Genome-wide technology for determining RNA stability in mammalian cells: historical perspective and recent advantages based on modified nucleotide labeling.

abstract：:Editing by ADAR enzymes is essential for mammalian life. Still, knowledge of the spatio-temporal editing patterns in mammals is limited. By use of 454 amplicon sequencing we examined the editing status of 12 regionally extracted mRNAs from porcine developing brain encompassing a total of 64 putative ADAR editing sites...

journal_title：RNA biology

authors： Venø MT,Bramsen JB,Bendixen C,Panitz F,Holm IE,Öhman M,Kjems J

更新日期：2012-08-01 00:00:00

abstract：:The development of rigorous molecular taxonomy pioneered by Carl Woese has freed evolution science to explore numerous cellular activities that lead to genome change in evolution. These activities include symbiogenesis, inter- and intracellular horizontal DNA transfer, incorporation of DNA from infectious agents, and ...

journal_title：RNA biology

authors： Shapiro JA

更新日期：2014-01-01 00:00:00

abstract：:The endoribonuclease toxins of the E. coli toxin-antitoxin systems arrest bacterial growth and protein synthesis by targeting cellular mRNAs. As an exception, E. coli MazF was reported to cleave also 16S rRNA at a single site and separate an anti-Shine-Dalgarno sequence-containing RNA fragment from the ribosome. We no...

journal_title：RNA biology

authors： Mets T,Lippus M,Schryer D,Liiv A,Kasari V,Paier A,Maiväli Ü,Remme J,Tenson T,Kaldalu N

更新日期：2017-01-02 00:00:00

abstract：:Studies on the regulation of gene expression in eukaryotes in the past 20 years have consistently revealed increasing levels of complexity. Thirty years ago it seemed that we had understood the basic principles of gene regulation in eukaryotes. It was thought that regulation of transcription was the first and most imp...

journal_title：RNA biology

authors： Collart MA,Reese JC

更新日期：2014-01-01 00:00:00

abstract：:Long non-coding RNAs have emerged as an important regulatory layer in biological systems. Of the various types of lncRNAs, one class (designated as divergent RNAs/XH), which is in head-to-head overlap with the coding genes, has emerged as a critical biotype that regulates development and cellular differentiation. This...

journal_title：RNA biology

authors： Prajapati B,Fatma M,Maddhesiya P,Sodhi MK,Fatima M,Dargar T,Bhagat R,Seth P,Sinha S

更新日期：2019-01-01 00:00:00

abstract：:The endoribonuclease RNase-L requires 2',5'-linked oligoadenylates for activation, and mediates antiviral and antiproliferative activities. We previously determined that RNase-L activation induces senescence; to determine potential mechanisms underlying this activity, we used microarrays to identify RNase-L-regulated ...

journal_title：RNA biology

authors： Andersen JB,Mazan-Mamczarz K,Zhan M,Gorospe M,Hassel BA

更新日期：2009-07-01 00:00:00

abstract：:RNA exosomes are large multi-subunit protein complexes involved in controlled and processive 3' to 5' RNA degradation. Exosomes form large molecular chambers and harbor multiple nuclease sites as well as RNA binding regions. This makes a quantitative kinetic analysis of RNA degradation with reliable parameter and erro...

journal_title：RNA biology

authors： Niederberger T,Hartung S,Hopfner KP,Tresch A

更新日期：2011-01-01 00:00:00

abstract：:Population differences observed for complex traits may be attributed to the combined effect of socioeconomic, environmental, genetic and epigenetic factors. To better understand population differences in complex traits, genome-wide genetic and gene expression differences among ethnic populations have been studied. Her...

journal_title：RNA biology

authors： Huang RS,Gamazon ER,Ziliak D,Wen Y,Im HK,Zhang W,Wing C,Duan S,Bleibel WK,Cox NJ,Dolan ME

更新日期：2011-07-01 00:00:00

abstract：:Seryl-tRNA synthetase (SerRS) catalyzes the ligation of serine to the 3'-end of serine tRNA (tRNA(Ser)), which is typical of the type-2 tRNAs characterized by a long extra arm. The SerRSs are divided into two types, the archaeal/eukaryal and bacterial types. In this study, we solved the crystal structures of the SerRS...

journal_title：RNA biology

authors： Itoh Y,Sekine S,Kuroishi C,Terada T,Shirouzu M,Kuramitsu S,Yokoyama S

更新日期：2008-07-01 00:00:00

abstract：:Viroids are the smallest autonomous infectious nucleic acids known today. They are non-coding, unencapsidated, circular RNAs with sizes ranging from 250 to 400 nucleotides and infect certain plants. These RNAs are transcribed by rolling-circle mechanisms in the plant host's nuclei (Pospiviroidae) or chloroplasts (Avsu...

