TERRA G-quadruplex stabilization behind the anti-multiple myeloma activity: Novel insights about resveratrol pleiotropic effects.

Resveratrol (RSV) is a nutraceutical compound belonging to the nonflavonoid polyphenol family, whose antioxidants, anti-inflammatory, and antitumoral properties have been widely investigated. The ability of RSV to provide beneficial effects for neurological, cardiovascular, and cancer disorders rekindled the interest to explore the molecular mechanisms behind its pleiotropic effects, which are due to the modulation of coding and noncoding genes involved in many key biological pathways. With a computational approach, including docking studies and thermodynamics calculations followed by 200-ns-long molecular dynamics and a clustering analysis, we hypothesized the stabilizing binding between RSV and G4 structures of telomeric repeat-containing RNA (TERRA), which is a tumor-suppressive long noncoding RNAs (lncRNA) involved in the regulation of telomere maintenance. In vitro studies performed on cellular models of multiple myeloma (MM) strengthened our hypothesis by highlighting that the antiproliferative and apoptotic effect induced by the treatment with RSV is associated with an increase of TERRA transcript and with upregulation of telomeric heterochromatin markers, such as H3K27Me3 and H4K20Me3, and of the hallmark of apoptosis, cleaved-poly(ADP-ribose) polymerase-1. Our results propose innovative insights underlying the multifaceted role of RSV in MM, by pointing out the role of this natural compound in an lncRNA-mediated regulation to counteract cellular immortality.

Recruitment of the m6A/m6Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48.

BACKGROUND: N6-methyladenosine (m6A), the most abundant internal modification on eukaryotic mRNA, and N6, 2'-O-dimethyladenosine (m6Am), are epitranscriptomic marks that function in multiple aspects of posttranscriptional regulation. Fat mass and obesity-associated protein (FTO) can remove both m6A and m6Am; however, little is known about how FTO achieves its substrate selectivity. RESULTS: Here, we demonstrate that ZBTB48, a C2H2-zinc finger protein that functions in telomere maintenance, associates with FTO and binds both mRNA and the telomere-associated regulatory RNA TERRA to regulate the functional interactions of FTO with target transcripts. Specifically, depletion of ZBTB48 affects targeting of FTO to sites of m6A/m6Am modification, changes cellular m6A/m6Am levels and, consequently, alters decay rates of target RNAs. ZBTB48 ablation also accelerates growth of HCT-116 colorectal cancer cells and modulates FTO-dependent regulation of Metastasis-associated protein 1 (MTA1) transcripts by controlling the binding to MTA1 mRNA of the m6A reader IGF2BP2. CONCLUSIONS: Our findings thus uncover a previously unknown mechanism of posttranscriptional regulation in which ZBTB48 co-ordinates RNA-binding of the m6A/m6Am demethylase FTO to control expression of its target RNAs.

Phase separation of hnRNPA1 and TERRA regulates telomeric stability.

Telomeres are repetitive DNA sequences and associated protein complexes located at the end of chromatin. As a result of the DNA replication ending issue, telomeric DNA shortens during each cell cycle. The shelterin protein complex caps telomeric ends and forms a high-order protein-DNA structure to protect telomeric DNA. The stability of telomeres is critical for cellular function and is related to the progression of many human diseases. Telomeric repeat-containing RNA (TERRA) is a noncoding RNA transcribed from telomeric DNA regions. TERRA plays an essential role in regulating and maintaining the stability of telomeres. Heterogeneous nuclear ribonucleoproteins (hnRNPs) are RNA-binding proteins associated with complex and diverse biological processes. HnRNPA1 can recognize both TERRA and telomeric DNA. Previous research reported that hnRNPA1, TERRA, and POT1, a component of the shelterin complex, worked coordinately and displaced replication protein A from telomeric ssDNA after DNA replication, promoting telomere capping to preserve genomic integrity. However, the detailed molecular mechanism has remained unclear for over twenty years. Our study revealed the molecular structure through which the hnRNPA1 UP1 domain interacts with TERRA. Through structural analysis, we identified critical residues on the interacting surface between UP1 and TERRA. Furthermore, we proved that nucleic acids significantly increase the phase separation ability of hnRNPA1 and disrupting the UP1-TERRA interaction extraordinarily affects hnRNPA1 droplet formation both in vitro and in vivo. Taken together, these data revealed the molecular mechanism of the droplet formation of hnRNPA1 and TERRA and the possible function of the droplets for maintaining genomic stability.

