Translation Start Site Research Articles

Discovery of Unannotated Small Open Reading Frames in Streptococcus pneumoniae D39 Involved in Quorum Sensing and Virulence Using Ribosome Profiling.

ABSTRACTStreptococcus pneumoniae, an opportunistic human pathogen, is the leading cause of community-acquired pneumonia and an agent of otitis media, septicemia, and meningitis. Although genomic and transcriptomic studies of S. pneumoniae have provided detailed perspectives on gene content and expression programs, they have lacked information pertaining to the translational landscape, particularly at a resolution that identifies commonly overlooked small open reading frames (sORFs), whose importance is increasingly realized in metabolism, regulation, and virulence. To identify protein-coding sORFs in S. pneumoniae, antibiotic-enhanced ribosome profiling was conducted. Using translation inhibitors, 114 novel sORFs were detected, and the expression of a subset of them was experimentally validated. Two loci associated with virulence and quorum sensing were examined in deeper detail. One such sORF, rio3, overlaps with the noncoding RNA srf-02 that was previously implicated in pathogenesis. Targeted mutagenesis parsing rio3 from srf-02 revealed that rio3 is responsible for the fitness defect seen in a murine nasopharyngeal colonization model. Additionally, two novel sORFs located adjacent to the quorum sensing receptor rgg1518 were found to impact regulatory activity. Our findings emphasize the importance of sORFs present in the genomes of pathogenic bacteria and underscore the utility of ribosome profiling for identifying the bacterial translatome.

Fruit ripening specific expression of β-D-N-acetylhexosaminidase (β-Hex) gene in tomato is transcriptionally regulated by ethylene response factor SlERF.E4

N-glycans and N-glycan processing enzymes are key players in regulating the ripening of tomato (Solanum lycopersicum) fruits, a model for fleshy fruit ripening. β-D-N-acetylhexosaminidase (β-Hex) is a N-glycan processing enzyme involved in fruit ripening. The suppression of β-Hex results in enhanced fruit shelf life and firmness in both climacteric and non-climacteric fruits. Previously, we have shown that ripening specific expression of β-Hex is regulated by RIPENING INHIBITOR (RIN), ABSCISIC ACID STRESS RIPENING 1 (SlASR1) and ethylene. However, the precise mechanism of ethylene-mediated regulation of β-Hex remains elusive. To gain insights into this, we have performed 5’ deletion mapping of tomato β-Hex promoter and a shorter promoter fragment (pD-200, 200 bp upstream to translational start site) is identified, which was found critical for spatio-temporal transcriptional regulation of β-Hex. Further, site specific mutagenesis in RIN and ASR1 binding sites in pD-200 provides key insights into ripening specific promoter activity. Furthermore, induction of GUS activity by ethylene, yeast one hybrid assay and EMSA identify Ethylene Response Factor SlERF.E4 as a positive regulator of β-Hex. Taken together, our study suggest that SlERF.E4 together with RIN and SlASR1 transcriptionally regulates β-Hex and all these three proteins are essential for fruit ripening specific expression of β-Hex in tomato.

EIF5B and eIF1A reorient initiator tRNA to allow ribosomal subunit joining.

Translation initiation defines the identity and quantity of a synthesized protein. The process is dysregulated in many human diseases1,2. A key commitment step is when the ribosomal subunits join at a translation start site on a messenger RNA to form a functional ribosome. Here, we combined single-molecule spectroscopy and structural methods using an in vitro reconstituted system to examine how the human ribosomal subunits join. Single-molecule fluorescence revealed when theuniversally conserved eukaryotic initiation factors eIF1A and eIF5B associate with and depart from initiation complexes. Guided by single-molecule dynamics, we visualized initiation complexes that contained both eIF1A and eIF5B using single-particle cryo-electron microscopy. The resulting structure revealed how eukaryote-specific contacts between the two proteins remodel the initiation complex to orient the initiator aminoacyl-tRNA in a conformation compatible with ribosomal subunit joining. Collectively, our findings provide a quantitative and architectural framework for the molecular choreography orchestrated by eIF1A and eIF5B during translation initiation in humans.

