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.

The alternative lengthening of telomeres mechanism jeopardizes telomere integrity if not properly restricted.

A substantial number of human cancers are telomerase-negative and elongate physiologically damaged telomeres through a break-induced replication (BIR)-based mechanism known as alternative lengthening of telomeres (ALT). We recently demonstrated that inhibiting the transcription of the telomeric long noncoding RNA TERRA suppresses telomere damage and ALT features, indicating that telomere transcription is a main trigger of ALT activity. Here we show that experimentally increased TERRA transcription not only increases ALT features, as expected, but also causes rapid loss of telomeric DNA through a pathway that requires the endonuclease Mus81. Our data indicate that the ALT mechanism can endanger telomere integrity if not properly controlled and point to TERRA transcription as a uniquely versatile target for therapy.

Genome-wide chromosomal association of Upf1 is linked to Pol II transcription in Schizosaccharomyces pombe.

Although the RNA helicase Upf1 has hitherto been examined mostly in relation to its cytoplasmic role in nonsense mediated mRNA decay (NMD), here we report high-throughput ChIP data indicating genome-wide association of Upf1 with active genes in Schizosaccharomyces pombe. This association is RNase sensitive, correlates with Pol II transcription and mRNA expression levels. Changes in Pol II occupancy were detected in a Upf1 deficient (upf1Δ) strain, prevalently at genes showing a high Upf1 relative to Pol II association in wild-type. Additionally, an increased Ser2 Pol II signal was detected at all highly transcribed genes examined by ChIP-qPCR. Furthermore, upf1Δ cells are hypersensitive to the transcription elongation inhibitor 6-azauracil. A significant proportion of the genes associated with Upf1 in wild-type conditions are also mis-regulated in upf1Δ. These data envisage that by operating on the nascent transcript, Upf1 might influence Pol II phosphorylation and transcription.

Spin-Selective Electron Transport Through Single Chiral Molecules.

The interplay between chirality and magnetism is a source of fascination among scientists for over a century. In recent years, chirality-induced spin selectivity (CISS) has attracted renewed interest. It is observed that electron transport through layers of homochiral molecules leads to a significant spin polarization of several tens of percent. Despite the abundant experimental evidence gathered through mesoscopic transport measurements, the exact mechanism behind CISS remains elusive. This study reports spin-selective electron transport through single helical aromatic hydrocarbons that are sublimed in vacuo onto ferromagnetic cobalt surfaces and examined with spin-polarized scanning tunneling microscopy (SP-STM) at a temperature of 5 K. Direct comparison of two enantiomers under otherwise identical conditions revealed magnetochiral conductance asymmetries of up to 50% when either the molecular handedness is exchanged or the magnetization direction of the STM tip or Co substrate is reversed. Importantly, the results rule out electron-phonon coupling and ensemble effects as primary mechanisms responsible for CISS.

PAR-TERRA is the main contributor to telomeric repeat-containing RNA transcripts in normal and cancer mouse cells.

Telomeric repeat-containing RNA (TERRA) molecules play important roles at telomeres, from heterochromatin regulation to telomerase activity control. In human cells, TERRA is transcribed from subtelomeric promoters located on most chromosome ends and associates with telomeres. The origin of mouse TERRA molecules is, however, unclear, as transcription from the pseudoautosomal PAR locus was recently suggested to account for the vast majority of TERRA in embryonic stem cells (ESC). Here, we confirm the production of TERRA from both the chromosome 18q telomere and the PAR locus in mouse embryonic fibroblasts, ESC, and various mouse cancer and immortalized cell lines, and we identify two novel sources of TERRA on mouse chromosome 2 and X. Using various approaches, we show that PAR-TERRA molecules account for the majority of TERRA transcripts, displaying an increase of two to four orders of magnitude compared to the telomeric 18q transcript. Finally, we present a SILAC-based pull-down screen revealing a large overlap between TERRA-interacting proteins in human and mouse cells, including PRC2 complex subunits, chromatin remodeling factors, DNA replication proteins, Aurora kinases, shelterin complex subunits, Bloom helicase, Coilin, and paraspeckle proteins. Hence, despite originating from distinct genomic regions, mouse and human TERRA are likely to play similar functions in cells.