Telomeric RNAs, TERRA, as a Potential Biomarker for Spermatozoa Quality.

Characterization of long non-coding telomeric repeat-containing RNAs in sperm of normozoospermic and oligoasthenozoospermic men as new biomarker of idiopathic male infertility. We conducted an observational prospective study with two groups of men with normal or orligoasthenozoospermic spermiogram, aged 40 and above. Fertility parameters were analyzed in men undergoing intracytoplasmic sperm injection with donor oocytes, to avoid the female factor. Telomeric RNAs and telomere length were measured by quantitative fluorescent in situ hybridization. Data from seminal parameters and in-vitro fertilization were assessed according to IVIRMA protocols. Patients with oligoasthenozoospermia, who had worse seminal parameters, also obtained embryos with lower inner-cell-mass quality (p = 0.04), despite using donor oocytes. While mean levels of telomeric RNAs were similar for both groups, the percentage of spermatozoa with more than 3 foci was higher in oligoasthenozoospermic men (p = 0.02). Regarding telomere length, oligoasthenozoospermic men had shorter mean, a higher accumulation of short telomeres (15th percentile; p = 0.03) and a lower percentage of very-long telomeres (85th percentile; p = 0.01). Finally, a positive correlation was found between telomeric-RNAs intensity and total progressive motility in the spermatozoa of normozoospermic patients (r = 0.5; p = 0.03). Telomeric parameters were altered in the spermatozoa of the oligoasthenozoospermic group, which also showed lower quality embryos. Interestingly, in the normozoospermic group, a correlation was found between progressive motility and telomeric RNA levels, suggesting that they could be a good biomarker of sperm quality. Further studies are required to confirm these results and translate them into the clinical practice.Trial registration number: 1711-MAD-109-CB, 07/07/2021.

Transcription of biological aging markers (ANRIL, P16INK4a, TBX2, and TERRA) and their correlations with severity of sulfur mustard exposure in veterans.

Sulfur mustard (SM) exposure has delayed harmful effects, including premature biological aging. This study aimed to evaluate the expression of aging markers (i.e., ANRIL, P16INK4a, TBX2, and TERRA) and assess their correlation with the severity of SM exposure in the long term. The study was conducted on two volunteer groups. 1) SM-exposed group, exposed to SM once in 1987 during the war; divided into three subgroups based on the injury severity, asymptomatic (without any clinical signs), mild, and severe; 2) Non-exposed group. In the SM-exposed group, ANRIL transcript was decreased, especially in subgroups of mild and severe. TBX2 transcript was also decreased in the total SM-exposed group. This decrease was more significant in the mild and severe subgroups than in asymptomatic ones. P16INK4a transcript was increased in the SM-exposed group, especially in the asymptomatic subgroup. The increase in TERRA transcript was also significant in all subgroups. There was a positive correlation between the TERRA transcript and the severity of injury, while this correlation was negative for the ANRIL. It is concluded that the delayed toxicity of SM may be associated with dysregulation of aging markers leading to premature cellular aging. These markers' alterations differed according to the severity of SM injury.

Leishmania major telomerase RNA knockout: From altered cell proliferation to decreased parasite infectivity.

This study focuses on the biological impacts of deleting the telomerase RNA from Leishmania major (LeishTER), a parasite responsible for causing leishmaniases, for which no effective treatment or prevention is available. TER is a critical player in the telomerase ribonucleoprotein complex, containing the template sequence copied by the reverse transcriptase component during telomere elongation. The success of knocking out both LeishTER alleles was confirmed, and no off-targets were detected. LmTER-/- cells share similar characteristics with other TER-depleted eukaryotes, such as altered growth patterns and partial G0/G1 cell cycle arrest in early passages, telomere shortening, and elevated TERRA expression. They also exhibit increased γH2A phosphorylation, suggesting that the loss of LeishTER induces DNA damage signaling. Moreover, pro-survival autophagic signals and mitochondrion alterations were shown without any detectable plasma membrane modifications. LmTER-/- retained the ability to transform into metacyclics, but their infectivity capacity was compromised. Furthermore, the overexpression of LeishTER was also deleterious, inducing a dominant negative effect that led to telomere shortening and growth impairments. These findings highlight TER's vital role in parasite homeostasis, opening discussions about its potential as a drug target candidate against Leishmania.

