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Rna splicing

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https://www.readbyqxmd.com/read/28723946/the-mitochondrial-genome-of-the-terrestrial-carnivorous-plant-utricularia-reniformis-lentibulariaceae-structure-comparative-analysis-and-evolutionary-landmarks
#1
Saura R Silva, Danillo O Alvarenga, Yani Aranguren, Helen A Penha, Camila C Fernandes, Daniel G Pinheiro, Marcos T Oliveira, Todd P Michael, Vitor F O Miranda, Alessandro M Varani
The carnivorous plants of the family Lentibulariaceae have attained recent attention not only because of their interesting lifestyle, but also because of their dynamic nuclear genome size. Lentibulariaceae genomes span an order of magnitude and include species with the smallest genomes in angiosperms, making them a powerful system to study the mechanisms of genome expansion and contraction. However, little is known about mitochondrial DNA (mtDNA) sequences of this family, and the evolutionary forces that shape this organellar genome...
2017: PloS One
https://www.readbyqxmd.com/read/28723513/the-natural-history-and-outcome-predictors-of-metastatic-castration-resistant-prostate-cancer
#2
REVIEW
Robert J van Soest, Jason A Efstathiou, Cora N Sternberg, Bertand Tombal
CONTEXT: Biomarkers for the treatment of metastatic castration-resistant prostate cancer (mCRPC) are urgently needed by clinicians to facilitate treatment decisions. OBJECTIVE: To review current prognostic and predictive biomarkers in mCRPC. EVIDENCE ACQUISITION: We performed a nonsystematic review of the literature from 2004 to August 2016 by searching in Medline. Cross-matching references were used to search for additional articles. We reviewed clinical research and review articles written in the English language...
December 2016: European Urology Focus
https://www.readbyqxmd.com/read/28722025/nanopore-long-read-rnaseq-reveals-widespread-transcriptional-variation-among-the-surface-receptors-of-individual-b-cells
#3
Ashley Byrne, Anna E Beaudin, Hugh E Olsen, Miten Jain, Charles Cole, Theron Palmer, Rebecca M DuBois, E Camilla Forsberg, Mark Akeson, Christopher Vollmers
Understanding gene regulation and function requires a genome-wide method capable of capturing both gene expression levels and isoform diversity at the single-cell level. Short-read RNAseq is limited in its ability to resolve complex isoforms because it fails to sequence full-length cDNA copies of RNA molecules. Here, we investigate whether RNAseq using the long-read single-molecule Oxford Nanopore MinION sequencer is able to identify and quantify complex isoforms without sacrificing accurate gene expression quantification...
July 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28718627/structural-basis-for-interaction-of-the-tandem-zinc-finger-domains-of-human-muscleblind-with-cognate-rna-from-human-cardiac-troponin-t
#4
Sangho Park, Priti Deka Phukan, Markus Zeeb, Maria A Martinez-Yamout, Helen Jane Dyson, Peter E Wright
The human muscleblind-like proteins (MBNL) regulate tissue-specific splicing by targeting cardiac troponin T and other pre-mRNAs; aberrant targeting of CUG and CCUG repeat expansions frequently accompanies the neuromuscular disease myotonic dystrophy. We show, using biolayer interferometry (Octet), and NMR spectroscopy, that the zinc finger domains of MBNL isoform 1 (MBNL1) are necessary and sufficient for binding CGCU sequences within the pre-mRNA of human cardiac troponin T (hcTnT). Protein constructs containing zinc fingers 1 and 2 (zf12) and zinc fingers 3 and 4 (zf34) of MBNL1 each fold into a compact globular tandem zinc finger structure that participates in RNA binding...
