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RNA transcription

Jade-Emmanuelle Deshaies, Lulzim Shkreta, Alexander J Moszczynski, Hadjara Sidibé, Sabrina Semmler, Aurélien Fouillen, Estelle R Bennett, Uriya Bekenstein, Laurie Destroismaisons, Johanne Toutant, Quentin Delmotte, Kathryn Volkening, Stéphanie Stabile, Anaïs Aulas, Yousra Khalfallah, Hermona Soreq, Antonio Nanci, Michael J Strong, Benoit Chabot, Christine Vande Velde
The RNA binding proteins TDP-43 (encoded by TARDBP) and hnRNP A1 (HNRNPA1) are each mutated in certain amyotrophic lateral sclerosis cases and are often mislocalized in cytoplasmic aggregates within motor neurons of affected patients. Cytoplasmic inclusions of TDP-43, which are accompanied by a depletion of nuclear TDP-43, are observed in most amyotrophic lateral sclerosis cases and nearly half of frontotemporal dementia cases. Here, we report that TDP-43 binds HNRNPA1 pre-mRNA and modulates its splicing, and that depletion of nuclear TDP-43 results in increased inclusion of a cassette exon in the HNRNPA1 transcript, and consequently elevated protein levels of an isoform containing an elongated prion-like domain, referred to as hnRNP A1B...
March 19, 2018: Brain: a Journal of Neurology
Haijun Xiao, Yanghong Xu, Chenzi Ni, Qiannan Zhang, Feiya Zhong, Jishuai Huang, Wei Liu, Leilei Peng, Yingguo Zhu, Jun Hu
In flowering plants, various RNA editing events occur in the mitochondria and chloroplasts as part of post-transcriptional processes. Although several PPRs and MORFs have been identified as RNA editing factors, the underlying mechanism of PPRs and the cooperation among these proteins are still obscure. Here, we identified a rice dual-localized PPR protein, OsPGL1. The loss of function of OsPGL1 resulted in defects in both chloroplast RNA editing of ndhD-878 and mitochondrial RNA editing of ccmFc-543, both of which could be restored via complementary validation...
March 17, 2018: Journal of Experimental Botany
Kathrin Theil, Margareta Herzog, Nikolaus Rajewsky
In mRNA sequences, 3' UTRs are thought to contain most elements that specifically regulate localization, turnover, and translation. Although high-throughput experiments indicate that many RNA-binding proteins (RBPs) also bind 5' UTRs, much less is known about specific post-transcriptional control exerted by 5' UTRs. GLD-1 is a conserved RBP and a translational repressor with essential roles in Caenorhabditis elegans germ cell development. Previously, we showed that GLD-1 binds highly conserved sites in both 3' and 5' UTRs...
March 20, 2018: Cell Reports
Pradipta Ray, Andrew Torck, Lilyana Quigley, Andi Wangzhou, Matthew Neiman, Chandranshu Rao, Tiffany Lam, Ji-Young Kim, Tae Hoon Kim, Michael Q Zhang, Gregory Dussor, Theodore J Price
Molecular neurobiological insight into human nervous tissues is needed to generate next generation therapeutics for neurological disorders like chronic pain. We obtained human Dorsal Root Ganglia (DRG) samples from organ donors and performed RNA-sequencing (RNA-seq) to study the human DRG (hDRG) transcriptional landscape, systematically comparing it with publicly available data from a variety of human and orthologous mouse tissues, including mouse DRG (mDRG). We characterized the hDRG transcriptional profile in terms of tissue-restricted gene co-expression patterns and putative transcriptional regulators, and formulated an information-theoretic framework to quantify DRG enrichment...
March 20, 2018: Pain
Patrycja Plewka, Agnieszka Thompson, Maciej Szymanski, Przemyslaw Nuc, Katarzyna Knop, Agnieszka Rasinska, Aleksandra Bialkowska, Zofia Szweykowska-Kulinska, Wojciech M Karlowski, Artur Jarmolowski
The Arabidopsis GUT15 RNA belongs to a class of noncoding RNAs that are expressed from the intergenic regions of protein-coding genes. We show that the RNA polymerase II transcribed GUT15 transcript serves as a precursor for two stable RNA species, a tRNA-like molecule and GUT15-tRF-F5, which are both encoded by the final intron in the GUT15 gene. The GUT15-encoded tRNA-like molecule cannot be autonomously transcribed by RNA polymerase III. However, this molecule contains a CCA motif, suggesting that it may enter the tRNA maturation pathway...
March 21, 2018: RNA Biology
Inuk Jung, Hyejin Kang, Jang Uk Kim, Hyeonsook Chang, Sun Kim, Woosuk Jung
BACKGROUND: Ginseng is a popular traditional herbal medicine in north-eastern Asia. It has been used for human health for over thousands of years. With the rise in global temperature, the production of Korean ginseng (Panax ginseng C.A.Meyer) in Korea have migrated from mid to northern parts of the Korean peninsula to escape from the various higher temperature related stresses. Under the high ambient temperature, vegetative growth was accelerated, which resulted in early flowering. This precocious phase change led to yield loss...
