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RNA biogenesis

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https://www.readbyqxmd.com/read/29784949/neuronal-activity-regulates-drosha-via-autophagy-in-spinal-muscular-atrophy
#1
Inês do Carmo G Gonçalves, Johanna Brecht, Maximilian P Thelen, Wiebke A Rehorst, Miriam Peters, Hyun Ju Lee, Susanne Motameny, Laura Torres-Benito, Darius Ebrahimi-Fakhari, Natalia L Kononenko, Janine Altmüller, David Vilchez, Mustafa Sahin, Brunhilde Wirth, Min Jeong Kye
Dysregulated miRNA expression and mutation of genes involved in miRNA biogenesis have been reported in motor neuron diseases including spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS). Therefore, identifying molecular mechanisms governing miRNA expression is important to understand these diseases. Here, we report that expression of DROSHA, which is a critical enzyme in the microprocessor complex and essential for miRNA biogenesis, is reduced in motor neurons from an SMA mouse model. We show that DROSHA is degraded by neuronal activity induced autophagy machinery, which is also dysregulated in SMA...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784765/dawdle-interacts-with-dicer-like-proteins-to-mediate-small-rna-biogenesis
#2
Shuxin Zhang, Yongchao Dou, Shengjun Li, Guodong Ren, David Chevalier, Chi Zhang, Bin Yu
DAWDLE (DDL) is a conserved forkhead-associated (FHA) domain-containing protein with essential roles in plant development and immunity. It acts in the biogenesis of microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), which regulate gene expression at the transcriptional and/or post-transcriptional levels. However, the functional mechanism of DDL and its impact on exogenous siRNAs remain elusive. Here we report that DDL is required for the biogenesis of siRNAs derived from sense transgenes and inverted-repeat transgenes...
May 21, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29782554/hijacking-of-multiple-phospholipid-biosynthetic-pathways-and-induction-of-membrane-biogenesis-by-a-picornaviral-3cd-protein
#3
Sravani Banerjee, David Aponte-Diaz, Calvin Yeager, Suresh D Sharma, Gang Ning, Hyung S Oh, Qingxia Han, Masato Umeda, Yuji Hara, Robert Y L Wang, Craig E Cameron
RNA viruses induce specialized membranous structures for use in genome replication. These structures are often referred to as replication organelles (ROs). ROs exhibit distinct lipid composition relative to other cellular membranes. In many picornaviruses, phosphatidylinositol-4-phosphate (PI4P) is a marker of the RO. Studies to date indicate that the viral 3A protein hijacks a PI4 kinase to induce PI4P by a mechanism unrelated to the cellular pathway, which requires Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1, GBF1, and ADP ribosylation factor 1, Arf1...
May 21, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29779866/nucleolar-function-in-lifespan-regulation
#4
REVIEW
Varnesh Tiku, Adam Antebi
The nucleolus is a prominent membraneless organelle residing within the nucleus. The nucleolus has been regarded as a housekeeping structure mainly known for its role in ribosomal RNA (rRNA) production and ribosome assembly. However, accumulating evidence has revealed its functions in numerous cellular processes that control organismal physiology, thereby taking the nucleolus much beyond its conventional role in ribosome biogenesis. Perturbations in nucleolar functions have been associated with severe diseases such as cancer and progeria...
April 27, 2018: Trends in Cell Biology
https://www.readbyqxmd.com/read/29778844/identification-of-micrornas-with-heat-stress-responsive-and-immune-properties-in-marsupenaeus-japonicus-based-on-next-generation-sequencing-and-bioinformatics-analysis-essential-regulators-in-the-heat-stress-host-interactions
#5
Jinbin Zheng, Jiawen Cao, Yong Mao, Yongquan Su, Jun Wang
Summer mortality syndrome is one of the most serious issue for Marsupenaeus japonicus aquaculture in China. Since it causes massive economic loss and threatens sustainability of M. japonicus aquaculture industry, thus, there is an urgent desire to reveal the heat stress-host interactions mechanisms that lead to mass mortalities of M. japonicus in hot summer months. MicroRNAs (miRNAs) are small noncoding RNAs that involved in regulation of diverse biological processes, including stress and immune response, and might serve as potential regulators in the heat stress-host interactions...
