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https://www.readbyqxmd.com/read/28212420/transcriptome-using-illumina-sequencing-reveals-the-traits-of-spermatogenesis-and-developing-testes-in-eriocheir-sinensis
#1
Gen-Liang Li, Hui Qian
Chinese mitten crab (Eriocheir sinensis) has the spermatozoa with typical aflagellate, decondensed chromatin, cup-shaped nuclei, and radial arms. However, the mechanism of spermatogenesis during which the specific spermatozoa are generated in this species is yet unclear. Here, the transcriptome of developing testis in E. sinensis was analyzed using the ways of RNA-seq and bioinformatics analysis to identify candidate genes potentially involved in development of testis and spermatogenesis. The Illumina HiSeq2500 sequencing of three replicons of samples produced a total of 145...
2017: PloS One
https://www.readbyqxmd.com/read/28210621/circular-rnas-in-cardiovascular-disease-an-overview
#2
REVIEW
Ximin Fan, Xinyu Weng, Yifan Zhao, Wei Chen, Tianyi Gan, Dachun Xu
Circular RNA (circRNA), a novel type of endogenous noncoding RNA (ncRNA), has become a research hotspot in recent years. CircRNAs are abundant and stably exist in creatures, and they are found with covalently closed loop structures in which they are quite different from linear RNAs. Nowadays, an increasing number of scientists have demonstrated that circRNAs may have played an essential role in the regulation of gene expression, especially acting as miRNA sponges, and have described the potential mechanisms of several circRNAs in diseases, hinting at their clinical therapeutic values...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28204845/mirnas-target-databases-developmental-methods-and-target-identification-techniques-with-functional-annotations
#3
REVIEW
Nagendra Kumar Singh
PURPOSE: microRNA (miRNA) regulates diverse biological mechanisms and metabolisms in plants and animals. Thus, the discoveries of miRNA has revolutionized the life sciences and medical research.The miRNA represses and cleaves the targeted mRNA by binding perfect or near perfect or imperfect complementary base pairs by RNA-induced silencing complex (RISC) formation during biogenesis process. One miRNA interacts with one or more mRNA genes and vice versa, hence takes part in causing various diseases...
February 15, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28203519/the-widespread-occurrence-of-trna-derived-fragments-in-saccharomyces-cerevisiae
#4
Kamilla Bąkowska-Żywicka, Anna M Mleczko, Marta Kasprzyk, Piotr Machtel, Marek Żywicki, Tomasz Twardowski
Short RNAs derived from the cleavage of tRNA molecules are observed in most organisms. Their occurrence seems to be induced by stress conditions, but still little is known about their biogenesis and functions. We find that the recovery of tRNA fragments depends on the RNA isolation method. Using an optimized RNA extraction protocol and northern blot hybridization technique, we show that the tRNA-derived fragments in yeast are widespread in 12 different growth conditions. We did not observe significant stress-dependent changes in the amounts of tRNA fragments pool...
December 2016: FEBS Open Bio
https://www.readbyqxmd.com/read/28196591/nuclear-pkc%C3%AE-ect2-rac1-and-ribosome-biogenesis-a-novel-axis-in-lung-tumorigenesis
#5
Martin J Baker, Mariana Cooke, Marcelo G Kazanietz
The RhoGEF Ect2 controls cell division and exerts oncogenic functions in multiple cancers. In this issue of Cancer Cell, Justilien et al. report that Ect2 is required for lung tumorigenesis and identified a role for this GEF in ribosomal RNA (rRNA) synthesis that is mediated by Rac1 and PKCι-dependent phosphorylation.
February 13, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28188847/pharmacological-inhibition-of-spinal-cord-injury-stimulated-ribosomal-biogenesis-does-not-affect-locomotor-outcome
#6
Ewa Kilanczyk, Kariena R Andres, Justin Hallgren, Sujata Saraswat Ohri, Marikki Laiho, Scott R Whittemore, Michal Hetman
After unresolved endoplasmic reticulum stress, recovery of protein synthesis including increased expression of ribosomal components and translation factors may induce cell death. Using a mouse model of moderate contusive spinal cord injury (SCI) at the T9 level, upregulation of ribosomal biogenesis was observed in the injury epicenter at 24h after trauma. Such upregulation coincided with endoplasmic reticulum stress response as previously reported in this model. It was also accompanied by changes in expression of many other genes associated with translational regulation...
