Suppressed Magnitude of Spectral Diffusion in Cube-Shaped CdSe/CdS Core/Shell Nanocrystals with Exceedingly Stable Photoluminescence.

Colloidal semiconductor nanocrystals are promising candidates for quantum light sources, yet their application has been impeded by photoluminescence instability due to blinking and spectral diffusion. This study introduces a new category of cube-shaped CdSe/CdS core/shell nanocrystals with exceptionally stable photoluminescence characteristics. Under continuous excitation, the emissive quantum state remained consistent without alterations of the charge state for 4000 s, and the average photon energy variation stayed within the bounds of spectral resolution throughout this extended duration. Systematic examination of single-nanocrystal photoluminescence, upon variation of the core and shell dimensions, revealed that a thicker CdS shell and increased core edge length significantly curtail spectral diffusion, considering that the nanocrystals possess well-controlled CdSe-CdS and facet-ligand interfaces. This study advances the optimization of colloidal semiconductor nanocrystals as high-performance quantum light sources.

Weakly Confined Semiconductor Nanocrystals Excel in Photochemical and Optoelectronic Properties: Evidence from Single-Dot Studies.

Single-molecule spectroscopy offers state-resolved measurements on charge-transfer reactions of single semiconductor nanocrystals, leading to the discovery of up to six single-charge transfer reactions with seven transient states for single CdSe/CdS core/shell nanocrystals with water (or oxygen) as the hole (or electron) acceptors. Kinetic rates of three photoinduced single-hole transfer reactions decrease significantly upon increasing the number of excess electrons in a nanocrystal, mainly due to efficient Auger nonradiative recombination of the charged single excitons. Conversely, the kinetic rates of three single-electron transfer reactions of an unexcited nanocrystal increase proportionally to the number of excess electrons in it. Results here reveal that charge-transfer reactions of nanocrystals, at the center of nearly all their functions, could only be deciphered at a state-resolved level on a single nanocrystal. Size-dependent studies validate the weakly confined semiconductor nanocrystals, instead of strongly confined ones (quantum dots), as optimal candidates for photochemical and optoelectronic applications.

Transient Photoinduced Pb2+ Disproportionation for Exciton Self-Trapping and Broadband Emission in Low-Dimensional Lead Halide Perovskites.

Low-dimensional lead halide perovskites with broadband emission hold great promise for single-component white-light-emitting (WLE) devices. The origin of their broadband emission has been commonly attributed to self-trapped excitons (STEs) composed of localized electronic polarization with a distorted lattice. Unfortunately, the exact electronic and structural nature of the STE species in these WLE materials remains elusive, hindering the rational design of high-efficiency WLE materials. In this study, by combining ultrafast transient absorption spectroscopy and ab initio calculations, we uncover surprisingly similar STE features in two prototypical low dimensional WLE perovskite single crystals: 1D (DMEDA)PbBr4 and 2D (EDBE)PbBr4, despite of their different dimensionalities. Photoexcited excitons rapidly localize to intrinsic STEs within ∼250 fs, contributing to the white light emission. Crucially, STEs in both systems exhibit characteristic absorption features akin to those of Pb+ and Pb3+. Further atomic level theoretical simulations confirm photoexcited electrons and holes are localized on the Pb2+ site to form Pb+- and Pb3+-like species, resembling transient photoinduced Pb2+ disproportionation. This study provides conclusive evidence on the key excited state species for exciton self-trapping and broadband emission in low dimensional lead halide WLE perovskites and paves the way for the rational design of high-efficiency WLE materials.

Sequence-dependent recruitment of SRSF1 and SRSF7 to intronless lncRNA NKILA promotes nuclear export via the TREX/TAP pathway.

