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https://www.readbyqxmd.com/read/28343630/de-novo-truncating-mutations-in-the-last-and-penultimate-exons-of-ppm1d-cause-an-intellectual-disability-syndrome
#1
Sandra Jansen, Sinje Geuer, Rolph Pfundt, Rachel Brough, Priyanka Ghongane, Johanna C Herkert, Elysa J Marco, Marjolein H Willemsen, Tjitske Kleefstra, Mark Hannibal, Joseph T Shieh, Sally Ann Lynch, Frances Flinter, David R FitzPatrick, Alice Gardham, Birgitta Bernhard, Nicola Ragge, Ruth Newbury-Ecob, Raphael Bernier, Malin Kvarnung, E A Helena Magnusson, Marja W Wessels, Marjon A van Slegtenhorst, Kristin G Monaghan, Petra de Vries, Joris A Veltman, Christopher J Lord, Lisenka E L M Vissers, Bert B A de Vries
Intellectual disability (ID) is a highly heterogeneous disorder involving at least 600 genes, yet a genetic diagnosis remains elusive in ∼35%-40% of individuals with moderate to severe ID. Recent meta-analyses statistically analyzing de novo mutations in >7,000 individuals with neurodevelopmental disorders highlighted mutations in PPM1D as a possible cause of ID. PPM1D is a type 2C phosphatase that functions as a negative regulator of cellular stress-response pathways by mediating a feedback loop of p38-p53 signaling, thereby contributing to growth inhibition and suppression of stress-induced apoptosis...
March 18, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28338294/paradoxical-gain-of-function-mutant-of-the-g-protein-coupled-receptor-prokr2-promotes-early-puberty
#2
Maki Fukami, Erina Suzuki, Yoko Izumi, Tomohiro Torii, Satoshi Narumi, Maki Igarashi, Mami Miyado, Momori Katsumi, Yasuko Fujisawa, Kazuhiko Nakabayashi, Kenichiro Hata, Akihiro Umezawa, Yoichi Matsubara, Junji Yamauchi, Tsutomu Ogata
The human genome encodes ~750 G-protein-coupled receptors (GPCRs), including prokineticin receptor 2 (PROKR2) involved in the regulation of sexual maturation. Previously reported pathogenic gain-of-function mutations of GPCR genes invariably encoded aberrant receptors with excessive signal transduction activity. Although in vitro assays demonstrated that an artificially created inactive mutant of PROKR2 exerted paradoxical gain-of-function effects when co-transfected with wild-type proteins, such a phenomenon has not been observed in vivo...
March 24, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28337997/the-mir-24-3p-p130cas-a-novel-axis-regulating-the-migration-and-invasion-of-cancer-cells
#3
Hoin Kang, Jun Gi Rho, Chongtae Kim, Hyosun Tak, Heejin Lee, Eunbyul Ji, Sojin Ahn, A-Ri Shin, Hyun-Il Cho, Yun Hyun Huh, Woo Keun Song, Wook Kim, Eun Kyung Lee
MicroRNAs (miRNAs) are small non-coding RNAs that negatively regulate gene expression by suppressing translation or facilitating mRNA decay. Differential expression of miRNAs is involved in the pathogenesis of several diseases including cancer. Here, we investigated the role of-miR-24-3p as a downregulated miRNA in metastatic cancer. miR-24-3p was decreased in metastatic cancer and lower expression of miR-24-3p was related to poor survival of cancer patients. Consistently, ectopic expression of miR-24-3p suppressed the cell migration, invasion, and proliferation of MCF7, Hep3B, B16F10, SK-Hep1, and PC-3 cells by directly targeting p130Cas...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28334903/n6-methyladenosine-alters-rna-structure-to-regulate-binding-of-a-low-complexity-protein
#4
Nian Liu, Katherine I Zhou, Marc Parisien, Qing Dai, Luda Diatchenko, Tao Pan
N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA), and affects almost every stage of the mRNA life cycle. The YTH-domain proteins can specifically recognize m6A modification to control mRNA maturation, translation and decay. m6A can also alter RNA structures to affect RNA-protein interactions in cells. Here, we show that m6A increases the accessibility of its surrounding RNA sequence to bind heterogeneous nuclear ribonucleoprotein G (HNRNPG). Furthermore, HNRNPG binds m6A-methylated RNAs through its C-terminal low-complexity region, which self-assembles into large particles in vitro...
