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https://www.readbyqxmd.com/read/29773992/functional-analysis-of-rna-interference-related-soybean-pod-borer-lepidoptera-genes-based-on-transcriptome-sequences
#1
Fanli Meng, Mingyu Yang, Yang Li, Tianyu Li, Xinxin Liu, Guoyue Wang, Zhanchun Wang, Xianhao Jin, Wenbin Li
RNA interference (RNAi) is useful for controlling pests of agriculturally important crops. The soybean pod borer (SPB) is the most important soybean pest in Northeastern Asia. In an earlier study, we confirmed that the SPB could be controlled via transgenic plant-mediated RNAi. Here, the SPB transcriptome was sequenced to identify RNAi-related genes, and also to establish an RNAi-of-RNAi assay system for evaluating genes involved in the SPB systemic RNAi response. The core RNAi genes, as well as genes potentially involved in double-stranded RNA (dsRNA) uptake were identified based on SPB transcriptome sequences...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/29760470/breast-cancer-associated-germline-structural-variants-harboring-small-noncoding-rnas-impact-post-transcriptional-gene-regulation
#2
Mahalakshmi Kumaran, Preethi Krishnan, Carol E Cass, Roland Hubaux, Wan Lam, Yutaka Yasui, Sambasivarao Damaraju
Copy Number Variants (CNVs) are a class of structural variations of DNA. Germline CNVs are known to confer disease susceptibility, but their role in breast cancer warrants further investigations. We hypothesized that breast cancer associated germline CNVs contribute to disease risk through gene dosage or other post-transcriptional regulatory mechanisms, possibly through tissue specific expression of CNV-embedded small-noncoding RNAs (CNV-sncRNAs). Our objectives are to identify breast cancer associated CNVs using a genome wide association study (GWAS), identify sncRNA genes embedded within CNVs, confirm breast tissue (tumor and normal) expression of the sncRNAs, correlate their expression with germline copy status and identify pathways influenced by the genes regulated by sncRNAs...
May 14, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29760316/unique-sex-determination-system-in-the-silkworm-bombyx-mori-current-status-and-beyond
#3
Susumu Katsuma, Takashi Kiuchi, Munetaka Kawamoto, Toshiaki Fujimoto, Ken Sahara
The silkworm Bombyx mori has been used for silk production for over 5,000 years. In addition to its contribution to sericulture, B. mori has played an important role in the field of genetics. Classical genetic studies revealed that a gene(s) with a strong feminizing activity is located on the W chromosome, but this W-linked feminizing gene, called Feminizer (Fem), had not been cloned despite more than 80 years of study. In 2014, we discovered that Fem is a precursor of a single W chromosome-derived PIWI-interacting RNA (piRNA)...
2018: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/29752750/comparative-expression-profile-of-micrornas-and-pirnas-in-three-ruminant-species-testes-using-next-generation-sequencing
#4
H Wang, J Zhong, Z Chai, J Zhu, J Xin
microRNA (miRNA) and piwi-interacting RNA (piRNA) are two classes small non-coding regulatory RNAs that play crucial roles in multiple biological processes such as spermatogenesis. However, there are no published studies on conjoint analysis of miRNA and piRNA profiles among cattle, yak and their interspecies (the dzo) using sequencing technology. Next-generation sequencing technology was used to profile miRNAs and piRNAs among those three ruminants to elucidate their functions. A total of 119, 14 and six differentially expressed miRNAs were obtained in cattle vs...
May 11, 2018: Reproduction in Domestic Animals, Zuchthygiene
https://www.readbyqxmd.com/read/29749606/interactions-between-short-and-long-noncoding-rnas
#5
REVIEW
Igor Ulitsky
It is now evident that noncoding RNAs play key roles in regulatory networks determining cell fate and behavior, in a myriad of different conditions, and across all species. Among these noncoding RNAs are short RNAs, such as microRNAs, snoRNAs, and piRNAs, and the functions of those are relatively well understood. Other noncoding RNAs are longer, and their modes of action and functions are also increasingly explored and deciphered. Short RNAs and long noncoding RNAs (lncRNAs) interact with each other with reciprocal consequences for their fates and functions...