New distributional records of Southern Ocean Isopoda based on vouchers from the Italian National Antarctic Museum (MNA, Section of Genoa).

Background: The order Isopoda Latreille, 1816 consists of species occurring in terrestrial, marine and freshwater environments. In the Southern Ocean (SO), this group is amongst the most speciose and occur at all depths. Isopoda biogeography, despite being studied since the first Antarctic expeditions, is still poorly known from a geographical point of view and shows large occurrence gaps for some groups in specific sectors of the SO. In this paper, we update the isopod checklists of the Ross Sea (RS) and of some peri-Antarctic areas, such as the South Orkney Islands (SOI) and the South Sandwich Islands (SSI), based on the study of museum vouchers curated by the Italian National Antarctic Museum (MNA, Section of Genoa). New information: A total of 279 MNA samples from 15 different expeditions were studied. From this material, consisting of 419 specimens, 41 accepted species distributed in 24 families and 51 genera were identified. Comparing this newly-obtained information with the GBIF (Global Biodiversity Information Facility) and OBIS (Ocean Biodiversity Information System) portal, 15 species are here reported for the first time in the Ross Sea, with five new records in the Ross Sea Marine Protected Area. All records are new for the Terra Nova Bay area, for which a checklist of this group has never been produced before.

Human ARMC6 binds in vitro to both cancer genes and telomeric RNA, favoring G-quadruplex structure recognition.

Armadillo repeat-containing proteins (ARMCs) are a large family found throughout eukaryotes, which play prominent roles in cell adhesion, signaling and cytoskeletal regulation. The ARMC6 protein is highly conserved in primates, including humans, but to date does not have a clear function beyond initial hints of a link to cancer and telomerase activity. We report here in vitro experiments showing ARMC6 binding to DNA promoter sequences from several cancer-related genes (e.g., EGFR, VEGF and c-MYC), and also to the telomeric RNA repeat (TERRA). ARMC6 binding activity appears to recognize G-quadruplex motifs, which are being increasingly implicated as structure-based protein binding sites in chromosome maintenance and repair. In vivo investigation of ARMC6 function revealed that when this protein is overexpressed in human cell lines, there is different expression of genes connected with oncogenic pathways and those implicated in downstream non-canonical telomerase pathways (e.g., VEGF, hTERT, c-MYC, ESM1, MMP3). ARMC6 is already known to interact with human shelterin protein TRF2 and telomerase. The protein binds G-quadruplex structures and does so preferentially to RNA over DNA. As such, this protein may be an example of how a non-canonical nucleic acid structural motif allows mediation between gene regulation and telomeric chromatin rearrangement pathways.

Yeast Npl3 regulates replicative senescence outside of TERRA R-loop resolution and co-transcriptional processing.

Eukaryotic cells without telomerase experience progressively shorter telomeres with each round of cell division until cell cycle arrest is initiated, leading to replicative senescence. When yeast TLC1, which encodes the RNA template of telomerase, is deleted, senescence is accompanied by increased expression of TERRA (non-coding telomere repeat-containing RNA). Deletion of Npl3, an RNA-processing protein with telomere maintenance functions, accelerates senescence in tlc1Δ cells and significantly increases TERRA levels. Using genetic approaches, we set out to determine how Npl3 is involved in regulating TERRA expression and maintaining telomere homeostasis. Even though Npl3 regulates hyperrecombination, we found that Npl3 does not help resolve RNA:DNA hybrids formed during TERRA synthesis in the same way as RNase H1 and H2. Furthermore, Rad52 is still required for cells to escape senescence by telomere recombination in the absence of Npl3. Npl3 also works separately from the THO/TREX pathway for processing nascent RNA for nuclear export. However, deleting Dot1, a histone methyltransferase involved in tethering telomeres to the nuclear periphery, rescued the accelerated senescence phenotype of npl3Δ cells. Thus, our study suggests that Npl3 plays an additional role in regulating cellular senescence outside of RNA:DNA hybrid resolution and co-transcriptional processing.