February 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334781/auf1-facilitates-microrna-mediated-gene-silencing
#5
Kyung-Won Min, Myung Hyun Jo, Soochul Shin, Sylvia Davila, Richard W Zealy, Soo Im Kang, Lawson T Lloyd, Sungchul Hohng, Je-Hyun Yoon
Eukaryotic mRNA decay is tightly modulated by RNA-binding proteins (RBPs) and microRNAs (miRNAs). RBP AU-binding factor 1 (AUF1) has four isoforms resulting from alternative splicing and is critical for miRNA-mediated gene silencing with a distinct preference of target miRNAs. Previously, we have shown that AUF1 facilitates miRNA loading to Argonaute 2 (AGO2), the catalytic component of the RNA-induced silencing complex. Here, we further demonstrate that depletion of AUF1 abolishes the global interaction of miRNAs and AGO2...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28328949/mcpip1-alias-regnase-1-binds-and-cleaves-mrna-of-c-ebp%C3%AE
#6
Barbara Lipert, Mateusz Wilamowski, Andrzej Gorecki, Jolanta Jura
CCAAT/enhancer-binding protein beta (C/EBPβ) is a transcription factor controlling a broad range of genes essential for homeostasis, including genes related to immune functions, inflammation, metabolism and growth. Monocyte chemoattractant protein-1-induced protein 1 (MCPIP1) also called as Regnase-1 is an RNase and has been shown to decrease the stability of short-lived transcripts coding for inflammation-related proteins, including IL-1β, IL-6, IL-2, IL-8, IL-12b, IER-3, c-Rel. We found previously that the half-life of the C/EBPβ transcript is regulated by MCPIP...
2017: PloS One
https://www.readbyqxmd.com/read/28323884/a-system-for-coordinated-analysis-of-translational-readthrough-and-nonsense-mediated-mrna-decay
#7
Stacey L Baker, J Robert Hogg
The nonsense-mediated mRNA decay (NMD) pathway degrades mRNAs containing premature termination codons, limiting the expression of potentially deleterious truncated proteins. This activity positions the pathway as a regulator of the severity of genetic diseases caused by nonsense mutations. Because many genetic diseases result from nonsense alleles, therapeutics inducing readthrough of premature termination codons and/or inhibition of NMD have been of great interest. Several means of enhancing translational readthrough have been reported to concomitantly inhibit NMD efficiency, but tools for systematic analysis of mammalian NMD inhibition by translational readthrough are lacking...
2017: PloS One
https://www.readbyqxmd.com/read/28318500/mutations-in-tmem260-cause-a-pediatric-neurodevelopmental-cardiac-and-renal-syndrome
#8
Asaf Ta-Shma, Tahir N Khan, Asaf Vivante, Jason R Willer, Pavle Matak, Chaim Jalas, Ben Pode-Shakked, Yishay Salem, Yair Anikster, Friedhelm Hildebrandt, Nicholas Katsanis, Orly Elpeleg, Erica E Davis
Despite the accelerated discovery of genes associated with syndromic traits, the majority of families affected by such conditions remain undiagnosed. Here, we employed whole-exome sequencing in two unrelated consanguineous kindreds with central nervous system (CNS), cardiac, renal, and digit abnormalities. We identified homozygous truncating mutations in TMEM260, a locus predicted to encode numerous splice isoforms. Systematic expression analyses across tissues and developmental stages validated two such isoforms, which differ in the utilization of an internal exon...
March 11, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28318367/combinatorial-control-of-messenger-rnas-by-pumilio-nanos-and-brain-tumor-proteins
#9
René M Arvola, Chase A Weidmann, Traci M Tanaka Hall, Aaron C Goldstrohm
Eukaryotes possess a vast array of RNA-binding proteins (RBPs) that affect mRNAs in diverse ways to control protein expression. Combinatorial regulation of mRNAs by RBPs is emerging as the rule. No example illustrates this as vividly as the partnership of three Drosophila RBPs, Pumilio, Nanos and Brain Tumor, which have overlapping functions in development, stem cell maintenance and differentiation, fertility and neurological processes. Here we synthesize thirty years of research with new insights into their molecular functions and mechanisms of action...
