Major Satellite Research Articles

Random Forest Regression Model for Estimation of the Growing Stock Volumes in Georgia, USA, Using Dense Landsat Time Series and FIA Dataset

The forest volumes are essential as they are directly related to the economic and environmental values of the forests. Satellite-based forest volume estimation was first developed in the 1990s, and the accuracy of the estimation has been improved over time. One of the satellite-based forest volume estimation issues is that it tends to overestimate the large volume class and underestimate the small volume class. Free availability of the major satellite imagery and the development of cloud-based computational platforms facilitate an immense amount of satellite imagery in the estimation. In this paper, we set three objectives: (1) to examine whether the long Landsat time series contributes to the improvement of the estimation accuracy, (2) to explore the effectiveness of forest disturbance record and land cover data as ancillary spatial data on the accuracy of the estimation, and (3) to apply the bias correction method to reduce the bias of the estimation. We computed three Tasseled-cap components from the Landsat data for preparation of short (2014–2016) and long (1984–2016) time series. Each data entity was analyzed with harmonic regressions resulting in the coefficients and the fitted values recorded as pixel values in a multilayer raster database. Data included Forest Inventory and Analysis (FIA) unit field inventory measurements provided by the United States Department of Agriculture Forest Service and the National Land Cover Database and disturbance history data added as ancillary information. The totality of the available data was organized into seven distinct Random Forest (RF) models with different variables compared against each other to identify the ones with the most satisfactory performance. A bias correction method was then applied to all the RF models to examine the effectiveness of the method. Among the seven models, the worst one used the coefficients and fitted values of the short Landsat time series only, and the best one used coefficients and fitted values of both short and long Landsat time series. Using the Out-of-bag (OOB) score, the best model was found to be 34.4% better than the worst one. The model that used only the long time series data had almost the same OOB score as the best model. The results indicate that the use of the long Landsat time series improves model performance. Contrary to the previous research employing forest disturbance data as a feature variable had almost no effect on OOB. The bias correction method reduced the relative size of the bias in the estimates of the best model from 3.79% to −1.47%, the bottom 10% bias by 12.5 points, and the top 10% bias by 9.9 points. Depending on the types of forest, important feature variables were differed, reflecting the relationship between the time series remote sensing data we computed for this research and the forests’ phenological characteristics. The availability of Light Detection And Ranging (LiDAR) data and accessibility of the precise locations of the FIA data are likely to improve the model estimates further.

Satellite DNA-Mediated Gene Expression Regulation: Physiological and Evolutionary Implication.

Satellite DNAs are tandemly repeated sequences organized in large clusters within (peri)centromeric and/or subtelomeric heterochromatin. However, in many species, satellite DNAs are not restricted to heterochromatin but are also dispersed as short arrays within euchromatin. Such genomic organization together with transcriptional activity seems to be a prerequisite for the gene-modulatory effect of satellite DNAs which was first demonstrated in the beetle Tribolium castaneum upon heat stress. Namely, enrichment of a silent histone mark at euchromatic repeats of a major beetle satellite DNA results in epigenetic silencing of neighboring genes. In addition, human satellite III transcripts induced by heat shock contribute to genome-wide gene silencing, providing protection against stress-induced cell death. Gene silencing mediated by satellite RNA was also shown to be fundamental for the early embryonic development of the mosquito Aedes aegypti. Apart from a physiological role during embryogenesis and heat stress response, activation of satellite DNAs in terms of transcription and proliferation can have an evolutionary impact. Spreading of satellite repeats throughout euchromatin promotes the variation of epigenetic landscapes and gene expression diversity, contributing to the evolution of gene regulatory networks and to genome adaptation in fluctuating environmental conditions.

