 4 | Viewed by 3848
Abstract
Although the pericentromeric regions of chromosomes that are enriched in tandemly repeated satellite DNA represent a significant part of eukaryotic genomes, they remain understudied, which is mainly due to interdisciplinary knowledge gaps. Recent studies suggest their important role in genome regulation, karyotype stability, [...] Read more.
Although the pericentromeric regions of chromosomes that are enriched in tandemly repeated satellite DNA represent a significant part of eukaryotic genomes, they remain understudied, which is mainly due to interdisciplinary knowledge gaps. Recent studies suggest their important role in genome regulation, karyotype stability, and evolution. Thus, the idea of satellite DNA as a junk part of the genome has been refuted. The integration of data regarding molecular composition, chromosome behaviour, and the details of the in situ organization of pericentromeric regions is of great interest. The objective of this work was a cytogenetic analysis of the interactions between pericentromeric regions from non-homologous chromosomes in mouse spermatocytes using immuno-FISH. We analysed two events: the associations between centromeric regions of the X chromosome and autosomes and the associations between the centromeric regions of the autosomal bivalents that form chromocenters. We concluded that the X chromosome forms temporary synaptic associations with different autosomes in early meiotic prophase I, which can normally be found until the pachytene–diplotene, without signs of pachytene arrest. These associations are formed between the satellite-DNA-rich centromeric regions of the X chromosome and different autosomes but do not involve the satellite-DNA-poor centromeric region of the Y chromosome. We suggest the hypothetical model of X chromosome competitive replacement from such associations during synaptic correction. We showed that the centromeric region of the X chromosome in association remains free of γH2Ax-dependent chromatin inactivation, while the Y chromosome is completely inactivated. This finding highlights the predominant role of associations between satellite DNA-rich regions of different chromosomes, including the X chromosome. We suppose that X-autosomal transient associations are a manifestation of an additional synaptic disorder checkpoint. These associations are normally corrected before the late diplotene stage. We revealed that the intense spreading conditions that were applied to the spermatocyte I nuclei did not lead to the destruction of stretched chromatin fibers of elongated chromocenters enriched in satellite DNA. The tight associations that we revealed between the pericentromeric regions of different autosomal bivalents and the X chromosome may represent the basis for a mechanism for maintaining the repeats stability in the autosomes and in the X chromosome. The consequences of our findings are discussed. Full article
(This article belongs to the Special Issue Heterochromatin Is No Longer the Dark Side of the Genome: A Themed Issue in Honor of Prof. Sergio Pimpinelli)
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32 pages, 6009 KiB  
Article
The Organization of Pericentromeric Heterochromatin in Polytene Chromosome 3 of the Drosophila melanogaster Line with the Rif11; SuURES Su(var)3-906 Mutations Suppressing Underreplication
by Tatyana Zykova, Mariya Maltseva, Fedor Goncharov, Lidia Boldyreva, Galina Pokholkova, Tatyana Kolesnikova and Igor Zhimulev
Cells 2021, 10(11), 2809; https://0-doi-org.brum.beds.ac.uk/10.3390/cells10112809 - 20 Oct 2021
Cited by 1 | Viewed by 2524
Abstract
Although heterochromatin makes up 40% of the Drosophila melanogaster genome, its organization remains little explored, especially in polytene chromosomes, as it is virtually not represented in them due to underreplication. Two all-new approaches were used in this work: (i) with the use of [...] Read more.
Although heterochromatin makes up 40% of the Drosophila melanogaster genome, its organization remains little explored, especially in polytene chromosomes, as it is virtually not represented in them due to underreplication. Two all-new approaches were used in this work: (i) with the use of a newly synthesized Drosophila line that carries three mutations, Rif11, SuURES and Su(var)3-906, suppressing the underreplication of heterochromatic regions, we obtained their fullest representation in polytene chromosomes and described their structure; (ii) 20 DNA fragments with known positions on the physical map as well as molecular genetic features of the genome (gene density, histone marks, heterochromatin proteins, origin recognition complex proteins, replication timing sites and satellite DNAs) were mapped in the newly polytenized heterochromatin using FISH and bioinformatics data. The borders of the heterochromatic regions and variations in their positions on arm 3L have been determined for the first time. The newly polytenized heterochromatic material exhibits two main types of morphology: a banding pattern (locations of genes and short satellites) and reticular chromatin (locations of large blocks of satellite DNA). The locations of the banding and reticular polytene heterochromatin was determined on the physical map. Full article
(This article belongs to the Special Issue Heterochromatin Is No Longer the Dark Side of the Genome: A Themed Issue in Honor of Prof. Sergio Pimpinelli)
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Review

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12 pages, 826 KiB  
Review
Chromosome Tug of War: Dicentric Chromosomes and the Centromere Strength Hypothesis
by Hunter J. Hill and Kent G. Golic
Cells 2022, 11(22), 3550; https://0-doi-org.brum.beds.ac.uk/10.3390/cells11223550 - 10 Nov 2022
Viewed by 1476
Abstract
It has been 70 years since the concept of varied centromere strengths was introduced based on the behavior of dicentric chromosomes. One of the key conclusions from those early experiments was that some centromeres could pull with sufficient force to break a dicentric [...] Read more.