February 7, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28188211/cluh-regulates-mitochondrial-metabolism-by-controlling-translation-and-decay-of-target-mrnas
#7
Désirée Schatton, David Pla-Martin, Marie-Charlotte Marx, Henriette Hansen, Arnaud Mourier, Ivan Nemazanyy, Alberto Pessia, Peter Zentis, Teresa Corona, Vangelis Kondylis, Esther Barth, Astrid C Schauss, Vidya Velagapudi, Elena I Rugarli
Mitochondria are essential organelles that host crucial metabolic pathways and produce adenosine triphosphate. The mitochondrial proteome is heterogeneous among tissues and can dynamically change in response to different metabolic conditions. Although the transcriptional programs that govern mitochondrial biogenesis and respiratory function are well known, posttranscriptional regulatory mechanisms remain unclear. In this study, we show that the cytosolic RNA-binding protein clustered mitochondria homologue (CLUH) regulates the expression of a mitochondrial protein network supporting key metabolic programs required under nutrient deprivation...
February 10, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28187419/dynamics-of-mirna-biogenesis-and-nuclear-transport
#8
Aneesh Kotipalli, Ravikumar Gutti, Chanchal K Mitra
MicroRNAs (miRNAs) are short noncoding RNA sequences ~22 nucleotides in length that play an important role in gene regulation-transcription and translation. The processing of these miRNAs takes place in both the nucleus and the cytoplasm while the final maturation occurs in the cytoplasm. Some mature miRNAs with nuclear localisation signals (NLS) are transported back to the nucleus and some remain in the cytoplasm. The functional roles of these miRNAs are seen in both the nucleus and the cytoplasm. In the nucleus, miRNAs regulate gene expression by binding to the targeted promoter sequences and affect either the transcriptional gene silencing (TGS) or transcriptional gene activation (TGA)...
December 22, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28185365/circrnas-biogenesis-properties-roles-and-their-relationships-with-liver-diseases-running-title-circular-rnas-and-liver-diseases
#9
REVIEW
Ting Yao, Qingqing Chen, Liyun Fu, Junming Guo
Circular RNAs (circRNAs) are a class of new found RNA molecules that have a special covalent loop structure without 5' cap and 3' tail. Researchers have found that circRNAs may be generated by intron-pairing-driven or lariat-driven circularization. They are cleared up via extracellular vesicles. They have some advantages such as stable, conservation, tissue specificity and so on. By severing as sponge of microRNAs, interacting with long non-coding RNAs, mRNA, or proteins, circRNAs regulate gene expression at transcriptional and post-transcriptional levels and contribute carcinogenesis...
February 10, 2017: Hepatology Research: the Official Journal of the Japan Society of Hepatology
https://www.readbyqxmd.com/read/28174252/trbp-maintains-mammalian-embryonic-neural-stem-cell-properties-by-enhancing-the-notch-signaling-pathway-as-a-novel-transcriptional-coactivator
#10
Sung-Hyun Byun, Juwan Kim, Dasol Han, Mookwang Kwon, Jae Youl Cho, Hui Xuan Ng, Samuel J Pleasure, Keejung Yoon
Transactivation response element RNA-binding protein (TRBP) is known to play important roles in human immunodeficiency virus (HIV) replication and microRNA biogenesis. However, recent studies implicate TRBP in a variety of biological processes as a mediator for cross-talk between signal transduction pathways. Here, we provide the first evidence that TRBP is required for efficient neurosphere formation, and expression of neural stem cell markers and Notch target genes in primary neural progenitor cells in vitro Consistent with this, introduction of TRBP into the mouse embryonic brain in utero increased the fraction of cells expressing Sox2 in the ventricular zone (VZ)...
February 7, 2017: Development
https://www.readbyqxmd.com/read/28174021/biogenesis-and-function-of-ago-associated-rnas
#11
REVIEW
Iben Daugaard, Thomas Birkballe Hansen
Numerous sophisticated high-throughput sequencing technologies have been developed over the past decade, and these have enabled the discovery of a diverse catalog of small non-coding (nc)RNA molecules that function as regulatory entities by associating with Argonaute (Ago) proteins. MicroRNAs (miRNAs) are currently the best-described class of post-transcriptional regulators that follow a specific biogenesis pathway characterized by Drosha/DGCR8 and Dicer processing. However, more exotic miRNA-like species that bypass particular steps of the canonical miRNA biogenesis pathway continue to emerge, with one of the most recent additions being the agotrons, which escape both Drosha/DGCR8- and Dicer-processing...