Heterochromatic Repeat Clustering Imposes a Physical Barrier on Homologous Recombination to Prevent Chromosomal Translocations

Mouse pericentromeric DNA is composed of tandem major satellite repeats, which are heterochromatinized and cluster together to form chromocenters containing homologous sequences from different chromosomes. These clusters are protected from DNA damage and are refractory to DNA repair through homologous recombination (HR). Moreover, double stranded DNA breaks (DSBs) occurring within chromocenters relocate away from the core domain to be repaired. The mechanisms by which pericentric heterochromatin imposes a barrier on HR and the implications of repeat clustering are unknown. Here, we compare the spatial recruitment of HR factors upon DSBs induced specifically in human and mouse pericentromeric heterochromatin, which differ in their capacity to form clusters. We show that while DSBs in human pericentromeric heterochromatin increase the accessibility of the domain by disrupting HP1 α dimerization, mouse pericentromeric heterochromatin repeat clustering imposes a physical barrier that requires many layers of decompaction to be accessed. Our results are consistent with a model in which the 3D organization of the different heterochromatic regions dictates the spatial activation of DNA repair pathways and is key to prevent the activation of HR within clustered repeats and the onset of chromosomal translocations.

Complex sequence organization of heterochromatin in the holocentric plant Cuscuta europaea elucidated by the computational analysis of nanopore reads

Repeat-rich regions of higher plant genomes are usually associated with constitutive heterochromatin, a specific type of chromatin that forms tightly packed nuclear chromocenters and chromosome bands. There is a large body of cytogenetic evidence that these chromosome regions are often composed of tandemly organized satellite DNA. However, comparatively little is known about the sequence arrangement within heterochromatic regions, which are difficult to assemble due to their repeated nature. Here, we explore long-range sequence organization of heterochromatin regions containing the major satellite repeat CUS-TR24 in the holocentric plant Cuscuta europaea. Using a combination of ultra-long read sequencing with assembly-free sequence analysis, we reveal the complex structure of these loci, which are composed of short arrays of CUS-TR24 interrupted frequently by emerging simple sequence repeats and targeted insertions of a specific lineage of LINE retrotransposons. These data suggest that the organization of satellite repeats constituting heterochromatic chromosome bands can be more complex than previously envisioned, and demonstrate that heterochromatin organization can be efficiently investigated without the need for genome assembly.

Distinct Regulation of the Expression of Satellite DNAs in the Beetle Tribolium castaneum.

In the flour beetle, Tribolium castaneum (peri)centromeric heterochromatin is mainly composed of a major satellite DNA TCAST1 interspersed with minor satellites. With the exception of heterochromatin, clustered satellite repeats are found dispersed within euchromatin. In order to uncover a possible satellite DNA function within the beetle genome, we analysed the expression of the major TCAST1 and a minor TCAST2 satellite during the development and upon heat stress. The results reveal that TCAST1 transcription was strongly induced at specific embryonic stages and upon heat stress, while TCAST2 transcription is stable during both processes. TCAST1 transcripts are processed preferentially into piRNAs during embryogenesis and into siRNAs during later development, contrary to TCAST2 transcripts, which are processed exclusively into piRNAs. In addition, increased TCAST1 expression upon heat stress is accompanied by the enrichment of the silent histone mark H3K9me3 on the major satellite, while the H3K9me3 level at TCAST2 remains unchanged. The transcription of the two satellites is proposed to be affected by the chromatin state: heterochromatin and euchromatin, which are assumed to be the prevalent sources of TCAST1 and TCAST2 transcripts, respectively. In addition, distinct regulation of the expression might be related to diverse roles that major and minor satellite RNAs play during the development and stress response.

Water Vapor Retrievals from Near-infrared Channels of the Advanced Medium Resolution Spectral Imager Instrument onboard the Fengyun-3D Satellite