May 17, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29776339/differential-gene-transcription-across-the-life-cycle-in-daphnia-magna-using-a-new-all-genome-custom-made-microarray
#6
Bruno Campos, Danielle Fletcher, Benjamín Piña, Romà Tauler, Carlos Barata
BACKGROUND: Unravelling the link between genes and environment across the life cycle is a challenging goal that requires model organisms with well-characterized life-cycles, ecological interactions in nature, tractability in the laboratory, and available genomic tools. Very few well-studied invertebrate model species meet these requirements, being the waterflea Daphnia magna one of them. Here we report a full genome transcription profiling of D. magna during its life-cycle. The study was performed using a new microarray platform designed from the complete set of gene models representing the whole transcribed genome of D...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29770436/all-i-s-on-the-radar-role-of-adar-in-gene-regulation
#7
REVIEW
Galina Shevchenko, Kevin V Morris
Adenosine to inosine (A-to-I) editing is the most abundant form of RNA modification in mammalian cells, which is catalyzed by adenosine deaminase acting on the double-stranded RNA (ADAR) protein family. A-to-I editing is currently known to be involved in the regulation of the immune system, RNA splicing, protein recoding, microRNA biogenesis, and formation of heterochromatin. Editing occurs within regions of double-stranded RNA, particularly within inverted Alu repeats, and is associated with many diseases including cancer, neurological disorders, and metabolic syndromes...
May 16, 2018: FEBS Letters
https://www.readbyqxmd.com/read/29763587/mice-exposed-to-bisphenol-a-exhibit-depressive-like-behavior-with-neurotransmitter-and-neuroactive-steroid-dysfunction
#8
Frances Xin, Erin Fischer, Christopher Krapp, Elizabeth N Krizman, Yemin Lan, Clementina Mesaros, Nathaniel W Snyder, Amita Bansal, Michael B Robinson, Rebecca A Simmons, Marisa S Bartolomei
Fetal exposure to endocrine disrupting chemicals (EDCs) has been associated with adverse neurobehavioral outcomes across the lifespan and can persist across multiple generations of offspring. However, the underlying mechanisms driving these changes are not well understood. We investigated the molecular perturbations associated with EDC-induced behavioral changes in first (F1) and second (F2) filial generations, using the model EDC bisphenol A (BPA). C57BL/6J dams were exposed to BPA from preconception until lactation through the diet at doses (10 μg/kg bw/d-lower dose or 10 mg/kg bw/d-upper dose) representative of human exposure levels...
May 18, 2018: Hormones and Behavior
https://www.readbyqxmd.com/read/29760712/the-function-of-micrornas-in-b-cell-development-lymphoma-and-their-potential-in-clinical-practice
#9
REVIEW
Bing Zheng, Zhijiang Xi, Rong Liu, Wei Yin, Zhiwei Sui, Boxu Ren, Heather Miller, Quan Gong, Chaohong Liu
B-cell formation, development, and differentiation are complex processes regulated by several mechanisms. Recently, there has been growing evidence indicating that microRNAs (miRNAs) are important for normal B-cell lineage development. miRNAs are small non-coding RNA molecules, about 20-22 nucleotide in length, that play an important role in regulating gene expression. They pair with specific messenger RNAs (mRNAs), resulting in mRNAs translational repression or degradation. Here, we review current research about the function of miRNAs in the aspects of B-cell physiology and pathology...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29760477/functional-interplay-between-e2f7-and-ribosomal-rrna-gene-transcription-regulates-protein-synthesis
#10
Amanda S Coutts, Shonagh Munro, Nicholas B La Thangue
A prerequisite for protein synthesis is the transcription of ribosomal rRNA genes by RNA polymerase I (Pol I), which controls ribosome biogenesis. UBF (upstream binding factor) is one of the main Pol I transcription factors located in the nucleolus that activates rRNA gene transcription. E2F7 is an atypical E2F family member that acts as a transcriptional repressor of E2F target genes, and thereby contributes to cell cycle arrest. Here, we describe an unexpected role for E2F7 in regulating rRNA gene transcription...
