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RNA transcription

Yunfeng Liu, Shengjun Li, Yuan Chen, Athen N Kimberlin, Edgar B Cahoon, Bin Yu
Uridine-rich small nuclear RNAs (snRNAs) are the basal components of the spliceosome and play essential roles in splicing. The biogenesis of the majority of snRNAs involves 3' end endonucleolytic cleavage of the nascent transcript from the elongating DNA-dependent RNA ploymerase II. However, the protein factors responsible for this process remain elusive in plants. Here, we show that DEFECTIVE in snRNA PROCESSING 1 (DSP1) is an essential protein for snRNA 3' end maturation in Arabidopsis. A hypomorphic dsp1-1 mutation causes pleiotropic developmental defects, impairs the 3' end processing of snRNAs, increases the levels of snRNA primary transcripts (pre-snRNAs), and alters the occupancy of Pol II at snRNA loci...
October 2016: PLoS Biology
Chun-Min Kang, Yan-Wei Hu, Ying Nie, Jia-Yi Zhao, Shu-Fen Li, Shuai Chu, Hai-Xia Li, Qing-Shui Huang, Yu-Rong Qiu
Early reports suggest that nuclear factor IA (NFIA) is important in the pathogenesis of glioma. Our previous study demonstrated that the long non‑coding RNA (lncRNA), RP5‑833A20.1, suppressed the expression of NFIA in THP‑1 macrophage-derived foam cells. However, the effect and possible mechanism of RP5‑833A20.1 on glioma remains to be fully elucidated, and whether the NFIA-dependent pathway is involved in its progression has not been investigated. In the present study, the mechanisms by which RP5‑833A20...
October 19, 2016: Molecular Medicine Reports
Hangfei Gao, Jiancao Gui, Liming Wang, Yan Xu, Yiqiu Jiang, Mingyue Xiong, Yongguang Cui
Aquaporins (AQPs) have been found to be associated with a number of diseases. However, the role of AQP‑1 in the pathogenesis of osteoarthritis remains unclear. We previously found that AQP‑1 expression was upregulated in osteoarthritic cartilage and strongly correlated with caspase‑3 expression and activity. The aim of this study was to further investigate the association of AQP‑1 expression with chondrocyte apoptosis in a rat model of osteoarthritis, using RNA interference to knock down AQP‑1. For this purspose, 72 male Sprague‑Dawley rats were randomly assigned to 3 groups as follows: the control group not treated surgically (n=24), the sham‑operated group (n=24), and the osteoarthritis group (n=24)...
October 24, 2016: International Journal of Molecular Medicine
Cuncun Chen, Min Wu, Wen Zhang, Wei Lu, Min Zhang, Zhanqing Zhang, Xiaonan Zhang, Zhenghong Yuan
Multi-layered mechanisms of virus host interaction exist for chronic hepatitis B virus (HBV) infection, which have been typically manifested at the microRNA level. Our previous study suggested that miRNA-939 (miR-939) may play a potential role in regulating HBV replication. Here we further investigated the mechanism by which miR-939 regulates HBV life cycle. We found that miR-939 inhibited the abundance of viral RNAs without direct miRNA-mRNA base pairing, but via host factors. Expression profiling and functional validation identified Jmjd3 as a target responsible for miR-939 induced anti-HBV effect...
October 25, 2016: Scientific Reports
Gudrun Böhmdorfer, Shriya Sethuraman, M Jordan Rowley, Michal Krzyszton, M Hafiz Rothi, Lilia Bouzit, Andrzej T Wierzbicki
RNA-mediated transcriptional gene silencing is a conserved process where small RNAs target transposons and other sequences for repression by establishing chromatin modifications. A central element of this process are long non-coding RNAs (lncRNA), which in Arabidopsis thaliana are produced by a specialized RNA polymerase known as Pol V. Here we show that non-coding transcription by Pol V is controlled by preexisting chromatin modifications located within the transcribed regions. Most Pol V transcripts are associated with AGO4 but are not sliced by AGO4...
October 25, 2016: ELife
Miguel Jesus Nunes Ramos, João Lucas Coito, Joana Fino, Jorge Cunha, Helena Silva, Patrícia Gomes de Almeida, Maria Manuela Ribeiro Costa, Sara Amâncio, Octávio S Paulo, Margarida Rocheta
RNA-seq of Vitis during early stages of bud development, in male, female and hermaphrodite flowers, identified new loci outside of annotated gene models, suggesting their involvement in sex establishment. The molecular mechanisms responsible for flower sex specification remain unclear for most plant species. In the case of V. vinifera ssp. vinifera, it is not fully understood what determines hermaphroditism in the domesticated subspecies and male or female flowers in wild dioecious relatives (Vitis vinifera ssp...