It has been 70 years since the concept of varied centromere strengths was introduced based on the behavior of dicentric chromosomes. One of the key conclusions from those early experiments was that some centromeres could pull with sufficient force to break a dicentric chromosome bridge, while others could not. In the ensuing decades there have been numerous studies to characterize strengths of the various components involved, such as the spindle, the kinetochore, and the chromosome itself. We review these various measurements to determine if the conclusions about centromere strength are supported by current evidence, with special attention to characterization of Drosophila melanogaster kinetochores upon which the original conclusions were based. Full article
(This article belongs to the Special Issue Heterochromatin Is No Longer the Dark Side of the Genome: A Themed Issue in Honor of Prof. Sergio Pimpinelli)
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19 pages, 1302 KiB  
Review
The Green Valley of Drosophila melanogaster Constitutive Heterochromatin: Protein-Coding Genes Involved in Cell Division Control
by Giovanni Messina, Yuri Prozzillo, Greta Bizzochi, Renè Massimiliano Marsano and Patrizio Dimitri
Cells 2022, 11(19), 3058; https://0-doi-org.brum.beds.ac.uk/10.3390/cells11193058 - 29 Sep 2022
Cited by 3 | Viewed by 1904
Abstract
Constitutive heterochromatin represents a significant fraction of eukaryotic genomes (10% in Arabidopsis, 20% in humans, 30% in D. melanogaster, and up to 85% in certain nematodes) and shares similar genetic and molecular properties in animal and plant species. Studies conducted over the [...] Read more.
Constitutive heterochromatin represents a significant fraction of eukaryotic genomes (10% in Arabidopsis, 20% in humans, 30% in D. melanogaster, and up to 85% in certain nematodes) and shares similar genetic and molecular properties in animal and plant species. Studies conducted over the last few years on D. melanogaster and other organisms led to the discovery of several functions associated with constitutive heterochromatin. This made it possible to revise the concept that this ubiquitous genomic territory is incompatible with gene expression. The aim of this review is to focus the attention on a group of protein-coding genes resident in D. melanogaster constitutive of heterochromatin, which are implicated in different steps of cell division. Full article
(This article belongs to the Special Issue Heterochromatin Is No Longer the Dark Side of the Genome: A Themed Issue in Honor of Prof. Sergio Pimpinelli)
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9 pages, 919 KiB  
Review
The Cell Biology of Heterochromatin
by Brandt Warecki and William Sullivan
Cells 2022, 11(7), 1247; https://0-doi-org.brum.beds.ac.uk/10.3390/cells11071247 - 06 Apr 2022
Cited by 1 | Viewed by 2749
Abstract
A conserved feature of virtually all higher eukaryotes is that the centromeres are embedded in heterochromatin. Here we provide evidence that this tight association between pericentric heterochromatin and the centromere is essential for proper metaphase exit and progression into telophase. Analysis of chromosome [...] Read more.
A conserved feature of virtually all higher eukaryotes is that the centromeres are embedded in heterochromatin. Here we provide evidence that this tight association between pericentric heterochromatin and the centromere is essential for proper metaphase exit and progression into telophase. Analysis of chromosome rearrangements that separate pericentric heterochromatin and centromeres indicates that they must remain associated in order to balance Cohesin/DNA catenation-based binding forces and centromere-based pulling forces during the metaphase–anaphase transition. In addition, a centromere embedded in heterochromatin facilitates nuclear envelope assembly around the entire complement of segregating chromosomes. Because the nuclear envelope initially forms on pericentric heterochromatin, nuclear envelope formation proceeds from the pole, thus providing time for incorporation of lagging and trailing chromosome arms into the newly formed nucleus. Additional analysis of noncanonical mitoses provides further insights into the functional significance of the tight association between heterochromatin and centromeres. Full article
(This article belongs to the Special Issue Heterochromatin Is No Longer the Dark Side of the Genome: A Themed Issue in Honor of Prof. Sergio Pimpinelli)
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17 pages, 2040 KiB  
Review
What Have We Learned in 30 Years of Investigations on Bari Transposons?
by Antonio Palazzo, Ruggiero Caizzi, Roberta Moschetti and René Massimiliano Marsano
Cells 2022, 11(3), 583; https://0-doi-org.brum.beds.ac.uk/10.3390/cells11030583 - 08 Feb 2022
Cited by 3 | Viewed by 1817
Abstract
Transposable elements (TEs) have been historically depicted as detrimental genetic entities that selfishly aim at perpetuating themselves, invading genomes, and destroying genes. Scientists often co-opt “special” TEs to develop new and powerful genetic tools, that will hopefully aid in changing the future of [...] Read more.
