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Rna splicing

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https://www.readbyqxmd.com/read/28811565/iss-pc-identifying-splicing-sites-via-physical-chemical-properties-using-deep-sparse-auto-encoder
#1
Zhao-Chun Xu, Peng Wang, Wang-Ren Qiu, Xuan Xiao
Gene splicing is one of the most significant biological processes in eukaryotic gene expression, such as RNA splicing, which can cause a pre-mRNA to produce one or more mature messenger RNAs containing the coded information with multiple biological functions. Thus, identifying splicing sites in DNA/RNA sequences is significant for both the bio-medical research and the discovery of new drugs. However, it is expensive and time consuming based only on experimental technique, so new computational methods are needed...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28810637/binding-of-line-1-rna-to-psf-transcriptionally-promotes-gage6-and-regulates-cell-proliferation-and-tumor-formation-in-vitro
#2
Jiao Lv, Ziyi Zhao
Hepatocellular carcinoma (HCC) has one of the highest mortality rates among numerous types of cancer. It has been demonstrated that in hepatitis B (HBV)-associated HCC, the expression of chimeric fusion transcript HBx-long interspersed nuclear element-1 (LINE-1) initiated by HBV integration is correlated with hepatocarcinogenesis and poor patient survival rates. Furthermore, increased rates of LINE-1 hypomethylation have been detected in HCC tissues compared with adjacent tissues. This suggests that individual LINE-1 RNA (L1 RNA) serves an important role in the processes of hepatocarcinogenesis...
August 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28808137/regulatory-rnps-a-novel-class-of-ribonucleoproteins-that-potentially-contribute-to-ribosome-heterogeneity
#3
Aaron R Poole, Ian Vicino, Hironori Adachi, Yi-Tao Yu, Michael D Hebert
Many ribonucleoproteins (RNPs), which are comprised of non-coding RNA and associated proteins, are involved in essential cellular processes such as translation and pre-mRNA splicing. One class of RNP is the small Cajal body-specific RNP (scaRNP), which contributes to the biogenesis of small nuclear RNPs (snRNPs) that are central components of the spliceosome. Three scaRNAs are internally processed, generating stable nucleolus-enriched RNAs of unknown function. Here we provide data that these RNAs become part of RNPs we term regulatory RNPs (regRNPs)...
August 14, 2017: Biology Open
https://www.readbyqxmd.com/read/28803727/elimination-of-toxic-microsatellite-repeat-expansion-rna-by-rna-targeting-cas9
#4
Ranjan Batra, David A Nelles, Elaine Pirie, Steven M Blue, Ryan J Marina, Harrison Wang, Isaac A Chaim, James D Thomas, Nigel Zhang, Vu Nguyen, Stefan Aigner, Sebastian Markmiller, Guangbin Xia, Kevin D Corbett, Maurice S Swanson, Gene W Yeo
Microsatellite repeat expansions in DNA produce pathogenic RNA species that cause dominantly inherited diseases such as myotonic dystrophy type 1 and 2 (DM1/2), Huntington's disease, and C9orf72-linked amyotrophic lateral sclerosis (C9-ALS). Means to target these repetitive RNAs are required for diagnostic and therapeutic purposes. Here, we describe the development of a programmable CRISPR system capable of specifically visualizing and eliminating these toxic RNAs. We observe specific targeting and efficient elimination of microsatellite repeat expansion RNAs both when exogenously expressed and in patient cells...
August 8, 2017: Cell
https://www.readbyqxmd.com/read/28802831/validation-of-a-targeted-rna-sequencing-assay-for-kinase-fusion-detection-in-solid-tumors
#5
Julie W Reeser, Dorrelyn Martin, Jharna Miya, Esko A Kautto, Ezra Lyon, Eliot Zhu, Michele R Wing, Amy Smith, Matthew Reeder, Eric Samorodnitsky, Hannah Parks, Karan R Naik, Joseph Gozgit, Nicholas Nowacki, Kurtis D Davies, Marileila Varella-Garcia, Lianbo Yu, Aharon G Freud, Joshua Coleman, Dara L Aisner, Sameek Roychowdhury
Kinase gene fusions are important drivers of oncogenic transformation and can be inhibited with targeted therapies. Clinical grade diagnostics using RNA sequencing to detect gene rearrangements in solid tumors are limited, and the few that are available require prior knowledge of fusion break points. To address this, we have analytically validated a targeted RNA sequencing assay (OSU-SpARKFuse) for fusion detection that interrogates complete transcripts from 93 kinase and transcription factor genes. From a total of 74 positive and 36 negative control samples, OSU-SpARKFuse had 93...