Transcriptional Regulation of the Chicken ASMT Gene- A Preliminary Analysis

ABSTRACT 1. Melatonin is an indole hormone that, among its myriad biological functions, regulates circadian and seasonal rhythms in animals. The ASMT gene plays an essential role in melatonin synthesis. However, in chickens, little is known about the regulatory elements governing its transcription. 2. The following study identified the transcription start site of the chicken ASMT gene by 5’-RACE. Then, the proximal minimal promoter was identified using a series of 5′ truncations of the ASMT promoter (e.g., -3502/+17, -2698/+17, -2003/+17, -1378/+17, and -254/+17). Site-directed mutagenesis, overexpression, and electrophoretic mobility shift assay (EMSA) were applied to show that the transcription factor Oct-1 binds to the promoter region of ASMT. 3. The translation start site was located 19 bp upstream from the translational start site. The luciferase reporter assay confirmed that the core promoter of chicken ASMT gene was in the -254/+17 region. Using site-directed mutagenesis, overexpression, and EMSA, Oct-1 bound the promoter of ASMT. 4. Overall, Oct1 plays an important role in the transcriptional regulation of chicken ASMT gene.

Abstract 5105: Comparing comprehensive NGS panel(s) based approach versus tissue whole exome sequencing (WES) using matched tissue and circulating tumor DNA from late-stage colorectal cancer patients

Abstract Background: The ctDNA shedding rate, concentration and stability are associated with tumor type, stage, ctDNA degradation and clearance mechanisms. Tumoral heterogeneity together with tissue of origin related genomic alterations adds complexity to genomic profiling. The value of NGS panels capable of detecting variants in both tissue and ctDNA are well recognized. Therefore, it is essential to assess the comprehensive NGS panel(s) performance in both liquid biopsy and tissue by comparing to tissue WES. In this study, we systematically conducted performance evaluation of llumina TruSight™ Oncology 500 gene (TSO500) NGS assay(s) using matched tissue and ctDNA specimens Methods: Matched tissue and plasma samples from seven treatment naive stage III/IV CRC patients were utilized for Illumina TSO500 sequencing and WES. Tissue samples were separately analyzed by both WES and the TSO500 tissue panel while extracted cfDNA was analyzed by TSO500 ctDNA panel. Illumina BaseSpace TruSight Oncology 500 platform (CombinedVariantOutput.tsv) was applied to select non-synonymous (frameshift, in-frame, nonsense, missense, translation start site, nonstop and splice site) variants in both cfDNA and tissue samples. Genes found to be mutated by tissue WES were filtered for corresponding mutated genes detected by TSO500 analysis. Next, using maftools, we characterize the most frequently mutated genes and the mutations observed for each patient sample. Results: 1,300 variants and 33 copy number variants were observed in the liquid biopsy samples whereas 1,199 variants, 9 genes with high copy number variations and 3 gene fusions were observed in the TSO500 tissue panel. Of these mutations, 889 variants (56.9%) were common between the liquid and tissue in the TSO500 panels. We observed a significant correlation across WES and TSO500-called variants (TSO500 tissue/TSO500 cfDNA r2=0.81, WES/TSO500 tissue r2=0.91 (47 variants), WES/TSO500 cfDNA r2=0.84 (17 variants). In the TSO tissue and cfDNA datasets, 19/20 most commonly mutated genes were the same, while FAT1 was the most commonly mutated gene in both tissue and ctDNA samples. In addition, only 2/20 (APC and TP53) most commonly mutated genes found in the tissue WES dataset were included in the top 20 for two TSO500 datasets. Furthermore, the RTK-RAS pathway had mutations in 22 genes in the liquid and tissue TSO500, by far the most of any pathway. Conclusions: Significant concordance between the TSO500 liquid biopsy and tissue datasets were demonstrated, but lesser concordance with the tissue WES dataset. The evidence supports the potential of leveraging both ctDNA and FFPE based genomic observation to enable precision oncology. A deeper analytical dive into each dataset is on-going. Citation Format: Dennis O'Rourke, Roman Alpatov, Danyi Wang, Zheng Feng, Juergen Scheuenpflug. Comparing comprehensive NGS panel(s) based approach versus tissue whole exome sequencing (WES) using matched tissue and circulating tumor DNA from late-stage colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5105.

Axl Expression in Renal Mesangial Cells Is Regulated by Sp1, Ap1, MZF1, and Ep300, and the IL-6/miR-34a Pathway.