October 24, 2016: Plant Molecular Biology
Ping Shuai, Yu Zhou, Bo Gong, Zhilin Jiang, Chong Yang, Hongji Yang, Dingding Zhang, Shikai Zhu
BACKGROUND: Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a newly discovered long intergenic noncoding RNA (lincRNA), has been reported to be aberrantly expressed in various cancers, and may serve as a novel potential biomarker for cancer prognosis. This meta-analysis was conducted to investigate the effects of MALAT1 on cancer prognosis and lymph node metastasis. METHODS: A quantitative meta-analysis was performed using a systematic search of PubMed, Medline and Web of Science databases to identify eligible papers on prognostic value of MALAT1 in cancers...
2016: SpringerPlus
Zoe Daniel, Angelina Swali, Richard Emes, Simon C Langley-Evans
BACKGROUND: Fetal exposure to a maternal low protein diet during rat pregnancy is associated with hypertension, renal dysfunction and metabolic disturbance in adult life. These effects are present when dietary manipulations target only the first half of pregnancy. It was hypothesised that early gestation protein restriction would impact upon placental gene expression and that this may give clues to the mechanism which links maternal diet to later consequences. METHODS: Pregnant rats were fed control or a low protein diet from conception to day 13 gestation...
2016: Genes & Nutrition
Donna M Bond, Nick W Albert, Robyn H Lee, Gareth B Gillard, Chris M Brown, Roger P Hellens, Richard C Macknight
BACKGROUND: Transcription factors (TFs) coordinate precise gene expression patterns that give rise to distinct phenotypic outputs. The identification of genes and transcriptional networks regulated by a TF often requires stable transformation and expression changes in plant cells. However, the production of stable transformants can be slow and laborious with no guarantee of success. Furthermore, transgenic plants overexpressing a TF of interest can present pleiotropic phenotypes and/or result in a high number of indirect gene expression changes...
2016: Plant Methods
Dillon Hawley, Hema Aluri, Helene Armaos, Gina Kim, Claire Kublin, Driss Zoukhri
PURPOSE: Gene expression and protein analysis studies require high-quality human tissue which is a challenge and difficult to obtain through live human biopsies. Human postmortem lacrimal gland (LG) and submandibular gland (SMG) tissues have the potential to provide an invaluable source for studying the mechanisms involved in LG and SMG dysfunction. Therefore, we aimed to test the suitability of post-mortem LG and SMG for molecular, biochemical, and cell biological studies. METHODS: LG and SMG tissue from healthy donors was collected and immediately placed in RNAlater solution and then shipped overnight at 4 °C...
2016: Molecular Vision
An Li, Shanzhong Gong, Kenneth A Johnson
Previous measurements of the rates of polymerization and pyrophosphate release with DNA templates showed that pyrophosphate (PPi) dissociation was fast following nucleotide incorporation so that it did not contribute to enzyme specificity (kcat/Km). Here, kinetic parameters governing nucleotide incorporation and PPi release were determined using an RNA template. Compared with a DNA template of the same sequence, the rate of chemistry increased by up to 10-fold (250 vs 24 s-1) while the rate of PPi release decreased to approximate 58 s-1, so that PPi release became the rate-limiting step...
October 24, 2016: Journal of Biological Chemistry
Weijie Ma, Haitao Wang, Wei Jing, Fuling Zhou, Lei Chang, Zhenfei Hong, Hailing Liu, Zhisu Liu, Yufeng Yuan
BACKGROUND: The expression profiles and biological relevance of long non-coding RNA XIST and its activator JPX in hepatocellular carcinoma (HCC) are not well elucidated. We measured JPX and XIST expression levels in HCC, evaluated their clinical significance in HCC progression, and verified their potential as biomarkers for diagnosing HCC. METHODS: JPX and XIST expression in 68 HCC tissues and adjacent normal tissues were evaluated by quantitative reverse transcription-PCR (qRT-PCR); their association with pathologic features and overall survival was analyzed...
October 21, 2016: Clinics and Research in Hepatology and Gastroenterology
E Saplaoura, F Kragler
Phloem serves as a highway for mobile signals in plants. Apart from sugars and hormones, proteins and RNAs are transported via the phloem and contribute to the intercellular communication coordinating growth and development. Different classes of RNAs have been found mobile and in the phloem exudate such as viral RNAs, small interfering RNAs (siRNAs), microRNAs, transfer RNAs, and messenger RNAs (mRNAs). Their transport is considered to be mediated via ribonucleoprotein complexes formed between phloem RNA-binding proteins and mobile RNA molecules...