Water vapor plays a key role in weather, climate and environmental research on local and global scales. Knowledge about atmospheric water vapor and its spatiotemporal variability is essential for climate and weather research. Because of the advantage of a unique temporal and spatial resolution, satellite observations provide global or regional water vapor distributions. The advanced Medium Resolution Spectral Imager (MERSI) instrument—that is, MERSI-II—onboard the Fengyun-3D (FY-3D) meteorological satellite, has been one of the major satellite sensors routinely providing precipitable water vapor (PWV) products to the community using near-infrared (NIR) measurements since June 2018. In this paper, the major updates related to the production of the NIR PWV products of MERSI-II are discussed for the first time. In addition, the water vapor retrieval algorithm based on the MERSI-II NIR channels is introduced and derivations are made over clear land areas, clouds, and sun-glint areas over the ocean. Finally, the status and samples of the MERSI-II PWV products are presented. The accuracy of MERSI-II PWV products is validated using ground-based GPS measurements. The results show that the accuracies of the water vapor products based on the updated MERSI-II instrument are significantly improved compared with those of MERSI, because MERSI-II provides a better channel setting and new calibration method. The root-mean-square error and relative bias of MERSI-II PWV products are typically 1.8–5.5 mm and −3.0% to −14.3%, respectively, and thus comparable with those of other global remote sensing products of the same type.

MeCP2 and Major Satellite Forward RNA Cooperate for Pericentric Heterochromatin Organization.

SummaryMethyl-CpG binding protein 2 (MeCP2) has historically been linked to heterochromatin organization, and in mouse cells it accumulates at pericentric heterochromatin (PCH), closely following major satellite (MajSat) DNA distribution. However, little is known about the specific function of MeCP2 in these regions. We describe the first evidence of a role in neurons for MeCP2 and MajSat forward (MajSat-fw) RNA in reciprocal targeting to PCH through their physical interaction. Moreover, MeCP2 contributes to maintenance of PCH by promoting deposition of H3K9me3 and H4K20me3. We highlight that the MeCP2B isoform is required for correct higher-order PCH organization, and underline involvement of the methyl-binding and transcriptional repression domains. The T158 residue, which is commonly mutated in Rett patients, is directly involved in this process. Our findings support the hypothesis that MeCP2 and the MajSat-fw transcript are mutually dependent for PCH organization, and contribute to clarify MeCP2 function in the regulation of chromatin architecture.

Topography and geology of Uranian mid-sized icy satellites in comparison with Saturnian and Plutonian satellites.

Newly processed global imaging and topographic mapping of Uranus's five major satellites reveal differences and similarities to mid-sized satellites at Saturn and Pluto. Three modes of internal heat redistribution are recognized. The broad similarity of Miranda's three oval resurfacing zones to those mapped on Enceladus and (subtly) on Dione are likely due to antipodal diapiric upwelling. Conversely, break-up and foundering of crustal blocks accompanied by extensive (cryo)volcanism is the dominant mode on both Charon and Ariel. Titania's fault network finds parallels on Rhea, Dione, Tethys and possibly Oberon. Differences in the geologic style of resurfacing in the satellite systems (e.g. plains on Charon, Dione, Tethys and perhaps Titania versus ridges on Miranda and Ariel) may be driven by differences in ice composition. Surface processes such as volatile transport may also be indicated by bright and dark materials on Oberon, Umbriel and Charon. The more complete and higher quality observations of the Saturnian and Plutonian mid-sized icy satellites by Cassini and New Horizons reveal a wealth of features and phenomena that cannot be perceived in the more limited Voyager coverage of the Uranian satellites, harbingers of many discoveries awaiting us on a return to Uranus. This article is part of a discussion meeting issue 'Future exploration of ice giant systems'.

The major satellite DNA families of the diploid Chenopodium album aggregate species: Arguments for and against the "library hypothesis".

