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https://www.readbyqxmd.com/read/29240690/high-throughput-sequencing-of-small-rna-transcriptomes-in-maize-kernel-identifies-mirnas-involved-in-embryo-and-endosperm-development
#1
Lijuan Xing, Ming Zhu, Min Zhang, Wenzong Li, Haiyang Jiang, Junjie Zou, Lei Wang, Miaoyun Xu
Maize kernel development is a complex biological process that involves the temporal and spatial expression of many genes and fine gene regulation at a transcriptional and post-transcriptional level, and microRNAs (miRNAs) play vital roles during this process. To gain insight into miRNA-mediated regulation of maize kernel development, a deep-sequencing technique was used to investigate the dynamic expression of miRNAs in the embryo and endosperm at three developmental stages in B73. By miRNA transcriptomic analysis, we characterized 132 known miRNAs and six novel miRNAs in developing maize kernel, among which, 15 and 14 miRNAs were commonly differentially expressed between the embryo and endosperm at 9 days after pollination (DAP), 15 DAP and 20 DAP respectively...
December 14, 2017: Genes
https://www.readbyqxmd.com/read/29240242/the-9p21-locus-a-potential-therapeutic-target-and-prognostic-marker-in-breast-cancer
#2
REVIEW
Mahdi Rivand, Mohammad-Sadegh Khorrami, Hamid Fiuji, Soodabeh Shahidsales, Malihe Hasanzadeh, Mir Hadi Jazayeri, Seyed Mahdi Hassanian, Gordon A Ferns, Nafiseh Saghafi, Amir Avan
Breast cancer is an important cause of cancer related mortality in women. Despite extensive efforts to identify valid biomarkers for risk stratification, there are relatively few with proven clinical utility. It is recognized that genetic factors play a major role in determining susceptibility to breast cancer. Recent genome-wide-association-studies and gene expression analysis have demonstrated that a locus on chromosome 9p21, which contains three genes; CDKN2B (encoding p15ink4b), CDKN2A (encoding p16ink4a and p14ARF) and the 3' end of CDKN2BAS [an antisense noncoding RNA in the INK4 locus (ANRIL)] are associated with an increased risk of this malignancy...
December 14, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29239765/immune-responses-transcriptional-and-post-transcriptional-networks-pass-the-baton
#3
Johannes Lichti, Christian Gallus, Elke Glasmacher
Diverse gene regulatory mechanisms impact on immune homeostasis, and a new model now emerges as fundamental in light of recent genome-wide studies. In this picture, transcriptional networks drive functional changes during immune activation, whereas autoregulatory feedback loops of post-transcriptional programs ensure the original cell lineage identity and subsequent immune resolution.
November 24, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/29237851/micrornas-regulate-the-sesquiterpenoid-hormonal-pathway-in-drosophila-and-other-arthropods
#4
Zhe Qu, William G Bendena, Wenyan Nong, Kenneth W Siggens, Fernando G Noriega, Zhen-Peng Kai, Yang-Yang Zang, Alex C Koon, Ho Yin Edwin Chan, Ting Fung Chan, Ka Hou Chu, Hon Ming Lam, Michael Akam, Stephen S Tobe, Jerome Ho Lam Hui
Arthropods comprise the majority of all described animal species, and understanding their evolution is a central question in biology. Their developmental processes are under the precise control of distinct hormonal regulators, including the sesquiterpenoids juvenile hormone (JH) and methyl farnesoate. The control of the synthesis and mode of action of these hormones played important roles in the evolution of arthropods and their adaptation to diverse habitats. However, the precise roles of non-coding RNAs, such as microRNAs (miRNAs), controlling arthropod hormonal pathways are unknown...
December 20, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29237394/prediction-of-mirna-and-identification-of-their-relationship-network-related-to-late-blight-disease-of-potato
#5
Mohammad Samir Farooqi, Animesh Kumar, D C Mishra, Sanjeev Kumar, Anil Rai, K K Chaturvedi, S B Lal, Anu Sharma
Late blight, is one of the most serious disease in potato caused by Phytophthora infestans. In spite of adopting so many agricultural practices this disease is still a threat for potato. Recent studies showed that microRNA (miRNA), an important gene expression regulator, plays a very important role in host-pathogen interaction by silencing genes either by destructing or blocking of translation of mRNA. To date only few miRNA have been discovered which are related to late blight disease of potato during host pathogen interaction...