August 8, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28800773/rattus-norvegicus-bn-shr-liver-and-heart-left-ventricle-ribosomal-rna-depleted-directional-rna-sequencing
#6
Emanuel Wyler, Sebastiaan van Heesch, Eleonora Adami, Norbert Hubner, Markus Landthaler
OBJECTIVE: The spontaneously hypertensive rat strain is a frequently used disease model. In a previous study, we measured translational efficiency from this strain and BN-Lx animals. Here, we describe long RNA sequencing reads from ribosomal RNA depleted samples from the same animals. This data can be used to investigate splicing-related events. RESULTS: RNA was extracted from rat liver and heart left ventricle from BN-Lx and SHR/Ola rats in biological replicates...
August 11, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28800125/large-introns-of-5-to-10-kilo-base-pairs-can-be-spliced-out-in-arabidopsis
#7
Ning Chang, Qingqing Sun, Jinglei Hu, Chuanjing An, And Hongbo Gao
Most of the eukaryotic genes contain introns, which are removed from the pre-RNA during RNA processing. In contrast to the introns in animals, which are usually several kilo base pairs (kb), those in plants generally are very small, which are mostly from dozens of base pairs (bp) to a few hundred bp. According to annotation version 10.0 of the genome of Arabidopsis thaliana, there are 127,854 introns in the nuclear genes; 99.23% of them are less than 1 kb, and only 16 introns are annotated to be larger than 5 kb, which are extremely large introns (ELI) in Arabidopsis...
August 11, 2017: Genes
https://www.readbyqxmd.com/read/28798494/identification-and-functional-characterization-of-the-sex-determining-gene-doublesex-in-the-sawfly-athalia-rosae%C3%A2-hymenoptera-tenthredinidae
#8
Shotaro Mine, Megumi Sumitani, Fugaku Aoki, Masatsugu Hatakeyama, Masataka G Suzuki
Sexual fate of the sawfly, Athalia rosae (Hymenoptera: Tenthredinidae) is determined by the complementary sex determination (CSD) mechanism as is the case in honeybees. However, to date, genes involved in sex determination have not been identified in this species. In this study, we attempted to identify orthologs of complementary sex-determiner (csd), feminizer (fem), and doublesex (dsx) from the A. rosae genome, all of which are crucial components of the sex determination cascade in the honeybee. As a result, we identified a sawfly ortholog of dsx (designated as Ardsx)...
2017: Applied Entomology and Zoology
https://www.readbyqxmd.com/read/28794490/a-transcriptome-atlas-of-rabbit-revealed-by-pacbio-single-molecule-long-read-sequencing
#9
Shi-Yi Chen, Feilong Deng, Xianbo Jia, Cao Li, Song-Jia Lai
It is widely acknowledged that transcriptional diversity largely contributes to biological regulation in eukaryotes. Since the advent of second-generation sequencing technologies, a large number of RNA sequencing studies have considerably improved our understanding of transcriptome complexity. However, it still remains a huge challenge for obtaining full-length transcripts because of difficulties in the short read-based assembly. In the present study we employ PacBio single-molecule long-read sequencing technology for whole-transcriptome profiling in rabbit (Oryctolagus cuniculus)...
August 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28792005/splicing-and-transcription-touch-base-co-transcriptional-spliceosome-assembly-and-function
#10
REVIEW
Lydia Herzel, Diana S M Ottoz, Tara Alpert, Karla M Neugebauer
Several macromolecular machines collaborate to produce eukaryotic messenger RNA. RNA polymerase II (Pol II) translocates along genes that are up to millions of base pairs in length and generates a flexible RNA copy of the DNA template. This nascent RNA harbours introns that are removed by the spliceosome, which is a megadalton ribonucleoprotein complex that positions the distant ends of the intron into its catalytic centre. Emerging evidence that the catalytic spliceosome is physically close to Pol II in vivo implies that transcription and splicing occur on similar timescales and that the transcription and splicing machineries may be spatially constrained...