Satellite DNA (satDNA) is one of the major fractions of the eukaryotic nuclear genome. Highly variable satDNA is involved in various genome functions, and a clear link between satellites and phenotypes exists in a wide range of organisms. However, little is known about the origin and temporal dynamics of satDNA. The “library hypothesis” indicates that the rapid evolutionary changes experienced by satDNAs are mostly quantitative. Although this hypothesis has received some confirmation, a number of its aspects are still controversial. A recently developed next-generation sequencing (NGS) method allows the determination of the satDNA landscape and could shed light on unresolved issues. Here, we explore low-coverage NGS data to infer satDNA evolution in the phylogenetic context of the diploid species of the Chenopodium album aggregate. The application of the Illumina read assembly algorithm in combination with Oxford Nanopore sequencing and fluorescent in situ hybridization allowed the estimation of eight satDNA families within the studied group, six of which were newly described. The obtained set of satDNA families of different origins can be divided into several categories, namely group-specific, lineage-specific and species-specific. In the process of evolution, satDNA families can be transmitted vertically and can be eliminated over time. Moreover, transposable element-derived satDNA families may appear repeatedly in the satellitome, creating an illusion of family conservation. Thus, the obtained data refute the “library hypothesis”, rather than confirming it, and in our opinion, it is more appropriate to speak about “the library of the mechanisms of origin”.

Response of turkey pectoralis major muscle satellite cells to hot and cold thermal stress: Effect of growth selection on satellite cell proliferation and differentiation

Satellite cell (SCs), the main progenitors for post-hatch poultry muscle growth, has maximal mitotic activity and sensitivity to temperature during the first week after hatch. The objective of the present study was to determine the effect of hot and cold temperatures on the proliferation and differentiation of SCs from pectoralis major (P. major) muscle of fast-growing 1-week-old Nicholas commercial (NC) turkeys compared to Randombred Control Line 2 (RBC2) turkeys representing commercial turkeys from 1966. Three temperature regimens were used: SCs proliferation at 38 °C (control) with differentiation at 43° or 33 °C; proliferation at 43° or 33 °C with differentiation at 38 °C; or both proliferation and differentiation at 43°, 38°, or 33°C. Satellite cell proliferation and differentiation increased at 43 °C and decreased at 33 °C in both lines. When a thermal challenge was administered during proliferation, greater stimulatory or suppressive effects on differentiation were observed compared to if the thermal challenge was applied only during differentiation in both lines. Expression of myoblast determination protein 1 during proliferation showed a higher increase in the NC line compared to the RBC2 line at 43 °C. Increased myogenin expression was observed in all hot treatment groups in the NC line but was only observed in the RBC2 line if the hot treatment was administered throughout proliferation and differentiation. Cold treatment suppressed myogenin expression independent of line. These results suggest turkey P. major muscle SCs are more sensitive to environmental temperatures during proliferation, and SCs from growth-selected NC turkeys are more sensitive to thermal stress compared to the RBC2 turkeys.

Helicase LSH/Hells regulates kinetochore function, histone H3/Thr3 phosphorylation and centromere transcription during oocyte meiosis

Centromeres are epigenetically determined nuclear domains strictly required for chromosome segregation and genome stability. However, the mechanisms regulating centromere and kinetochore chromatin modifications are not known. Here, we demonstrate that LSH is enriched at meiotic kinetochores and its targeted deletion induces centromere instability and abnormal chromosome segregation. Superresolution chromatin analysis resolves LSH at the inner centromere and kinetochores during oocyte meiosis. LSH knockout pachytene oocytes exhibit reduced HDAC2 and DNMT-1. Notably, mutant oocytes show a striking increase in histone H3 phosphorylation at threonine 3 (H3T3ph) and accumulation of major satellite transcripts in both prophase-I and metaphase-I chromosomes. Moreover, knockout oocytes exhibit centromere fusions, ectopic kinetochore formation and abnormal exchange of chromatin fibers between paired bivalents and asynapsed chromosomes. Our results indicate that loss of LSH affects the levels and chromosomal localization of H3T3ph and provide evidence that, by maintaining transcriptionally repressive heterochromatin, LSH may be essential to prevent deleterious meiotic recombination events at repetitive centromeric sequences.