Balancing act: BRCA2's elaborate management of telomere replication through control of G-quadruplex dynamicity.

In billion years of evolution, eukaryotes preserved the chromosome ends with arrays of guanine repeats surrounded by thymines and adenines, which can form stacks of four-stranded planar structure known as G-quadruplex (G4). The rationale behind the evolutionary conservation of the G4 structure at the telomere remained elusive. Our recent study has shed light on this matter by revealing that telomere G4 undergoes oscillation between at least two distinct folded conformations. Additionally, tumor suppressor BRCA2 exhibits a unique mode of interaction with telomere G4. To elaborate, BRCA2 directly interacts with G-triplex (G3)-derived intermediates that form during the interconversion of the two different G4 states. In doing so, BRCA2 remodels the G4, facilitating the restart of stalled replication forks. In this review, we succinctly summarize the findings regarding the dynamicity of telomeric G4, emphasize its importance in maintaining telomere replication homeostasis, and the physiological consequences of losing G4 dynamicity at the telomere.

Terra Firma-Forme Dermatosis: A Heart-Shaped Dark Lesion in a Boy.

Terra firma-forme dermatosis is an acquired and idiopathic disorder with an underestimated incidence. It is characterized by brownish skin pigmentation, forming asymptomatic plaques that give a soiled skin appearance. Soap and water have a minor effect; however, friction with 70% ethyl or isopropyl alcohol immediately eliminates plaques to a normal skin appearance, thus being the ideal method for diagnosis and treatment. The lack of familiarity with this disease possibly contributes to an alarming underdiagnosis. In this report, the authors present a case of terra firma-forme occurring in a 14-year-old Mexican patient who presented with a heart-shaped pigmented lesion in the pubic area.

Geographical distribution of the mesozooplankton community in highly productive coastal polynyas of the Ross Sea region marine protected area (RSR MPA) during early summer.

We investigated the recent spatial variation in the mesozooplankton community on the broad shelf of the RSR MPA during the bloom season. The mesozooplankton community was geographically divided into three regions: the Terra Nova Bay polynya, the Ross Sea polynya, and the marginal polynya. Larval euphausiids were dominant in the two polynya regions, whereas copepods were predominant in the marginal polynya region. Salinity, sea ice, and dissolved oxygen related to the different water mass compositions were the most significant factors distinguishing the mesozooplankton community. The key environmental variable separating the three groups was salinity. In accordance with the relatively high mesozooplankton abundance in the polynya regions, the occurrence and size of the polynyas in the December Ross Sea are thought to affect the spatial distribution of mesozooplankton. Consequently, this study indicates that two polynyas in the Ross Sea are vital habitats for krill during summer. Our observation results provide fundamental information for evaluating marine ecosystems and establishing a management plan for the RSR MPA.

TERRA ONTseq: a long-read-based sequencing pipeline to study the human telomeric transcriptome.

The long noncoding RNA TERRA is transcribed from telomeres in virtually all eukaryotes with linear chromosomes. In humans, TERRA transcription is driven in part by promoters comprising CpG dinucleotide-rich repeats of 29 bp repeats, believed to be present in half of the subtelomeres. Thus far, TERRA expression has been analyzed mainly using molecular biology-based approaches that only generate partial and somehow biased results. Here, we present a novel experimental pipeline to study human TERRA based on long-read sequencing (TERRA ONTseq). By applying TERRA ONTseq to different cell lines, we show that the vast majority of human telomeres produce TERRA and that the cellular levels of TERRA transcripts vary according to their chromosomes of origin. Using TERRA ONTseq, we also identified regions containing TERRA transcription start sites (TSSs) in more than half of human subtelomeres. TERRA TSS regions are generally found immediately downstream from 29 bp repeat-related sequences, which appear to be more widespread than previously estimated. Finally, we isolated a novel TERRA promoter from the highly expressed subtelomere of the long arm of Chromosome 7. With the development of TERRA ONTseq, we provide a refined picture of human TERRA biogenesis and expression and we equip the scientific community with an invaluable tool for future studies.

Planktonic, benthic and sympagic copepods collected from the desalination unit of Mario Zucchelli Research Station in Terra Nova Bay (Ross Sea, Antarctica).

