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Rna splicing

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https://www.readbyqxmd.com/read/28938739/sequence-variants-of-khdrbs1-as-high-penetrance-susceptibility-risks-for-primary-ovarian-insufficiency-by-mis-regulating-mrna-alternative-splicing
#1
Binbin Wang, Lin Li, Ying Zhu, Wei Zhang, Xi Wang, Beili Chen, Tengyan Li, Hong Pan, Jing Wang, Kehkooi Kee, Yunxia Cao
STUDY QUESTION: Does a novel heterozygous KHDRBS1 variant, identified using whole-exome sequencing (WES) in two patients with primary ovarian insufficiency (POI) in a pedigree, cause defects in mRNA alternative splicing? SUMMARY ANSWER: The heterozygous variant of KHDRBS1 was confirmed to cause defects in alternative splicing of many genes involved in DNA replication and repair. WHAT IS KNOWN ALREADY: Studies in mice revealed that Khdrbs1 deficient females are subfertile, which manifests as delayed sexual maturity and significantly reduced numbers of secondary and pre-antral follicles...
October 1, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28935721/the-spliceosomal-proteins-ppih-and-prpf4-exhibit-bipartite-binding
#2
Caroline Rajiv, S RaElle Jackson, Simon Cocklin, Elan Z Eisenmesser, Tara Davis
Pre-mRNA splicing is a dynamic, multi-step process that is catalyzed by the RNA: protein complex called the spliceosome. The spliceosome contains a core set of RNAs and proteins that are conserved in all organisms that perform splicing. In higher organisms, PPIH directly interacts with the core protein PRPF4 and both integrate into the pre-catalytic spliceosome as part of the tri-snRNP sub-complex. As a first step to understand the protein interactions that dictate PPIH and PRPF4 function, we expressed and purified soluble forms of each protein and formed a complex between them...
September 21, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28934506/clip-seq-analysis-of-multi-mapped-reads-discovers-novel-functional-rna-regulatory-sites-in-the-human-transcriptome
#3
Zijun Zhang, Yi Xing
Crosslinking or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-seq/RIP-seq reads are short, existing computational tools focus on uniquely mapped reads, while reads mapped to multiple loci are discarded. We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectation-maximization algorithm to assign multi-mapped reads and calls peaks combining uniquely and multi-mapped reads. To demonstrate the utility of CLAM, we applied it to a wide range of public CLIP-seq/RIP-seq datasets involving numerous splicing factors, microRNAs and m6A RNA methylation...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934490/number-of-inadvertent-rna-targets-for-morpholino-knockdown-in-danio-rerio-is-largely-underestimated-evidence-from-the-study-of-ser-arg-rich-splicing-factors
#4
Marine Joris, Marie Schloesser, Denis Baurain, Marc Hanikenne, Marc Muller, Patrick Motte
Although the involvement of Ser/Arg-rich (SR) proteins in RNA metabolism is well documented, their role in vertebrate development remains elusive. We, therefore, elected to take advantage of the zebrafish model organism to study the SR genes' functions using the splicing morpholino (sMO) microinjection and the programmable site-specific nucleases. Consistent with previous research, we revealed discrepancies between the mutant and morphant phenotypes and we show that these inconsistencies may result from a large number of unsuspected inadvertent morpholino RNA targets...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934473/the-conserved-au-dinucleotide-at-the-5-end-of-nascent-u1-snrna-is-optimized-for-the-interaction-with-nuclear-cap-binding-complex
#5
Chung-Shu Yeh, Shang-Lin Chang, Jui-Hui Chen, Hsuan-Kai Wang, Yue-Chang Chou, Chun-Hsiung Wang, Shih-Hsin Huang, Amy Larson, Jeffrey A Pleiss, Wei-Hau Chang, Tien-Hsien Chang
Splicing is initiated by a productive interaction between the pre-mRNA and the U1 snRNP, in which a short RNA duplex is established between the 5' splice site of a pre-mRNA and the 5' end of the U1 snRNA. A long-standing puzzle has been why the AU dincucleotide at the 5'-end of the U1 snRNA is highly conserved, despite the absence of an apparent role in the formation of the duplex. To explore this conundrum, we varied this AU dinucleotide into all possible permutations and analyzed the resulting molecular consequences...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934469/hnrnp-l-controls-hpv16-rna-polyadenylation-and-splicing-in-an-akt-kinase-dependent-manner