Axl receptor tyrosine kinase expression in the kidney contributes to a variety of inflammatory renal disease by promoting glomerular proliferation. Axl expression in the kidney is negligible in healthy individuals but upregulated under inflammatory conditions. Little is known about Axl transcriptional regulation. We analyzed the 4.4 kb mouse Axl promoter region and found that many transcription factor (TF)-binding sites and regulatory elements are located within a 600 bp fragment proximal to the translation start site. Among four TFs (Sp1, Ap1, MZF1, and Ep300) identified, Sp1 was the most potent TF that promotes Axl expression. Luciferase assays confirmed the siRNA results and revealed additional mechanisms that regulate Axl expression, including sequences encoding a 5′-UTR mini-intron and potential G-quadruplex forming regions. Deletion of the Axl 5′-UTR mini-intron resulted in a 3.2-fold increases in luciferase activity over the full-length UTR (4.4 kb Axl construct). The addition of TMPyP4, a G-quadruplex stabilizer, resulted in a significantly decreased luciferase activity. Further analysis of the mouse Axl 3′-UTR revealed a miRNA-34a binding site, which inversely regulates Axl expression. The inhibitory role of miRNA-34a in Axl expression was demonstrated in mesangial cells using miRNA-34a mimicry and in primary kidney cells with IL-6 stimulated STAT3 activation. Taken together, Axl expression in mouse kidney is synergistically regulated by multiple factors, including TFs and secondary structures, such as mini-intron and G-quadruplex. A unique IL6/STAT3/miRNA-34a pathway was revealed to be critical in inflammatory renal Axl expression.

Generation of FLAG-tagged Arx knock-in mouse model.

The Aristaless-related homeobox (ARX) is a paired-like homeodomain transcription factor playing important roles in brain development. Patients with mutations in ARX have a spectrum of neurodevelopmental disorders such as epilepsy, intellectual disability, and autism spectrum disorder, with or without structural abnormalities of the brain such as lissencephaly (smooth brain), microcephaly (small brain), and/or agenesis of the corpus callosum. Mouse models have provided important clues on the pathophysiologic roles of ARX in these disorders. However, successfully isolating specific in vivo complexes of ARX, with DNA and proteins, has remained as a challenge. To facilitate in vivo detection of ARX complexes, we generated a mouse line containing one epitope of FLAG-tag (1 × FLAG) targeted at the translational start site of the endogenous Arx gene using CRSPR/Cas9 strategy. Homozygous Flag-Arx mice are viable and fertile without gross abnormality, suggesting that the FLAG-tag does not perturb the normal function of ARX. Using a FLAG antibody, we successfully detected ARX with immunofluorescent staining and pulled down ARX in embryonic brain tissues. This Flag-Arx mouse line will be a useful tool to isolate ARX complexes from mouse tissues for many applications.

Characterization of molecular and immune landscape of microvascular invasion in hepatocellular carcinoma and prognostic significance.