2016: Enzymes
Richard Lindqvist, Filip Mundt, Jonathan D Gilthorpe, Silke Wölfel, Nelson O Gekara, Andrea Kröger, Anna K Överby
BACKGROUND: Neurotropic flaviviruses such as tick-borne encephalitis virus (TBEV), Japanese encephalitis virus (JEV), West Nile virus (WNV), and Zika virus (ZIKV) are causative agents of severe brain-related diseases including meningitis, encephalitis, and microcephaly. We have previously shown that local type I interferon response within the central nervous system (CNS) is involved in the protection of mice against tick-borne flavivirus infection. However, the cells responsible for mounting this protective response are not defined...
October 24, 2016: Journal of Neuroinflammation
Miri Danan-Gotthold, Clotilde Guyon, Matthieu Giraud, Erez Y Levanon, Jakub Abramson
BACKGROUND: In order to become functionally competent but harmless mediators of the immune system, T cells undergo a strict educational program in the thymus, where they learn to discriminate between self and non-self. This educational program is, to a large extent, mediated by medullary thymic epithelial cells that have a unique capacity to express, and subsequently present, a large fraction of body antigens. While the scope of promiscuously expressed genes by medullary thymic epithelial cells is well-established, relatively little is known about the expression of variants that are generated by co-transcriptional and post-transcriptional processes...
October 24, 2016: Genome Biology
Yuanfei Zhou, Tingxing Song, Jie Peng, Zheng Zhou, Hongkui Wei, Rui Zhou, Siwen Jiang, Jian Peng
Sirtuin 1 (SIRT1) regulates adipocyte and osteoblast differentiation. However, the underlying mechanism should be investigated. This study revealed that SIRT1 acts as a crucial repressor of adipogenesis. RNA-interference-mediated SIRT1 knockdown or genetic ablation enhances adipogenic potential, whereas SIRT1 overexpression inhibits adipogenesis in mesenchymal stem cells (MSCs). SIRT1 also deacetylates the histones of sFRP1, sFRP2, and Dact1 promoters; inhibits the mRNA expression of sFRP1, sFRP2, and Dact1; activates Wnt signaling pathways; and suppresses adipogenesis...
October 20, 2016: Oncotarget
Agata Swiatkowska, Paulina Zydowicz, Joanna Sroka, Jerzy Ciesiołka
The p53 tumour suppressor protein is one of the major factors responsible for cell cycle regulation and protection against cancer development. This is why it is often referred to as "the guardian of the genome". On the other hand, mutations in the p53 gene are connected with more than 50% of tumours of various types. The thirty-six years of extensive research on the p53 gene and its protein products have shown how sophisticated the p53-based cell system control is. An additional level of complexity of the p53 research is connected with at least twelve p53 isoforms which have been identified in the cell...
October 25, 2016: Acta Biochimica Polonica
Huiting Zhao, Yali Du, Pengfei Gao, Shujie Wang, Jianfang Pan, Yusuo Jiang
Chemosensory genes play a central role in sensing chemical signals and guiding insect behavior. The Chinese honeybee, Apis cerana cerana, is one of the most important insect species in China in terms of resource production, and providing high-quality products for human consumption, and also serves as an important pollinator. Communication and foraging behavior of worker bees is likely linked to a complex chemosensory system. Here, we used transcriptome sequencing on adult A. c. cerana workers of different ages to identify the major chemosensory gene families and the differentially expressed genes(DEGs), and to investigate their expression profiles...
2016: PloS One
D F Paulo, A M L Azeredo-Espin, L E C Canesin, R Vicentini, A C M Junqueira
MicroRNAs (miRNAs) are small noncoding RNAs that modulate gene expression through post-transcriptional regulation. Here, we report the identification and characterization of miRNAs in two closely related screwworm flies with different feeding habits: Cochliomyia hominivorax and Cochliomyia macellaria. The New World screwworm, C. hominivorax, is an obligatory parasite of warm-blooded vertebrates, whereas the secondary screwworm, C. macellaria, is a free-living organism that feeds on decaying organic matter. Here, the small RNA transcriptomes of adults and third-instar larvae of both species were sequenced...
October 24, 2016: Insect Molecular Biology
J-P Yang, X-J Yang, L Xiao, Y Wang
OBJECTIVE: To investigate long noncoding RNA PVT1 expression in the serum of cervical cancer patients, and to evaluate serum PVT1 level as a diagnostic biomarker for cervical cancer. PATIENTS AND METHODS: Eighty-eight cervical cancer patients, 64 cervical intraepithelial neoplasia patients, 25 breast cancer patients, 25 ovarian cancer patients, and 111 healthy control subjects were enrolled into this study. PVT1 serum level in these participants and PVT1 expression in 20 pairs of cervical cancer tissues and adjacent paired normal tissues was measured by quantitative reverse transcription-polymerase chain reaction...
October 2016: European Review for Medical and Pharmacological Sciences
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