#6
Naoko Kajitani, Jacob Glahder, Chengjun Wu, Haoran Yu, Kersti Nilsson, Stefan Schwartz
Inhibition of the Akt kinase activates HPV16 late gene expression by reducing HPV16 early polyadenylation and by activating HPV16 late L1 mRNA splicing. We identified 'hot spots' for RNA binding proteins at the early polyA signal and at splice sites on HPV16 late mRNAs. We observed that hnRNP L was associated with sequences at all HPV16 late splice sites and at the early polyA signal. Akt kinase inhibition resulted in hnRNP L dephosphorylation and reduced association of hnRNP L with HPV16 mRNAs. This was accompanied by an increased binding of U2AF65 and Sam68 to HPV16 mRNAs...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934425/human-bocavirus-capsid-messenger-rna-detection-in-children-with-pneumonia
#7
Robert Schlaberg, Krow Ampofo, Keith D Tardif, Chris Stockmann, Keith E Simmon, Weston Hymas, Steven Flygare, Brett Kennedy, Anne Blaschke, Karen Eilbeck, Mark Yandell, Jon A McCullers, Derek J Williams, Kathryn Edwards, Sandra R Arnold, Anna Bramley, Seema Jain, Andrew T Pavia
Background: The role of human bocavirus (HBoV) in respiratory illness is uncertain. HBoV genomic DNA is frequently detected in both ill and healthy children. We hypothesized that spliced viral capsid messenger RNA (mRNA) produced during active replication might be a better marker for acute infection. Methods: As part of the Etiology of Pneumonia in the Community (EPIC) study, children aged <18 years who were hospitalized with community-acquired pneumonia (CAP) and children asymptomatic at the time of elective outpatient surgery (controls) were enrolled...
September 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28934014/nucleoplasmic-nup98-controls-gene-expression-by-regulating-a-dexh-d-box-protein
#8
Juliana S Capitanio, Ben Montpetit, Richard W Wozniak
The nucleoporin Nup98 has been linked to the regulation of transcription and RNA metabolism, (1-3) but the mechanisms by which Nup98 contributes to these processes remains largely undefined. Recently, we uncovered interactions between Nup98 and several DExH/D-box proteins (DBPs), a protein family well-known for modulating gene expression and RNA metabolism. (4-6) Analysis of Nup98 and one of these DBPs, DHX9, showed that they directly interact, their association is facilitated by RNA, and Nup98 binding stimulates DHX9 ATPase activity...
September 21, 2017: Nucleus
https://www.readbyqxmd.com/read/28933584/circular-rna-hsa_circ_0001982-promotes-breast-cancer-cell-carcinogenesis-through-decreasing-mir-143
#9
Yi-Yin Tang, Ping Zhao, Tian-Ning Zou, Jia-Jun Duan, Rong Zhi, Si-Yuan Yang, De-Chun Yang, Xiao-Li Wang
Circular RNAs (circRNAs) are a type of noncoding RNAs generated from back-splicing, which have been verified to mediate multiple tumorigenesis. With the development of high-throughput sequencing, massive circRNAs are discovered in tumorous tissue. However, the potential physiological effect of circRNAs in breast cancer is still unknown. The purpose of this study is to investigate the expression profile of circRNA in breast cancer tissue and explore the in-depth regulatory mechanism in breast cancer tumorigenesis...
September 21, 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/28932105/changes-in-alternative-splicing-as-pharmacodynamic-markers-for-sudemycin-d6
#10
Morgan Thurman, Jacob van Doorn, Barbara Danzer, Thomas R Webb, Stefan Stamm
OBJECTIVE: The aim of the study was to define pharmacodynamic markers for sudemycin D6, an experimental cancer drug that changes alternative splicing in human blood. METHODS: Blood samples from 12 donors were incubated with sudemycin D6 for up to 24 hours, and at several time points total RNA from lymphocytes was prepared and the pre-messenger RNA (mRNA) splicing patterns were analyzed with reverse transcription-polymerase chain reaction. RESULTS: Similar to immortalized cells, blood lymphocytes change alternative splicing due to sudemycin D6 treatment...