The TREX-TAP pathway is vital for mRNA export. For spliced mRNA, the TREX complex is recruited during splicing; however, for intronless mRNA, recruitment is sequence dependent. However, the export of cytoplasmic long noncoding RNA (lncRNA) is poorly characterized. We report the identification of a cytoplasmic accumulation region (CAR-N) in the intronless lncRNA, NKILA. CAR-N removal led to strong nuclear retention of NKILA, and CAR-N insertion promoted the export of cDNA transcripts. In vitro RNP purification via CAR-N, mass spectrometry, and siRNA screening revealed that SRSF1 and SRSF7 were vital to NKILA export, and identified a cluster of SRSF1/7 binding sites within a 55 nucleotide sequence in CAR-N. Significant nuclear enrichment of NKILA was observed for NKILA lacking CAR-N or the cluster of binding sites in knock-in models. Depletion of TREX-TAP pathway components resulted in strong nuclear retention of NKILA. RNA and protein immunoprecipitation verified that SRSF1/7 were bound to NKILA and interacted with UAP56 and ALYREF. Moreover, NKILA lacking CAR-N was unable to inhibit breast cancer cell migration. We concluded that the binding of SRSF1/7 to clustered motifs in CAR-N facilitated TREX recruitment, promoting the export of NKILA, and confirmed the importance of NKILA localization to its function.

Synthesis of Weakly Confined, Cube-Shaped, and Monodisperse Cadmium Chalcogenide Nanocrystals with Unexpected Photophysical Properties.

Zinc-blende CdSe, CdS, and CdSe/CdS core/shell nanocrystals with a structure-matched shape (cube-shaped, edge length ≤30 nm) are synthesized via a universal scheme. With the edge length up to five times larger than exciton diameter of the bulk semiconductors, the nanocrystals exhibit novel properties in the weakly confined size regime, such as near-unity single exciton and biexciton photoluminescence (PL) quantum yields, single-nanocrystal PL nonblinking, mixed PL decay dynamics of exciton and free carriers with sub-microsecond monoexponential decay lifetime, and stable yet extremely narrow PL full width at half maximum (FWHM < 0.1 meV) at 1.8 K. Their monodisperse edge length, shape, and facet structure enable demonstration of unexpected yet size-dependent PL properties at room temperature, including unusually broad and abnormally size-dependent PL FWHM (∼100 meV), nonmonotonic size dependence of PL peak energy, and dual-peak single-exciton PL. Calculations suggest that these unusual properties should be originated from the band-edge electron/hole states of the dynamic-exciton, whose exciton binding energy is too small to hold the photogenerated electron-hole pair as a bonded Wannier exciton in a weakly confined nanocrystal.

XAB2 depletion induces intron retention in POLR2A to impair global transcription and promote cellular senescence.

XAB2 is a multi-functional protein participating processes including transcription, splicing, DNA repair and mRNA export. Here, we report POLR2A, the largest catalytic subunit of RNA polymerase II, as a major target gene down-regulated after XAB2 depletion. XAB2 depletion led to severe splicing defects of POLR2A with significant intron retention. Such defects resulted in substantial loss of POLR2A at RNA and protein levels, which further impaired global transcription. Treatment of splicing inhibitor madrasin induced similar reduction of POLR2A. Screen using TMT-based quantitative proteomics identified several proteins involved in mRNA surveillance including Dom34 with elevated expression. Inhibition of translation or depletion of Dom34 rescued the expression of POLR2A by stabilizing its mRNA. Immuno-precipitation further confirmed that XAB2 associated with spliceosome components important to POLR2A expression. Domain mapping revealed that TPR motifs 2-4 and 11 of XAB2 were critical for POLR2A expression by interacting with SNW1. Finally, we showed POLR2A mediated cell senescence caused by XAB2 deficiency. Depletion of XAB2 or POLR2A induced cell senescence by up-regulation of p53 and p21, re-expression of POLR2A after XAB2 depletion alleviated cellular senescence. These data together support that XAB2 serves as a guardian of POLR2A expression to ensure global gene expression and antagonize cell senescence.

Cholesterol content in cell membrane maintains surface levels of ErbB2 and confers a therapeutic vulnerability in ErbB2-positive breast cancer.

