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Chen Yan, Yaqing Chen, Wewei Kong, Liya Fu, Yunde Liu, Qingjuan Yao, Yuhua Yuan
Accumulating evidences indicate ectopic expression of noncoding RNAs are responsible for breast cancer progression. Increased non-coding RNA PVT1, the host gene of microRNA-1207-5p (miR-1207-5p), has been associated with breast cancer proliferation. However, how PVT1 functions in breast cancer is still not clear. In this study, we show a PVT1 derived microRNA, miR-1207-5p, which promotes the proliferation of breast cancer cells by directly regulating STAT6. We first confirm the positive correlated expression pattern between PVT1 and miR-1207-5p by observing consistent induced expression by estrogen, and overexpression in breast cancer cell lines and breast cancer patient specimens...
February 24, 2017: Cancer Science
Kira S Makarova, Feng Zhang, Eugene V Koonin
Class 1 CRISPR-Cas systems are characterized by effector modules consisting of multiple subunits. Class 1 systems comprise about 90% of all CRISPR-Cas loci identified in bacteria and archaea and can target both DNA and RNA.
February 23, 2017: Cell
Rajiv C McCoy, Jon Wakefield, Joshua M Akey
Regulatory variation influencing gene expression is a key contributor to phenotypic diversity, both within and between species. Unfortunately, RNA degrades too rapidly to be recovered from fossil remains, limiting functional genomic insights about our extinct hominin relatives. Many Neanderthal sequences survive in modern humans due to ancient hybridization, providing an opportunity to assess their contributions to transcriptional variation and to test hypotheses about regulatory evolution. We developed a flexible Bayesian statistical approach to quantify allele-specific expression (ASE) in complex RNA-seq datasets...
February 23, 2017: Cell
Anthony Szempruch, Mitchell Guttman
Exposure to ultraviolet light leads to a cell-wide DNA damage response that includes a global reduction in transcription. Williamson et al., identify a protein involved in this process as well as a noncoding RNA produced by alternative processing of RNA transcribed from the same gene that promotes recovery from the repressed state.
February 23, 2017: Cell
Oriya Vardi, Inbal Shamir, Elisheva Javasky, Alon Goren, Itamar Simon
Avoiding biases in next generation sequencing (NGS) library preparation is crucial for obtaining reliable sequencing data. Recently, a new library preparation method has been introduced which has eliminated the need for the ligation step. This method, termed SMART (switching mechanism at the 5' end of the RNA transcript), is based on template switching reverse transcription. To date, there has been no systematic analysis of the additional biases introduced by this method. We analysed the genomic distribution of sequenced reads prepared from genomic DNA using the SMART methodology and found a strong bias toward long (≥12bp) poly dA/dT containing genomic loci...
2017: PloS One
Ruixue Li, Dandan Chen, Taichu Wang, Yizhen Wan, Rongfang Li, Rongjun Fang, Yuting Wang, Fei Hu, Hong Zhou, Long Li, Weiguo Zhao
MicroRNAs (miRNAs) play important regulatory roles by targeting mRNAs for cleavage or translational repression. Identification of miRNA targets is essential to better understanding the roles of miRNAs. miRNA targets have not been well characterized in mulberry (Morus alba). To anatomize miRNA guided gene regulation under drought stress, transcriptome-wide high throughput degradome sequencing was used in this study to directly detect drought stress responsive miRNA targets in mulberry. A drought library (DL) and a contrast library (CL) were constructed to capture the cleaved mRNAs for sequencing...
2017: PloS One
Maria Angela Gomes de Castro, Claudia Höbartner, Felipe Opazo
Continuous improvements in imaging techniques are challenging biologists to search for more accurate methods to label cellular elements. This is particularly relevant for diffraction-unlimited fluorescence imaging, where the perceived resolution is affected by the size of the affinity probes. This is evident when antibodies, which are 10-15 nm in size, are used. Previously it has been suggested that RNA aptamers (~3 nm) can be used to detect cellular proteins under super-resolution imaging. However, a direct comparison between several aptamers and antibodies is needed, to clearly show the advantages and/or disadvantages of the different probes...