February 4, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28148795/hepatitis-b-virus-encoded-mirna-controls-viral-replication
#12
Xi Yang, Hongfeng Li, Huahui Sun, Hongxia Fan, Yaqi Hu, Min Liu, Xin Li, Hua Tang
: microRNAs (miRNAs) are a class of small single-stranded non-coding functional RNAs. Hepatitis B virus (HBV) is an enveloped DNA virus with virions and subviral forms of particles that lack a core. It was not known whether HBV encodes miRNAs. Here, we identified an HBV-encoded miRNA (called HBV-miR-3) by deep sequencing and northern blot. HBV-miR-3 is located at nts 373-393 of the HBV genome and was generated from 3.5Kb, 2,4Kb and 2.1Kb HBV in classic miRNA biogenesis (Drosha-Dicer dependent) manner...
February 1, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28145468/the-srnaome-mining-revealed-existence-of-unique-signature-small-rnas-derived-from-5-8srrna-from-piper-nigrum-and-other-plant-lineages
#13
Srinivasan Asha, E V Soniya
Small RNAs derived from ribosomal RNAs (srRNAs) are rarely explored in the high-throughput data of plant systems. Here, we analyzed srRNAs from the deep-sequenced small RNA libraries of Piper nigrum, a unique magnoliid plant. The 5' end of the putative long form of 5.8S rRNA (5.8SLrRNA) was identified as the site for biogenesis of highly abundant srRNAs that are unique among the Piperaceae family of plants. A subsequent comparative analysis of the ninety-seven sRNAomes of diverse plants successfully uncovered the abundant existence and precise cleavage of unique rRF signature small RNAs upstream of a novel 5' consensus sequence of the 5...
February 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28143451/distinct-prostate-cancer-related-mrna-cargo-in-extracellular-vesicle-subsets-from-prostate-cell-lines
#14
Elisa Lázaro-Ibáñez, Taral R Lunavat, Su Chul Jang, Carmen Escobedo-Lucea, Jorge Oliver-De La Cruz, Pia Siljander, Jan Lötvall, Marjo Yliperttula
BACKGROUND: Multiple types of extracellular vesicles (EVs), including microvesicles (MVs) and exosomes (EXOs), are released by all cells constituting part of the cellular EV secretome. The bioactive cargo of EVs can be shuffled between cells and consists of lipids, metabolites, proteins, and nucleic acids, including multiple RNA species from non-coding RNAs to messenger RNAs (mRNAs). In this study, we hypothesized that the mRNA cargo of EVs could differ based on the EV cellular origin and subpopulation analyzed...
February 1, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28143407/widespread-changes-in-mrna-stability-contribute-to-quiescence-specific-gene-expression-patterns-in-a-fibroblast-model-of-quiescence
#15
Elizabeth L Johnson, David G Robinson, Hilary A Coller
BACKGROUND: Quiescence, reversible exit from the cell division cycle, is characterized by large-scale changes in steady-state gene expression, yet mechanisms controlling these changes are in need of further elucidation. In order to characterize the effects of post-transcriptional control on the quiescent transcriptome in human fibroblasts, we determined mRNA decay rates for over 10,000 genes using a transcription shut-off time-course. RESULTS: We found that ~500 of the genes monitored exhibited significant changes in decay rate upon quiescence induction...
February 1, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28139767/drosophila-cg3303-is-an-essential-endoribonuclease-linked-to-tdp-43-mediated-neurodegeneration
#16
Pietro Laneve, Lucia Piacentini, Assunta Maria Casale, Davide Capauto, Ubaldo Gioia, Ugo Cappucci, Valerio Di Carlo, Irene Bozzoni, Patrizio Di Micco, Veronica Morea, Carmela Antonia Di Franco, Elisa Caffarelli
Endoribonucleases participate in almost every step of eukaryotic RNA metabolism, acting either as degradative or biosynthetic enzymes. We previously identified the founding member of the Eukaryotic EndoU ribonuclease family, whose components display unique biochemical features and are flexibly involved in important biological processes, such as ribosome biogenesis, tumorigenesis and viral replication. Here we report the discovery of the CG3303 gene product, which we named DendoU, as a novel family member in Drosophila...