May 14, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29758258/nuclear-mrna-surveillance-mechanisms-function-and-links-to-human-disease
#11
REVIEW
Pragyan Singh, Upasana Saha, Sunirmal Paira, Biswadip Das
Production of export-competent mRNAs involves transcription and a series of dynamic processing and modification events of pre-messenger RNAs in the nucleus. Mutations in the genes encoding the transcription and mRNP processing machinery and the complexities involved in the biogenesis events lead to the formation of aberrant messages. These faulty transcripts are promptly eliminated by the nuclear RNA exosome and its cofactors to safeguard the cells and organisms from genetic catastrophe. Mutations in the components of the core nuclear exosome and its cofactors lead to the tissue-specific dysfunction of exosomal activities, which are linked to diverse human diseases and disorders...
May 11, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29757215/the-rules-and-functions-of-nucleocytoplasmic-shuttling-proteins
#12
REVIEW
Xuekun Fu, Chao Liang, Fangfei Li, Luyao Wang, Xiaoqiu Wu, Aiping Lu, Guozhi Xiao, Ge Zhang
Biological macromolecules are the basis of life activities. There is a separation of spatial dimension between DNA replication and RNA biogenesis, and protein synthesis, which is an interesting phenomenon. The former occurs in the cell nucleus, while the latter in the cytoplasm. The separation requires protein to transport across the nuclear envelope to realize a variety of biological functions. Nucleocytoplasmic transport of protein including import to the nucleus and export to the cytoplasm is a complicated process that requires involvement and interaction of many proteins...
May 12, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29755516/synaptic-paths-to-neurodegeneration-the-emerging-role-of-tdp-43-and-fus-in-synaptic-functions
#13
REVIEW
Shuo-Chien Ling
TAR DNA-binding protein-43 KDa (TDP-43) and fused in sarcoma (FUS) as the defining pathological hallmarks for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), coupled with ALS-FTD-causing mutations in both genes, indicate that their dysfunctions damage the motor system and cognition. On the molecular level, TDP-43 and FUS participate in the biogenesis and metabolism of coding and noncoding RNAs as well as in the transport and translation of mRNAs as part of cytoplasmic mRNA-ribonucleoprotein (mRNP) granules...
2018: Neural Plasticity
https://www.readbyqxmd.com/read/29755439/dicer-like-proteins-regulate-sexual-development-via-the-biogenesis-of-perithecium-specific-micrornas-in-a-plant-pathogenic-fungus-fusarium-graminearum
#14
Wenping Zeng, Jie Wang, Ying Wang, Jing Lin, Yanping Fu, Jiatao Xie, Daohong Jiang, Tao Chen, Huiquan Liu, Jiasen Cheng
Ascospores act as the primary inoculum of Fusarium graminearum , which causes the destructive disease Fusarium head blight (FHB), or scab. MicroRNAs (miRNAs) have been reported in the F. graminearum vegetative stage, and Fgdcl2 is involved in microRNA-like RNA (milRNA) biogenesis but has no major impact on vegetative growth, abiotic stress or pathogenesis. In the present study, we found that ascospore discharge was decreased in the Fgdcl1 deletion mutant, and completely blocked in the double-deletion mutant of Fgdcl1 and Fgdcl2 ...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29754835/identification-and-expression-analysis-of-long-noncoding-rnas-in-embryogenesis-and-larval-metamorphosis-of-ciona-savignyi
#15
Jiankai Wei, Bo Dong
Long noncoding RNAs (lncRNAs) play important roles in diverse developmental and pathological processes through chromatin reprogramming, cis regulation and posttranscriptional modification. They have been extensively studied in both vertebrates and invertebrates. However, the information of lncRNAs in urochordate is still lacking. In this study, we used the RNA-Seq data from three developmental stages (18, 21 and 42 hours post fertilization, hpf) of embryos and larvae in Ciona savignyi to identify candidate lncRNAs and analyze their expression profiles...