2017: PloS One
Nirjal Bhattarai, James H McLinden, Jinhua Xiang, M Meleah Mathahs, Warren N Schmidt, Thomas M Kaufman, Jack T Stapleton
Among human RNA viruses, hepatitis C virus (HCV) is unusual in that it causes persistent infection in the majority of infected people. To establish persistence, HCV evades host innate and adaptive immune responses by multiple mechanisms. Recent studies identified virus genome-derived small RNAs (vsRNAs) in HCV-infected cells; however, their biological significance during human HCV infection is unknown. One such vsRNA arising from the hepatitis C virus (HCV) E2 coding region impairs T cell receptor (TCR) signaling by reducing expression of a Src-kinase regulatory phosphatase (PTPRE) in vitro...
February 24, 2017: PLoS Pathogens
Xu Chen, Haiyan Ye, Shilin Li, Baihai Jiao, Jianqin Wu, Peibin Zeng, Limin Chen
Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease caused by a novel bunyavirus (SFTS virus, SFTSV). At present there is still no specific antiviral treatment for SFTSV; To understand which cells support SFTSV life cycle and whether SFTSV infection activates host innate immunity, four different cell lines (Vero, Hela, Huh7.5.1, and Huh7.0) were infected with SFTSV. Intracellular/extracellular viral RNA and expression of IFNα, and IFNß were detected by real-time RT- PCR following infection...
2017: PloS One
Chandra Shekhar Pareek, Paweł Błaszczyk, Piotr Dziuba, Urszula Czarnik, Leyland Fraser, Przemysław Sobiech, Mariusz Pierzchała, Yaping Feng, Haja N Kadarmideen, Dibyendu Kumar
BACKGROUND: RNA-seq is a useful next-generation sequencing (NGS) technology that has been widely used to understand mammalian transcriptome architecture and function. In this study, a breed-specific RNA-seq experiment was utilized to detect putative single nucleotide polymorphisms (SNPs) in liver tissue of young bulls of the Polish Red, Polish Holstein-Friesian (HF) and Hereford breeds, and to understand the genomic variation in the three cattle breeds that may reflect differences in production traits...
2017: PloS One
Corina I Schanzenbach, Benedikt Kirchner, Susanne E Ulbrich, Michael W Pfaffl
The most critical phase of pregnancy is the first three weeks following insemination. During this period about 50% of high yielding lactating cows suffer embryonic loss prior to implantation, which poses a high economic burden on dairy farmers. Early diagnosis of pregnancy in cattle is therefore essential for monitoring breeding outcome and efficient production intervals. Regulated microRNAs (miRNAs) that reach easily accessible body fluids via a 'liquid biopsy' could be a new class of pregnancy predicting biomarkers...
2017: PloS One
Yani Zhang, Yingjie Wang, Qisheng Zuo, Dong Li, Wenhui Zhang, Fei Wang, Yanqin Ji, Jing Jin, Zhenyu Lu, Man Wang, Chen Zhang, Bichun Li
An efficient genome editing approach had been established to construct the stable transgenic cell lines in the domestic chicken (Gallus gallus domesticus) at present. Our objectives were to investigate gene function in the differentiation process of chicken embryonic stem cells (ESCs) into spermatogonial stem cells(SSCs). Three guides RNA (gRNAs) were designed to knockout the Stra8 gene, and knockout efficiency was evaluated in domestic chicken cells using cleavage activity of in vitro transcription of gRNA, Luciferase-SSA assay, T7 endonuclease I assay(T7E1) and TA clone sequence...
2017: PloS One
Pin Yu, Yanfeng Xu, Wei Deng, Linlin Bao, Lan Huang, Yuhuan Xu, Yanfeng Yao, Chuan Qin
Middle East respiratory syndrome (MERS), which is caused by a newly discovered coronavirus (CoV), has recently emerged. It causes severe viral pneumonia and is associated with a high fatality rate. However, the pathogenesis, comparative pathology and inflammatory cell response of rhesus macaques and common marmosets experimentally infected with MERS-CoV are unknown. We describe the histopathological, immunohistochemical, and ultrastructural findings from rhesus macaque and common marmoset animal models of MERS-CoV infection...
2017: PloS One
Yuko Yamada, Masakatsu Takanashi, Katsuko Sudo, Shinobu Ueda, Shin-Ichiro Ohno, Masahiko Kuroda
MicroRNA 29b (miR-29b) replacement therapy is effective for suppressing fibrosis in a mouse model. However, to develop clinical applications for miRNA mimics, the side effects of nucleic acid drugs have to be addressed. In this study, we focused on miRNA mimics in order to develop therapies for idiopathic pulmonary fibrosis. We developed a single-stranded RNA, termed "miR-29b Psh-match," that has a unique structure to avoid problems associated with the therapeutic uses of miRNAs. A comparison of miR-29b Psh-match and double-stranded one, termed "miR-29b mimic" indicated that the single-stranded form was significantly effective towards fibrosis according to both in vivo and in vitro experiments...