BACKGROUND: ErbB2 overexpression identifies a subset of breast cancer as ErbB2-positive and is frequently associated with poor clinical outcomes. As a membrane-embedded receptor tyrosine kinase, cell surface levels of ErbB2 are regulated dynamically by membrane physical properties. The present study aims to investigate the influence of membrane cholesterol contents on ErbB2 status and cellular responses to its tyrosine kinase inhibitors. METHODS: The cholesterol abundance was examined in ErbB2-positive breast cancer cells using filipin staining. Cellular ErbB2 localizations were investigated by immunofluorescence with altered membrane cholesterol contents. The inhibitory effects of the cholesterol-lowering drug lovastatin were assessed using cell proliferation, apoptosis, immunoblotting and immunofluorescence assays. The synergistic effects of lovastatin with the ErbB2 inhibitor lapatinib were evaluated using an ErbB2-positive breast cancer xenograft mouse model. RESULTS: Membrane cholesterol contents positively correlated with cell surface distribution of ErbB2 through increasing the rigidity and decreasing the fluidity of cell membranes. Reduction in cholesterol abundance assisted the internalization and degradation of ErbB2. The cholesterol-lowering drug lovastatin significantly potentiated the inhibitory effects of ErbB2 kinase inhibitors, accompanied with enhanced ErbB2 endocytosis. Lovastatin also synergized with lapatinib to strongly suppress the in vivo growth of ErbB2-positive breast cancer xenografts. CONCLUSION: The cell surface distribution of ErbB2 was closely regulated by membrane physical properties governed by cholesterol contents. The cholesterol-lowering medications can hence be exploited for potential combinatorial therapies with ErbB2 kinase inhibitors in the clinical treatment of ErbB2-positive breast cancer.

Nuclear retention element recruits U1 snRNP components to restrain spliced lncRNAs in the nucleus.

In contrast to cytoplasmic localization of spliced mRNAs, many spliced lncRNAs are localized in the nucleus. To investigate the mechanism, we used lncRNA MEG3 as a reporter and mapped a potent nuclear retention element (NRE), deletion of this element led to striking export of MEG3 from the nucleus to the cytoplasm. Insertion of the NRE resulted in nuclear retention of spliced lncRNA as well as spliced mRNA. We further purified RNP assembled on the NRE in vitro and identified the proteins by mass spectrometry. Screen using siRNA revealed depletion of U1 snRNP components SNRPA, SNRNP70 or SNRPD2 caused significant cytoplasmic localization of MEG3 reporter transcripts. Co-knockdown these factors in HFF1 cells resulted in an increased cytoplasmic distribution of endogenous lncRNAs. Together, these data support a model that U1 snRNP components restrain spliced lncRNAs in the nucleus via the interaction with nuclear retention element.

Aurora-A Kinase: A Potent Oncogene and Target for Cancer Therapy.

The Aurora kinase family is comprised of three serine/threonine kinases, Aurora-A, Aurora-B, and Aurora-C. Among these, Aurora-A and Aurora-B play central roles in mitosis, whereas Aurora-C executes unique roles in meiosis. Overexpression or gene amplification of Aurora kinases has been reported in a broad range of human malignancies, pointing to their role as potent oncogenes in tumorigenesis. Aurora kinases therefore represent promising targets for anticancer therapeutics. A number of Aurora kinase inhibitors (AKIs) have been generated; some of which are currently undergoing clinical evaluation. Recent studies have unveiled novel unexpected functions of Aurora kinases during cancer development and the mechanisms underlying the anticancer actions of AKIs. In this review, we discuss the most recent advances in Aurora-A kinase research and targeted cancer therapy, focusing on the oncogenic roles and signaling pathways of Aurora-A kinases in promoting tumorigenesis, the recent preclinical and clinical AKI data, and potential alternative routes for Aurora-A kinase inhibition.

HuR antagonizes the effect of an intronic pyrimidine-rich sequence in regulating WT1 +/-KTS isoforms.