July 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28717189/cdk5-mediated-phosphorylation-of-xbp1s-contributes-to-its-nuclear-translocation-and-activation-in-mpp-induced-parkinson-s-disease-model
#5
Feng-Juan Jiao, Qing-Zhi Wang, Pei Zhang, Jian-Guo Yan, Zheng Zhang, Feng He, Qian Zhang, Ze-Xi Lv, Xiang Peng, Hong-Wei Cai, Bo Tian
Parkinson's disease (PD) is an irreversible and progressive neurodegenerative disorder characterized by the selective loss of dopaminergic neurons of the substantia nigra pars compacta. Growing evidence indicates that endoplasmic reticulum stress is a hallmark of PD; however, its exact contribution to the disease process remains poorly understood. Here, we used molecular biology methods and RNA-Seq analysis to explored an unexpected role of spliced X-Box binding protein 1 (XBP1s) in the nervous system. In this study, we determined that the IRE1α/XBP1 pathway is activated in MPP(+)-treated neurons...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717182/widespread-alternative-exon-usage-in-clinically-distinct-subtypes-of-invasive-ductal-carcinoma
#6
Sunniva Stordal Bjørklund, Anshuman Panda, Surendra Kumar, Michael Seiler, Doug Robinson, Jinesh Gheeya, Ming Yao, Grethe I Grenaker Alnæs, Deborah Toppmeyer, Margit Riis, Bjørn Naume, Anne-Lise Børresen-Dale, Vessela N Kristensen, Shridar Ganesan, Gyan Bhanot
Cancer cells can have different patterns of exon usage of individual genes when compared to normal tissue, suggesting that alternative splicing may play a role in shaping the tumor phenotype. The discovery and identification of gene variants has increased dramatically with the introduction of RNA-sequencing technology, which enables whole transcriptome analysis of known, as well as novel isoforms. Here we report alternative splicing and transcriptional events among subtypes of invasive ductal carcinoma in The Cancer Genome Atlas (TCGA) Breast Invasive Carcinoma (BRCA) cohort...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717044/congenital-myotonic-dystrophy-an-rna-mediated-disease-across-a-developmental-continuum
#7
REVIEW
Sujatha Jagannathan, Robert K Bradley
Thomas and colleagues (pp. 1122-1133) demonstrate severe dysregulation of developmentally regulated alternative splicing and polyadenylation in congenital myotonic dystrophy (CDM). In doing so, they also highlight the importance of these post-transcriptional processes during normal fetal muscle development. Finally, they generate and characterize a mouse model of CDM that lacks all three Muscleblind-like proteins.
June 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28716651/significance-of-a-to-i-rna-editing-of-transcripts-modulating-pharmacokinetics-and-pharmacodynamics
#8
REVIEW
Masataka Nakano, Miki Nakajima
RNA editing is a post-transcriptional process that alters the nucleotide sequence of RNA transcripts to generate transcriptome diversity. Among the various types of RNA editing, adenosine-to-inosine (A-to-I) RNA editing is the most frequent type of RNA editing in mammals. Adenosine deaminases acting on RNA (ADAR) enzymes, ADAR1 and ADAR2, convert adenosines in double-stranded RNA structures into inosines by hydrolytic deamination. Inosine forms a base pair with cytidine as if it were guanosine; therefore, the conversion may affect the amino acid sequence, splicing, microRNA targeting, and miRNA maturation...
July 14, 2017: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28716526/slc45a3-elk4-functions-as-a-long-non-coding-chimeric-rna
#9
Fujun Qin, Yanmei Zhang, Jia Liu, Hui Li
Gene fusions in cancer typically lead to the expression of a fusion protein or disrupt the expression of one of the parental genes. Here we report a new phenomenon whereby a fusion transcript functions as a long non-coding chimeric RNA (lnccRNA). This fusion RNA, SLC45A3-ELK4, generated by cis-splicing between neighboring genes, was found in prostate cancer. The fusion RNA encodes the same protein as ELK4. Intriguingly, we found that the fusion RNA level is less than 1% of wild type ELK4, unlikely to perturb the general pool of ELK4 protein...
July 14, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28714225/leveraging-splice-affecting-variant-predictors-and-a-minigene-validation-system-to-identify-mendelian-disease-causing-variants-amongst-exon-captured-variants-of-uncertain-significance
#10
Zachry T Soens, Justin Branch, Shijing Wu, Zhisheng Yuan, Yumei Li, Hui Li, Keqing Wang, Mingchu Xu, Lavan Rajan, Fabiana L Motta, Renata T Simões, Irma Lopez-Solache, Radwan Ajlan, David G Birch, Peiquan Zhao, Fernanda B Porto, Juliana Sallum, Robert K Koenekoop, Ruifang Sui, Rui Chen
The genetic heterogeneity of Mendelian disorders results in a significant proportion of patients that are unable to be assigned a confident molecular diagnosis after conventional exon sequencing and variant interpretation. Here we evaluated how many patients with an inherited retinal disease (IRD) have variants of uncertain significance (VUS's) that are disrupting splicing in a known IRD gene by means other than affecting the canonical dinucleotide splice site. Three in silico splice-affecting variant predictors were leveraged to annotate and prioritize variants for splicing functional validation...
