CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli.

abstract：:We investigated the gene-expression variation among humans by analysing previously published mRNA-seq and ribosome footprint profiling of heart left-ventricles from healthy donors. We ranked the genes according to their coefficient of variation values and found that the top 5% most variable genes had special features ...

journal_title：RNA biology

authors： Domitrovic T,Moreira MH,Carneiro RL,Ribeiro-Alves M,Palhano FL

更新日期：2020-12-11 00:00:00

abstract：:I am honored to have been asked to contribute to this memorial issue, although I cannot claim to have known Carl Woese well. Carl's insights and the discoveries that his research group made over the years certainly stimulated my own research program, and at several points early on, interactions with him were pivotal i...

journal_title：RNA biology

authors： Gray MW

更新日期：2014-01-01 00:00:00

abstract：:Wobble uridines (U34) are generally modified in all species. U34 modifications can be essential in metazoans but are not required for viability in fungi. In this review, we provide an overview on the types of modifications and how they affect the physico-chemical properties of wobble uridines. We describe the molecula...

journal_title：RNA biology

authors： Schaffrath R,Leidel SA

更新日期：2017-09-02 00:00:00

abstract：:Significant structural and mechanistic similarities between the spliceosomal snRNAs and catalytically critical domains of self-splicing group II introns have led to the hypothesis that the spliceosomes and group II introns may be evolutionarily related. We have previously shown that in vitro-transcribed, protein-free ...

journal_title：RNA biology

authors： Jaladat Y,Zhang B,Mohammadi A,Valadkhan S

更新日期：2011-05-01 00:00:00

abstract：:The question of how cysteinyl-tRNA(Cys) is synthesized in organisms that lack a canonical cysteinyl-tRNA synthetase (CysRS) is an important open question in understanding protein synthesis. The prolyl-tRNA synthetase (ProRS) of wide ranging organisms has the ability to mis-activate cysteine without editing. This raise...

journal_title：RNA biology

authors： Zhang CM,Hou YM

更新日期：2004-05-01 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：:tRNA molecules undergo extensive post-transcriptional processing to generate the mature functional tRNA species that are essential for translation in all organisms. These processing steps include the introduction of numerous specific chemical modifications to nucleotide bases and sugars; among these modifications, met...

journal_title：RNA biology

authors： Swinehart WE,Jackman JE

更新日期：2015-01-01 00:00:00

abstract：:In a series of conceptual articles published around the millennium, Carl Woese emphasized that evolution of cells is the central problem of evolutionary biology, that the three-domain ribosomal tree of life is an essential framework for reconstructing cellular evolution, and that the evolutionary dynamics of functiona...

journal_title：RNA biology

authors： Koonin EV

更新日期：2014-01-01 00:00:00

abstract：:5-fluorouracil (5-FU) was isolated as an inhibitor of thymidylate synthase, which is important for DNA synthesis. The drug was later found to also affect the conserved 3'-5' exoribonuclease EXOSC10/Rrp6, a catalytic subunit of the RNA exosome that degrades and processes protein-coding and non-coding transcripts. Work ...

journal_title：RNA biology

authors： Xie B,Becker E,Stuparevic I,Wery M,Szachnowski U,Morillon A,Primig M

更新日期：2019-06-01 00:00:00

abstract：:Selenoproteins are a unique class of proteins that contain the 21st amino acid, selenocysteine (Sec). Addition of Sec into a protein is achieved by recoding of the UGA stop codon. All 25 mammalian selenoprotein mRNAs possess a 3' UTR stem-loop structure, the Selenocysteine Insertion Sequence (SECIS), which is required...

journal_title：RNA biology

authors： Cockman EM,Narayan V,Willard B,Shetty SP,Copeland PR,Driscoll DM

更新日期：2019-12-01 00:00:00

abstract：:In the last years, a number of nuclear genes restoring cytoplasmic male sterility (CMS) have been cloned in various crop species. The majority of these genes have been shown to encode pentatricopeptide repeat proteins (PPR) that act by specifically suppressing the expression of sterility-causing mitochondrial transcri...

journal_title：RNA biology

authors： Dahan J,Mireau H

更新日期：2013-01-01 00:00:00

abstract：:As a mental framework for the transition of self-replicating biological forms, the RNA world concept stipulates a dual function of RNAs as genetic substance and catalyst. The chaperoning function is found intrinsic to ribozymes involved in protein synthesis and tRNA maturation, enriching the primordial RNA world with ...

journal_title：RNA biology

authors： Son A,Horowitz S,Seong BL

更新日期：2021-01-01 00:00:00

abstract：:The ribosome binding site of Escherichia coli rpoS mRNA, encoding the stationary sigma-factor RpoS, is sequestered by an inhibitory stem-loop structure (iss). Translational activation of rpoS mRNA at low temperature and during exponential growth includes Hfq-facilitated duplex formation between rpoS and the small regu...