WT1 + KTS and -KTS isoforms only differ in 3 amino acids in protein sequence but show significant functional difference. The +/-KTS isoforms were generated by alternative usage of 2 adjacent 5' splice sites at RNA level, however, how these 2 isoforms are regulated is still elusive. Here we report the identification of an intronic pyrimidine-rich sequence that is critical for the ratio of +/-KTS isoforms, deletion or partial replacement of the sequence led to full/significant shift to -KTS isoform. To identify trans-factors that can regulate +/-KTS isoforms via the binding to the element, we performed RNP assembly using in vitro transcribed RNA with or without the pyrimidine-rich sequence. Mass spectrometry analysis of purified RNPs showed that the element associated with many splicing factors. Co-transfection of these factors with WT1 reporter revealed that HuR promoted the production of -KTS isoform at the reporter level. RNA immuno-precipitation experiment indicated that HuR interacted with the pyrimidine-rich element in WT1 intron 9. We further presented evidence that transient or stable over-expression of HuR led to enhanced expression of endogenous -KTS isoform. Moreover, knockdown of HuR resulted in decreased expression of endogenous -KTS isoform in 293T, SW620, SNU-387 and AGS cell lines. Together, these data indicate that HuR binds to the pyrimidine-rich sequence and antagonize its effect in regulating WT1 +/-KTS isoforms.

Evidence that a consensus element found in naturally intronless mRNAs promotes mRNA export.

We previously showed that mRNAs synthesized from three genes that naturally lack introns contain a portion of their coding sequence, known as a cytoplasmic accumulation region (CAR), which is essential for stable accumulation of the intronless mRNAs in the cytoplasm. The CAR in each mRNA is unexpectedly large, ranging in size from ∼160 to 285 nt. Here, we identified one or more copies of a 10-nt consensus sequence in each CAR. To determine whether this element (designated CAR-E) functions in cytoplasmic accumulation of intronless mRNA, we multimerized the most conserved CAR-E and inserted it upstream of ß-globin cDNA, which is normally retained/degraded in the nucleus. Significantly, the tandem CAR-E, but not its antisense counterpart, rescued cytoplasmic accumulation of ß-globin cDNA transcripts. Moreover, dinucleotide mutations in the CAR-E abolished this rescue. We show that the CAR-E, but not the mutant CAR-E, associates with components of the TREX mRNA export machinery, the Prp19 complex and U2AF2. Moreover, knockdown of these factors results in nuclear retention of the intronless mRNAs. Together, these data suggest that the CAR-E promotes export of intronless mRNA by sequence-dependent recruitment of the mRNA export machinery.

Export and stability of naturally intronless mRNAs require specific coding region sequences and the TREX mRNA export complex.

A great deal is known about the export of spliced mRNAs, but little is known about the export of mRNAs encoded by human cellular genes that naturally lack introns. Here, we investigated the requirements for export of three naturally intronless mRNAs (HSPB3, IFN-α1, and IFN-ß1). Significantly, we found that all three mRNAs are stable and accumulate in the cytoplasm, whereas size-matched random RNAs are unstable and detected only in the nucleus. A portion of the coding region confers this stability and cytoplasmic localization on the naturally intronless mRNAs and a cDNA transcript, which is normally retained in the nucleus and degraded. A polyadenylation signal, TREX mRNA export components, and the mRNA export receptor TAP are required for accumulation of the naturally intronless mRNAs in the cytoplasm. We conclude that naturally intronless mRNAs contain specific sequences that result in efficient packaging into the TREX mRNA export complex, thereby supplanting the splicing requirement for efficient mRNA export.

Robust and Efficient Out-of-Plane Exciton Transport in Two-Dimensional Perovskites via Ultrafast Förster Energy Transfer.

Two-dimensional (2D) perovskites, comprising inorganic semiconductor layers separated by organic spacers, hold promise for light harvesting and optoelectronic applications. Exciton transport in these materials is pivotal for device performance, often necessitating deliberate alignment of the inorganic layers with respect to the contacting layers to facilitate exciton transport. While much attention has focused on in-plane exciton transport, little has been paid to out-of-plane interlayer transport, which presumably is sluggish and unfavorable. Herein, by time-resolved photoluminescence, we unveil surprisingly efficient out-of-plane exciton transport in 2D perovskites, with diffusion coefficients (up to ∼0.1 cm2 s-1) and lengths (∼100 nm) merely a few times smaller or comparable to their in-plane counterparts. We unambiguously confirm that the out-of-plane exciton diffusion coefficient corresponds to a subpicosecond interlayer exciton transfer, governed by the Förster resonance energy transfer (FRET) mechanism. Intriguingly, in contrast to temperature-sensitive intralayer band-like transport, the interlayer exciton transport exhibits negligible temperature dependence, implying a lowest-lying bright exciton state in 2D perovskites, irrespective of spacer molecules. The robust and ultrafast interlayer exciton transport alleviates the constraints on crystal orientation that are crucial for the design of 2D perovskite-based light harvesting and optoelectronic devices.

