Review

Authors: Jitendra Thakur, Jenika Packiaraj, Steven Henikoff...

Satellite DNA consists of abundant tandem repeats that play important roles in cellular processes, including chromosome segregation, genome organization and chromosome end protection. Most satellite DNA repeat units are either of nucleosomal length or 5-10 bp long and occupy centromeric, pericentromeric or telomeric regions. Due to high repetitiveness, satellite DNA sequences have largely been absent from genome assemblies. Although few conserved satellite-specific sequence motifs have been identified, DNA curvature, dyad symmetries and inverted repeats are features of various satellite DNAs in several organisms. Satellite DNA sequences are either embedded in highly compact gene-poor heterochromatin or specialized chromatin that is distinct from euchromatin. Nevertheless, some satellite DNAs are transcribed into non-coding RNAs that may play important roles in satellite DNA function. Intriguingly, satellite DNAs are among the most rapidly evolving genomic elements, such that a large fraction is species-specific in most organisms. Here we describe the different classes of satellite DNA sequences, their satellite-specific chromatin features, and how these features may contribute to satellite DNA biology and evolution. We also discuss how the evolution of functional satellite DNA classes may contribute to speciation in plants and animals.

Topics: Animals; Centromere; Chromatin; DNA, Satellite; Evolution, Molecular; Humans; Species Specificity

PubMed: 33919233
DOI: 10.3390/ijms22094309

Review

Authors: Franziska Brändle, Benjamin Frühbauer, Madhav Jagannathan...

Simple non-coding tandem repeats known as satellite DNA are observed widely across eukaryotes. These repeats occupy vast regions at the centromere and pericentromere of chromosomes but their contribution to cellular function has remained incompletely understood. Here, we review the literature on pericentromeric satellite DNA and discuss its organization and functions across eukaryotic species. We specifically focus on chromocenters, DNA-dense nuclear foci that contain clustered pericentromeric satellite DNA repeats from multiple chromosomes. We first discuss chromocenter formation and the roles that epigenetic modifications, satellite DNA transcripts and sequence-specific satellite DNA-binding play in this process. We then review the newly emerging functions of chromocenters in genome encapsulation, the maintenance of cell fate and speciation. We specifically highlight how the rapid divergence of satellite DNA repeats impacts reproductive isolation between closely related species. Together, we underline the importance of this so-called 'junk DNA' in fundamental biological processes.

Topics: Cell Nucleus; Centromere; Cluster Analysis; DNA, Satellite; Heterochromatin

PubMed: 35144860
DOI: 10.1016/j.semcdb.2022.02.005

Review

Authors: Jaclyn M Fingerhut, Yukiko M Yamashita

Satellite DNAs are arrays of tandem repeats found in the eukaryotic genome. They are mainly found in pericentromeric heterochromatin and have been believed to be mostly inert, leading satellite DNAs to be erroneously regarded as junk. Recent studies have started to elucidate the function of satellite DNA, yet little is known about the peculiar case where satellite DNA is found within the introns of protein coding genes, resulting in incredibly large introns, a phenomenon termed intron gigantism. Studies in Drosophila demonstrated that satellite DNA-containing introns are transcribed with the gene and require specialized mechanisms to overcome the burdens imposed by the extremely long stretches of repetitive DNA. Whether intron gigantism confers any benefit or serves any functional purpose for cells and/or organisms remains elusive. Here we review our current understanding of intron gigantism: where it is found, the challenges it imposes, how it is regulated and what purpose it may serve.

Topics: Animals; DNA, Satellite; Drosophila; Gigantism; Heterochromatin; Introns

PubMed: 35469677
DOI: 10.1016/j.semcdb.2022.04.010

Review

Authors: Glennis A Logsdon, Evan E Eichler

The complete sequence of a human genome provided our first comprehensive view of the organization of satellite DNA associated with heterochromatin. We review how our understanding of the genetic architecture and epigenetic properties of human centromeric DNA have advanced as a result. Preliminary studies of human and nonhuman ape centromeres reveal complex, saltatory mutational changes organized around distinct evolutionary layers. Pockets of regional hypomethylation within higher-order α-satellite DNA, termed centromere dip regions, appear to define the site of kinetochore attachment in all human chromosomes, although such epigenetic features can vary even within the same chromosome. Sequence resolution of satellite DNA is providing new insights into centromeric function with potential implications for improving our understanding of human biology and health.

Topics: Humans; DNA, Satellite; Centromere; Kinetochores; DNA; Heterochromatin

PubMed: 36672831
DOI: 10.3390/genes14010092

Authors: Manuel A Garrido-Ramos, Miroslav Plohl, Eva Šatović-Vukšić...

A significant portion of eukaryotic genomes consists of non-coding repetitive DNA sequences arranged in tandem arrays, known as satellite DNA (satDNA) [...].

Topics: DNA, Satellite; Genomics; Humans; Animals

PubMed: 39336813
DOI: 10.3390/genes15091223

Authors: Susan A Gerbi

Structures known as chromocenters, comprising satellite DNA and proteins such as D1 or HMGA1, help to contain DNA inside the nucleus between cell divisions.

