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exon junction complex

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https://www.readbyqxmd.com/read/29153833/structure-of-the-post-catalytic-spliceosome-from-saccharomyces-cerevisiae
#1
Rui Bai, Chuangye Yan, Ruixue Wan, Jianlin Lei, Yigong Shi
Removal of an intron from a pre-mRNA by the spliceosome results in the ligation of two exons in the post-catalytic spliceosome (known as the P complex). Here, we present a cryo-EM structure of the P complex from Saccharomyces cerevisiae at an average resolution of 3.6 Å. The ligated exon is held in the active site through RNA-RNA contacts. Three bases at the 3' end of the 5' exon remain anchored to loop I of U5 small nuclear RNA, and the conserved AG nucleotides of the 3'-splice site (3'SS) are specifically recognized by the invariant adenine of the branch point sequence, the guanine base at the 5' end of the 5'SS, and an adenine base of U6 snRNA...
November 4, 2017: Cell
https://www.readbyqxmd.com/read/29151891/the-exon-junction-complex-factor-y14-is-dynamic-in-the-nucleus-of-the-beetle-tribolium-castaneum-during-late-oogenesis
#2
Artem M Kiselev, Irina S Stepanova, Leonid S Adonin, Florina M Batalova, Vladimir N Parfenov, Dmitry S Bogolyubov, Olga I Podgornaya
Background: The oocyte chromosomes of the red flour beetle, Tribolium castaneum, are gathered into a knot, forming a karyosphere at the diplotene stage of meiotic prophase. Chromatin rearrangement, which is a characteristic feature of oocyte maturation, is well documented. The T. castaneum karyosphere is surrounded by a complex extrachromosomal structure termed the karyosphere capsule. The capsule contains the vast majority of oocyte RNA. We have previously shown using a BrUTP assay that oocyte chromosomes in T...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/29052934/the-contribution-of-alternative-splicing-to-genetic-risk-for-psychiatric-disorders
#3
REVIEW
Emma Reble, Aidan Dineen, Cathy L Barr
A genetic contribution to psychiatric disorders has clearly been established and genome-wide association studies now provide the location of risk genes and genetic variants associated with risk. However, the mechanism by which these genes and variants contribute to psychiatric disorders is mostly undetermined. This is in part because non-synonymous protein coding changes cannot explain the majority of variants associated with complex genetic traits. Based on this, it is predicted that these variants are causing gene expression changes, including changes to alternative splicing...
October 20, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/28986317/acute-hypoxia-stress-induced-abundant-differential-expression-genes-and-alternative-splicing-events-in-heart-of-tilapia
#4
Jun Hong Xia, Hong Lian Li, Bi Jun Li, Xiao Hui Gu, Hao Ran Lin
Hypoxia is one of the critical environmental stressors for fish in aquatic environments. Although accumulating evidences indicate that gene expression is regulated by hypoxia stress in fish, how genes undergoing differential gene expression and/or alternative splicing (AS) in response to hypoxia stress in heart are not well understood. Using RNA-seq, we surveyed and detected 289 differential expressed genes (DEG) and 103 genes that undergo differential usage of exons and splice junctions events (DUES) in heart of a hypoxia tolerant fish, Nile tilapia, Oreochromis niloticus following 12h hypoxic treatment...
October 3, 2017: Gene
https://www.readbyqxmd.com/read/28924040/a-b-z-junction-induced-by-an-a-a-mismatch-in-gac-repeats-in-the-gene-for-cartilage-oligomeric-matrix-protein-promotes-binding-with-the-hz%C3%AE-adar1-protein
#5
Narendar Kolimi, Yogeeshwar Ajjugal, Thenmalarchelvi Rathinavelan
GAC repeat expansion from five to seven in the exonic region of the gene for cartilage oligomeric matrix protein (COMP) leads to pseudoachondroplasia, a skeletal abnormality. However, the molecular mechanism by which GAC expansions in the COMP gene lead to skeletal dysplasias is poorly understood. Here, we used MD simulations which indicate that an A...A mismatch in a d(GAC)6.d(GAC)6 duplex induces negative supercoiling, leading to a local B-to-Z DNA transition. This transition facilitates the binding of d(GAC)7...