2017: Biomarker Insights
https://www.readbyqxmd.com/read/28927841/maternal-provision-of-transformer-2-is-required-for-female-development-and-embryo-viability-in-the-wasp-nasonia-vitripennis
#11
Elzemiek Geuverink, Anna H Rensink, Inge Rondeel, Leo W Beukeboom, Louis van de Zande, Eveline C Verhulst
In insect sex determination a primary signal starts the genetic sex determination cascade that, in most insect orders, is subsequently transduced down the cascade by a transformer (tra) ortholog. Only a female-specifically spliced tra mRNA yields a functional TRA-protein that forms a complex with TRA2, encoded by a transformer-2 (tra2) ortholog, to act as a sex specific splicing regulator of the downstream transcription factors doublesex (dsx) and fruitless (fru). Here, we identify the tra2 ortholog of the haplodiploid parasitoid wasp N...
September 16, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28927534/alternative-rna-splicing-and-gastric-cancer
#12
REVIEW
Ying Li, Yuan Yuan
Alternative splicing (AS) linked to diseases, especially to tumors. Recently, more and more studies focused on the relationship between AS and gastric cancer (GC). This review surveyed the hot topic from four aspects: First, the common types of AS in cancer, including exon skipping, intron retention, mutually exclusive exon, alternative 5 ' or 3' splice site, alternative first or last exon and alternative 3' untranslated regions. Second, basic mechanisms of AS and its relationship with cancer. RNA splicing in eukaryotes follows the GT-AG rule by both cis-elements and trans-acting factors regulatory...
July 2017: Mutation Research
https://www.readbyqxmd.com/read/28927531/discriminating-rna-variants-with-single-molecule-allele-specific-fish
#13
REVIEW
Martyna O Urbanek, Wlodzimierz J Krzyzosiak
DNA mutations of various types often affect the cellular localization and function of gene products. The role of mutant transcripts in the pathogenesis of human disease is increasingly recognized. Among the pathogenic RNA variants are transcripts with single nucleotide substitutions, small insertions or deletions, aberrantly or alternatively spliced transcripts and RNAs derived from fused genes. To discriminate among transcripts, particularly those of low abundance, showing small or large sequence differences, a highly sensitive and specific RNA imaging method is required...
July 2017: Mutation Research
https://www.readbyqxmd.com/read/28923960/igh-isotype-specific-b-cell-receptor-expression-influences-b-cell-fate
#14
Pei Tong, Alessandra Granato, Teng Zuo, Neha Chaudhary, Adam Zuiani, Seung Seok Han, Rakesh Donthula, Akritee Shrestha, Debattama Sen, Jennifer M Magee, Michael P Gallagher, Cees E van der Poel, Michael C Carroll, Duane R Wesemann
Ig heavy chain (IgH) isotypes (e.g., IgM, IgG, and IgE) are generated as secreted/soluble antibodies (sIg) or as membrane-bound (mIg) B cell receptors (BCRs) through alternative RNA splicing. IgH isotype dictates soluble antibody function, but how mIg isotype influences B cell behavior is not well defined. We examined IgH isotype-specific BCR function by analyzing naturally switched B cells from wild-type mice, as well as by engineering polyclonal Ighγ1/γ1 and Ighε/ε mice, which initially produce IgG1 or IgE from their respective native genomic configurations...
September 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28920960/long-noncoding-rna-egfr-as1-mediates-epidermal-growth-factor-receptor-addiction-and-modulates-treatment-response-in-squamous-cell-carcinoma
#15
Daniel S W Tan, Fui Teen Chong, Hui Sun Leong, Shen Yon Toh, Dawn P Lau, Xue Lin Kwang, Xiaoqian Zhang, Gopinath M Sundaram, Gek San Tan, Mei Mei Chang, Boon Tin Chua, Wan Teck Lim, Eng Huat Tan, Mei Kim Ang, Tony K H Lim, Prabha Sampath, Balram Chowbay, Anders J Skanderup, Ramanuj DasGupta, N Gopalakrishna Iyer
Targeting EGFR is a validated approach in the treatment of squamous-cell cancers (SCCs), although there are no established biomarkers for predicting response. We have identified a synonymous mutation in EGFR, c.2361G>A (encoding p.Gln787Gln), in two patients with head and neck SCC (HNSCC) who were exceptional responders to gefitinib, and we showed in patient-derived cultures that the A/A genotype was associated with greater sensitivity to tyrosine kinase inhibitors (TKIs) as compared to the G/A and G/G genotypes...
