Abstract:The central dogma of molecular biology describes the flow of genetic information within the biological system. According to the classical central dogma, RNA can only play its role in life through translation. With the development of molecular biology, rapidly growing evidence shows that RNAs perform a vast array of functions within organisms even without translation. Moreover, RNA can fold into different types aside from linear RNA. Here, we summarized the four forms of RNA for their post transcriptional fate: non-translation, part-translation, de novo-translation and over-translation. Non-translation means the RNAs can’t be translated to proteins as many non-coding RNAs do. Part-translation describes a phenomenon that the RNA can’t translate into a peptide chain using all the information as a template, but only a part of it. Whereas the de novo-translation refers to the classical translation process. Over-translation means the RNA can encode a protein using more than their own genetic information, which only occurs in circular RNAs. The diversity of RNA’s fate extends largely our understanding of translation above the classical central dogma. Further understanding of the fate of RNA post transcription will put forward more challenging demand on the research for the functions of RNA, and meanwhile, will also present the potential solutions for comprehensive understanding of the functions of RNA.

Abstract:The expression of eukaryotic genes are regulated at multiple levels, including transcription, translation, post-translational modification. Long non-coding RNAs (lncRNAs) are defined as non-protein coding transcripts longer than 200 nucleotides that play extensive roles in regulation of gene expression. They usually interact with DNA, mRNA and protein to regulate histone modification, DNA methylation, transcription activation or inhibition, mRNA splicing. LncRNAs are poorly conserved throughout evolution between widely divergent species, while also express specifically in different cells, tissues and differential stages. It is preferred to conduct research on lncRNAs expressed in cells of immune system because the development and differentiation of immune cells are controlled by delicate and specified gene regulation. In addition, the research focused on the lncRNAs in immune system can provide more comprehensive understanding of the mechanisms of regulation on immune system and thus contribute to developing new treatment of immune related diseases. The topics of this article are the classification of non-coding RNA, their general molecular mechanisms, and the specific regulation mechanisms involved in T cells, B cells and innate immune cells and cytokines.

Abstract:The tRNA-derived RNA fragments (tRFs) and tRNA halves (tiRNAs) are derived from mature transfer RNAs (tRNAs) or precursor tRNAs through specific cleavage at different sites. They are belonged to small non-coding RNA molecules widely existing in prokaryotic and eukaryotic transcriptome. tRFs are classified into tRF-5s, tRF-3s and tRF-1s. tRF-5s and tRF-3s are generated from the cleavage between D-ring and anticodon loop to 5′-end, and T-ring to 3′-end of mature tRNAs, respectively. tRF-1s are from the 3′ trailer fragment of precursor tRNAs. The sizes of tRFs are 14-30 nt. tiRNAs, 29-50 nt in length, are divided into 5′ tiRNAs and 3′ tiRNAs. They are generated within the anti-codon loop. tRFs and tiRNAS have a variety of biological functions. They can be not only stress-activated signal molecules but also coordinators of gene expression. Moreover, tRFs and tiRNAs are associated with the occurrence of a variety of human diseases such as cancers, neurodegenerative diseases, hereditary metabolic diseases, and infectious diseases. Thus, they may become a new type of biomarkers for the diagnosis of these diseases. In this paper, the classification of tRFs and tiRNAs, their biological functions, and their relationships with human diseases were reviewed.

Abstract:C2H2 zinc finger proteins represent the largest family of transcription factors in mammalian. Their C2H2 zinc finger arrays are highly variable, indicating that most of them have unique DNA binding motifs, regulating different genes and playing diversified roles. However, the detailed regulatory functions of many C2H2 zinc finger proteins are unknown because of the unclear target sequences. The prediction of DNA-binding preferences of C2H2 zinc finger proteins is a commendable approach to figure it out. In this review, the canonical recognition pattern of C2H2 zinc fingers binding DNA was described. The prediction models of DNA-binding preferences of C2H2 zinc finger proteins according to their methods, training datasets, and golden standard datasets were summarized. This review is of great benefit to the comprehensive understanding of the prediction models of DNA-binding preferences of C2H2 zinc finger proteins. All of these information will facilitate the further theoretical and applied studies of C2H2 zinc finger proteins.

Abstract:LncRNA-GAS5 can act as a “sponge” for microRNA-21 (miR-21) by competitively sequestering miR-21 from binding target mRNAs. Moreover, miR-21 directly regulates PTEN and TPM1 via imperfect complementary target base pairing．We confirmed miR-21 regulates PTEN and TPM1 protein expression without significantly affecting PTEN and TPM1 mRNA expression via imperfect complementary target binding in HEK293T and HeLa cells. Furthermore, Overexpressing miR-21 could significantly shorten half-lives of PTEN and TPM1, miR-21 enhanced PTEN and TPM1 decay．Cells were transfected with lncRNA-GAS5 expression vector, we found lncRNA-GAS5 competitively bound miR-21 and increased the half-lives of PTEN and TPM1. Besides, miR-21 bound with lncRNA-GAS5 could lead rapid decay of lncRNA-GAS5. This study indicates lncRNA-GAS5 functions as a miR-21 “sponge” that inhibits mRNA degradation of the miR-21 imperfect complementary targets PTEN and TPM1, and miR-21 also could regulate lncRNA-GAS5 stability by base pairing．Further exploration of the mechanisms may improve our understanding of the lncRNA-miRNA-mRNA sophisticated regulatory feedback loop.