March 20, 2017: RNA Biology
https://www.readbyqxmd.com/read/28315363/sider2-retroposon-mediated-mrna-decay-in-leishmania-is-coupled-to-translation
#10
Hiva Azizi, Michaela Müller-McNicoll, Barbara Papadopoulou
We previously reported that Short Interspersed Degenerate Retroposons of the SIDER2 subfamily predominantly located within 3' untranslated regions (UTRs) of Leishmania transcripts promote rapid turnover that is initiated by endonucleolytic cleavage. Here, we investigated whether SIDER2-mediated mRNA decay is linked to translation. We show that preventing translation initiation by inserting a hairpin structure at the 5'-end of a SIDER2-containing mRNA blocks degradation. Similarly, global inhibition of translation elongation by cycloheximide or termination by puromycin causes stabilisation of SIDER2-containing transcripts...
March 14, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/28298237/irfinder-assessing-the-impact-of-intron-retention-on-mammalian-gene-expression
#11
Robert Middleton, Dadi Gao, Aubin Thomas, Babita Singh, Amy Au, Justin J-L Wong, Alexandra Bomane, Bertrand Cosson, Eduardo Eyras, John E J Rasko, William Ritchie
Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing data. Analysis of 2573 samples showed that IR occurs in all tissues analyzed, affects over 80% of all coding genes and is associated with cell differentiation and the cell cycle. Frequently retained introns are enriched for specific RNA binding protein sites and are often retained in clusters in the same gene...
March 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/28292421/rna-methylation-clears-the-way
#12
Cassandra Kontur, Antonio Giraldez
During the maternal-to-zygotic transition, maternal mRNAs are cleared by multiple distinct but interrelated pathways. A recent study in Nature by Zhao et al. (2017) finds that YTHDF2, a reader of N(6)- methylation, facilitates maternal mRNA decay, introducing an additional facet of control over transcript fate and developmental reprogramming.
March 13, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28288699/longevity-regulation-by-nmd-mediated-mrna-quality-control
#13
Heehwa G Son, Seung-Jae V Lee
Proper maintenance of biological components is crucial for longevity and healthy aging. Although the role of homeostatic maintenance systems for DNA and protein in longevity is established, it remained largely unknown for RNA. In our recent work, we show that nonsense-mediated mRNA decay (NMD) promotes longevity in the roundworm C. elegans by enhancing RNA quality control. We find that the activity of NMD decreases during aging, raising the possibility that RNA quality declines in old animals. We then show that key components of NMD complex are required for long lifespan in C...
March 14, 2017: BMB Reports
https://www.readbyqxmd.com/read/28287067/translational-control-of-mrnas-by-3-untranslated-region-binding-proteins
#14
Akio Yamashita, Osamu Takeuchi
Eukaryotic gene expression is precisely regulated at all points between transcription and translation. In this review, we focus on translational control mediated by the 3'-untranslated regions (UTRs) of mRNAs. mRNA 3'-UTRs contain cis-acting elements that function in the regulation of protein translation or mRNA decay. RNA binding proteins that bind to these cis-acting elements regulate mRNA translation via various mechanisms targeting the mRNA cap structure, the eukaryotic initiation factor 4E (eIF4E)-eIF4G complex, ribosomes, and the poly (A) tail...
March 13, 2017: BMB Reports
https://www.readbyqxmd.com/read/28283058/5-end-nicotinamide-adenine-dinucleotide-cap-in-human-cells-promotes-rna-decay-through-dxo-mediated-denadding
#15
Xinfu Jiao, Selom K Doamekpor, Jeremy G Bird, Bryce E Nickels, Liang Tong, Ronald P Hart, Megerditch Kiledjian
Eukaryotic mRNAs generally possess a 5' end N7 methyl guanosine (m(7)G) cap that promotes their translation and stability. However, mammalian mRNAs can also carry a 5' end nicotinamide adenine dinucleotide (NAD(+)) cap that, in contrast to the m(7)G cap, does not support translation but instead promotes mRNA decay. The mammalian and fungal noncanonical DXO/Rai1 decapping enzymes efficiently remove NAD(+) caps, and cocrystal structures of DXO/Rai1 with 3'-NADP(+) illuminate the molecular mechanism for how the "deNADding" reaction produces NAD(+) and 5' phosphate RNA...