e16162 Background: Partial hepatectomy is potentially curative treatment in selected patients (pts) with hepatocellular carcinoma (HCC). Microvascular invasion (MVI) is one of the strongest predictors of prognosis and recurrence of HCC. In this study, we analyzed the gene mutation signature and immune factors associated with MVI, and the prognostic value. Methods: Pts who were diagnosed with HCC between Jan 2018 and Sep 2020 in Cancer Hospital of Chinese Academy of Medical Sciences were retrospectively enrolled in this study. Next-generation sequencing (NGS) was performed on tumor tissues after radical partial hepatectomy. The different immune makers (PD1, PD-L1, CD3, CD8, CD68, and CD163) of tumor-infiltrating lymphocytes (TILs) were identified with immunofluorescence-based microenvironment analysis panel (MAP). Results: In the MVI+ group (n = 39, 59.1 %), there were significantly more pts with larger tumor size, and capsules invasion by tumors. The mutation spectra revealed that 61 (92.4%) pts harbored somatic mutations and the most frequently mutated gene was telomerase reverse transcriptase (TERT), which was present in 31.8% (n = 20) HCC pts. Mutations in the promoter of TERT were found in 95.2% (20/21) pts. 90.0% (18/20) had one hotspot point mutation located 124bp upstream of the translation start site. The mutation frequency in the TERT promoter was significantly higher in the MVI+ group compared with the MVI- group (41.0% vs. 14.8%, p < 0.05). Pts with TERT promoter mutations tend to be MVI+ rather than MVI- and more HCC driver mutations were detected in MVI+ pts with TERT promoter mutations (p < 0.05). Based on MAP, we found MVI+ pts had significantly lower CD3+ TILs (p < 0.05). The multivariable analysis indicated that pts with copy number variations (CNV, hazard ratios [HR] 2.62, 95% confidence interval [CI] 1.07-6.40; p = 0.028), elevated PT/INR (HR 0.29, 95% CI 0.11-0.77; p = 0.008), and lower serum prealbumin concentration (PALB, HR 3.03, 95% CI 1.08-8.51; p = 0.027) had significantly shorter recurrence-free survival (RFS) after surgery. Similar findings were also observed for immune factors within cancer parenchyma, including CD68+ (HR 7.14, 95% CI 0.95-53.55; p = 0.025), CD163+ (HR 3.07, 95% CI 1.10-8.53; p = 0.023), CD68+/CD163- (HR 11.35, 95% CI 1.51-85.05; p = 0.003), CD68+/CD163+ (HR 3.51, 95% CI 1.4-8.79; p = 0.004), which indicated tumor-associated macrophage (TAM) infiltration was independent risk factor for RFS. Conclusions: In this study, we characterized the molecular and immune landscape of MVI in HCC patients. MVI presence highly correlated with adverse biological markers, mutations in the promoter of TERT, and higher CD3+ TILs. Some risk factors of HCC recurrence were identified, including CNV, PT/INR, CA 19-9, PALB, and TAM. Transcriptional alterations and immune tumor microenvironment change may contribute to MVI in HCC.

Identification of h-TERT Promoter Mutations in Germline DNA from North Indian Lung Carcinoma Patients.

Lung cancer is a severe and the leading cause of cancer related deaths worldwide. The recurrent h-TERT promoter mutations have been implicated in various cancer types. Thus, the present study is extended to analyze h-TERT promoter mutations from the North Indian lung carcinoma patients. Total 20 histopathologically and clinically confirmed cases of lung cancer were enrolled in this study. The genomic DNA was extracted from venous blood and subjected to amplification using appropriate h-TERT promoter primers. Amplified PCR products were subjected for DNA Sanger sequencing for the identification of novel h-TERT mutations. Further, these identified h-TERT promoter mutations were analysed for the prediction of pathophysiological consequences using bioinformatics tools such as Tfsitescan and CIIDER. The average age of patients was 45 ± 8years which was categorized in early onset of lung cancer with predominance of male patients by 5.6 fold. Interestingly, h-TERT promoter mutations were observed highly frequent in lung cancer. Identified mutations include c. G272A, c. T122A, c. C150A, c. 123 del C, c. C123T, c. G105A, c. 107 Ins A, c. 276 del C corresponding to -168 G>A, -18T>A, -46 C>A, -19 del C, -19 C>T, -1 G>A, -3 Ins A, -172 del C respectively from the translation start site in the promoter of the telomerase reverse transcriptase gene which are the first time reported in germline genome from lung cancer. Strikingly, c. -18T>A [C.T122A] was found the most prevalent variant with 75% frequency. Notwithstanding, other mutations viz c. -G168A [c. G272A] and c. -1 G>A [c. G105A] were found to be at 35% and 15% frequency respectively whilst the rest of the mutations were present at 10% and 5% frequency. Additionally, bioinformatics analysis revealed that these mutations can lead to either loss or gain of various transcription factor binding sites in the h-TERT promoter region. Henceforth, these mutations may play a pivotal role in h-TERT gene expression. Taken together, these identified novel promoter mutations may alter the epigenetics and subsequently various transcription factor binding sites which are of great functional significance. Thereby, it is plausible that these germline mutations may involve either as predisposing factor or direct participation in the pathophysiology of lung cancer through entangled molecular mechanisms.