August 9, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/28791797/emerging-roles-of-hnrnpa1-in-modulating-malignant-transformation
#11
REVIEW
Rajat Roy, Yueyang Huang, Michael J Seckl, Olivier E Pardo
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are RNA-binding proteins associated with complex and diverse biological processes such as processing of heterogeneous nuclear RNAs (hnRNAs) into mature mRNAs, RNA splicing, transactivation of gene expression, and modulation of protein translation. hnRNPA1 is the most abundant and ubiquitously expressed member of this protein family and has been shown to be involved in multiple molecular events driving malignant transformation. In addition to selective mRNA splicing events promoting expression of specific protein variants, hnRNPA1 regulates the gene expression and translation of several key players associated with tumorigenesis and cancer progression...
August 8, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28790308/transcriptome-profiling-of-mouse-brains-with-qki-deficient-oligodendrocytes-reveals-major-alternative-splicing-defects-including-self-splicing
#12
Lama Darbelli, Karine Choquet, Stéphane Richard, Claudia L Kleinman
The qkI gene encodes a family of RNA binding proteins alternatively spliced at its 3' end, giving rise to three major spliced isoforms: QKI-5, QKI-6 and QKI-7. Their expression is tightly regulated during brain development with nuclear QKI-5 being the most abundant during embryogenesis followed by QKI-6 and QKI-7 that peak during myelination. Previously, we generated a mouse conditional qkI allele where exon 2 is excised using Olig2-Cre resulting in QKI-deficient oligodendrocytes (OLs). These mice have dysmyelination and die at the third post-natal week...
August 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28790111/amiloride-an-old-diuretic-drug-is-a-potential-therapeutic-agent-for-multiple-myeloma
#13
Elizabeta Rojas, Luis Corchete, Laura San Segundo, Juan F Martínez-Blanch, Francisco M Codoñer, Teresa Paíno, Noemi Puig, Ramón García-Sanz, Maria Victoria Mateos, Enrique M Ocio, Irena Misiewicz-Krzeminska, Norma C Gutiérrez
<br />The search for new drugs that control the continuous relapses of multiple myeloma is still required. Here, we report for the first time the potent anti-myeloma activity of amiloride, an old potassium-sparing diuretic approved for the treatment of hypertension and edema due to heart failure.<br /><br />Experimental Design:  <p>Myeloma cell lines and primary samples were used to evaluate cytotoxicity of amiloride. In vivo studies were carried out in a xenograft mouse model. The mechanisms of action were investigated using RNA-Seq, qRT-PCR, immunoblotting and immunofluorescence assays...
August 8, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28789987/regulation-of-splicing-and-circularisation-of-rna-in-epithelial-mesenchymal-plasticity
#14
REVIEW
Daniel P Neumann, Gregory J Goodall, Philip A Gregory
Interconversions between epithelial and mesenchymal states, often referred to as epithelial mesenchymal transition (EMT) and its reverse MET, play important roles in embryonic development and are recapitulated in various adult pathologies including cancer progression. These conversions are regulated by complex transcriptional and post-transcriptional mechanisms including programs of alternative splicing which are orchestrated by specific splicing factors. This review will focus on the latest developments in our understanding of the splicing factors regulating epithelial mesenchymal plasticity associated with cancer progression and the induction of pluripotency, including potential roles for circular RNAs (circRNAs) which have been recently implicated in these processes...
August 5, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28789862/genome-wide-identification-and-characterization-of-putative-lncrnas-in-the-diamondback-moth-plutella-xylostella-l
#15
Yue Wang, Tingting Xu, Weiyi He, Xiujing Shen, Qian Zhao, Jianlin Bai, Minsheng You
Long non-coding RNAs (lncRNAs) are of particular interest because of their contributions to many biological processes. Here, we present the genome-wide identification and characterization of putative lncRNAs in a global insect pest, Plutella xylostella. A total of 8096 lncRNAs were identified and classified into three groups. The average length of exons in lncRNAs was longer than that in coding genes and the GC content was lower than that in mRNAs. Most lncRNAs were flanked by canonical splice sites, similar to mRNAs...