March 19, 2018: BMC Systems Biology
A-K Reinhold, E Jentho, S T Schäfer, M Bauer, H L Rittner
Epigenetics, i.e. an altered reading of the genome without altering the genes themselves is a growing scientific field. A distinction is made between changes in the DNA by modification of the histones and non-coding RNA that alter the messenger (m)RNAs. Epigenetic modifications can be triggered by personal circumstances or other external factors and therefore influence the occurrence of diseases. Epigenetics are therefore of particular interest to anesthesiologists, pain specialists and intensive care physicians, as anesthetic drugs may have a long-term influence on protein transcription leading for example to alterations in neurocognition after anesthesia, chronification of postoperative pain and immune response in sepsis...
March 20, 2018: Der Anaesthesist
Andrea Cipriano, Monica Ballarino
The completion of the human genome sequence together with advances in sequencing technologies have shifted the paradigm of the genome, as composed of discrete and hereditable coding entities, and have shown the abundance of functional noncoding DNA. This part of the genome, previously dismissed as "junk" DNA, increases proportionally with organismal complexity and contributes to gene regulation beyond the boundaries of known protein-coding genes. Different classes of functionally relevant nonprotein-coding RNAs are transcribed from noncoding DNA sequences...
2018: Frontiers in Molecular Biosciences
Ioannis Panagopoulos, Ludmila Gorunova, Hege Kilen Andersen, Astrid Bergrem, Anders Dahm, Kristin Andersen, Francesca Micci, Sverre Heim
Background: Acquired primary chromosomal changes in cancer are sometimes found as sole karyotypic abnormalities. They are specifically associated with particular types of neoplasia, essential in establishing the neoplasm, and they often lead to the generation of chimeric genes of pathogenetic, diagnostic, and prognostic importance. Thus, the report of new primary cancer-specific chromosomal aberrations is not only of scientific but also potentially of clinical interest, as is the detection of their gene-level consequences...
2018: Experimental Hematology & Oncology
Hadas Pahima, Simona Reina, Noa Tadmor, Daniella Dadon-Klein, Anna Shteinfer-Kuzmine, Nathalie M Mazure, Vito De Pinto, Varda Shoshan-Barmatz
The voltage-dependent anion channel 1 (VDAC1), an outer mitochondria membrane (OMM) protein, serves as a mitochondrial gatekeeper, mediating the transport of nucleotides, Ca2+ and other metabolites across the OMM. VDAC1 also plays a central role in mitochondria-mediated apoptosis by facilitating the release of apoptotic proteins and by association with both pro- and anti-apoptotic proteins. Tumor cells, which are constantly exposed to hypoxic conditions, affect the cell via the transcription factor hypoxia-inducible factor (HIF) that induces transcriptional activity...
February 27, 2018: Oncotarget
Keshi Ma, Wenshuo Shi, Mengyue Xu, Jiaxi Liu, Feixiong Zhang
It remains unclear whether plant lncRNAs are responsive to Ca2+ -channel blocking. When using the Ca2+ -channel blocker, LaCl3 , to treat germinated wheat seeds for 24 h, we found that both root length and mitosis were inhibited in the LaCl3 -treated groups. The effect of the Ca2+ -channel blocker was verified in three ways: a [Ca2+ ]cyt decrease detected using Fluo-3/AM staining, a decrease in the Ca content measured using inductively coupled plasma mass spectrometry, and an inhibition of Ca2+ influx detected using Non-invasive Micro-test Technology...
2018: Frontiers in Plant Science
Ahmad Al-Attar, Steven R Presnell, Jody L Clasey, Douglas E Long, R Grace Walton, Morgan Sexton, Marlene E Starr, Philip A Kern, Charlotte A Peterson, Charles T Lutz
Natural killer (NK) lymphocyte-mediated cytotoxicity and cytokine secretion control infections and cancers, but these crucial activities decline with age. NK cell development, homeostasis, and function require IL-15 and its chaperone, IL-15 receptor alpha (IL-15Rα). Macrophages and dendritic cells (DC) are major sources of these proteins. We had previously postulated that additional IL-15 and IL-15Rα is made by skeletal muscle and adipose tissue. These sources may be important in aging, when IL-15-producing immune cells decline...
2018: Frontiers in Immunology
Daiqiang Liu, Yaqun Zhou, Yawen Peng, Peng Su, Zheng Li, Qiaoqiao Xu, Ye Tu, Xuebi Tian, Hui Yang, Zhen Wu, Wei Mei, Feng Gao
Morphine tolerance remains an intractable problem, which hinders its prolonged use in clinical practice. Endoplasmic reticulum (ER) stress has been proved to play a fundamental role in the pathogenesis of Alzheimer's disease, diabetes, atherosclerosis, cancer, etc. In this study, we provide the first direct evidence that ER stress may be a significant driver of morphine tolerance. Binding immunoglobulin protein (BiP), the ER stress marker, was significantly upregulated in neurons in spinal dorsal horn in rats being treated with morphine for 7 days...