September 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28895891/alignment-of-mitotic-chromosomes-in-human-cells-involves-sr-like-splicing-factors-btf-and-trap150
#6
Sapna Varia, Divya Cheedu, Michael Markey, Keshia Torres-Shafer, Vishnu Priya Battini, Athanasios Bubulya, Paula A Bubulya
Serine-arginine-rich (SR) or SR-like splicing factors interact with exon junction complex proteins during pre-mRNA processing to promote mRNA packaging into mature messenger ribonucleoproteins (mRNPs) and to dictate mRNA stability, nuclear export, and translation. The SR protein family is complex, and while many classical SR proteins have well-defined mRNA processing functions, those of other SR-like proteins is unclear. Here, we show that depletion of the homologous non-classical serine-arginine-rich (SR) splicing factors Bcl2-associated transcription factor (Btf or BCLAF) and thyroid hormone receptor-associated protein of 150 kDa (TRAP150) causes mitotic defects...
September 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28874828/srsf1-suppresses-selection-of-intron-distal-5-splice-site-of-dok7-intron-4-to-generate-functional-full-length-dok-7-protein
#7
Khalid Bin Ahsan, Akio Masuda, Mohammad Alinoor Rahman, Jun-Ichi Takeda, Mohammad Nazim, Bisei Ohkawara, Mikako Ito, Kinji Ohno
Dok-7 is a non-catalytic adaptor protein that facilitates agrin-induced clustering of acetylcholine receptors (AChR) at the neuromuscular junction. Alternative selection of 5' splice sites (SSs) of DOK7 intron 4 generates canonical and frame-shifted transcripts. We found that the canonical full-length Dok-7 enhanced AChR clustering, whereas the truncated Dok-7 did not. We identified a splicing cis-element close to the 3' end of exon 4 by block-scanning mutagenesis. RNA affinity purification and mass spectrometry revealed that SRSF1 binds to the cis-element...
September 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28776093/identification-of-an-atypical-microdeletion-generating-the-rnf135-suz12-chimeric-gene-and-causing-a-position-effect-in-an-nf1-patient-with-overgrowth
#8
Luca Ferrari, Giulietta Scuvera, Arianna Tucci, Donatella Bianchessi, Francesco Rusconi, Francesca Menni, Elena Battaglioli, Donatella Milani, Paola Riva
Neurofibromatosis type I (NF1) microdeletion syndrome, which is present in 4-11% of NF1 patients, is associated with a severe phenotype as it is caused by the deletion of NF1 and other genes in the 17q11.2 region. The variable expressivity of the disease makes it challenging to establish genotype-phenotype correlations, which also affects prognosis and counselling. We here describe a 3-year-old NF1 patient with an atypical deletion and a complex phenotype. The patient showed overgrowth, café au lait spots, inguinal freckling, and neurological abnormalities...
October 2017: Human Genetics
https://www.readbyqxmd.com/read/28653984/multiple-isoforms-of-anril-in-melanoma-cells-structural-complexity-suggests-variations-in-processing
#9
Debina Sarkar, Ali Oghabian, Pasani K Bodiyabadu, Wayne R Joseph, Euphemia Y Leung, Graeme J Finlay, Bruce C Baguley, Marjan E Askarian-Amiri
The long non-coding RNA ANRIL, antisense to the CDKN2B locus, is transcribed from a gene that encompasses multiple disease-associated polymorphisms. Despite the identification of multiple isoforms of ANRIL, expression of certain transcripts has been found to be tissue-specific and the characterisation of ANRIL transcripts remains incomplete. Several functions have been associated with ANRIL. In our judgement, studies on ANRIL functionality are premature pending a more complete appreciation of the profusion of isoforms...
June 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28637711/the-exon-junction-complex-and-srp54-contribute-to-hedgehog-signaling-via-ci-rna-splicing-in-drosophila-melanogaster
#10
Elisa Garcia-Garcia, Jamie C Little, Daniel Kalderon
Hedgehog (Hh) regulates the Cubitus interruptus (Ci) transcription factor in Drosophila melanogaster by activating full-length Ci-155 and blocking processing to the Ci-75 repressor. However, the interplay between the regulation of Ci-155 levels and activity, as well as processing-independent mechanisms that affect Ci-155 levels, have not been explored extensively. Here, we identified Mago Nashi (Mago) and Y14 core Exon Junction Complex (EJC) proteins, as well as the Srp54 splicing factor, as modifiers of Hh pathway activity under sensitized conditions...