December 13, 2017: MicroRNA
https://www.readbyqxmd.com/read/29236054/genome-wide-profiling-of-small-rnas-and-degradome-revealed-conserved-regulations-of-mirnas-on-auxin-responsive-genes-during-fruit-enlargement-in-peaches
#6
Mengya Shi, Xiao Hu, Yu Wei, Xu Hou, Xue Yuan, Jun Liu, Yueping Liu
Auxin has long been known as a critical phytohormone that regulates fruit development in plants. However, due to the lack of an enlarged ovary wall in the model plants Arabidopsis and rice, the molecular regulatory mechanisms of fruit division and enlargement remain unclear. In this study, we performed small RNA sequencing and degradome sequencing analyses to systematically explore post-transcriptional regulation in the mesocarp at the hard core stage following treatment of the peach (Prunus persica L.) fruit with the synthetic auxin α-naphthylacetic acid (NAA)...
December 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29235467/in-situ-functional-dissection-of-rna-cis-regulatory-elements-by-multiplex-crispr-cas9-genome-engineering
#7
Qianxin Wu, Quentin R V Ferry, Toni A Baeumler, Yale S Michaels, Dimitrios M Vitsios, Omer Habib, Roland Arnold, Xiaowei Jiang, Stefano Maio, Bruno R Steinkraus, Marta Tapia, Paolo Piazza, Ni Xu, Georg A Holländer, Thomas A Milne, Jin-Soo Kim, Anton J Enright, Andrew R Bassett, Tudor A Fulga
RNA regulatory elements (RREs) are an important yet relatively under-explored facet of gene regulation. Deciphering the prevalence and functional impact of this post-transcriptional control layer requires technologies for disrupting RREs without perturbing cellular homeostasis. Here we describe genome-engineering based evaluation of RNA regulatory element activity (GenERA), a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 platform for in situ high-content functional analysis of RREs...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29234933/micrornas-and-metastasis-small-rnas-play-big-roles
#8
Jongchan Kim, Fan Yao, Zhenna Xiao, Yutong Sun, Li Ma
MicroRNAs (miRNAs) are small non-coding RNAs regulating post-transcriptional gene expression. They play important roles in many biological processes under physiological or pathological conditions, including development, metabolism, tumorigenesis, metastasis, and immune response. Over the past 15 years, significant insights have been gained into the roles of miRNAs in cancer. Depending on the cancer type, miRNAs can act as oncogenes, tumor suppressors, or metastasis regulators. In this review, we focus on the role of miRNAs as components of molecular networks regulating metastasis...
December 12, 2017: Cancer Metastasis Reviews
https://www.readbyqxmd.com/read/29234348/diurnal-transcriptome-and-gene-network-represented-through-sparse-modeling-in-brachypodium-distachyon
#9
Satoru Koda, Yoshihiko Onda, Hidetoshi Matsui, Kotaro Takahagi, Yukiko Yamaguchi-Uehara, Minami Shimizu, Komaki Inoue, Takuhiro Yoshida, Tetsuya Sakurai, Hiroshi Honda, Shinto Eguchi, Ryuei Nishii, Keiichi Mochida
We report the comprehensive identification of periodic genes and their network inference, based on a gene co-expression analysis and an Auto-Regressive eXogenous (ARX) model with a group smoothly clipped absolute deviation (SCAD) method using a time-series transcriptome dataset in a model grass, Brachypodium distachyon. To reveal the diurnal changes in the transcriptome in B. distachyon, we performed RNA-seq analysis of its leaves sampled through a diurnal cycle of over 48 h at 4 h intervals using three biological replications, and identified 3,621 periodic genes through our wavelet analysis...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29233752/mammalian-zygotic-genome-activation
#10
REVIEW
Petr Svoboda
Zygotic genome activation (ZGA) denotes the initiation of gene expression after fertilization. It is part of the complex oocyte-to-embryo transition (OET) in which a highly specialized cell - the oocyte - is fertilized and transformed into a zygote that gives rise to an embryo that will develop into a newborn. From the perspective of gene expression, the OET reflects reprogramming of germ cell gene expression into the new developmental program of the zygote. This reprogramming occurs at transcriptional and post-transcriptional levels...