Alternative translation and retrotranslocation of cytosolic C3 that detects cytoinvasive bacteria

Complement C3 was originally regarded as a serum effector protein, although recent data has emerged suggesting that intracellular C3 can also regulate basic cellular processes. Despite the growing interest in intracellular C3 functions, the mechanism behind its generation has not been demonstrated. In this study we show that C3 can be expressed from an alternative translational start site, resulting in C3 lacking the signal peptide, which is therefore translated in the cytosol. In contrast to the secreted form, alternatively translated cytosolic C3 is not glycosylated, is present mainly in a reduced state, and is turned over by the ubiquitin–proteasome system. C3 can also be retrotranslocated from the endoplasmic reticulum into the cytosol, structurally resembling secreted C3. Finally, we demonstrate that intracellular cytosolic C3 can opsonize invasive Staphylococcus aureus within epithelial cell, slowing vacuolar escape as well as impacting bacterial survival on subsequent exposure to phagocytes. Our work therefore reveals the existence and origin of intracellular, cytosolic C3, and demonstrates functions for cytosolic C3 in intracellular detection of cytoinvasive pathogens.

Introns in yeast regulate translation to generate protein and cellular function

While RNA splicing has been recognized as an important mode of eukaryotic gene regulation, the role that introns themselves play in gene expression and proteome diversity has been less clear. Here, we describe how the intron of GCR1, a transcription factor that regulates glycolytic gene expression, contains intronic elements that control translation initiated from an in‐frame, intronic‐AUG. Moreover, the intronic elements regulate translation under stress conditions. To understand how the translation start site within the intron is recognized, we analyzed the structures and functions of sequences around the start site. These studies reveal an internal ribosome entry site (IRES) that regulates translation initiation from within the intron. In addition to this sequence, we find that a ribosomal protein, Rps25, regulates utilization of the intronic AUG. These data suggest that splicing regulation and intron retention set up a novel mode of translational control. When we analyzed all intron‐containing genes in yeast, we discovered that this architecture—an intronic AUG that is in frame with the annotated stop codon—is found in other intron‐containing genes. Moreover, the proteins generated appear to be functional, particularly under stress conditions. Together these studies illustrate a role for introns in translational control and tuning the proteome in response to environmental conditions.

An alternative downstream translation start site in the non-TIR adaptor Scimp enables selective amplification of CpG DNA responses in mouse macrophages.

Toll‐like receptor (TLR) signaling relies on Toll/interleukin‐1 receptor homology (TIR) domain‐containing adaptor proteins that recruit downstream signaling molecules to generate tailored immune responses. In addition, the palmitoylated transmembrane adaptor protein family member Scimp acts as a non‐TIR‐containing adaptor protein in macrophages, scaffolding the Src family kinase Lyn to enable TLR phosphorylation and proinflammatory signaling responses. Here we report the existence of a smaller, naturally occurring translational variant of Scimp (Scimp TV1), which is generated through leaky scanning and translation at a downstream methionine. Scimp TV1 also scaffolds Lyn, but in contrast to full‐length Scimp, it is basally rather than lipopolysaccharide (LPS)‐inducibly phosphorylated. Macrophages from mice that selectively express Scimp TV1, but not full‐length Scimp, have impaired sustained LPS‐inducible cytokine responses. Furthermore, in granulocyte macrophage colony‐stimulating factor‐derived myeloid cells that express high levels of Scimp, selective overexpression of Scimp TV1 enhances CpG DNA‐inducible cytokine production. Unlike full‐length Scimp that localizes to the cell surface and filopodia, Scimp TV1 accumulates in intracellular compartments, particularly the Golgi. Moreover, this variant of Scimp is not inducibly phosphorylated in response to CpG DNA, suggesting that it may act via an indirect mechanism to enhance TLR9 responses. Our findings thus reveal the use of alternative translation start sites as a previously unrecognized mechanism for diversifying TLR responses in the innate immune system.

Removal of an Internal Translational Start Site from mRNA While Retaining Expression of the Full-Length Protein

Removal of an Internal Translational Start Site from mRNA While Retaining Expression of the Full-Length Protein

Removal of an Internal Translational Start Site from mRNA While Retaining Expression of the Full-Length Protein.