August 2017: Genetics
https://www.readbyqxmd.com/read/28623893/evolutionary-origin-of-type-iv-classical-cadherins-in-arthropods
#11
Mizuki Sasaki, Yasuko Akiyama-Oda, Hiroki Oda
BACKGROUND: Classical cadherins are a metazoan-specific family of homophilic cell-cell adhesion molecules that regulate morphogenesis. Type I and type IV cadherins in this family function at adherens junctions in the major epithelial tissues of vertebrates and insects, respectively, but they have distinct, relatively simple domain organizations that are thought to have evolved by independent reductive changes from an ancestral type III cadherin, which is larger than derived paralogs and has a complicated domain organization...
June 17, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28566540/the-exon-junction-complex-senses-energetic-stress-and-regulates-contractility-and-cell-architecture-in-cardiac-myocytes
#12
Olivier A Pierrat, Anju Paudyal, James Woodruff, Olga Koroleva, Samuel Boateng
The Exon Junction Complex (EJC) is the main mechanism by which cells select specific mRNAs for translation into protein. We hypothesised that the EJC is involved in the regulation of gene expression during the stress response in cardiac myocytes, with implications for the failing heart. In cultured rat neonatal myocytes, we examined the cellular distribution of two EJC components eIF4A3 and mago nashi homologue (Mago) in response to metabolic stress. There was significant relocalisation of eIF4A3 and Mago from the nucleus to cytoplasm following 18 hours of hypoxia...
May 31, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28539927/a-comprehensive-analysis-of-alternative-splicing-in-paleopolyploid-maize
#13
Wenbin Mei, Sanzhen Liu, James C Schnable, Cheng-Ting Yeh, Nathan M Springer, Patrick S Schnable, William B Barbazuk
Identifying and characterizing alternative splicing (AS) enables our understanding of the biological role of transcript isoform diversity. This study describes the use of publicly available RNA-Seq data to identify and characterize the global diversity of AS isoforms in maize using the inbred lines B73 and Mo17, and a related species, sorghum. Identification and characterization of AS within maize tissues revealed that genes expressed in seed exhibit the largest differential AS relative to other tissues examined...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28539829/multifaceted-regulation-of-gene-expression-by-the-apoptosis-and-splicing-associated-protein-complex-and-its-components
#14
REVIEW
Bhagyashree Deka, Kusum Kumari Singh
The differential deposition of RNA-binding proteins (RBPs) on pre-mRNA mediates the processes of gene expression. One of the complexes containing RBPs that play a crucial part in RNA metabolism is the apoptosis-and splicing-associated protein (ASAP) complex. In this review, we present a summary of the structure of ASAP complex and its localization. Also, we discuss the findings by different groups on various functions of the subunits of the ASAP complex in RNA metabolism. The subunits of the ASAP complex are RNPS1, Acinus and SAP18...
2017: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/28502770/an-atomic-structure-of-the-human-spliceosome
#15
Xiaofeng Zhang, Chuangye Yan, Jing Hang, Lorenzo I Finci, Jianlin Lei, Yigong Shi
Mechanistic understanding of pre-mRNA splicing requires detailed structural information on various states of the spliceosome. Here we report the cryo electron microscopy (cryo-EM) structure of the human spliceosome just before exon ligation (the C(∗) complex) at an average resolution of 3.76 Å. The splicing factor Prp17 stabilizes the active site conformation. The step II factor Slu7 adopts an extended conformation, binds Prp8 and Cwc22, and is poised for selection of the 3'-splice site. Remarkably, the intron lariat traverses through a positively charged central channel of RBM22; this unusual organization suggests mechanisms of intron recruitment, confinement, and release...