Herschel-PACS photometry of the five major moons of Uranus

Aims.We aim to determine far-infrared fluxes at 70, 100, and 160μm for the five major Uranus satellites, Titania, Oberon, Umbriel, Ariel, and Miranda. Our study is based on the available calibration observations at wavelengths taken with the PACS photometer aboard theHerschelSpace Observatory.Methods.The bright image of Uranus was subtracted using a scaled Uranus point spread function (PSF) reference established from all maps of each wavelength in an iterative process removing the superimposed moons. The photometry of the satellites was performed using PSF photometry. Thermophysical models of the icy moons were fitted to the photometry of each measurement epoch and auxiliary data at shorter wavelengths.Results.The best-fit thermophysical models provide constraints for important properties of the moons, such as surface roughness and thermal inertia. We present the first thermal infrared radiometry longward of 50μm for the four largest Uranian moons, Titania, Oberon, Umbriel, and Ariel, at epochs with equator-on illumination. Due to this inclination geometry, heat transport took place to the night side so that thermal inertia played a role, allowing us to constrain that parameter. Also, we found some indication for differences in the thermal properties of leading and trailing hemispheres. The total combined flux contribution of the four major moons relative to Uranus is 5.7 × 10−3, 4.8 × 10−3, and 3.4 × 10−3at 70, 100, and 160μm, respectively. We therefore precisely specify the systematic error of the Uranus flux by its moons when Uranus is used as a far-infrared prime flux calibrator. Miranda is considerably fainter and always close to Uranus, impeding reliable photometry.Conclusions.We successfully demonstrate an image processing technique for PACS photometer data that allows us to remove a bright central source and reconstruct point source fluxes on the order of 10−3of the central source as close as ≈3 × the half width at half maximum of the PSF. We established improved thermophysical models of the five major Uranus satellites. Our derived thermal inertia values resemble those of trans-neptunian object (TNO) dwarf planets, Pluto and Haumea, more than those of smaller TNOs and Centaurs at heliocentric distances of about 30 AU.

Molecular Analysis of the Microbial Community Developing in Continuous Culture of Methylococcus sp. Concept-8 on Natural Gas

The composition of the microbial community formed in the course of long-term (over 60 days) continuous cultivation of an obligate methanotroph Methylococcus sp. Concept-8 on natural gas in a 50-L bioreactor at 42°C and pH 5.6 was monitored. Stable growth with high optical density of the culture (average OD540 = 13.5), specific growth rate of 0.2 h–1, and biomass yield of 4.0–4.5 g dry matter L–1 continued for 50 days. During the subsequent period of regime instability, optical density decreased sharply, down to OD540 = 4. Formate, acetate, and a number of unidentified fatty acids derived from oxidation of methane homologs were detected in the culture liquid. Microscopy revealed the highest share of satellite bacteria (10–15% of the total cell number) during the period of stable growth, while it dropped to 4.5% during growth decline. Molecular profiling of the community composition based on 16S rRNA gene sequence analysis revealed members of the genera Cohnella, Brevibacillus, Azospirillim, Thermomonas, Cupriavidus, and Paenibacillus among the major microbial satellites responsible for utilization of metabolites and the products of lysis of the methanotroph cells. During the phase of growth instability, the relative abundance of Brevibacillus decreased drastically; these organisms were most likely responsible for acetate oxidation. Isolates obtained by means of cultivation represented only a minor part of microbial diversity revealed in the community by molecular analysis. Isolation of the cultures of Brevibacillus and Cupriavidus species representing the functionally important components of the community opens the way for targeted construction of associations with strain Concept-8, which will display high productivity and stable growth.

CRISPR/Cas9-Induced Breaks in Heterochromatin, Visualized by Immunofluorescence.

CRISPR/Cas9 technology can be used to investigate how double-strand breaks (DSBs) occurring in constitutive heterochromatin are getting repaired. This technology can be used to induce specific breaks on mouse pericentromeric heterochromatin, by using a guide RNA specific for the major satellite repeats and co-expressing it with Cas9. Those clean DSBs can be visualized later by confocal microscopy. More specifically, immunofluorescence can be used to visualize the main factors of each DSB repair pathway and quantify their percentage and pattern of recruitment at the heterochromatic region.

Knockdown of Death-Associated Protein Expression Induces Global Transcriptome Changes in Proliferating and Differentiating Muscle Satellite Cells.