Background: Distributional data on planktonic, benthic and sympagic copepods collected in the framework of the XXXIVth Expeditions of the Italian National Antarctic Programme (PNRA) to the Ross Sea sector from 2018-2019 are here provided. These occurrences correspond to specimens collected from the 25 µm filters used in the desalination plant of the Italian research station "Mario Zucchelli" (MZS), located in the Terra Nova Bay area (TNB; Ross Sea, Antarctica). This dataset is a contribution to the Antarctic Biodiversity Portal, the thematic Antarctic node for both the Ocean Biogeographic Information System (AntOBIS) and the Global Biodiversity Information Facility Antarctic Biodiversity Information Facility (ANTABIF). The dataset was uploaded and integrated with the SCAR-AntOBIS database (the geospatial component of SCAR-MarBIN). Please follow the guidelines from the SCAR Data Policy (ISSN 1998-0337) when using the data. If you have any questions regarding this dataset, please contact us via the contact information provided in the metadata or via data-biodiversity-aq@naturalsciences.be. Issues with the dataset can be reported at the biodiversity-aq GitHub project. New information: We describe the diversity of marine copepods Terra Nova Bay sampled by the filters installed in the desalination unit (DU) of the Italian research station "Mario Zucchelli" described in recent work. The opening of the intake pipe of the DU is positioned at a depth of 4 m and allowed a total of 2,116 specimens to be sampled and recognised. In addition, new occurrence records of copepod genera and species are reported in the same zone. We provide an overview of the marine copepod diversity reported for TNB. The total of 2,116 individuals corresponds to 14 genera and 15 species and is represented by 136 occurrence records in this dataset. Around 52% of the total number of species are new records for the TNB area. The publication of this data paper was funded by the Belgian Science Policy Office (BELSPO, contract n°FR/36/AN1/AntaBIS) in the Framework of EU-Lifewatch as a contribution to the SCAR Antarctic biodiversity portal (biodiversity.aq).

TERRA and the alternative lengthening of telomeres: a dangerous affair.

Eukaryotic telomeres are transcribed into the long noncoding RNA TERRA. A fraction of TERRA remains associated with telomeres by forming RNA:DNA hybrids dubbed telR-loops. TERRA and telR-loops are essential to promote telomere elongation in human cancer cells that maintain telomeres through a homology-directed repair pathway known as alternative lengthening of telomeres or ALT. However, TERRA and telR-loops compromise telomere integrity and cell viability if their levels are not finely tuned. The study of telomere transcription in ALT cells will enormously expand our understanding of the ALT mechanism and of how genome integrity is maintained. Moreover, telomere transcription, TERRA and telR-loops are likely to become exceptionally suited targets for the development of novel anti-cancer therapies.

Genomic insights of Fictibacillus terranigra sp. nov., a versatile metabolic bacterium from Amazonian Dark Earths.

The Amazon rainforest, a hotspot for biodiversity, is a crucial research area for scientists seeking novel microorganisms with ecological and biotechnological significance. A key region within the Amazon rainforest is the Amazonian Dark Earths (ADE), noted for supporting diverse plant and microbial communities, and its potential as a blueprint for sustainable agriculture. This study delineates the isolation, morphological traits, carbon source utilization, and genomic features of Fictibacillus terranigra CENA-BCM004, a candidate novel species of the Fictibacillus genus isolated from ADE. The genome of Fictibacillus terranigra was sequenced, resulting in 16 assembled contigs, a total length of 4,967,627 bp, and a GC content of 43.65%. Genome annotation uncovered 3315 predicted genes, encompassing a wide range of genes linked to various metabolic pathways. Phylogenetic analysis indicated that CENA-BCM004 is a putative new species, closely affiliated with other unidentified Fictibacillus species and Bacillus sp. WQ 8-8. Moreover, this strain showcased a multifaceted metabolic profile, revealing its potential for diverse biotechnological applications. It exhibited capabilities to antagonize pathogens, metabolize multiple sugars, mineralize organic matter compounds, and solubilize several minerals. These insights substantially augment our comprehension of microbial diversity in ADE and underscore the potential of Fictibacillus terranigra as a precious resource for biotechnological endeavors. The genomic data generated from this study will serve as a foundational resource for subsequent research and exploration of the biotechnological capabilities of this newly identified species.