May 18, 2017: Cell
https://www.readbyqxmd.com/read/28440616/discovery-and-characterization-of-a-eukaryotic-initiation-factor-4a-3-selective-inhibitor-that-suppresses-nonsense-mediated-mrna-decay
#16
Misa Iwatani-Yoshihara, Masahiro Ito, Yoshihiro Ishibashi, Hideyuki Oki, Toshio Tanaka, Daisuke Morishita, Takashi Ito, Hiromichi Kimura, Yasuhiro Imaeda, Samuel Aparicio, Atsushi Nakanishi, Tomohiro Kawamoto
Eukaryotic initiation factor 4A-3 (eIF4A3) is an Asp-Glu-Ala-Asp (DEAD) box-family adenosine triphosphate (ATP)-dependent RNA helicase. Subtypes eIF4A1 and eIF4A2 are required for translation initiation, but eIF4A3 participates in the exon junction complex (EJC) and functions in RNA metabolism including nonsense-mediated RNA decay (NMD). No small molecules for NMD inhibition via selective inhibition of eIF4A3 have been discovered. Here, we identified allosteric eIF4A3 inhibitors from a high-throughput screening campaign...
May 10, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28404883/mir-29a-regulates-the-proliferation-and-differentiation-of-retinal-progenitors-by-targeting-rbm8a
#17
Yi Zhang, Bingqiao Shen, Dandan Zhang, Yuyao Wang, Zhimin Tang, Ni Ni, Xiaoliang Jin, Min Luo, Hao Sun, Ping Gu
During development, tight regulation of the expansion of retinal progenitor cells (RPCs) and their differentiation into neuronal and glial cells is important for retinal formation and function. Our study demonstrated that microRNA (miR)-29a modulated the proliferation and differentiation of RPCs by suppressing RBM8A (one of the factors in the exon junction complex). Particularly, overexpression of miR-29a reduced RPC proliferation but accelerated RPC differentiation. By contrast, reduction of endogenous miR-29a elicited the opposite effects...
May 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28402567/nonsense-mediated-mrna-decay-in-tetrahymena-is-ejc-independent-and-requires-a-protozoa-specific-nuclease
#18
Miao Tian, Wentao Yang, Jing Zhang, Huai Dang, Xingyi Lu, Chengjie Fu, Wei Miao
Nonsense-mediated mRNA decay (NMD) is essential for removing premature termination codon-containing transcripts from cells. Studying the NMD pathway in model organisms can help to elucidate the NMD mechanism in humans and improve our understanding of how this biologically important process has evolved. Ciliates are among the earliest branching eukaryotes; their NMD mechanism is poorly understood and may be primordial. We demonstrate that highly conserved Upf proteins (Upf1a, Upf2 and Upf3) are involved in the NMD pathway of the ciliate, Tetrahymena thermophila...
June 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28400409/drosha-targets-its-own-transcript-to-modulate-alternative-splicing
#19
Dooyoung Lee, Jin-Wu Nam, Chanseok Shin
The nuclear RNase III enzyme DROSHA interacts with its cofactor DGCR8 to form the Microprocessor complex, which initiates microRNA (miRNA) maturation by cleaving hairpin structures embedded in primary transcripts. Apart from its central role in the biogenesis of miRNAs, DROSHA is also known to recognize and cleave miRNA-like hairpins in a subset of transcripts without apparent small RNA production. Here, we report that the human DROSHA transcript is one such noncanonical target of DROSHA. Mammalian DROSHA genes have evolved a conserved hairpin structure spanning a specific exon-intron junction, which serves as a substrate for the Microprocessor in human cells but not in murine cells...
July 2017: RNA
https://www.readbyqxmd.com/read/28393127/novel-junctophilin-2-mutation-a405s-is-associated-with-basal-septal-hypertrophy-and-diastolic-dysfunction
#20
Ann P Quick, Andrew P Landstrom, Qiongling Wang, David L Beavers, Julia O Reynolds, Giselle Barreto-Torres, Viet Tran, Jordan Showell, Leonne E Philippen, Shaine A Morris, Darlene Skapura, J Martijn Bos, Steen E Pedersen, Robia G Pautler, Michael J Ackerman, Xander H T Wehrens
BACKGROUND: Hypertrophic cardiomyopathy (HCM), defined as asymmetric left ventricular hypertrophy, is a leading cause of cardiac death in the young. Perturbations in calcium (Ca(2+)) handling proteins have been implicated in the pathogenesis of HCM. JPH2-encoded junctophilin 2 is a major component of the junctional membrane complex, the subcellular microdomain involved in excitation-contraction coupling. We hypothesized that a novel JPH2 mutation identified in patients with HCM is causally linked to HCM, and alters intracellular Ca(2+) signaling in a pro-hypertrophic manner...
February 2017: JACC. Basic to Translational Science
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