journal_title：RNA biology

authors： Hammann C,Steger G

更新日期：2012-06-01 00:00:00

abstract：:Bacterial small RNAs (sRNAs) are a class of structural RNAs that often regulate mRNA targets via post-transcriptional base pair interactions. We determined features that discriminate functional from non-functional interactions and assessed the influence of these features on genome-wide target predictions. For this pur...

journal_title：RNA biology

authors： Richter AS,Backofen R

更新日期：2012-07-01 00:00:00

abstract：:RNA interference (RNAi) is a powerful tool for gene functional analysis of plant-parasitic nematodes (PPNs). RNAi involving soaking in a dsRNA solution and in planta methods is commonly applied in the study of gene function in PPNs. However, certain problems restrict the application of these methods. Therefore, more c...

journal_title：RNA biology

authors： Ding S,Wang D,Xu C,Yang S,Cheng X,Peng X,Chen C,Xie H

更新日期：2020-12-14 00:00:00

abstract：:Alternative splicing (AS) in response to changing external conditions often requires alterations in the ability of sequence-specific RNA-binding proteins to bind to cis-acting sequences in their target pre-mRNA. While daily oscillations in AS events have been described in several organisms, cis-acting sequences that c...

journal_title：RNA biology

authors： Goldammer G,Neumann A,Strauch M,Müller-McNicoll M,Heyd F,Preußner M

更新日期：2018-01-01 00:00:00

abstract：:In mammals, the genic disequilibrium between males (XY) and females (XX) is resolved through the inactivation of one of the X-chromosomes in females. X-chromosome inactivation (XCI) takes place in all mammalian species, but has mainly been studied in the mouse model where it was shown to be controlled by the interplay...

journal_title：RNA biology

authors： Vallot C,Rougeulle C

更新日期：2013-08-01 00:00:00

abstract：:Regulation of protein synthesis is an essential step of gene expression. This process is under the control of cis-acting RNA elements and trans-acting factors. Gemin5 is a multifunctional RNA-binding protein organized in distinct domains. The protein bears a non-canonical RNA-binding site, designated RBS1, at the C-te...

journal_title：RNA biology

authors： Francisco-Velilla R,Embarc-Buh A,Rangel-Guerrero S,Basu S,Kundu S,Martinez-Salas E

更新日期：2020-09-01 00:00:00

abstract：:microRNAs (miRNAs) are critical regulators of gene expression. For elucidating functional roles of miRNAs, it is critical to identify their direct targets. There are debates about whether pulldown of biotinylated miRNA mimics can be used to identify miRNA targets or not. Here we show that biotin-labelled miR-34a can b...

journal_title：RNA biology

authors： Awan HM,Shah A,Rashid F,Wei S,Chen L,Shan G

更新日期：2018-01-02 00:00:00

abstract：:Ribosome biogenesis drives cell growth and proliferation, but mechanisms that modulate this process remain poorly understood. For a long time, small rRNA sequences have been widely treated as non-specific degradation products and neglected as garbage sequences. Recently, we identified a new class of antisense ribosoma...

journal_title：RNA biology

authors： Zhou X,Chen X,Wang Y,Feng X,Guang S

更新日期：2017-11-02 00:00:00

abstract：:Amplification or overexpression of neuronal MYC (MYCN) is associated with poor prognosis of human neuroblastoma. Three isoforms of the MYCN protein have been described as well as a protein encoded by an antisense transcript (MYCNOS) that originates from the opposite strand at the MYCN locus. Recent findings suggest th...

journal_title：RNA biology

authors： Vadie N,Saayman S,Lenox A,Ackley A,Clemson M,Burdach J,Hart J,Vogt PK,Morris KV

更新日期：2015-01-01 00:00:00

abstract：:Translation begins at AUG, GUG, or UUG codons in bacteria. Start codon recognition occurs in the P site, which may help explain this first-position degeneracy. However, the molecular basis of start codon specificity remains unclear. In this study, we measured the codon dependence of 30S•mRNA•tRNAfMet and 30S•mRNA•tRNA...

journal_title：RNA biology

authors： Roy B,Liu Q,Shoji S,Fredrick K

更新日期：2018-01-01 00:00:00

abstract：:Proper base-pairing of a miRNA with its target mRNA is a key step in miRNA-mediated mRNA repression. RNA remodelling by RNA-binding proteins (RBPs) can improve access of miRNAs to their target mRNAs. The largest isoform p45 of the RBP AUF1 has previously been shown to remodel viral or AU-rich RNA elements. Here, we sh...

journal_title：RNA biology

authors： Sänger L,Bender J,Rostowski K,Golbik R,Lilie H,Schmidt C,Behrens SE,Friedrich S