A Comparative Analysis of UAV Photogrammetric Software Performance for Forest 3D Modeling: A Case Study Using AgiSoft Photoscan, PIX4DMapper, and DJI Terra.

Three-dimensional (3D) modeling of trees has many applications in various areas, such as forest and urban planning, forest health monitoring, and carbon sequestration, to name a few. Unmanned Aerial Vehicle (UAV) photogrammetry has recently emerged as a low cost, rapid, and accurate method for 3D modeling of urban and forest trees replacing the costly traditional methods such as plot measurements and surveying. There are numerous commercial and open-source software programs available, each processing UAV data differently to generate forest 3D modeling and photogrammetric products, including point clouds, Digital Surface Models (DSMs), Canopy Height Models (CHMs), and orthophotos in forest areas. The objective of this study is to compare the three widely-used commercial software packages, namely, AgiSoft Photoscan (Metashape) V 1.7.3, PIX4DMapper (Pix4D) V 4.4.12, and DJI Terra V 3.7.6 for processing UAV data over forest areas from three perspectives: point cloud density and reconstruction quality, computational time, DSM assessment for height accuracy (z) and ability of tree detection on DSM. Three datasets, captured by UAVs on the same day at three different flight altitudes, were used in this study. The first, second, and third datasets were collected at altitudes of 60 m, 100 m, and 120 m, respectively over a forested area in Tully, New York. While the first and third datasets were taken horizontally, the second dataset was taken 20 degrees off-nadir to investigate the impact of oblique images. Results show that Pix4D and AgiSoft generate 2.5 times denser point clouds than DJI Terra. However, reconstruction quality evaluation using the Iterative Closest Point method (ICP) shows DJI Terra has fewer gaps in the point cloud and performed better than AgiSoft and Pix4D in generating a point cloud of trees, power lines and poles despite producing a fewer number of points. In other words, the outperformance in key points detection and an improved matching algorithm are key factors in generating improved final products. The computational time comparison demonstrates that the processing time for AgiSoft and DJI Terra is roughly half that of Pix4D. Furthermore, DSM elevation profiles demonstrate that the estimated height variations between the three software range from 0.5 m to 2.5 m. DJI Terra's estimated heights are generally greater than those of AgiSoft and Pix4D. Furthermore, DJI Terra outperforms AgiSoft and Pix4D for modeling the height contour of trees, buildings, and power lines and poles, followed by AgiSoft and Pix4D. Finally, in terms of the ability of tree detection, DJI Terra outperforms AgiSoft and Pix4D in generating a comprehensive DSM as a result of fewer gaps in the point cloud. Consequently, it stands out as the preferred choice for tree detection applications. The results of this paper can help 3D model users to have confidence in the reliability of the generated 3D models by comprehending the accuracy of the employed software.

Telomere-specific regulation of TERRA and its impact on telomere stability.

TERRA is a class of telomeric repeat-containing RNAs that are expressed from telomeres in multiple organisms. TERRA transcripts play key roles in telomere maintenance and their physiological levels are essential to maintain the integrity of telomeric DNA. Indeed, deregulated TERRA expression or its altered localization can impact telomere stability by multiple mechanisms including fueling transcription-replication conflicts, promoting resection of chromosome ends, altering the telomeric chromatin, and supporting homologous recombination. Therefore, a fine-tuned control of TERRA is important to maintain the integrity of the genome. Several studies have reported that different cell lines express substantially different levels of TERRA. Most importantly, TERRA levels markedly vary among telomeres of a given cell type, indicating the existence of telomere-specific regulatory mechanisms which may help coordinate TERRA functions. TERRA molecules contain distinct subtelomeric sequences, depending on their telomere of origin, which may instruct specific post-transcriptional modifications or mediate distinct functions. In addition, all TERRA transcripts share a repetitive G-rich sequence at their 3' end which can form DNA:RNA hybrids and fold into G-quadruplex structures. Both structures are involved in TERRA functions and can critically affect telomere stability. In this review, we examine the mechanisms controlling TERRA levels and the impact of their telomere-specific regulation on telomere stability. We compare evidence obtained in different model organisms, discussing recent advances as well as controversies in the field. Furthermore, we discuss the importance of DNA:RNA hybrids and G-quadruplex structures in the context of TERRA biology and telomere maintenance.