Topics: Cell Nucleus; DNA; DNA, Satellite; Heterochromatin

PubMed: 29771237
DOI: 10.7554/eLife.37234

Review

Authors: Đurđica Ugarković, Antonio Sermek, Sven Ljubić...

Tandemly repeated satellite DNAs are major components of centromeres and pericentromeric heterochromatin which are crucial chromosomal elements responsible for accurate chromosome segregation. Satellite DNAs also contribute to genome evolution and the speciation process and are important for the maintenance of the entire genome inside the nucleus. In addition, there is increasing evidence for active and tightly regulated transcription of satellite DNAs and for the role of their transcripts in diverse processes. In this review, we focus on recent discoveries related to the regulation of satellite DNA expression and the role of their transcripts, either in heterochromatin establishment and centromere function or in gene expression regulation under various biological contexts. We discuss the role of satellite transcripts in the stress response and environmental adaptation as well as consequences of the dysregulation of satellite DNA expression in cancer and their potential use as cancer biomarkers.

Topics: Centromere; DNA, Satellite; Gene Expression Regulation; Heterochromatin

PubMed: 35885937
DOI: 10.3390/genes13071154

Review

Authors: Giuseppe Biamonti, Claire Vourc'h

Nuclear stress bodies (nSBs) are unique subnuclear organelles which form in response to heat shock. They are initiated through a direct interaction between heat shock transcription factor 1 (HSF1) and pericentric tandem repeats of satellite III sequences and correspond to active transcription sites for noncoding satellite III transcripts. Given their unusual features, nSBs are distinct from other known transcription sites. In stressed cells, they are thought to participate in rapid, transient, and global reprogramming of gene expression through different types of mechanisms including chromatin remodeling and trapping of transcription and splicing factors. The analysis of these atypical and intriguing structures uncovers new facets of the relationship between nuclear organization and nuclear function.

Topics: Animals; DNA, Satellite; Intranuclear Space; Organelles; Stress, Physiological; Transcription, Genetic

PubMed: 20516127
DOI: 10.1101/cshperspect.a000695

Authors: Liane P Fernandes, Rocio Enriquez-Gasca, Poppy A Gould...

Mammalian genomes are a battleground for genetic conflict between repetitive elements and KRAB-zinc finger proteins (KZFPs). We asked whether KZFPs can regulate cell fate by using ZFP819, which targets a satellite DNA array, ZP3AR. ZP3AR coats megabase regions of chromosome 7 encompassing genes encoding ZSCAN4, a master transcription factor of totipotency. Depleting ZFP819 in mouse embryonic stem cells (mESCs) causes them to transition to a 2-cell (2C)-like state, whereby the ZP3AR array switches from a poised to an active enhancer state. This is accompanied by a global erosion of heterochromatin roadblocks, which we link to decreased SETDB1 stability. These events result in transcription of active LINE-1 elements and impaired differentiation. In summary, ZFP819 and TRIM28 partner up to close chromatin across , to promote exit from totipotency. We propose that satellite DNAs may control developmental fate transitions by barcoding and switching off master transcription factor genes.

Topics: Animals; Mice; DNA, Satellite; Mammals; Oligonucleotide Array Sequence Analysis; Repressor Proteins; Transcription Factors; Chromosomes

PubMed: 36306355
DOI: 10.1126/sciadv.abp8085

Authors: Nadine Heidi Brückmann, Christina Bøg Pedersen, Henrik Jørn Ditzel...

Repression of repetitive DNA is important for maintaining genomic stability, but is often perturbed in cancer. For instance, the megabase satellite domain at chromosome 1q12 is a common site of genetic rearrangements, such as translocations and deletions. Polycomb-group proteins can be observed as large subnuclear domains called polycomb bodies, the composition and cellular function of which has remained elusive. This study demonstrates that polycomb bodies are canonical subunits of the multiprotein polycomb repressive complex 1 deposited on 1q12 pericentromeric satellite DNA, which are normally maintained as constitutive heterochromatin by other mechanisms. Furthermore, the data reveal that polycomb bodies are exclusive to premalignant and malignant cells, being absent in normal cells. For instance, polycomb bodies are present in melanocytic cells of nevi and conserved in primary and metastatic melanomas. Deposition of polycomb on the 1q12 satellite DNA in melanoma development correlated with reduced DNA methylation levels. In agreement with this, inhibition of DNA methyltransferases, with the hypomethylating agent guadecitabine (SGI-110), was sufficient for polycomb body formation on pericentromeric satellites in primary melanocytes. This suggests that polycomb bodies form in cancer cells with global DNA demethylation to control the stability of pericentromeric satellite DNA. These results reveal a novel epigenetic perturbation specific to premalignant and malignant cells that may be used as an early diagnostic marker for detection of precancerous changes and a new therapeutic entry point. Pericentromeric satellite DNA is epigenetically reprogrammed into polycomb bodies as a premalignant event with implications for transcriptional activity and genomic stability. .

Topics: DNA, Satellite; Epigenesis, Genetic; Humans; Neoplasms; Precancerous Conditions; Transfection

PubMed: 29330295
DOI: 10.1158/1541-7786.MCR-17-0477