May 10, 2018: FEBS Letters
https://www.readbyqxmd.com/read/29743438/improved-boronate-affinity-electrophoresis-by-optimization-of-the-running-buffer-for-a-single-step-separation-of-pirna-from-mouse-testis-total-rna
#6
Yusuke Sato, Daijiro Iwasawa, Kuo Ping Hui, Rena Nakagomi, Seiichi Nishizawa
Here we examined optimization of the running buffer in boronate affinity electrophoresis for improved separation of PIWI-interacting RNA (piRNA) with 2'-O-methylated ribose in 3'-terminal nucleotide. The use of Good's buffer, such as HEPES, significantly increased the separation efficiency for piRNA over normal RNA with free 3'-terminal ribose, and retained an ability to resolve the difference by at least 4-nucleotide lengths in the target piRNAs. We also demonstrated a single-step separation of piRNA from mouse testis total RNA...
2018: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
https://www.readbyqxmd.com/read/29740006/identification-of-target-genes-regulated-by-the-drosophila-histone-methyltransferase-eggless-reveals-a-role-of-decapentaplegic-in-apoptotic-signaling
#7
Igojo Kang, Yourim Choi, Sueun Jung, Jae Yun Lim, Dooyoung Lee, Sumeet Gupta, Woongjoon Moon, Chanseok Shin
Epigenetic gene regulation is essential for developmental processes. Eggless (Egg), the Drosophila orthologue of the mammalian histone methyltransferase, SETDB1, is known to be involved in the survival and differentiation of germline stem cells and piRNA cluster transcription during Drosophila oogenesis; however the detailed mechanisms remain to be determined. Here, using high-throughput RNA sequencing, we investigated target genes regulated by Egg in an unbiased manner. We show that Egg plays diverse roles in particular piRNA pathway gene expression, some long non-coding RNA expression, apoptosis-related gene regulation, and Decapentaplegic (Dpp) signaling during Drosophila oogenesis...
May 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29735660/longevity-and-transposon-defense-the-case-of-termite-reproductives
#8
Daniel Elsner, Karen Meusemann, Judith Korb
Social insects are promising new models in aging research. Within single colonies, longevity differences of several magnitudes exist that can be found elsewhere only between different species. Reproducing queens (and, in termites, also kings) can live for several decades, whereas sterile workers often have a lifespan of a few weeks only. We studied aging in the wild in a highly social insect, the termite Macrotermes bellicosus , which has one of the most pronounced longevity differences between reproductives and workers...
May 7, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29735528/a-critical-role-for-nucleoporin-358-nup358-in-transposon-silencing-and-pirna-biogenesis-in-drosophila
#9
Rasesh Y Parikh, Haifan Lin, Vamsi K Gangaraju
Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs that bind Piwi proteins to silence transposons and to regulate gene expression. In Drosophila germ cells, the Aubergine (Aub)-Argonaute 3 (Ago3)-dependent ping-pong cycle generates most germline piRNAs. Loading of anti-sense piRNAs amplified by this cycle enables Piwi to enter the nucleus and silence transposons. Nuclear localization is crucial for Piwi function in transposon silencing, but how this process is regulated remains unknown. It is also not known whether any of the components of the nuclear pore complex (NPC) directly function in the piRNA pathway...
May 7, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29733347/disruption-of-tdrd5-decouples-the-stepwise-processing-of-long-precursor-transcripts-during-pachytene-pirna-biogenesis
#10
Yu H Sun, Feng Jiang, Xin Zhiguo Li
No abstract text is available yet for this article.
May 3, 2018: Biology of Reproduction
https://www.readbyqxmd.com/read/29730207/sports1-0-a-tool-for-annotating-and-profiling-non-coding-rnas-optimized-for-rrna-and-trna-derived-small-rnas
#11
Junchao Shi, Eun-A Ko, Kenton M Sanders, Qi Chen, Tong Zhou
High-throughput RNA-seq has revolutionized the process of small RNA (sRNA) discovery, leading to a rapid expansion of sRNA categories. In addition to the previously well-characterized sRNAs such as microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNA (snoRNAs), recent emerging studies have spotlighted on tRNA-derived sRNAs (tsRNAs) and rRNA-derived sRNAs (rsRNAs) as new categories of sRNAs that bear versatile functions. Since existing software and pipelines for sRNA annotation are mostly focused on analyzing miRNAs or piRNAs, here we developed the sRNA annotation pipeline optimized for rRNA- and tRNA- derived sRNAs (SPORTS1...