Mechanisms of RNA export and nuclear retention.

With the identification of huge amount of noncoding RNAs in recent years, the concept of RNA localization has extended from traditional mRNA export to RNA export of mRNA and ncRNA as well as nuclear retention of ncRNA. This review aims to summarize the recent findings from studies on the mechanisms of export of different RNAs and nuclear retention of some lncRNAs in higher eukaryotes, with a focus on splicing-dependent TREX recruitment for the export of spliced mRNA and the sequence-dependent mechanism of mRNA export in the absence of splicing. In addition, evidence to support the involvement of m6 A modification in RNA export with the coordination between the methylase complex and TREX complex as well as sequence-dependent nuclear retention of lncRNA is recapitulated. Finally, a model of sequence-dependent RNA localization is proposed along with the many questions that remain to be answered. This article is categorized under: RNA Export and Localization > RNA Localization RNA Export and Localization > Nuclear Export/Import.

MS2-MBP-Based Affinity Purification of Nucleus- or Cytoplasm-Localized lncRNA-Protein Complexes Formed In Vivo.

With recent emergence of huge number of long noncoding RNAs (lncRNAs), purification of lncRNA-protein (lncRNP) complexes is fundamental to understand the role of lncRNA and its biological function. However, lncRNP purification is still a daunting challenge. Here we describe a protocol to purify lncRNP formed in vivo with MS2-MBP-based affinity purification. Inducible lncRNA tagged with MS2 RNA hairpins is introduced into cells of interest, and RNP on tagged lncRNA is formed in vivo. MS2-MBP fusion protein is expressed in Escherichia coli and purified with amylose resin and HiTrap heparin column. The MS2 part of MS2-MBP fusion protein binds to the hairpins, and MBP part binds to amylose resin. We also describe a protocol to separate the nucleus and the cytoplasm so that lncRNP localized in the nucleus or cytoplasm can be individually purified. The amount of lncRNP purified is well sufficient for mass spectrometry analysis.

Band-Edge Energy Levels of Dynamic Excitons in Cube-Shaped CdSe/CdS Core/Shell Nanocrystals.

An electron-hole pair in a cube-shaped CdSe/CdS core/shell nanocrystal exists in the form of dynamic excitons across the strongly and weakly confined regimes under ambient temperatures. Photochemical doping is applied to distinguish the band-edge electron and hole levels, confirming an effective mass model with universal constants. Reduction of the optical bandgap upon epitaxy of the CdS shells is caused by lowering the band-edge electron level and barely affecting the band-edge hole level. Similar shifts of the electron levels, yet retaining the hole levels, can switch the order in energy of the three lowest-energy transitions. Thermal distribution of 1-4 electrons among the two thermally accessible electron levels follows number-counting statistics, instead of Fermi-Dirac distribution.

Application of RNA subcellular fraction estimation method to explore RNA localization regulation.

RNA localization is involved in multiple biological processes. Recent advances in subcellular fractionation-based sequencing approaches uncovered localization pattern on a global scale. Most of existing methods adopt relative localization ratios (such as ratios of separately normalized transcripts per millions of different subcellular fractions without considering the difference in total RNA abundances in different fractions), however, absolute ratios may yield different results on the preference to different cellular compartment. Experimentally, adding external Spike-in RNAs to different fractionation can be used to obtain absolute ratios. In addition, a spike-in independent computational approach based on multiple linear regression model can also be used. However, currently, no custom tool is available. To solve this problem, we developed a method called subcellular fraction abundance estimator to correctly estimate relative RNA abundances of different subcellular fractionations. The ratios estimated by our method were consistent with existing reports. By applying the estimated ratios for different fractions, we explored the RNA localization pattern in cell lines and also predicted RBP motifs that were associated with different localization patterns. In addition, we showed that different isoforms of same genes could exhibit distinct localization patterns. To conclude, we believed our tool will facilitate future subcellular fractionation-related sequencing study to explore the function of RNA localization in various biological problems.