The CRISPR-Cas9 gene-editing system, based on genome repair mechanisms, enables the generation of gene-modified mouse models more quickly and easily relative to traditional homologous recombination. The CRISPR-Cas9 system is particularly attractive when a single-point mutation is desired. The gap junction protein, Connexin 43 (Cx43), is encoded by gene Gja1, which has a single coding exon and cannot be spliced. However, Gja1 produces not only full-length Cx43 protein but up to six N-terminus truncated isoforms by a process known as internal translation, the result of ribosomal translation initiation at internal AUG (Methionine) start sites. GJA1-20k is the most commonly generated truncated isoform of Cx43 initiated at the AUG codon at position 213 of Gja1 mRNA. Because residue 213 occurs at the end of the last transmembrane domain of Cx43, GJA1-20k is effectively the 20 kDa C-terminus tail of Cx43 as an independent protein. Previous investigators identified, in cells, that a critical role of GJA1-20k is to facilitate trafficking of full-length Cx43 gap junction hemichannels to the plasma membrane. To examine this phenomenon in vivo, a mutant mouse with a Gja1 point-mutation was generated that replaces the ATG (Methionine) at residue 213 with TTA (Leucine, M213L mutation). The result of M213L is that Gja1 mRNA and full-length Cx43 are still generated, yet the translation of Gja1-20k is significantly reduced. This report focuses on choosing the restriction enzyme site to develop a one amino acid mutated (Gja1M213L/M213L) mouse model. This protocol describes genetically modified mice by the CRISPR-Cas9 system and rapid genotyping by combining PCR and restriction enzyme treatments.

Beginners guide to ribosome profiling

Beginners guide to ribosome profiling

Evolutionarily conserved inhibitory uORFs sensitize Hox mRNA translation to start codon selection stringency

Translation start site selection in eukaryotes is influenced by context nucleotides flanking the AUG codon and by levels of the eukaryotic translation initiation factors eIF1 and eIF5. In a search of mammalian genes, we identified five homeobox (Hox) gene paralogs initiated by AUG codons in conserved suboptimal context as well as 13 Hox genes that contain evolutionarily conserved upstream open reading frames (uORFs) that initiate at AUG codons in poor sequence context. An analysis of published cap analysis of gene expression sequencing (CAGE-seq) data and generated CAGE-seq data for messenger RNAs (mRNAs) from mouse somites revealed that the 5' leaders of Hox mRNAs of interest contain conserved uORFs, are generally much shorter than reported, and lack previously proposed internal ribosome entry site elements. We show that the conserved uORFs inhibit Hox reporter expression and that altering the stringency of start codon selection by overexpressing eIF1 or eIF5 modulates the expression of Hox reporters. We also show that modifying ribosome homeostasis by depleting a large ribosomal subunit protein or treating cells with sublethal concentrations of puromycin leads to lower stringency of start codon selection. Thus, altering global translation can confer gene-specific effects through altered start codon selection stringency.

Translation initiation landscape profiling reveals hidden open-reading frames required for the pathogenesis of tomato yellow leaf curl Thailand virus.

Plant viruses with densely packed genomes employ noncanonical translational strategies to increase the coding capacity for viral function. However, the diverse translational strategies used make it challenging to define the full set of viral genes. Here, using tomato yellow leaf curl Thailand virus (TYLCTHV, genus Begomovirus) as a model system, we identified genes beyond the annotated gene sets by experimentally profiling in vivo translation initiation sites (TISs). We found that unanticipated AUG TISs were prevalent and determined that their usage involves alternative transcriptional and/or translational start sites and is associated with flanking mRNA sequences. Specifically, two downstream in-frame TISs were identified in the viral gene AV2. These TISs were conserved in the begomovirus lineage and led to the translation of different protein isoforms localized to cytoplasmic puncta and at the cell periphery, respectively. In addition, we found translational evidence of an unexplored gene, BV2. BV2 is conserved among TYLCTHV isolates and localizes to the endoplasmic reticulum and plasmodesmata. Mutations of AV2 isoforms and BV2 significantly attenuated disease symptoms in tomato (Solanum lycopersicum). In conclusion, our study pinpointing in vivo TISs untangles the coding complexity of a plant viral genome and, more importantly, illustrates the biological significance of the hidden open-reading frames encoding viral factors for pathogenicity.

Rosiglitazone Ameliorates Spinal Cord Injury via Inhibiting Mitophagy and Inflammation of Neural Stem Cells.