Geometry-Induced Spin Filtering in Photoemission Maps from WTe_{2} Surface States.

We demonstrate that an important quantum material WTe_{2} exhibits a new type of geometry-induced spin filtering effect in photoemission, stemming from low symmetry that is responsible for its exotic transport properties. Through the laser-driven spin-polarized angle-resolved photoemission Fermi surface mapping, we showcase highly asymmetric spin textures of electrons photoemitted from the surface states of WTe_{2}. Such asymmetries are not present in the initial state spin textures, which are bound by the time-reversal and crystal lattice mirror plane symmetries. The findings are reproduced qualitatively by theoretical modeling within the one-step model photoemission formalism. The effect could be understood within the free-electron final state model as an interference due to emission from different atomic sites. The observed effect is a manifestation of time-reversal symmetry breaking of the initial state in the photoemission process, and as such it cannot be eliminated, but only its magnitude influenced, by special experimental geometries.

Scaling and Confinement in Ultrathin Chalcogenide Films as Exemplified by GeTe.

Chalcogenides such as GeTe, PbTe, Sb2 Te3 , and Bi2 Se3 are characterized by an unconventional combination of properties enabling a plethora of applications ranging from thermo-electrics to phase change materials, topological insulators, and photonic switches. Chalcogenides possess pronounced optical absorption, relatively low effective masses, reasonably high electron mobilities, soft bonds, large bond polarizabilities, and low thermal conductivities. These remarkable characteristics are linked to an unconventional bonding mechanism characterized by a competition between electron delocalization and electron localization. Confinement, that is, the reduction of the sample dimension as realized in thin films should alter this competition and modify chemical bonds and the resulting properties. Here, pronounced changes of optical and vibrational properties are demonstrated for crystalline films of GeTe, while amorphous films of GeTe show no similar thickness dependence. For crystalline films, this thickness dependence persists up to remarkably large thicknesses above 15 nm. X-ray diffraction and accompanying simulations employing density functional theory relate these changes to thickness dependent structural (Peierls) distortions, due to an increased electron localization between adjacent atoms upon reducing the film thickness. A thickness dependence and hence potential to modify film properties for all chalcogenide films with a similar bonding mechanism is expected.

In Vitro Characterization of the Physical Interactions between the Long Noncoding RNA TERRA and the Telomeric Proteins TRF1 and TRF2.

RNA-protein interactions drive key cellular pathways such as protein translation, nuclear organization and genome stability maintenance. The human telomeric protein TRF2 binds to the long noncoding RNA TERRA through independent domains, including its N-terminal B domain. We previously demonstrated that TRF2 B domain binding to TERRA supports invasion of TERRA into telomeric double stranded DNA, leading to the formation of telomeric RNA:DNA hybrids. The other telomeric protein TRF1, which also binds to TERRA, suppresses this TRF2-associated activity by preventing TERRA-B domain interactions. Herein, we show that the binding of both TRF1 and TRF2 to TERRA depends on the ability of the latter to form G-quadruplex structures. Moreover, a cluster of arginines within the B domain is largely responsible for its binding to TERRA. On the other side, a patch of glutamates within the N-terminal A domain of TRF1 mainly accounts for the inhibition of TERRA-B domain complex formation. Finally, mouse TRF2 B domain binds to TERRA, similarly to its human counterpart, while mouse TRF1 A domain lacks the inhibitory activity. Our data shed further light on the complex crosstalk between telomeric proteins and RNAs and suggest a lack of functional conservation in mouse.

Conservation of Nickel Ion Single-Active Site Character in a Bottom-Up Constructed π-Conjugated Molecular Network.