March 9, 2017: Cell
https://www.readbyqxmd.com/read/28277968/vascular-plant-one-zinc-finger-protein-2-is-localized-both-to-the-nucleus-and-stress-granules-under-heat-stress-in-arabidopsis
#16
Misaki Koguchi, Kanako Yamasaki, Tomoko Hirano, Masa H Sato
VASCULAR PLANT ONE-ZINC FINGER (VOZ)1/ and VOZ2 have an ability to bind to the specific cis-element in the AVP1 promoter of Arabidopsis, which function on the PhyB-dependent flowering and possibly in various stress responses as potential transcription factors, although nuclear localization of VOZ proteins is still unclear. In this study, we found that VOZ2 is dispersed throughout the cytoplasm under normal growth conditions, whereas VOZ2 but is transferred not only to the nucleus but also to the cytoplasmic foci under heat stress conditions...
February 25, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28277935/the-pre-mrna-retention-and-splicing-complex-controls-expression-of-the-mediator-subunit-med20
#17
Yang Zhou, Marcus J O Johansson
The heterotrimeric pre-mRNA retention and splicing (RES) complex, consisting of Bud13p, Snu17p and Pml1p, promotes splicing and nuclear retention of a subset of intron-containing pre-mRNAs. Yeast cells deleted for individual RES genes show growth defects that are exacerbated at elevated temperatures. Although the growth phenotypes correlate to the splicing defects in the individual mutants, the underlying mechanism is unknown. Here, we show that the temperature sensitive (Ts) growth phenotype of bud13Δ and snu17Δ cells is a consequence of inefficient splicing of MED20 pre-mRNA, which codes for a subunit of the Mediator complex; a co-regulator of RNA polymerase II transcription...
February 17, 2017: RNA Biology
https://www.readbyqxmd.com/read/28277929/both-exo-and-endo-nucleolytic-activities-of-rnase-j1-from-staphylococcus-aureus-are-manganese-dependent-and-active-on-triphosphorylated-5-ends
#18
Stéphane Hausmann, Vanessa Andrade Guimarães, Dominique Garcin, Natalia Baumann, Patrick Linder, Peter Redder
RNA decay and RNA maturation are important steps in the regulation of bacterial gene expression. RNase J, which is present in about half of bacterial species, has been shown to possess both endo- and 5' to 3' exo-ribonuclease activities. The exonucleolytic activity is clearly involved in the degradation of mRNA and in the maturation of at least the 5'end of 16S rRNA in the two Firmicutes Staphylococcus aureus and Bacillus subtilis. The endoribonuclease activity of RNase J from a number of species has been shown to be weak in vitro and 3-D structural data of different RNase J orthologs has not provided a clear explanation for the molecular basis of this activity...
March 1, 2017: RNA Biology
https://www.readbyqxmd.com/read/28277618/the-within-host-dynamics-of-infection-in-trans-generationally-primed-flour-beetles
#19
Ann T Tate, Peter Andolfatto, Jeffery P Demuth, Andrea L Graham
Many taxa exhibit plastic immune responses initiated after primary microbial exposure that provide increased protection against disease-induced mortality and the fitness costs of infection. In several arthropod species, this protection can even be passed from parents to offspring through a phenomenon called trans-generational immune priming. Here, we first demonstrate that trans-generational priming is a repeatable phenomenon in flour beetles (Tribolium castaneum) primed and infected with Bacillus thuringiensis (Bt)...
March 9, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28276441/rna-surveillance-via-nonsense-mediated-mrna-decay-is-crucial-for-longevity-in-daf-2-insulin-igf-1-mutant-c-elegans
#20
Heehwa G Son, Mihwa Seo, Seokjin Ham, Wooseon Hwang, Dongyeop Lee, Seon Woo A An, Murat Artan, Keunhee Seo, Rachel Kaletsky, Rachel N Arey, Youngjae Ryu, Chang Man Ha, Yoon Ki Kim, Coleen T Murphy, Tae-Young Roh, Hong Gil Nam, Seung-Jae V Lee
Long-lived organisms often feature more stringent protein and DNA quality control. However, whether RNA quality control mechanisms, such as nonsense-mediated mRNA decay (NMD), which degrades both abnormal as well as some normal transcripts, have a role in organismal aging remains unexplored. Here we show that NMD mediates longevity in C. elegans strains with mutations in daf-2/insulin/insulin-like growth factor 1 receptor. We find that daf-2 mutants display enhanced NMD activity and reduced levels of potentially aberrant transcripts...
March 9, 2017: Nature Communications
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