Abstract:Intervertebral disc degeneration is believed to originate in the nucleus pulposus (NP) region, it is important to obtain greater numbers of active NP cells for the study and therapy of disc degenerative disease (DDD). Human induced pluripotent stem cells (iPSCs) are a powerful tool for modeling human development and disease, as well as for their potential applications in regenerative medicine. We isolated NP cells from DDD patients with our improved method, and reprogramed primary NP cells into iPSCs with Sendai virus vectors encoding 4 factors. Successful reprogramming of iPSCs was verified by specific surface markers and teratoma, and differentiation of iPSCs into NP-like cells was performed in culture plate and hydrogel, with skin fibroblast derived-iPSC used as control. It was demonstrated that iPSCs derived from NP cells were featured with normal karyotype, and showed expression of pluripotency markers and were able to form teratoma in nude mice. NP induction of iPSCs resulted in their expression of NP cell specific matrix proteins and related genes. NP derived-iPSCs without induction also showed a basal level of expression of some NP-like phenotype characteristics. What’s more, NP derived-iPSCs prefer to differentiate into NP-like cells in hydrogel rather than in culture plate.This is the first protocol for generation of iPSCs from NP cells of DDD patients, and we successfully differentiated this iPSCs into NP-like cells in hydrogel. This method opens a window in the treatment of DDD by using patient-specific NP cells in a relatively simple and straight forward manner.

Abstract:Age-related cognitive impairment, for instance Alzheimer’s disease (AD), is a chronic, progressive, neurodegeneration disease. The concentration of endogenous formaldehyde (FA) positively correlates with the severity of cognitive impairments in AD patients. However, the FA concentrations used in the previous studies were usually higher than the physiological and pathological levels in aging people. To elucidate the relationship between FA and the pathogenesis of AD, it is necessary to investigate the effect of long-term exposure of neurons to low concentration of FA, which is consistent with the pathological FA concentration. In this study, we established a cell culture method to simulate the chronic low-concentration FA exposure by using a serial passage strategy. Murine neuroblastoma N2a cells and primary murine hippocampal neurons were exposed to a simulated pathological FA concentration referred to AD patients. During the long-term of culture, FA gradually accumulated in the medium and impaired N2a cells. High performance liquid chromatography, cell viability assay and lactate dehydrogenase assay showed that, the FA-elimination capacity of N2a cell decreases with the incubation time, accompanied with inhibition of cell growth and increase in cell death. Holographic microscopy showed that long-term simulated pathological FA exposure attenuated the cells’ adhesive morphology. Cells exposed to FA became thicker, exhibiting impairment of neuronal processes. The number of primary neurites in primary hippocampal neurons were reduced by FA exposure, suggesting a decrease in the connectivity between neurons. Formaldehyde accumulation promoted Tau phosphorylation at its Thr181 and Ser396 epitopes, which may be one of the factors leading to decrease in primary neurites. Our findings indicate that accumulation of simulated pathological concentration of FA impairs neurons, induces Tau hyperphosphrylation and decreases neural connectivity, which would lead to neural dysfunction and eventually contribute to the pathogenesis of age-related cognitive impairment.

Abstract:Stereopsis is not only the perception of static depth information, but also involves the ability to detect dynamic stereoscopic motion. This study investigated the motion-in-depth (MID) perception in dynamic random dot stereogram (DRDS) among the population of inexperienced normal vision observers, and the role of visual perceptual training for MID perception. There were three sessions in the main experiment: in the pre-training session, subjects were instructed to discriminate the motion direction of DRDS moving in depth (toward or away from the observer). Then subjects went through a perceptual training session to improve their sensitivity for the motion detection discrimination. A post-training session was carried out to evaluate the outcome of the training process. A control experiment involving only pre-training and post-training sessions was carried out to clarify the influence of repeated practice on visual performance improvement. Participants showed low direction discrimination ability for MID perception of DRDS in the pre-training session, their performance was significantly improved after the perceptual training session. However, large individual difference existed for fully perceiving the binocular disparity information during perceptual learning session. Moreover, the training effect was equivalently retained after six months. The subjects’ performances in the control experiment did not show significantly difference between pre-training and post-training sessions. These findings demonstrate that difficulties for DRDS motion perception exist for inexperienced observers, and highlight the role of visual perceptual training.

Abstract:Recently discovered light-driven Na pumps are novel optogenetic tools. Activated by light, they actively transport Na outward across cell membrane. However, the mechanism of Na transport remains elusive. Visible absorption spectra, fluorescence spectra and ITC results of NdR2, a light-driven Na pump, indicated that Na may not bind to NdR2 in the ground state. Moreover, Na transport kinetics and functional assay suggested that Na transport might be altered at acidic pH. This pH-dependent transport of Na may shed light on and the mechanism of Na transport in NaRs.