January 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28138067/structure-and-dynamics-of-bacterial-ribosome-biogenesis
#17
REVIEW
Joseph H Davis, James R Williamson
Bacterial ribosome biogenesis has been an active area of research for more than 30 years and has served as a test-bed for the development of new biochemical, biophysical and structural techniques to understand macromolecular assembly generally. Recent work inspecting the process in vivo has advanced our understanding of the role of ribosome biogenesis factors, the co-transcriptional nature of assembly, the kinetics of the process under sub-optimal conditions, and the rRNA folding and ribosome protein binding pathways...
March 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28134914/comparative-genomics-of-two-jute-species-and-insight-into-fibre-biogenesis
#18
Md Shahidul Islam, Jennifer A Saito, Emdadul Mannan Emdad, Borhan Ahmed, Mohammad Moinul Islam, Abdul Halim, Quazi Md Mosaddeque Hossen, Md Zakir Hossain, Rasel Ahmed, Md Sabbir Hossain, Shah Md Tamim Kabir, Md Sarwar Alam Khan, Md Mursalin Khan, Rajnee Hasan, Nasima Aktar, Ummay Honi, Rahin Islam, Md Mamunur Rashid, Xuehua Wan, Shaobin Hou, Taslima Haque, Muhammad Shafiul Azam, Mahdi Muhammad Moosa, Sabrina M Elias, A M Mahedi Hasan, Niaz Mahmood, Md Shafiuddin, Saima Shahid, Nusrat Sharmeen Shommu, Sharmin Jahan, Saroj Roy, Amlan Chowdhury, Ashikul Islam Akhand, Golam Morshad Nisho, Khaled Salah Uddin, Taposhi Rabeya, S M Ekramul Hoque, Afsana Rahman Snigdha, Sarowar Mortoza, Syed Abdul Matin, Md Kamrul Islam, M Z H Lashkar, Mahboob Zaman, Anton Yuryev, Md Kamal Uddin, Md Sharifur Rahman, Md Samiul Haque, Md Monjurul Alam, Haseena Khan, Maqsudul Alam
Jute (Corchorus sp.) is one of the most important sources of natural fibre, covering ∼80% of global bast fibre production(1). Only Corchorus olitorius and Corchorus capsularis are commercially cultivated, though there are more than 100 Corchorus species(2) in the Malvaceae family. Here we describe high-quality draft genomes of these two species and their comparisons at the functional genomics level to support tailor-designed breeding. The assemblies cover 91.6% and 82.2% of the estimated genome sizes for C...
January 30, 2017: Nature Plants
https://www.readbyqxmd.com/read/28134793/trm112-a-protein-activator-of-methyltransferases-modifying-actors-of-the-eukaryotic-translational-apparatus
#19
REVIEW
Gabrielle Bourgeois, Juliette Létoquart, Nhan van Tran, Marc Graille
Post-transcriptional and post-translational modifications are very important for the control and optimal efficiency of messenger RNA (mRNA) translation. Among these, methylation is the most widespread modification, as it is found in all domains of life. These methyl groups can be grafted either on nucleic acids (transfer RNA (tRNA), ribosomal RNA (rRNA), mRNA, etc.) or on protein translation factors. This review focuses on Trm112, a small protein interacting with and activating at least four different eukaryotic methyltransferase (MTase) enzymes modifying factors involved in translation...
January 27, 2017: Biomolecules
https://www.readbyqxmd.com/read/28134598/circular-rnas-an-emerging-type-of-rna-in-cancer
#20
Li-Dan Hou, Jing Zhang
Circular RNAs (circRNAs), a novel type of widespread and diverse endogenous non-coding RNAs (ncRNAs), which are different from the linear RNAs, form a covalently closed continuous loop without 5' or 3' polarities. The majority of circRNAs are abundant, conserved and stable across different species, and exhibit tissue/developmental-stage-specific characteristics. They are generated primarily through a type of alternative RNA splicing called "back-splicing," in which a downstream splice donor is joined to an upstream splice acceptor through splice skipping or direct splice...
January 1, 2017: International Journal of Immunopathology and Pharmacology
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