2017: PloS One
Tatiana A Soboleva, Brian J Parker, Maxim Nekrasov, Gene Hart-Smith, Ying Jin Tay, Wei-Quan Tng, Marc Wilkins, Daniel Ryan, David J Tremethick
The replacement of histone H2A with its variant forms is critical for regulating all aspects of genome organisation and function. The histone variant H2A.B appeared late in evolution and is most highly expressed in the testis followed by the brain in mammals. This raises the question of what new function(s) H2A.B might impart to chromatin in these important tissues. We have immunopurified the mouse orthologue of H2A.B, H2A.B.3, from testis chromatin and found this variant to be associated with RNA processing factors and RNA Polymerase (Pol) II...
February 24, 2017: PLoS Genetics
Rémi Foissac, Phi Villageois, Bérengère Chignon-Sicard, Charalambos Georgiou, Olivier Camuzard, Christian Dani
BACKGROUND: Autologous fat grafting has become an essential procedure in breast reconstructive surgery. However, molecular knowledge of different adipose donor sites remains inadequate. Tissue regeneration studies have shown that it is essential to match the Hox code of transplanted cells and host tissues to achieve correct repair. This study aims to provide a better molecular understanding of adipose tissue. METHODS: Over the course of 1 year, the authors prospectively included 15 patients and studied seven adipose areas: chin, breast, arm, abdomen, thigh, hip, and knee...
March 2017: Plastic and Reconstructive Surgery
Li Jin, Ming Quan Lin, Zhe Hao Piao, Jae Yeong Cho, Gwi Ran Kim, Sin Young Choi, Yuhee Ryu, Simei Sun, Hae Jin Kee, Myung Ho Jeong
OBJECTIVE: Gallic acid, a natural chemical found in plants, has been reported to show antioxidant, anticancer, and anti-inflammatory effects. We investigated the efficacy of a short-term or long-term treatment with gallic acid in N-nitro-L-arginine methyl ester (L-NAME)-induced hypertensive mice and the underlying regulatory mechanism. METHODS: Hypertension was sufficiently induced after 2 weeks of L-NAME administration. Cardiac remodeling was assessed by echocardiography...
February 22, 2017: Journal of Hypertension
Annika Mutanen, Jouko Lohi, Päivi Heikkilä, Hannu Jalanko, Mikko P Pakarinen
OBJECTIVE: Although liver disease is a major complication of parenteral nutrition (PN) for intestinal failure (IF), its pathogenesis remains unclear. We investigated potential molecular mechanisms of liver injury in pediatric onset IF. METHODS: Liver expression of canalicular phospholipid (ABCB4), bile acid (ABCB11), and sterol (ABCG5/8) transporters, their upstream regulators LXR and FXR as well as pro-inflammatory cytokines interleukin-6 (IL6) and tumor necrosis factor (TNF) were investigated among patients with IF [age median 3...
February 23, 2017: Annals of Surgery
J Yuan, X Liu, Y Chen, Y Zhao, P Liu, L Zhao, W Han
To explore the effect of SOX2 on osteogenic differentiation of dental pulp stem cells (DPSCs) and to develop a new method for facilitating osteogenic differentiation of DPSCs. SOX2-overexpressing human DPSCs (DPSCs-SOX2) were established through retrovirus infection. Differentiation was induced with osteogenic differentiation medium and further evaluated by alkaline phosphatase (ALP) staining and qPCR. Following the differentiation procedure, the mechanism of SOX2 on osteogenic differentiation of DPSCs was analyzed using genome RNA microarray and flow cytometry...
January 30, 2017: Cellular and Molecular Biology
Wei Wei, Anqi Mao, Bin Tang, Qiufang Zeng, Shennan Gao, Lu Lu, Wenpeng Li, James X Du, Jiwen Li, Jiemin Wong, Lujian Liao
Lysine crotonylation on histones is a recently identified post-translational modification that has been demonstrated to associate with active promoters and to directly stimulate transcription. Given that crotonyl-CoA is essential for the acyl transfer reaction and it is a metabolic intermediate widely localized within the cell, we postulate that lysine crotonylation on non-histone proteins could also widely exist. Using specific antibody enrichment followed by high-resolution mass spectrometry analysis, we identified hundreds of crotonylated proteins and lysine residues...
February 24, 2017: Journal of Proteome Research
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