September 18, 2017: Nature Medicine
https://www.readbyqxmd.com/read/28919899/emerging-roles-and-landscape-of-translating-mrnas-in-plants
#16
REVIEW
Gaurav Sablok, Jonathan J Powell, Kemal Kazan
Plants use a wide range of mechanisms to adapt to different environmental stresses. One of the earliest responses displayed under stress is rapid alterations in stress responsive gene expression that has been extensively analyzed through expression profiling such as microarrays and RNA-sequencing. Recently, expression profiling has been complemented with proteome analyses to establish a link between transcriptional and the corresponding translational changes. However, proteome profiling approaches have their own technical limitations...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28919308/alternative-splicing-in-cancers-from-aberrant-regulation-to-new-therapeutics
#17
REVIEW
Xiaowei Song, Zhenyu Zeng, Huanhuan Wei, Zefeng Wang
Alternative splicing is one of the most common mechanisms for gene regulation in humans, and plays a vital role to increase the complexity of functional proteins. In this article, we seek to provide a general review on the relationships between alternative splicing and tumorigenesis. We briefly introduce the basic rules for regulation of alternative splicing, and discuss recent advances on dynamic regulation of alternative splicing in cancers by highlighting the roles of a variety of RNA splicing factors in tumorigenesis...
September 14, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28919079/structure-of-an-intron-lariat-spliceosome-from-saccharomyces-cerevisiae
#18
Ruixue Wan, Chuangye Yan, Rui Bai, Jianlin Lei, Yigong Shi
The disassembly of the intron lariat spliceosome (ILS) marks the end of a splicing cycle. Here we report a cryoelectron microscopy structure of the ILS complex from Saccharomyces cerevisiae at an average resolution of 3.5 Å. The intron lariat remains bound in the spliceosome whereas the ligated exon is already dissociated. The step II splicing factors Prp17 and Prp18, along with Cwc21 and Cwc22 that stabilize the 5' exon binding to loop I of U5 small nuclear RNA (snRNA), have been released from the active site assembly...
September 21, 2017: Cell
https://www.readbyqxmd.com/read/28918420/computer-analysis-of-glioma-transcriptome-profiling-alternative-splicing-events
#19
Vladimir N Babenko, Natalya V Gubanova, Anatoly O Bragin, Irina V Chadaeva, Gennady V Vasiliev, Irina V Medvedeva, Alexey S Gaytan, Alexey L Krivoshapkin, Yuriy L Orlov
Here we present the analysis of alternative splicing events on an example of glioblastoma cell culture samples using a set of computer tools in combination with database integration. The gene expression profiles of glioblastoma were obtained from cell culture samples of primary glioblastoma which were isolated and processed for RNA extraction. Transcriptome profiling of normal brain samples and glioblastoma were done by Illumina sequencing. The significant differentially expressed exon-level probes and their corresponding genes were identified using a combination of the splicing index method...
September 18, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28917667/amyloid-%C3%AE-42-clearance-and-neuroprotection-mediated-by-x-box-binding-protein-1-signaling-decline-with-aging-in-the-drosophila-brain
#20
María S Marcora, Lautaro F Belfiori-Carrasco, Nadia I Bocai, Laura Morelli, Eduardo M Castaño
The unfolded protein response (UPR) may be pathogenically related to Alzheimer's disease. Yet, the effects of chronic amyloid-β42 (Aβ42) accumulation and UPR activation upon neurotoxicity remain unclear. Here, we show that neuronal Aβ42 expression in Drosophila activated the inositol-requiring protein-1/X-box binding protein 1 (XBP1) UPR branch before the onset of behavioral impairment and persisted with aging. Early upregulation of hsc3/BiP, a target of XBP1 and activating transcription factor 6 pathways, was also sustained in old animals...
August 24, 2017: Neurobiology of Aging
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