On-surface chemistry holds the potential for ultimate miniaturization of functional devices. Porphyrins are promising building-blocks in exploring advanced nanoarchitecture concepts. More stable molecular materials of practical interest with improved charge transfer properties can be achieved by covalently interconnecting molecular units. On-surface synthesis allows to construct extended covalent nanostructures at interfaces not conventionally available. Here, we address the synthesis and properties of covalent molecular network composed of interconnected constituents derived from halogenated nickel tetraphenylporphyrin on Au(111). We report that the π-extended two-dimensional material exhibits dispersive electronic features. Concomitantly, the functional Ni cores retain the same single-active site character of their single-molecule counterparts. This opens new pathways when exploiting the high robustness of transition metal cores provided by bottom-up constructed covalent nanomeshes.

Value of PET imaging for radiation therapy.

This comprehensive review written by experts in their field gives an overview on the current status of incorporating positron emission tomography (PET) into radiation treatment planning. Moreover, it highlights ongoing studies for treatment individualisation and per-treatment tumour response monitoring for various primary tumours. Novel tracers and image analysis methods are discussed. The authors believe this contribution to be of crucial value for experts in the field as well as for policy makers deciding on the reimbursement of this powerful imaging modality.

Molecular Level Synthesis of InFeO3 and InFeO3/Fe2O3 Nanocomposites.

New heterometallic In-Fe alkoxides [InFe(OtBu)4(PyTFP)2] (1), [InFe2(OneoPen)9(Py)] (2), and [InFe3(OneoPen)12] (3) were synthesized and structurally characterized. The arrangement of metal centers in mixed-metal framework was governed by the In:Fe ratio and the coordination preferences of Fe(III) and In(III) centers to be in tetrahedral and octahedral environments, respectively. 3 displayed a star-shaped so-called "Mitsubishi" motif with the central In atom coordinated with three tetrahedral {Fe(OneoPen)4}- anionic units. The deterministic structural influence of the larger In atom was evident in 1 and 2 which displayed the coordination of neutral coligands to achieve the desired coordination number. Thermal decomposition studies of compounds 1-3 under inert conditions with subsequent powder diffraction studies revealed the formation of Fe2O3 and In2O3 in the case of 3 and 2, whereas 1 intriguingly produced elemental In and Fe. In contrary, the thermal decomposition of 1-3 under ambient conditions produced a ternary oxide, InFeO3, with additional Fe2O3 present as a secondary phase in a different stoichiometric ratio predetermined through the In:Fe ratio in 2 and 3. The intimate mixing of different phases in InFeO3/Fe2O3 nanocomposites was confirmed by transmission electron microscopy of solid residues obtained after the decomposition of 1 and 2. The pure InFeO3 particles demonstrated ferromagnetic anomalies around 170 K as determined by temperature-dependent field-cooled and zero-field-cooled magnetization experiments. A first-order magnetic transition with an increase in the ZFC measurements was explained by temperature-induced reduction of the Fe-Fe distance and the corresponding increase in superexchange.

Primary sellar melanocytoma.

PURPOSE: We present an up-to-date review of all published cases of sellar melanocytoma, a benign melanocytic neoplasm arising from melanocytes present in the leptomeninges surrounding the pituitary. METHODS: Both the Medline and Embase databases were searched for case reports or case series of patients with a sellar mass consisting of melanocytes. RESULTS: All 14 identified patients developed symptoms due to compression of the surrounding structures. Symptoms included pituitary dysfunction and visual impairment. All patients received a transsphenoidal resection as first-line treatment. The diagnosis is made on pathological examination but deciding whether a sellar melanocytic tumor is best classified as a melanocytoma or a melanoma is not straightforward. DISCUSSION: Genetic analyses can help differentiate between central nervous system origin and metastasis of a cutaneous melanoma with the presence of a GNAQ and GNA11 mutations or a BRAF mutation, respectively. First choice treatment is complete resection, and in case of incomplete resection or recurrence additional radiotherapy is advised.

New Acetophenones and Chromenes from the Leaves of Melicope barbigera A. Gray.