December 9, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29232857/mir-34a-regulates-sperm-motility-in-zebrafish
#11
Wenjie Guo, Binyue Xie, Shuting Xiong, Xufang Liang, Jian-Fang Gui, Jie Mei
Increasing attention has been focused on the role of microRNAs in post-transcription regulation during spermatogenesis. Recently, the miR-34 family has been shown to be involved in the spermatogenesis, but the clear function of the miR-34 family in spermatogenesis is still obscure. Here we analyzed the function of miR-34a, a member of the miR-34 family, during spermatogenesis using miR-34a knockout zebrafish generated by the clustered regularly interspaced short palindromic repeats/associated protein 9 (CRISPR/Cas9) system...
December 10, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29231896/differential-expression-of-serum-micrornas-supports-cd4%C3%A2-%C2%BA-t-cell-differentiation-into-th2-th17-cells-in-severe-equine-asthma
#12
Alicja Pacholewska, Matthias F Kraft, Vincent Gerber, Vidhya Jagannathan
MicroRNAs (miRNAs) regulate post-transcriptional gene expression and may be exported from cells via exosomes or in partnership with RNA-binding proteins. MiRNAs in body fluids can act in a hormone-like manner and play important roles in disease initiation and progression. Hence, miRNAs are promising candidates as biomarkers. To identify serum miRNA biomarkers in the equine model of asthma we investigated small RNA derived from the serum of 34 control and 37 asthmatic horses. These samples were used for next generation sequencing, novel miRNA identification and differential miRNA expression analysis...
December 12, 2017: Genes
https://www.readbyqxmd.com/read/29231756/higher-levels-of-circulating-timp-4-in-preeclampsia-is-strongly-associated-with-clinical-parameters-and-microrna
#13
Valéria C Sandrim, Solange Diniz, Nibia Mariana Eleuterio, Karina B Gomes, Luci Maria S Dusse, Ricardo C Cavalli
BACKGROUND: Preeclampsia results in maternal and fetal complications and some studies have reported the role of MMPs and TIMPs in its pathophysiology. Therefore, the aim of this study was to compare plasma TIMP-4 levels in preeclampsia and healthy pregnant; and to correlate these levels with clinical parameters and expression of Let7a-5p (3´UTR post-transcriptionally regulation) Methods: TIMP-4 was measured by ELISA and miR-Let7a-5p expression by qPCR. RESULTS: Elevated plasma TIMP-4 levels in preeclampsia compared to healthy pregnant was found 1450 ± 411 vs...
December 12, 2017: Clinical and Experimental Hypertension: CHE
https://www.readbyqxmd.com/read/29231262/mir-24-3p-promotes-cell-migration-and-proliferation-in-lung-cancer-by-targeting-sox7
#14
Liang Yan, Jinzhu Ma, Yiping Zhu, Jiawei Zan, Zhen Wang, Liefeng Ling, Qiang Li, Jun Lv, Shimei Qi, Yingya Cao, Ying Liu, Long Cao, Yao Zhang, Zhilin Qi, Liuwang Nie
Lung cancer (LC) is one of the leading causes of cancer-related death in the world. miR-24-3p plays critical roles in many cancer types, including LC. In this study, we first investigated whether miR-24-3p promoted LC cell migration and proliferation in vitro. We used three bioinformatics algorithms to predict the miR-24-3p target gene to study the molecular mechanism by which miR-24-3p contributes to LC progression. Then, we used the luciferase reporter assay to identify whether SOX7 was a direct target of miR-24-3p...
December 12, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29230236/post-transcriptional-regulation-of-pcsk9-by-mir-191-mir-222-and-mir-224
#15
Parisa Naeli, Fatemeh Mirzadeh Azad, Mahshid Malakootian, Nabil G Seidah, Seyed J Mowla
Since proprotein convertase subtilisin kexin 9 (PCSK9) discovery, a gene involved in LDL metabolism regulation and cardiovascular diseases (CVD), many therapeutic strategies have been introduced for direct targeting of PCSK9. The main goal of these strategies has been to reduce PCSK9 protein level either by application of antibodies or inhibition of its production. In this study, we have tried to discover microRNAs (miRNAs) which can target, and hence regulate, PCSK9 expression. Using bioinformatics tools, we selected three microRNAs with binding sites on 3'-UTR of PCSK9...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29230098/circular-rnas-a-novel-type-of-non-coding-rna-and-their-potential-implications-in-antiviral-immunity
#16
REVIEW
Man Wang, Fei Yu, Wei Wu, Yuan Zhang, Wenguang Chang, Murugavel Ponnusamy, Kun Wang, Peifeng Li
Circular RNAs (circRNAs), a novel type of non-coding RNAs (ncRNAs), are ubiquitously expressed in eukaryotic cells during post-transcriptional processes. Unlike linear RNAs, circRNAs form covalent-closed continuous loops without 5' to 3' polarities and poly (A) tails. With advances in high-throughput sequencing technology, numerous circRNAs have been identified in plants, animals and humans. Notably, circRNAs display cell-type, tissue-type and developmental-stage specific expression patterns in eukaryotic transcriptome, which reveals their significant regulatory functions in gene expression...