更新日期：2020-09-29 00:00:00

abstract：:MicroRNAs (miRNAs) are key regulators of gene expression and play critical roles in modulating metabolism, development and physiology in animals and plants. miRNA levels are transcriptionally and post-transcriptionally controlled for their proper function. Recent studies have shown that RNA-binding proteins play impor...

journal_title：RNA biology

authors： Ren G,Yu B

更新日期：2012-12-01 00:00:00

abstract：:The NOVA (neuro-oncological ventral antigen) protein family, composed of two paralogs, NOVA1 and NOVA2, consists of RNA-binding proteins involving in processes such as alternative splicing and transport of some target mRNAs. The function of NOVA has been well studied, and increasing evidence has shown that NOVA protei...

journal_title：RNA biology

authors： Tang S,Zhao Y,He X,Zhu J,Chen S,Wen J,Deng Y

更新日期：2020-06-01 00:00:00

abstract：:Transcription termination delineates the 3' ends of transcripts, prevents otherwise runaway RNA polymerase (RNAP) from intruding into downstream genes and regulatory elements, and enables release of the RNAP for recycling. While other eukaryotic RNAPs require complex cis-signals and/or accessory factors to achieve the...

journal_title：RNA biology

authors： Arimbasseri AG,Maraia RJ

更新日期：2016-01-01 00:00:00

abstract：:Nonsense-mediated decay (NMD) is a RNA surveillance pathway that degrades subsets of normal and aberrant mRNAs. Mutations that perturb NMD cause neurological disorders in humans, suggesting that NMD has roles in the brain. Recently, it was shown that NMD is repressed during neural development to allow for the stabiliz...

journal_title：RNA biology

authors： Karam R,Wilkinson M

更新日期：2012-01-01 00:00:00

abstract：:The PDCD1 gene encodes PD-1, an important immune checkpoint protein and key immunotherapy target to treat cancer. PDCD1 is alternatively spliced to generate an exon 3-skipped isoform PD-1Δ3 that has been suggested to play an antagonistic role to PD-1, but the mechanism underlying alternative splicing of PDCD1 has neve...

journal_title：RNA biology

authors： Sun J,Bai J,Jiang T,Gao Y,Hua Y

更新日期：2019-12-01 00:00:00

abstract：:We had previously proposed that the post-transcriptional regulation through microRNA as a mechanism for incomplete penetrance and variable expressivity, leads to lack of correlation between genotype and phenotype. Here we report the validation of miRNA-target interactions we predicted earlier and demonstrate the regul...

journal_title：RNA biology

authors： Ahluwalia JK,Soni K,Sivasubbu S,Brahmachari V

更新日期：2012-03-01 00:00:00

abstract：:Transcriptional regulation of microRNA (miRNA) expression is one of the least understood aspects of miRNA biogenesis. In C. elegans the list of miRNAs whose transcriptional control has been described in some detail is currently limited to four: let-7, lin-4, lsy-6, and mir-61. Each of these genes has been shown experi...

journal_title：RNA biology

authors： Turner MJ,Slack FJ

更新日期：2009-01-01 00:00:00

abstract：:Alternative splicing (AS) plays a central role during cell-fate determination. However, how the core spliceosomal factors (CSFs) are involved in this process is poorly understood. Here, we report the down-regulation of the U2AF1 CSF during stem cell differentiation. To investigate its function in stemness and differen...

journal_title：RNA biology

authors： Laaref AM,Manchon L,Bareche Y,Lapasset L,Tazi J

更新日期：2020-06-01 00:00:00

abstract：:The human genome contains some thousands of long non coding RNAs (lncRNAs). Many of these transcripts are presently considered crucial regulators of gene expression and functionally implicated in developmental processes in Eukaryotes. Notably, despite a huge number of lncRNAs are expressed in the Central Nervous Syste...

journal_title：RNA biology

authors： Bevilacqua V,Gioia U,Di Carlo V,Tortorelli AF,Colombo T,Bozzoni I,Laneve P,Caffarelli E

更新日期：2015-01-01 00:00:00

abstract：:Processing bodies (P-bodies) are cytoplasmatic mRNP granules containing non-translating mRNAs and proteins from the mRNA decay and silencing machineries. The mechanism of P-body assembly has been typically addressed by depleting P-body components. Here we apply a complementary approach and establish an automated cell-...

journal_title：RNA biology

authors： Martínez JP,Pérez-Vilaró G,Muthukumar Y,Scheller N,Hirsch T,Diestel R,Steinmetz H,Jansen R,Frank R,Sasse F,Meyerhans A,Díez J

更新日期：2013-11-01 00:00:00