July 17, 2017: Human Mutation
https://www.readbyqxmd.com/read/28712387/srsf2-directly-inhibits-intron-splicing-to-suppresses-cassette-exon-inclusion
#11
Heegyum Moon, Sunghee Cho, Tiing Jen Loh, Ha Na Jang, Yongchao Liu, Namjeong Choi, Jagyeong Oh, Jiyeon Ha, Jianhua Zhou, Sungchan Cho, Dong-Eun Kim, Michael B Ye, Xuexiu Zheng, Haihong Shen
SRSF2, a Serine-Arginine rich (SR) protein, is a splicing activator that mediates exon inclusion and exclusion events equally well. Here we show SRSF2 directly suppresses intron splicing to suppress cassette exon inclusion in SMN pre-mRNA. Through a serial mutagenesis, we demonstrate that a 10 nt RNA sequence surrounding the branch-point (BP), is important for SRSF2-mediated inhibition of cassette exon inclusion through directly interacting with SRSF2. We conclude that SRSF2 inhibits intron splicing to promote exon exclusion...
July 17, 2017: BMB Reports
https://www.readbyqxmd.com/read/28709000/regulatory-expansion-in-mammals-of-multivalent-hnrnp-assemblies-that-globally-control-alternative-splicing
#12
Serge Gueroussov, Robert J Weatheritt, Dave O'Hanlon, Zhen-Yuan Lin, Ashrut Narula, Anne-Claude Gingras, Benjamin J Blencowe
Alternative splicing (AS) patterns have diverged rapidly during vertebrate evolution, yet the functions of most species- and lineage-specific splicing events are not known. We observe that mammalian-specific AS events are enriched in transcript sequences encoding intrinsically disordered regions (IDRs) of proteins, in particular those containing glycine/tyrosine repeats that mediate formation of higher-order protein assemblies implicated in gene regulation and human disease. These evolutionary changes impact nearly all members of the hnRNP A and D families of RNA binding proteins...
July 13, 2017: Cell
https://www.readbyqxmd.com/read/28707655/-the-fus-protein-physiological-functions-and-a-role-in-amyotrophic-lateral-sclerosis
#13
A D Efimova, R K Ovchinnikov, A Yu Roman, A V Maltsev, V V Grigoriev, E A Kovrazhkina, V I Skvortsova
Certain forms of amyotrophic lateral sclerosis (ALS) are associated with an altered compartmentalization of FUS and its aggregation in the cytoplasm of motoneurons. FUS is a DNA/RNA-binding protein that is involved in DNA repair and the regulation of transcription, splicing, RNA transport, and local translation. Two theories have been proposed to explain the mechanism of the pathophysiological process in ALS. The theories attribute degeneration of motor neurons to either loss or gain of FUS function. The review describes the main physiological functions of FUS and considers evidence for each of the theories of ALS pathogenesis...
May 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28707092/the-determinants-of-alternative-rna-splicing-in-human-cells
#14
REVIEW
Tatsiana V Ramanouskaya, Vasily V Grinev
Alternative splicing represents an important level of the regulation of gene function in eukaryotic organisms. It plays a critical role in virtually every biological process within an organism, including regulation of cell division and cell death, differentiation of tissues in the embryo and the adult organism, as well as in cellular response to diverse environmental factors. In turn, studies of the last decade have shown that alternative splicing itself is controlled by different mechanisms. Unfortunately, there is no clear understanding of how these diverse mechanisms, or determinants, regulate and constrain the set of alternative RNA species produced from any particular gene in every cell of the human body...
July 13, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28706200/global-transcriptome-analysis-identifies-differentially-expressed-genes-related-to-lipid-metabolism-in-wagyu-and-holstein-cattle
#15
Wanlong Huang, Yuntao Guo, Weihua Du, Xiuxiu Zhang, Ai Li, Xiangyang Miao
Fat deposition of beef cattle varies between breeds. However, the regulation mechanism is still not elucidated completely at molecular level. In the present study, we comparatively analyzed transcriptome of subcutaneous adipose tissue between Wagyu and Holstein cattle with a significant difference in fat deposition to identify key genes associated with fat metabolism and adipogenesis by high-throughput RNA-seq technology. A total of 59,149,852 and 69,947,982 high quality reads were generated, respectively. With further analysis, 662 differentially expressed genes were identified...