August 5, 2017: Genomics
https://www.readbyqxmd.com/read/28789596/circular-rna-hsa_circ_0001564-facilitates-tumorigenesis-of-osteosarcoma-via-sponging-mir-29c-3p
#16
Ji-Feng Li, Yu-Ze Song
Circular RNAs are a novel type of non-coding RNAs generated from back splicing, which has been verified to mediate multiple tumorigenesis. However, the role of circular RNA in osteosarcoma is still unclear. In this study, we preliminarily screened the circular RNAs expression profiles in osteosarcoma and investigated the potential regulation mechanism. The circular RNAs expression profiles in osteosarcoma were screened using circular RNA microarray analysis, and results showed that there were 1152 circular RNAs upregulated and 915 circular RNAs downregulated in tumor tissue compared to adjacent tissue...
August 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28783698/maintenance-of-macrophage-transcriptional-programs-and-intestinal-homeostasis-by-epigenetic-reader-sp140
#17
Stuti Mehta, D Alexander Cronkite, Megha Basavappa, Tahnee L Saunders, Fatemeh Adiliaghdam, Hajera Amatullah, Sara A Morrison, Jose D Pagan, Robert M Anthony, Pierre Tonnerre, Georg M Lauer, James C Lee, Sreehaas Digumarthi, Lorena Pantano, Shannan J Ho Sui, Fei Ji, Ruslan Sadreyev, Chan Zhou, Alan C Mullen, Vinod Kumar, Yang Li, Cisca Wijmenga, Ramnik J Xavier, Terry K Means, Kate L Jeffrey
Epigenetic "readers" that recognize defined posttranslational modifications on histones have become desirable therapeutic targets for cancer and inflammation. SP140 is one such bromodomain- and plant homeodomain (PHD)-containing reader with immune-restricted expression, and single-nucleotide polymorphisms (SNPs) within SP140 associate with Crohn's disease (CD). However, the function of SP140 and the consequences of disease-associated SP140 SNPs have remained unclear. We show that SP140 is critical for transcriptional programs that uphold the macrophage state...
March 3, 2017: Science Immunology
https://www.readbyqxmd.com/read/28782559/trap-seq-an-rna-sequencing-based-pipeline-for-the-identification-of-genetrap-insertions-in-mammalian-cells
#18
Cristina Mayor-Ruiz, Orlando Dominguez, Oscar Fernandez-Capetillo
The development of haploid mammalian cell lines, coupled to next generation sequencing, has recently facilitated forward genetic screenings in mammals. For mutagenesis, retrovirus- or transposon-based genetraps are frequently used. Current methods to map genetrap insertions are based on inverse- or splinkerette-PCR, which despite their efficacy are prone to artifacts and do not provide information about expression of the targeted gene. Here, we describe a new RNA-sequencing based method (Trap(Seq)) to map genetrap insertions...
August 4, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28776911/long-non-coding-rnas-as-an-epigenetic-regulator-in-human-cancers
#19
REVIEW
Yutaka Kondo, Keiko Shinjo, Keisuke Katsushima
Recent studies have demonstrated the important multiple roles of long non-coding RNAs (lncRNAs) during oncogenic transformation. Because the coding genome accounts for a small amount of total DNA, and many mutations leading to cancer occur in the non-coding genome, it is plausible that the dysregulation of such non-coding transcribes might also affect tumor phenotypes. Indeed, to date, lncRNAs have been reported to affect diverse biological processes through the regulation of mRNA stability, RNA splicing, chromatin structure, and miRNA-mediated gene regulation by acting as miRNA sponges...
August 4, 2017: Cancer Science
https://www.readbyqxmd.com/read/28776436/chimeric-nup98-nsd1-transcripts-from-the-cryptic-t-5-11-q35-2-p15-4-in-adult-de-novo-acute-myeloid-leukemia
#20
Jarno L Kivioja, Jesus M Lopez Martí, Ashwini Kumar, Mika Kontro, Henrik Edgren, Alun Parsons, Tuija Lundán, Maija Wolf, Kimmo Porkka, Caroline A Heckman
The t(5;11)(q35;p15.4) is a clinically significant marker of poor prognosis in acute myeloid leukemia (AML), which is difficult to detect due to sub-telomeric localization of the breakpoints. To facilitate the detection of this rearrangement, we studied NUP98-NSD1 transcript variants in patients with the t(5;11) using paired-end RNA sequencing and standard molecular biology techniques. We discovered three NUP98-NSD1 transcripts with two fusion junctions (NUP98 exon 11-12/NSD1 exon 6), alternative 5' donor site in NUP98 exon 7, and NSD1 exon 7 skipping...
August 4, 2017: Leukemia & Lymphoma
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