2018: Frontiers in Molecular Neuroscience
Nazmul Haque, Ryota Ouda, Chao Chen, Keiko Ozato, J Robert Hogg
Control of type I interferon production is crucial to combat infection while preventing deleterious inflammatory responses, but the extent of the contribution of post-transcriptional mechanisms to innate immune regulation is unclear. Here, we show that human zinc finger RNA-binding protein (ZFR) represses the interferon response by regulating alternative pre-mRNA splicing. ZFR expression is tightly controlled during macrophage development; monocytes express truncated ZFR isoforms, while macrophages induce full-length ZFR to modulate macrophage-specific alternative splicing...
March 20, 2018: Nature Communications
Jeffrey S Mugridge, Ryan W Tibble, Marcin Ziemniak, Jacek Jemielity, John D Gross
The conserved decapping enzyme Dcp2 recognizes and removes the 5' eukaryotic cap from mRNA transcripts in a critical step of many cellular RNA decay pathways. Dcp2 is a dynamic enzyme that functions in concert with the essential activator Dcp1 and a diverse set of coactivators to selectively and efficiently decap target mRNAs in the cell. Here we present a 2.84 Å crystal structure of K. lactis Dcp1-Dcp2 in complex with coactivators Edc1 and Edc3, and with substrate analog bound to the Dcp2 active site. Our structure shows how Dcp2 recognizes cap substrate in the catalytically active conformation of the enzyme, and how coactivator Edc1 forms a three-way interface that bridges the domains of Dcp2 to consolidate the active conformation...
March 20, 2018: Nature Communications
Lian Hu, Hong Zeng, Nenghui Liu
To investigate the expression of H19 long non-coding RNA (lncRNA) and zinc finger E-box-binding protein 1 (ZEB1) in the trophoblast of women with spontaneous abortion.
 Methods: A total of 20 women underwent miscarriage were enrolled as a miscarriage group, while 20 women underwent artificial abortion were enrolled as a control group. Reverse transcriptional fluorescence quantitative polymerase chain reaction (RT-qPCR) was used to detect the expression of H19 lncRNA and miR-200, and Western blot was used to detect the expression of ZEB1...
February 28, 2018: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
David Harrich, Hongping Jin
The HIV-1 tat gene encodes a small 86-104 amino acid protein depending on the HIV-1 strain. Tat is essential for HIV-1 replication through interactions with numerous cellular transcription factors. The interaction between Tat and P-TEFb, which is a cellular protein complex composed of cyclin T1 and CDK9, delivers P-TEFb to the newly transcribed viral mRNAs where phosphorylation of RNA polymerase II by CDK9 leads to highly efficient mRNA transcription. It has long been recognized that Tat is a potential anti-HIV-1 target and possibly a viral Achilles' heel...
March 20, 2018: Biochemical Journal
Ethan A G Baker, Jill L Wegrzyn, Uzay U Sezen, Taylor Falk, Patricia E Maloney, Detlev R Vogler, Annette Delfino-Mix, Camille Jensen, Jeffry Mitton, Jessica Wright, Brian Knaus, Hardeep Rai, Richard Cronn, Daniel Gonzalez-Ibeas, Hans A Vasquez-Gross, Randi A Famula, Jun-Jun Liu, Lara M Kueppers, David B Neale
Conifers are the dominant plant species throughout the high latitude boreal forests as well as some lower latitude temperate forests of North America, Europe, and Asia. As such, they play an integral economic and ecological role across much of the world. This study focused on the characterization of needle transcriptomes from four ecologically important and understudied North American white pines within the Pinus subgenus Strobus. The populations of many Strobus species are challenged by native and introduced pathogens, native insects, and abiotic factors...
March 20, 2018: G3: Genes—Genomes—Genetics
Xin-Xin Yu, Wei-Lin Qiu, Liu Yang, Lin-Chen Li, Yu-Wei Zhang, Cheng-Ran Xu
Pancreatic endocrine lineages are derived from pancreatic progenitors that undergo a cell fate transition requiring a switch from low to high Ngn3 expression. However, the underlying chromatin regulatory mechanisms are unclear. Here, we performed epigenomic analysis of gene regulatory loci featuring histone marks in cells with low or high level of Ngn3 expression. In combination with transcriptomic analysis, we discovered that in Ngn3-high cells, the removal of H3K27me3 was associated with the activation of key transcription factors and the establishment of primed and active enhancers...
March 20, 2018: Development
Samantha Leong, Yue Zhao, Noyal M Joseph, Natasha S Hochberg, Sonali Sarkar, Jane Pleskunas, David Hom, Subitha Lakshminarayanan, C Robert Horsburgh, Gautam Roy, Jerrold J Ellner, W Evan Johnson, Padmini Salgame
Several studies have identified blood transcriptomic signatures that can distinguish active from latent Tuberculosis (TB). The purpose of this study was to assess how well these existing gene profiles classify TB disease in a South Indian population. RNA sequencing was performed on whole blood PAXgene samples collected from 28 TB patients and 16 latently TB infected (LTBI) subjects enrolled as part of an ongoing household contact study. Differential gene expression and clustering analyses were performed and compared with explicit predictive testing of TB and LTBI individuals based on established gene signatures...
March 2018: Tuberculosis
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