May 10, 2018: Marine Genomics
https://www.readbyqxmd.com/read/29751497/epigenetic-regulation-of-atp-binding-cassette-protein-a1-abca1-gene-expression-a-new-era-to-alleviate-atherosclerotic-cardiovascular-disease
#16
Mohamed Zaiou, Ahmed Bakillah
The most important function of high density lipoprotein (HDL) is its ability to remove cholesterol from cells and tissues involved in the early stages of atherosclerosis back to the liver for excretion. The ATP-binding cassette transporters ABCA1 and ABCG1 are responsible for the major part of cholesterol efflux to HDL in macrophage foam cells. Thus, promoting the process of reverse cholesterol transport (RCT) by upregulating mainly ABCA1 remains one of the potential targets for the development of new therapeutic agents against atherosclerosis...
May 3, 2018: Diseases (Basel)
https://www.readbyqxmd.com/read/29750247/tp53-dependent-and-independent-signaling-underlies-the-pathogenesis-and-possible-prevention-of-acrofacial-dysostosis-cincinnati-type
#17
Kristin E N Watt, Cynthia L Neben, Shawn Hall, Amy E Merrill, Paul A Trainor
Ribosome biogenesis is a global process required for growth and proliferation in all cells, but disruptions in this process surprisingly lead to tissue-specific phenotypic disorders termed ribosomopathies. Pathogenic variants in the RNA Polymerase (Pol) I subunit POLR1A cause Acrofacial Dysostosis - Cincinnati type, which is characterized by craniofacial and limb anomalies. In a zebrafish model of Acrofacial Dysostosis - Cincinnati type, we demonstrate that polr1a-/- mutants exhibit deficient 47S rRNA transcription, reduced monosomes and polysomes and, consequently, defects in protein translation...
May 10, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29749606/interactions-between-short-and-long-noncoding-rnas
#18
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/29749474/pgc1%C3%AE-promotes-cisplatin-resistance-in-human-ovarian-carcinoma-cells-through-upregulation-of-mitochondrial-biogenesis
#19
Luyan Shen, Boyang Sun, Jiyao Sheng, Sihang Yu, Yanqing Li, Huadan Xu, Jing Su, Liankun Sun
The induction of lesions in nuclear and mitochondrial DNA by cisplatin is only a small component of its cytostatic/cytotoxic activity. The signaling pathway network in the nucleus and cytoplasm may contribute to chemotherapeutic resistance. Peroxisome proliferator-activated receptor-coactivator 1α (PGC1α)-mediated mitochondrial biogenesis regulates mitochondrial structural and the functional adaptive response against chemotherapeutic stress, and may be a therapeutic target. However, this regulatory network is complex and depends upon tumor types and environments, which require further investigation...
May 9, 2018: International Journal of Oncology
https://www.readbyqxmd.com/read/29747424/alterations-of-oxidative-phosphorylation-complexes-in-papillary-thyroid-carcinoma
#20
Franz A Zimmermann, Daniel Neureiter, Wolfgang Sperl, Johannes A Mayr, Barbara Kofler
The papillary thyroid carcinoma (PTC) is the most common malignant tumor of the thyroid gland, with disruptive mutations in mitochondrial complex I subunits reported at very low frequency. Furthermore, metabolic diversity of PTC has been postulated owing to variable messenger RNA (mRNA) expression of genes encoding subunits of the oxidative phosphorylation (OXHPOS) complexes. The aim of the present study was to evaluate the metabolic diversity of the OXPHOS system at the protein level by using immunohistochemical staining...
May 9, 2018: Cells
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