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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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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 β-globin cDNA, which is normally retained/degraded in the nucleus. Significantly, the tandem CAR-E, but not its antisense counterpart, rescued cytoplasmic accumulation of β-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.

Investigates the characteristics of glycidyl methacrylate-DNA adducts formation in vitro in China. Importance of DNA modification on chemical carcinogenesis; Use of ultra violet spectroscopy Specificity of binding sites.

The emerging two-dimensional (2D) Dion-Jacobson (DJ) perovskites with bidentate ligands have attracted significant attention due to enhanced structural stability compared with conventional Ruddlesden-Popper (RP) perovskites with monodentate ligands linked by van der Waals interactions. However, how the pure chemical bond lattice interacts with excited state excitons and its impact on the exciton nature and dynamics in 2D DJ-perovskites, particularly in comparison to RP-perovskites, remains unexplored. Herein, by a combined spectroscopy study on excitonic and structural dynamics, we reveal a persistent exciton dressed by a weak polaronic effect in DJ-perovskite due to their rigid and harmonic lattice, in striking contrast to significantly screened exciton polaron observed in RP-perovskites. Despite the similar exciton binding energy (∼0.3 eV) in both n = 1 DJ- and RP-perovskites with near-identical crystal structure, photoexcitation results in a slightly screened exciton with minimal structural relaxation and a retained binding energy of ∼0.29 eV in DJ-perovskites but strongly screened exciton polaron with a binding energy of ∼0.13 eV in RP-perovskites. Structural dynamics further highlight the rigid and harmonic lattice motion in DJ-perovskites, as opposed to the thermally activated anharmonic lattice in RP-perovskites, arising from their distinct bonding modes. Our study offers insights into modulating excited state properties in 2D perovskites, simulating the rational design of hybrid semiconductors with tailored properties and functionalities.

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)PbBr 4 and 2D (EDBE)PbBr 4 , 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 Pb 3+ . Further atomic level theoretical simulations confirm photoexcited electrons and holes are localized on the Pb 2+ site to form Pb + - and Pb 3+ -like species, resembling transient photoinduced Pb 2+ 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.

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., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

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., (© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.)

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., Competing Interests: XQ, YZ, LS, QM, JY, LA, JX, GC, HZ, CJ, XG, HL, YY No competing interests declared, CL Reviewing Editor, eLife, (© 2021, Qiao et al.)

RNA-protein complexes are essential for the function of different RNAs, yet purification of specific RNA-protein complexes can be complicated and is a major obstacle in understanding the mechanism of regulatory RNAs. Here we present a protocol to purify RNA-protein complexes assembled in vitro based on biotin-streptavidin affinity. In vitro transcribed RNA is labeled with (32)P and biotin, ribonucleoprotein particles or RNPs are assembled by incubation of RNA in nuclear extract and fractionated using gel filtration, and RNP fractions are pooled for biotin-streptavidin affinity purification. The amount of RNA-protein complexes purified following this protocol is sufficient for mass spectrometry.

Aim: To investigate the clinicopathological significance of the expression of fibrous sheath interacting protein 1 (FSIP1) in breast cancer, serum samples, and wound fluid from patients with breast cancer., Methods: Wound fluid and serum samples from female patients with primary breast cancer, recurrent and metastatic breast cancer, and benign tumors were analyzed for FSIP1 expression using ELISA. 286 paraffin-embedded surgical specimens from breast cancer patients with at least 5 years of follow-up were included for FSIP1 expression assay using immunohistochemistry., Results: Expression of FSIP1 protein was significantly higher in breast cancer tissues compared to tumor-adjacent tissues (p = 0.001). Strong correlation was observed between FSIP1 expression and human epidermal growth factor receptor 2 (Her-2) or Ki67 expression in breast cancer (p = 0.027 and 0.002, respectively). Similarly, serum level of FSIP1 was higher in patients with recurrent and metastatic breast cancer compared to that of primary breast cancer (7, 713 ± 3, 065 vs. 4, 713 ± 3, 065 pg/ml, p = 0.003). Finally, patients with high FSIP1 expression showed a worse post-operative disease-specific survival (p = 0.024)., Conclusion: FSIP1 may play an important role in the tumorigenesis and invasion of breast cancer and is a potential biomarker for breast cancer diagnosis or prognosis.

A great deal of progress in understanding gene expression has been made using in vitro systems. For most studies, functional assays are carried out using extracts that are prepared in bulk from 10-50 or more liters of cells grown in suspension. However, these large-scale preparations are not amenable to rapidly testing in vitro effects that result from a variety of in vivo cellular treatments or conditions. This journal video article shows a method for preparing functional small-scale nuclear extracts, using HeLa cells as an example. This method is carried out using as few as three 150 mm plates of cells grown as adherent monolayers. To illustrate the efficiency of the small-scale extracts, we show that they are as active as bulk nuclear extracts for coupled RNA Polymerase II transcription/splicing reactions. To demonstrate the utility of the extract protocol, we show that splicing is abolished in extracts prepared from HeLa cells treated with the splicing inhibitor drug E7107. The small-scale protocol should be generally applicable to any process or cell type that can be investigated in vitro using cellular extracts. These include patient cells that are only available in limited quantities or cells exposed to numerous agents such as drugs, DNA damaging agents, RNAi, or transfection, which require the use of small cell populations. In addition, small amounts of freshly grown cells are convenient and/or required for some applications.

The TREX complex, which functions in mRNA export, is recruited to mRNA during splicing. Both the splicing machinery and the TREX complex are concentrated in 20-50 discrete foci known as nuclear speckle domains. In this study, we use a model system where DNA constructs are microinjected into HeLa cell nuclei, to follow the fates of the transcripts. We show that transcripts lacking functional splice sites, which are inefficiently exported, do not associate with nuclear speckle domains but are instead distributed throughout the nucleoplasm. In contrast, pre-mRNAs containing functional splice sites accumulate in nuclear speckles, and our data suggest that splicing occurs in these domains. When the TREX components UAP56 or Aly are knocked down, spliced mRNA, as well as total polyA+ RNA, accumulates in nuclear speckle domains. Together, our data raise the possibility that pre-mRNA undergoes splicing in nuclear speckle domains, before their release by TREX components for efficient export to the cytoplasm.

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.