The dichloromethane extract from leaves of Melicope barbigera (Rutaceae), endemic to the Hawaiian island of Kaua'i, yielded four new and three previously known acetophenones and 2H-chromenes, all found for the first time in M. barbigera. The structures of the new compounds obtained from the dichloromethane extract after purification by chromatographic methods were unambiguously elucidated by spectroscopic analyses including 1D/2D NMR spectroscopy and HRESIMS. The absolute configuration was determined by modified Mosher's method. Compounds 2, 4 and the mixture of 6 and 7 exhibited moderate cytotoxic activities against the human ovarian cancer cell line A2780 with IC50 values of 30.0 and 75.7 µM for 2 and 4, respectively, in a nuclear shrinkage cytotoxicity assay.

Oral batyl alcohol supplementation rescues decreased cardiac conduction in ether phospholipid-deficient mice.

Plasmalogens (Pls) are a class of membrane phospholipids which serve a number of essential biological functions. Deficiency of Pls is associated with common disorders such as Alzheimer's disease or ischemic heart disease. A complete lack of Pls due to genetically determined defective biosynthesis gives rise to rhizomelic chondrodysplasia punctata (RCDP), characterized by a number of severe disabling pathologic features and death in early childhood. Frequent cardiac manifestations of RCDP include septal defects, mitral valve prolapse, and patent ductus arteriosus. In a mouse model of RCDP, reduced nerve conduction velocity was partially rescued by dietary oral supplementation of the Pls precursor batyl alcohol (BA). Here, we examine the impact of Pls deficiency on cardiac impulse conduction in a similar mouse model (Gnpat KO). In-vivo electrocardiographic recordings showed that the duration of the QRS complex was significantly longer in Gnpat KO mice than in age- and sex-matched wild-type animals, indicative of reduced cardiac conduction velocity. Oral supplementation of BA for 2 months resulted in normalization of cardiac Pls levels and of the QRS duration in Gnpat KO mice but not in untreated animals. BA treatment had no effect on the QRS duration in age-matched wild-type mice. These data suggest that Pls deficiency is associated with increased ventricular conduction time which can be rescued by oral BA supplementation.

In-Gap States and Band-Like Transport in Memristive Devices.

Point defects such as oxygen vacancies cause emergent phenomena such as resistive switching in transition-metal oxides, but their influence on the electron-transport properties is far from being understood. Here, we employ direct mapping of the electronic structure of a memristive device by spectromicroscopy. We find that oxygen vacancies result in in-gap states that we use as input for single-band transport simulations. Because the in-gap states are situated below the Fermi level, they do not contribute to the current directly but impact the shape of the conduction band. Accordingly, we can describe our devices with band-like transport and tunneling across the Schottky barrier at the interface.

Fission yeast Cactin restricts telomere transcription and elongation by controlling Rap1 levels.

The telomeric transcriptome comprises multiple long non-coding RNAs generated by transcription of linear chromosome ends. In a screening performed in Schizosaccharomyces pombe, we identified factors modulating the cellular levels of the telomeric transcriptome. Among these factors, Cay1 is the fission yeast member of the conserved family of Cactins, uncharacterized proteins crucial for cell growth and survival. In cay1∆ mutants, the cellular levels of the telomeric factor Rap1 are drastically diminished due to defects in rap1+ pre-mRNA splicing and Rap1 protein stability. cay1∆ cells accumulate histone H3 acetylated at lysine 9 at telomeres, which become transcriptionally desilenced, are over-elongated by telomerase and cause chromosomal aberrations in the cold. Overexpressing Rap1 in cay1+ deleted cells significantly reverts all telomeric defects. Additionally, cay1∆ mutants accumulate unprocessed Tf2 retrotransposon RNA through Rap1-independent mechanisms. Thus, Cay1 plays crucial roles in cells by ultimately harmonizing expression of transcripts originating from seemingly unrelated genomic loci.

Human cactin interacts with DHX8 and SRRM2 to assure efficient pre-mRNA splicing and sister chromatid cohesion.