Death-associated protein (DAP) undergoes substantial changes in expression during turkey skeletal muscle development, decreasing from the 18 day embryonic stage to 1 day posthatch, and again from 1 day posthatch to 16 weeks of age. These changes suggest that DAP plays an important role at critical stages of the developmental process. The objective of this study was to elucidate the role of DAP in muscle development by examining the effect of reduced DAP expression on global gene expression in proliferating and differentiating turkey pectoralis major muscle satellite cells. Small interfering RNA was used to knock down expression of DAP and the transcriptome was subsequently profiled using a turkey skeletal muscle long oligonucleotide microarray. Microarray data were corroborated using quantitative real-time PCR. In proliferating cells, 458 loci, resulting in 378 uniquely annotated genes, showed differential expression (false discovery rate, FDR < 0.05). Pathway analysis highlighted altered eukaryotic translational initiation factors (eIFs) signaling, protein ubiquitination, sirtuin signaling, and mechanistic target of rapamycin (mTOR) signaling as the primary pathways affected in the knockdown proliferating cells. The findings underpinned the potential DAP involvement in cell proliferation of turkey satellite cells through the coordination between protein synthesis and cell cycle. In differentiating cells, 270 loci, accounting for 189 unique genes, showed differential expression (FDR < 0.05). Decreased expression of genes encoding various myofibrillar proteins and proteins involved in sarcoplasmic reticulum calcium flux suggests that DAP may affect regulation of calcium homeostasis and cytoskeleton signaling. This study provides the first evidence that reduced expression of DAP significantly alters the transcriptome profile of pectoralis major muscle satellite cells, thereby reducing proliferation and differentiation.

Identifying and Quantifying Pixel-Level Uncertainty among Major Satellite Derived Global Land Cover Products

Accurate global land cover (GLC), as a key input for scientific communities, is important for a wide variety of applications. In order to understand the current suitability and limitation of GLC products, the discrepancy and pixel-level uncertainty in major GLC products in three epochs are assessed in this study by using an integrated uncertainty index (IUI) that combines the thematic uncertainty and local classification accuracy uncertainty. The results show that the overall spatial agreements (Ao values) between GLC products are lower than 58%, and the total areas of forests are very consistent in major GLC products, but significant differences are found in different forest classes. The misclassification among different forest classes and mosaic types can account for about 20% of the total disagreements. The mean IUI almost reaches 0.5, and high uncertainty mostly occurs in transition zones and heterogeneous areas across the world. Further efforts are needed to make in the land cover classifications in areas with high uncertainty. Designing a classification scheme for climate models, with explicit definitions of land cover classes in the threshold of common attributes, is urgently needed. Information of the pixel-level uncertainty in major GLC products not only give important implications for the specific application, but also provide a quite important basis for land cover fusion.

MIWI prevents aneuploidy during meiosis by cleaving excess satellite RNA.

MIWI, a murine member of PIWI proteins mostly expressed during male meiosis, is crucial for piRNA biogenesis, post-transcriptional regulation, and spermiogenesis. However, its meiotic function remains unknown. Here, we report that MIWI deficiency alters meiotic kinetochore assembly, significantly increases chromosome misalignment at the meiosis metaphase I plate, and causes chromosome mis-segregation. Consequently, Miwi-deficient mice show elevated aneuploidy in metaphase II and spermatid death. Furthermore, in Miwi-null and Miwi slicer-deficient mutants, major and minor satellite RNAs from centromeric and pericentromeric satellite repeats accumulate in excess. Over-expression of satellite repeats in wild-type spermatocytes also causes elevated chromosome misalignment, whereas reduction of both strands of major or minor satellite RNAs results in lower frequencies of chromosome misalignment. We show that MIWI, guided by piRNA, cleaves major satellite RNAs, generating RNA fragments that may form substrates for subsequent Dicer cleavage. Furthermore, Dicer cleaves all satellite RNAs in conjunction with MIWI. These findings reveal a novel mechanism in which MIWI- and Dicer-mediated cleavage of the satellite RNAs prevents the over-expression of satellite RNAs, thus ensuring proper kinetochore assembly and faithful chromosome segregation during meiosis.