Background Neurodegenerative diseases, such as Alzheimer's disease, and traumatic brain and spinal cord injury (SCI) are prevalent in clinical practice. Inhibition of hyperactive inflammation and proliferation of endogenous neural stem cells (NSCs) is a promising treatment strategy for SCI. Our previous studies demonstrated the beneficial effects of rosiglitazone (Rosi) on SCI, but its roles in inflammation inhibition and proliferation of NSCs are unknown. Methods SCI in a rat model was established, and the effects of Rosi on motor functions were assessed. The effects of Rosi on NSC proliferation and the underlying mechanisms were explored in details. Results We showed that Rosi ameliorated impairment of moto functions in SCI rats, inhibited inflammation, and promoted proliferation of NSCs in vivo. Rosi increased ATP production through enhancing glycolysis but not oxidative phosphorylation. Rosi reduced mitophagy by downregulating PTEN-induced putative kinase 1 (PINK1) transcription to promote NSC proliferation, which was effectively reversed by an overexpression of PINK1 in vitro. Through KEGG analysis and experimental validations, we discovered that Rosi reduced the expression of forkhead box protein O1 (FOXO1) which was a critical transcription factor of PINK1. Three FOXO1 consensus sequences (FCSs) were found in the first intron of the PINK1 gene, which could be potentially binding to FOXO1. The proximal FCS (chr 5: 156680169–156680185) from the translation start site exerted a more significant influence on PINK1 transcription than the other two FCSs. The overexpression of FOXO1 entirely relieved the inhibition of PINK1 transcription in the presence of Rosi. Conclusions Besides inflammation inhibition, Rosi suppressed mitophagy by reducing FOXO1 to decrease the transcription of PINK1, which played a pivotal role in accelerating the NSC proliferation.

Correlated Expression of the Opsin Retrogene LWS-R and its Host Gene in Two Poeciliid Fishes.

The important role of retrogenes in genome evolution and species differentiation is becoming increasingly accepted. One synapomorphy among cyprinodontoid fish is a retrotransposed version of a long-wavelength sensitive (LWS) opsin gene, LWS-R, within an intron of the gephyrin (GPHN) gene. These two genes display opposing orientations. It had been speculated that LWS-R hijacks the cis-regulatory elements of GPHN for transcription, but whether their expression is correlated had remained unclear. Here, in silico predictions identified putative promoters upstream of the translation start site of LWS-R, indicating that its transcription is driven by its own promoter rather than by the GPHN promoter. However, consistent expression ratios of LWS-R:GPHN in the eyeball and brain of fishes indicate that the respective gene transcriptions are correlated. Co-expression is potentially modulated by histone exchange during GPHN transcription. Two isoforms were detected in this study, i.e., intron-free and intron-retaining. Intron-free LWS-R was only expressed in the eyeball of fishes, whereas intron-retaining LWS-R occurred in both eyeball and brain. Expression of vision-associated LWS-R beyond the eyeball supports that it is co-expressed with more ubiquitous GPHN.

Lipase family member N is a novel target gene for CCAAT/enhancer-binding protein α in type 2 diabetic model mouse liver.

CCAAT/enhancer-binding protein α (C/EBPα) is a transcription factor abundantly expressed in the liver and white adipose tissue (WAT). In this study, we investigated the mechanism by which C/EBPα regulates the lipase family member N (Lipn) gene in the mouse liver. Mouse Lipn consists of non-coding exon 1 and the translation start site located in exon 2. Lipn expression in the fatty liver of ob/ob mice was significantly higher than that in OB/OB mice and was significantly repressed by liver-specific C/EBPα deficiency. Lipn expression in ob/ob mice was detected in the liver, epididymal WAT (eWAT), subcutaneous WAT (sWAT), brown adipose tissue (BAT), and skeletal muscle, but not in the kidney, brain, and heart. Lipn expression in the liver, eWAT, and sWAT of wild-type mice was undetectable, although C/EBPα was highly expressed in these tissues. The database analysis revealed four putative C/EBP-responsive elements (CEBPREs), highly homologous with the typical CEBPRE consensus sequence at positions -2,686/-2,678, -1,364/-1,356, -106/-98, and -45/-37 from the transcription start site (+1) of Lipn. Reporter assays using reporter constructs with serial or internal deletions of the 5'-flanking regions of Lipn showed that two functional CEBPREs (-106/-98 and -45/-37) in the Lipn promoter region are essential for enhancing Lipn transcriptional activity by C/EBPα. Electrophoretic mobility shift assay showed that C/EBPα/β binds to CEBPRE (-106/-98). These results suggest that C/EBPα and type 2 diabetic environment may be required for hepatic Lipn expression.