Cactins constitute a family of eukaryotic proteins broadly conserved from yeast to human and required for fundamental processes such as cell proliferation, genome stability maintenance, organismal development and immune response. Cactin proteins have been found to associate with the spliceosome in several model organisms, nevertheless their molecular functions await elucidation. Here we show that depletion of human cactin leads to premature sister chromatid separation, genome instability and cell proliferation arrest. Moreover, cactin is essential for efficient splicing of thousands of pre-mRNAs, and incomplete splicing of the pre-mRNA of sororin (also known as CDCA5), a cohesin-associated factor, is largely responsible for the aberrant chromatid separation in cactin-depleted cells. Lastly, cactin physically and functionally interacts with the spliceosome-associated factors DHX8 and SRRM2. We propose that cellular complexes comprising cactin, DHX8 and SRRM2 sustain precise chromosome segregation, genome stability and cell proliferation by allowing faithful splicing of specific pre-mRNAs. Our data point to novel pathways of gene expression regulation dependent on cactin, and provide an explanation for the pleiotropic dysfunctions deriving from cactin inactivation in distant eukaryotes.

Stem-loop RNA labeling can affect nuclear and cytoplasmic mRNA processing.

The binding of sequence-specific RNA-interacting proteins, such as the bacteriophage MS2 or PP7 coat proteins, to their corresponding target sequences has been extremely useful and widely used to visualize single mRNAs in vivo. However, introduction of MS2 stem-loops into yeast mRNAs has recently been shown to lead to the accumulation of RNA fragments, suggesting that the loops impair mRNA decay. This result was questioned, because fragment occurrence was mainly assessed using ensemble methods, and their cellular localization and its implications had not been addressed on a single transcript level. Here, we demonstrate that the introduction of either MS2 stem-loops (MS2SL) or PP7 stem-loops (PP7SL) can affect the processing and subcellular localization of mRNA. We use single-molecule fluorescence in situ hybridization (smFISH) to determine the localization of three independent mRNAs tagged with the stem-loop labeling systems in glucose-rich and glucose starvation conditions. Transcripts containing MS2SL or PP7SL display aberrant localization in both the nucleus and the cytoplasm. These defects are most prominent in glucose starvation conditions, with nuclear mRNA processing being altered and stem-loop fragments abnormally enriching in processing bodies (PBs). The mislocalization of SL-containing RNAs is independent of the presence of the MS2 or PP7 coat protein (MCP or PCP).

Stress and Alzheimer's disease.

Alzheimer's disease (AD) is the leading cause of dementia worldwide. Due to demographic change in higher income countries and rising life expectancy in middle- and low-income countries, the prevalence of AD will increase significantly in the coming years. In the search for effective AD prevention, the role of stress in the development of AD has come into focus. There is increasing evidence that chronic exposure to stress is a risk factor for AD and may also adversely affect the course of the disease. In our review, we present the current literature on the association of specific personality traits and the risk of developing AD. We also report on findings on dementia risk in patients with posttraumatic stress disorder. Furthermore, we describe the role of anxiety symptoms in AD and give a brief overview over the biological mechanisms behind the association of stress and AD.

TERRA promotes telomerase-mediated telomere elongation in Schizosaccharomyces pombe.

Telomerase-mediated telomere elongation provides cell populations with the ability to proliferate indefinitely. Telomerase is capable of recognizing and extending the shortest telomeres in cells; nevertheless, how this mechanism is executed remains unclear. Here, we show that, in the fission yeast Schizosaccharomyces pombe, shortened telomeres are highly transcribed into the evolutionarily conserved long noncoding RNA TERRA A fraction of TERRA produced upon telomere shortening is polyadenylated and largely devoid of telomeric repeats, and furthermore, telomerase physically interacts with this polyadenylated TERRA in vivo We also show that experimentally enhanced transcription of a manipulated telomere promotes its association with telomerase and concomitant elongation. Our data represent the first direct evidence that TERRA stimulates telomerase recruitment and activity at chromosome ends in an organism with human-like telomeres.