Digitization of Astronegatives of the Pulkovo Glass Library: Positions of Saturn’s Major Satellites in the Period 1972–1982 in the Gaia DR2 System

We present the results of the re-reduction of Pulkovo photographic plates with images of Saturn’s major satellites in the Gaia DR2 catalog system (169 plates, 3007 individual positions). Astronegatives were taken with the 26-inch refractor at the Pulkovo Observatory between 1972 and 1982. The intrinsic accuracy of measurement of astronegatives using the Pulkovo MDD system was 1 μm (20 mas on the 26-inch refractor scale). The mean values of O–C differences when compared with the most up-to-date ephemerides vary within ±20 mas. The errors of the annual mean differences are usually better than 20 mas. There is a close agreement between the presented Pulkovo series and the results of the re-reduction of similar USNO observations (mean seasonal differences are less than 50 mas in modulus). Considering that different implementations of modern ephemerides give satellite positions that vary within ±50 mas for the time interval under study, we can conclude that the Pulkovo series is highly informative for improving the motion models of the major satellites of Saturn.

Increasing methylation of sperm rDNA and other repetitive elements in the aging male mammalian germline.

In somatic cells/tissues, methylation of ribosomal DNA (rDNA) increases with age and age‐related pathologies, which has a direct impact on the regulation of nucleolar activity and cellular metabolism. Here, we used bisulfite pyrosequencing and show that methylation of the rDNA transcription unit including upstream control element (UCE), core promoter, 18S rDNA, and 28S rDNA in human sperm also significantly increases with donor's age. This positive correlation between sperm rDNA methylation and biological age is evolutionarily conserved among mammals with widely different life spans such as humans, marmoset, bovine, and mouse. Similar to the tandemly repeated rDNA, methylation of human α‐satellite and interspersed LINE1 repeats, marmoset α‐satellite, bovine alpha‐ and testis satellite I, mouse minor and major satellite, and LINE1‐T repeats increases in the aging male germline, probably related to their sperm histone packaging. Deep bisulfite sequencing of single rDNA molecules in human sperm revealed that methylation does not only depend on donor's age, but also depend on the region and sequence context (A vs. G alleles). Both average rDNA methylation of all analyzed DNA molecules and the number of fully (>50%) methylated alleles, which are thought to be epigenetically silenced, increase with donor's age. All analyzed CpGs in the sperm rDNA transcription unit show comparable age‐related methylation changes. Unlike other epigenetic aging markers, the rDNA clock appears to operate in similar ways in germline and soma in different mammalian species. We propose that sperm rDNA methylation, directly or indirectly, influences nucleolar formation and developmental potential in the early embryo.

Transposons and satellite DNA: on the origin of the major satellite DNA family in the Chenopodium genome

Extensive and complex links exist between transposable elements (TEs) and satellite DNA (satDNA), which are the two largest fractions of eukaryotic genome. These relationships have a crucial effect on genome structure, function and evolution. Here, we report a novel case of mutual relationships between TEs and satDNA. In the genomes of Chenopodium s. str. species, the deletion derivatives of tnp2 conserved domain of the newly discovered CACTA-like TE Jozin are involved in generating monomers of the most abundant satDNA family of the Chenopodium satellitome. The analysis of the relative positions of satDNA and different TEs utilizing assembled Illumina reads revealed several associations between satDNA arrays and the transposases of putative CACTA-like elements when an ~ 40 bp fragment of tnp2 served as the start monomer of the satDNA array. The high degree of identity of the consensus satDNA monomers of the investigated species and the tnp2 fragment (from 82.1 to 94.9%) provides evidence of the genesis of CficCl-61-40 satDNA family monomers from analogous regions of their respective parental elements. The results were confirmed via molecular genetic methods and Oxford Nanopore sequencing. The discovered phenomenon leads to the continuous replenishment of species genomes with new identical satDNA monomers, which in turn may increase species satellitomes similarity.