May 3, 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29728561/heterochromatin-protein-1a-functions-for-pirna-biogenesis-predominantly-from-pericentric-and-telomeric-regions-in-drosophila
#12
Ryan Yee Wei Teo, Amit Anand, Vishweshwaren Sridhar, Katsutomo Okamura, Toshie Kai
In metazoan germline, Piwi-interacting RNAs (piRNAs) provide defence against transposons. Piwi-piRNA complex mediates transcriptional silencing of transposons in nucleus. Heterochromatin protein 1a (HP1a) has been proposed to function downstream of Piwi-piRNA complex in Drosophila. Here we show that HP1a germline knockdown (HP1a-GLKD) leads to a reduction in the total and Piwi-bound piRNAs mapping to clusters and transposons insertions, predominantly in the regions close to telomeres and centromeres, resulting in derepression of a limited number of transposons from these regions...
May 4, 2018: Nature Communications
https://www.readbyqxmd.com/read/29722951/-epigenetics-of-male-infertility-an-update
#13
REVIEW
Qi-Jie Zhang, Jie Xu, Chao Qin
Epigenetic factors play an important role in male infertility though about 60%-65% of the disease is idiopathic and its underlying causes are not yet clear. Many studies have indicated that epigenetic modifications, including DNA methylation, histone tail modifications, chromatin remodeling, and non-coding RNAs, may be involved in idiopathic male infertility. Abnormal methylation is associated with decreased sperm quality and fertility. It is known that 1 881 miRNAs are related to male fertility and such non-coding RNAs as piRNA, IncRNA, and circRNA play a regulating role in male reproduction...
June 2017: Zhonghua Nan Ke Xue, National Journal of Andrology
https://www.readbyqxmd.com/read/29712752/molecular-dissection-of-a-natural-transposable-element-invasion
#14
Robert Kofler, Kirsten-André Senti, Viola Nolte, Ray Tobler, Christian Schlötterer
The first tracking of the dynamics of a natural invasion by a transposable element (TE) provides unprecedented details on the establishment of host defense mechanisms against TEs. We captured a D. simulans population at an early stage of a P - element invasion and studied the spread of the TE in replicated experimentally evolving populations kept under hot and cold conditions. We analyzed the factors controlling the invasion by NGS, RNA-FISH, and gonadal dysgenesis assays. Under hot conditions, the P - element spread rapidly for 20 generations, but no further spread was noted later on...
April 30, 2018: Genome Research
https://www.readbyqxmd.com/read/29703750/identification-of-substrates-of-the-small-rna-methyltransferase-hen1-in-mouse-spermatogonial-stem-cells-and-analysis-of-its-methyl-transfer-domain
#15
Ling Peng, Fengjuan Zhang, Renfu Shang, Xueyan Wang, Jiayi Chen, James J Chou, Jinbiao Ma, Ligang Wu, Ying Huang
Small noncoding RNAs (sncRNAs) regulate many genes in eukaryotic cells. Hua enhancer 1 (Hen1) is a 2'-O-methyltransferase that adds a methyl group to the 2'-OH of 3'-terminal nucleotide of sncRNAs. The types and properties of sncRNAs may vary among different species, and the domain composition, structure, and function of Hen1 proteins differ accordingly. In mammals, Hen1 specifically methylates sncRNAs called p-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs). However, other types of sncRNAs that are methylated by Hen1 have not yet been reported, and the structures and the substrates of mammalian Hen1 remain unknown...
April 27, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29701755/domain-functional-analyses-of-piwil1-and-pabpc1-indicate-their-synergistic-roles-in-protein-translation-via-3-utrs-of-meiotic-mrnas
#16
Yaoyao Wu, Kaibiao Xu, Huayu Qi
Translational regulation plays a central role during post-meiotic development of male germ cells. Previous studies suggested that PIWIL1, a PIWI-interacting RNA (piRNA) binding protein that is critical for sperm development, participates in the maintenance and translational regulation of post-meiotic mRNAs in haploid spermatids. However, how PIWIL1 regulates protein translation remains largely unclear. Using biochemical assays, we show here that PIWIL1 utilizes different domains to interact with post-meiotic mRNAs and PABPC1, a general protein translation regulator...