July 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28705773/recent-progress-in-circular-rnas-in-human-cancers
#16
Guanqun Huang, Shuaihu Li, Nuo Yang, Yongdong Zou, Duo Zheng, Tian Xiao
Circular RNAs (circRNAs) are a large class of endogenous RNAs, formed by exon skipping or back-splicing events as covalently closed loops, which are expressed abundantly in mammalian cells. Although their biological functions remain largely unknown, recent studies show that circRNAs have three main functions in mammalian cells. First, circRNAs can regulate transcription and RNA splicing. Second, circRNAs function as microRNA (miRNA) sponges. Third, they can be translated into protein driven by N(6)-methyladenosine modification...
July 11, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28705764/a-survey-of-ddx21-activity-during-rev-rre-complex-formation
#17
John A Hammond, Li Zhou, Rajan Lamichhane, Hui-Yi Chu, David P Millar, Larry Gerace, James R Williamson
HIV-1 requires a specialized nuclear export pathway to transport unspliced and partially spliced viral transcripts to the cytoplasm. Central to this pathway is the viral protein Rev, which binds to the Rev response element in stem IIB located on unspliced viral transcripts and subsequently oligomerizes in a cooperative manner. Previous work identified a number of cellular DEAD-box helicases as in vivo binding partners of Rev, and siRNA experiments indicated a functional role for many in the HIV replication cycle...
July 10, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28702594/lpi-etslp-lncrna-protein-interaction-prediction-using-eigenvalue-transformation-based-semi-supervised-link-prediction
#18
Huan Hu, Chunyu Zhu, Haixin Ai, Li Zhang, Jian Zhao, Qi Zhao, Hongsheng Liu
RNA-protein interactions are essential for understanding many important cellular processes. In particular, lncRNA-protein interactions play important roles in post-transcriptional gene regulation, such as splicing, translation, signaling and even the progression of complex diseases. However, the experimental validation of lncRNA-protein interactions remains time-consuming and expensive, and only a few theoretical approaches are available for predicting potential lncRNA-protein associations. Here, we presented eigenvalue transformation-based semi-supervised link prediction (LPI-ETSLP) to uncover the relationship between lncRNAs and proteins...
July 12, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28701519/nineteen-complex-related-factor-prp45-is-required-for-the-early-stages-of-cotranscriptional-spliceosome-assembly
#19
Martina Hálová, Ondřej Gahura, Martin Převorovský, Zdeněk Cit, Marian Novotný, Anna Valentová, Kateřina Abrhámová, František Půta, Petr Folk
Splicing in S. cerevisiae has been shown to proceed cotranscriptionally, but the nature of the coupling remains a subject of debate. Here, we examine the effect of nineteen complex-related splicing factor Prp45 (a homolog of SNW1/SKIP) on cotranscriptional splicing. RNA-sequencing and RT-qPCR showed elevated pre-mRNA levels but only limited reduction of spliced mRNAs in cells expressing C-terminally truncated Prp45, Prp45(1-169). Assays with a series of reporters containing the AMA1 intron with regulatable splicing confirmed decreased splicing efficiency and showed the leakage of unspliced RNAs in prp45(1-169) cells...
July 12, 2017: RNA
https://www.readbyqxmd.com/read/28701145/an-in-vitro-technique-to-identify-the-rna-binding-site-sequences-for-rna-binding-proteins
#20
SunKyung Choi, Chungoo Park, Kyoon Eon Kim, Kee K Kim
RNA-protein interactions play a major role in gene regulation. Although many techniques to analyze RNA-protein interactions have been developed, noteworthy challenges such as determining the RNA sequences that bind RNA-binding proteins (RBPs) remain unsolved. Here, we describe a novel technique using a 4-thio-uridine-incorporated RNA pool to identify the RBP-binding consensus sequences for RBPs produced by in vitro transcription and translation. To confirm the fidelity of this approach, we determined the consensus RBP-binding sequence for RBFOX2, UGC(A/U)(A/U)NU, which is very similar to the known RBFOX2-binding sequence, UGCAUG...
July 1, 2017: BioTechniques
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