Transposable elements (TEs) have been historically depicted as detrimental genetic entities that selfishly aim at perpetuating themselves, invading genomes, and destroying genes. Scientists often co-opt “special” TEs to develop new and powerful genetic tools, that will hopefully aid in changing the future of the human being. However, many TEs are gentle, rarely unleash themselves to harm the genome, and bashfully contribute to generating diversity and novelty in the genomes they have colonized, yet they offer the opportunity to develop new molecular tools. In this review we summarize 30 years of research focused on the Bari transposons. Bari is a “normal” transposon family that has colonized the genomes of several Drosophila species and introduced genomic novelties in the melanogaster species. We discuss how these results have contributed to advance the field of TE research and what future studies can still add to the current knowledge. Full article
(This article belongs to the Special Issue Heterochromatin Is No Longer the Dark Side of the Genome: A Themed Issue in Honor of Prof. Sergio Pimpinelli)
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9 pages, 956 KiB  
Review
Shining Light on the Dark Side of the Genome
by Lori L. Wallrath, Felipe Rodriguez-Tirado and Pamela K. Geyer
Cells 2022, 11(3), 330; https://0-doi-org.brum.beds.ac.uk/10.3390/cells11030330 - 19 Jan 2022
Cited by 5 | Viewed by 2062
Abstract
Heterochromatin has historically been considered the dark side of the genome. In part, this reputation derives from its concentration near centromeres and telomeres, regions of the genome repressive to nuclear functions such as DNA replication and transcription. The repetitive nature of heterochromatic DNA [...] Read more.
Heterochromatin has historically been considered the dark side of the genome. In part, this reputation derives from its concentration near centromeres and telomeres, regions of the genome repressive to nuclear functions such as DNA replication and transcription. The repetitive nature of heterochromatic DNA has only added to its “darkness”, as sequencing of these DNA regions has been only recently achieved. Despite such obstacles, research on heterochromatin blossomed over the past decades. Success in this area benefitted from efforts of Sergio Pimpinelli and colleagues who made landmark discoveries and promoted the growth of an international community of researchers. They discovered complexities of heterochromatin, demonstrating that a key component, Heterochromatin Protein 1a (HP1a), uses multiple mechanisms to associate with chromosomes and has positive and negative effects on gene expression, depending on the chromosome context. In addition, they updated the work of Carl Waddington using molecular tools that revealed how environmental stress promotes genome change due to transposable element movement. Collectively, their research and that of many others in the field have shined a bright light on the dark side of the genome and helped reveal many mysteries of heterochromatin. Full article
(This article belongs to the Special Issue Heterochromatin Is No Longer the Dark Side of the Genome: A Themed Issue in Honor of Prof. Sergio Pimpinelli)
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17 pages, 988 KiB  
Review
When Down Is Up: Heterochromatin, Nuclear Organization and X Upregulation
by Reem Makki and Victoria H. Meller
Cells 2021, 10(12), 3416; https://0-doi-org.brum.beds.ac.uk/10.3390/cells10123416 - 04 Dec 2021
Cited by 3 | Viewed by 2294
Abstract
Organisms with highly differentiated sex chromosomes face an imbalance in X-linked gene dosage. Male Drosophila solve this problem by increasing expression from virtually every gene on their single X chromosome, a process known as dosage compensation. This involves a ribonucleoprotein complex that is [...] Read more.
Organisms with highly differentiated sex chromosomes face an imbalance in X-linked gene dosage. Male Drosophila solve this problem by increasing expression from virtually every gene on their single X chromosome, a process known as dosage compensation. This involves a ribonucleoprotein complex that is recruited to active, X-linked genes to remodel chromatin and increase expression. Interestingly, the male X chromosome is also enriched for several proteins associated with heterochromatin. Furthermore, the polytenized male X is selectively disrupted by the loss of factors involved in repression, silencing, heterochromatin formation or chromatin remodeling. Mutations in many of these factors preferentially reduce male survival or enhance the lethality of mutations that prevent normal recognition of the X chromosome. The involvement of primarily repressive factors in a process that elevates expression has long been puzzling. Interestingly, recent work suggests that the siRNA pathway, often associated with heterochromatin formation and repression, also helps the dosage compensation machinery identify the X chromosome. In light of this finding, we revisit the evidence that links nuclear organization and heterochromatin to regulation of the male X chromosome. Full article
(This article belongs to the Special Issue Heterochromatin Is No Longer the Dark Side of the Genome: A Themed Issue in Honor of Prof. Sergio Pimpinelli)
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