April 25, 2018: Biology of Reproduction
https://www.readbyqxmd.com/read/29696996/a-technical-assessment-of-the-porcine-ejaculated-spermatozoa-for-a-sperm-specific-rna-seq-analysis
#17
Marta Gòdia, Fabiana Quoos Mayer, Julieta Nafissi, Anna Castelló, Joan Enric Rodríguez-Gil, Armand Sánchez, Alex Clop
The study of the boar sperm transcriptome by RNA-seq can provide relevant information on sperm quality and fertility and might contribute to animal breeding strategies. However, the analysis of the spermatozoa RNA is challenging as these cells harbor very low amounts of highly fragmented RNA, and the ejaculates also contain other cell types with larger amounts of non-fragmented RNA. Here, we describe a strategy for a successful boar sperm purification, RNA extraction and RNA-seq library preparation. Using these approaches our objectives were: (i) to evaluate the sperm recovery rate (SRR) after boar spermatozoa purification by density centrifugation using the non-porcine-specific commercial reagent BoviPureTM ; (ii) to assess the correlation between SRR and sperm quality characteristics; (iii) to evaluate the relationship between sperm cell RNA load and sperm quality traits and (iv) to compare different library preparation kits for both total RNA-seq (SMARTer Universal Low Input RNA and TruSeq RNA Library Prep kit) and small RNA-seq (NEBNext Small RNA and TailorMix miRNA Sample Prep v2) for high-throughput sequencing...
April 26, 2018: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/29694837/planarian-flatworms-as-a-new-model-system-for-understanding-epigenetic-regulation-of-stem-cell-pluripotency-and-differentiation
#18
REVIEW
Anish Dattani, Divya Sridhar, Aziz Aboobaker
Planarian flatworms possess pluripotent stem cells (neoblasts) that are able to differentiate into all cell types that constitute the adult body plan. Consequently, planarians possess remarkable regenerative capabilities. Transcriptomic studies have revealed that gene expression is coordinated to maintain neoblast pluripotency, and ensure correct lineage specification during differentiation. But as yet they have not revealed how this regulation of expression is controlled. In this review, we propose that planarians represent a unique and effective system to study the epigenetic regulation of these processes in an in vivo context...
April 22, 2018: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29691221/small-ncrna-seq-results-of-human-tissues-variations-depending-on-sample-integrity
#19
Nicole Ludwig, Tobias Fehlmann, Valentina Galata, Andre Franke, Christina Backes, Eckart Meese, Andreas Keller
BACKGROUND: Although mature miRNAs are relatively stable in vivo, RNA degradation can have a substantial influence on small noncoding RNA (sncRNA) profiles. METHODS: Using different tissue storage conditions and RNA isolation procedures, we analyzed the integrity and quality of RNA isolates from human lung and heart tissues. We sequenced a total of 64 RNA samples and quantified the effect of RNA degradation, DNA contamination, and other confounding factors on the sncRNA-seq data...
April 24, 2018: Clinical Chemistry
https://www.readbyqxmd.com/read/29690553/pirna-profiling-of-dengue-virus-type-2-infected-asian-tiger-mosquito-and-midgut-tissues
#20
Yanhai Wang, Binbin Jin, Peiwen Liu, Jing Li, Xiaoguang Chen, Jinbao Gu
The Asian tiger mosquito, Aedes albopictus , is a competent vector for the majority of arboviruses. The mosquito innate immune response is a primary determinant for arthropod-borne virus transmission, and the midgut is the first barrier to pathogen transmission. Mosquito antiviral immunity is primarily mediated by the small interfering RNA pathway. However, the roles that the P-element induced wimpy testis (PIWI)-interacting RNA (piRNA) pathway play in antiviral immunity in Ae. albopictus and its midgut still need further exploration...
April 22, 2018: Viruses
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