Association of human breast cancer CD44-/CD24- cells with delayed distant metastasis.

Tumor metastasis remains the main cause of breast cancer-related deaths, especially delayed breast cancer distant metastasis. The current study assessed the frequency of CD44-/CD24- breast cancer cells in 576 tissue specimens for associations with clinicopathological features and metastasis and investigated the underlying molecular mechanisms. The results indicated that higher frequency (≥19.5%) of CD44-/CD24- cells was associated with delayed postoperative breast cancer metastasis. Furthermore, CD44-/CD24-triple negative breast cancer (TNBC) cells spontaneously converted into CD44+/CD24-cancer stem cells (CSCs) with properties similar to CD44+/CD24-CSCs from primary human breast cancer cells and parental TNBC cells in terms of stemness marker expression, self-renewal, differentiation, tumorigenicity, and lung metastasis in vitro and in NOD/SCID mice. RNA sequencing identified several differentially expressed genes (DEGs) in newly converted CSCs and RHBDL2, one of the DEGs, expression was upregulated. More importantly, RHBDL2 silencing inhibited the YAP1/USP31/NF-κB signaling and attenuated spontaneous CD44-/CD24- cell conversion into CSCs and their mammosphere formation. These findings suggest that the frequency of CD44-/CD24- tumor cells and RHBDL2 may be valuable for prognosis of delayed breast cancer metastasis, particularly for TNBC.

Polymorphisms in predicted microRNA-binding sites in integrin genes and breast cancer: ITGB4 as prognostic marker.

Integrins control the cell attachment to the extracellular matrix and play an important role in mediating cell proliferation, migration and survival. A number of important cancer-associated integrin genes can be regulated by microRNAs (miRNAs) that bind to their target sites in the 3' untranslated regions. We examined the effect of single-nucleotide polymorphisms (SNPs) in predicted miRNA target sites of six integrin genes (ITGA3, ITGA6, ITGAv, ITGB3, ITGB4 and ITGB5) on breast cancer (BC) risk and clinical outcome. Six SNPs were genotyped in 749 Swedish incident BC cases with detailed clinical data and up to 15 years of follow-up together with 1493 matched controls. We evaluated associations between genotypes and BC risk and clinical tumour characteristics. Survival probabilities were compared between different subgroups. As a novel finding, several SNPs seemed to associate with the hormone receptor status. The strongest association was observed between the A allele of the SNP rs743554 in the ITGB4 gene and oestrogen receptor-negative tumours [odds ratio 2.09, 95% confidence intervals (CIs) 1.19-3.67]. The same SNP was associated with survival. The A allele carriers had a worse survival compared with the wild-type genotype carriers (hazard ratio 2.11, 95% CIs 1.21-3.68). The poor survival was significantly associated with the aggressive tumour characteristics: high grade, lymph node metastasis and high stage. None of the SNPs was significantly associated with BC risk. As the ITGB4 SNP seems to influence tumour aggressiveness and survival, it may have prognostic value in the clinic.

Identification of splicing silencers and enhancers in sense Alus: a role for pseudoacceptors in splice site repression.

Auxiliary splicing signals in introns play an important role in splice site selection, but these elements are poorly understood. We show that a subset of serine/arginine (SR)-rich proteins activate a cryptic 3' splice site in a sense Alu repeat located in intron 4 of the human LST1 gene. Utilization of this cryptic splice site is controlled by juxtaposed Alu-derived splicing silencers and enhancers between closely linked short tandem repeats TNFd and TNFe. Systematic mutagenesis of these elements showed that AG dinucleotides that were not preceded by purine residues were critical for repressing exon inclusion of a chimeric splicing reporter. Since the splice acceptor-like sequences are present in excess in exonic splicing silencers, these signals may contribute to inhibition of a large number of pseudosites in primate genomes.