2017: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29229900/post-transcriptional-3%C3%A2-utr-cleavage-of-mrna-transcripts-generates-thousands-of-stable-uncapped-autonomous-rna-fragments
#17
Yuval Malka, Avital Steiman-Shimony, Eran Rosenthal, Liron Argaman, Leonor Cohen-Daniel, Eliran Arbib, Hanah Margalit, Tommy Kaplan, Michael Berger
The majority of mammalian genes contain one or more alternative polyadenylation sites. Choice of polyadenylation sites was suggested as one of the underlying mechanisms for generating longer/shorter transcript isoforms. Here, we demonstrate that mature mRNA transcripts can undergo additional cleavage and polyadenylation at a proximal internal site in the 3'-UTR, resulting in two stable, autonomous, RNA fragments: a coding sequence with a shorter 3'-UTR (body) and an uncapped 3'-UTR sequence downstream of the cleavage point (tail)...
December 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/29229387/mir-124-3p-affects-the-formation-of-intramuscular-fat-through-alterations-in-branched-chain-amino-acid-consumption-in-sheep
#18
Yangyang Pan, Jiongjie Jing, Liying Qiao, Jianhua Liu, Junxing Zhao, Lixia An, Baojun Li, Weiwei Wang, Chen Liang, Wenzhong Liu
Intramuscular fat is used to determine meat quality in animals; however, factors affecting branched chain amino acid (BCAA) catabolism, which fuels adipogenesis and lipogenesis, remain unclear. To better understand the post-transcriptional influence on BCAA catabolism during adipogenesis, we investigated the role of miR-124-3p. Stromal vascular fraction (SVF) cells were isolated from skeletal muscle of sheep, and induced to differentiate. We determined the roles of miR-124-3p and its predicted target, branched chain keto acid dehydrogenase E1, alpha polypeptide (BCKDHA), in adipogenic differentiation and lipogenesis of SVFs after overexpressing or inhibiting miR-124-3p or BCKDHA, respectively...
December 8, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29229384/crystal-structure-of-the-chloroplast-rna-editing-factor-morf2
#19
Jingyu Yang, Min Zhang, Xiao Wang
RNA editing is a post-transcription process that alters the genetic information on RNA molecules. In plastids and mitochondria of flowering plants, the multiple organellar RNA editing factors (MORFs) interact with the PLS-type pentatricopeptide repeat (PPR) proteins and participate in RNA editing of cytidine-to-uridine conversion. The PPR proteins recognize cytidine targets around the editing sites, and the MORF proteins modulate the RNA-binding activity of the PPR proteins. Here, we report the structure of the Arabidopsis thaliana chloroplast MORF2 at 2...
December 8, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29228623/linking-creb-function-with-altered-metabolism-in-murine-fibroblast-based-model-cell-lines
#20
André Steven, Sandra Leisz, Claudia Wickenhauser, Kristin Schulz, Dimitrios Mougiakakos, Rolf Kiessling, Carsten Denkert, Barbara Seliger
The cAMP-responsive element binding protein CREB is frequently overexpressed and activated in tumors of distinct histology, leading to enhanced proliferation, migration, invasion and angiogenesis as well as reduced apoptosis. The de-regulated expression of CREB might be linked with transcriptional as well as post-transcriptional regulation mechanisms. We show here that altered CREB expression levels and function are associated with changes in the cellular metabolism. Using comparative proteome-based analysis an altered expression pattern of proteins involved in the cellular metabolism in particular in glycolysis was found upon CREB down-regulation in HER-2/neu-transfected cell lines...
November 14, 2017: Oncotarget
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