journal_title：RNA biology

authors： Resch A,Većerek B,Palavra K,Bläsi U

更新日期：2010-11-01 00:00:00

abstract：:Physical entanglement, and particularly knots arise spontaneously in equilibrated polymers that are sufficiently long and densely packed. Biopolymers are no exceptions: knots have long been known to occur in proteins as well as in encapsidated viral DNA. The rapidly growing number of RNA structures has recently made i...

journal_title：RNA biology

authors： Burton AS,Di Stefano M,Lehman N,Orland H,Micheletti C

更新日期：2016-01-01 00:00:00

abstract：:RBM10 is an RNA binding protein and alternative splicing regulator frequently mutated in lung adenocarcinomas. Recent results indicate that RBM10 inhibits proliferation of lung cancer cells by promoting skipping of exon 9 of the gene NUMB, a frequent alternative splicing change in lung cancer generating a negative reg...

journal_title：RNA biology

authors： Hernández J,Bechara E,Schlesinger D,Delgado J,Serrano L,Valcárcel J

更新日期：2016-01-01 00:00:00

abstract：:RNA-binding proteins (RBPs) are key regulators of posttranscriptional processes such as RNA maturation, localization, turnover and translation. Despite their dysregulation in various diseases including cancer, the landscape of RBP expression in human cancer has not been well elucidated. Here, we built a comprehensive ...

journal_title：RNA biology

authors： Zhang B,Babu KR,Lim CY,Kwok ZH,Li J,Zhou S,Yang H,Tay Y

更新日期：2020-02-01 00:00:00

abstract：:MicroRNA (miRs) are short non-coding RNAs that fine-tune the regulation of gene expression to coordinate a wide range of biological processes. MicroRNAs are transcribed from miR genes and primary miR transcripts are processed to approximately 22 nucleotide single strand mature forms that function as repressors of tran...

journal_title：RNA biology

authors： Desvignes T,Contreras A,Postlethwait JH

更新日期：2014-01-01 00:00:00

abstract：:Riboswitches are cis-encoded, cis-acting RNA elements that directly sense a physiological signal. Signal response results in a change in RNA structure that impacts gene expression. Elements of this type play an important role in bacteria, where they regulate a variety of fundamental cellular pathways. Riboswitch-media...

journal_title：RNA biology

authors： Smith AM,Fuchs RT,Grundy FJ,Henkin TM

更新日期：2010-01-01 00:00:00

abstract：:De novo addition of telomeric sequences can occur at broken chromosomes and must be well controlled, which is essential during programmed DNA reorganization processes. In ciliated protozoa an extreme form of DNA-reorganization is observed during macronuclear differentiation after sexual reproduction leading to the eli...

journal_title：RNA biology

authors： Fuhrmann G,Jönsson F,Weil PP,Postberg J,Lipps HJ

更新日期：2016-08-02 00:00:00

abstract：:Oncogenic viruses are associated with approximately 15% of human cancers. In viral infections, microRNAs play an important role in host-pathogen interactions. miR-21 is a highly conserved non-coding RNA that not only regulates the development of oncogenic viral diseases, but also responds to the regulation of intracel...

journal_title：RNA biology

authors： He G,Ding J,Zhang Y,Cai M,Yang J,Cho WC,Zheng Y

更新日期：2021-01-27 00:00:00

abstract：:Amphioxus is the closest living proxy for exploring the evolutionary origin of the immune system in vertebrates. To understand the immune responses of amphioxus to lipopolysaccharide (LPS), 5 ribosomal RNA (rRNA)-depleted libraries of amphioxus were constructed, including one control (0 h) library and 4 treatment libr...

journal_title：RNA biology

authors： Zhang QL,Zhu QH,Xie ZQ,Xu B,Wang XQ,Chen JY

更新日期：2017-12-02 00:00:00

abstract：:The Hedgehog (HH) signaling pathway has important roles in tumorigenesis and in embryonal patterning. The Glioma-associated oncogene 1 (GLI1) is a key molecule in HH signaling, acting as a transcriptional effector and, moreover, is considered to be a potential therapeutic target for several types of cancer. To extend ...

journal_title：RNA biology

authors： Shimokawa T,Rahman MF,Tostar U,Sonkoly E,Ståhle M,Pivarcsi A,Palaniswamy R,Zaphiropoulos PG

更新日期：2013-02-01 00:00:00

abstract：:In metazoan organisms, alternative splicing is a central mechanism for the regulation of gene expression. However, many questions remain about the underlying molecular mechanisms. Our recent work suggests that U1 snRNP-independent premRNA splicing occurs in humans, which contributes to the regulation of alternative sp...

journal_title：RNA biology

authors： Fukumura K,Inoue K

更新日期：2009-09-01 00:00:00

abstract：:YchF is one of two universally conserved GTPases with unknown cellular function. As a first step toward elucidating YchF's cellular role, we performed a detailed biochemical characterization of the protein from Escherichia coli. Our data from fluorescence titrations not only confirmed the surprising finding that YchFE...

journal_title：RNA biology

authors： Becker M,Gzyl KE,Altamirano AM,Vuong A,Urban K,Wieden HJ

更新日期：2012-10-01 00:00:00

abstract：:Interactions between glioma cells and their local environment are critical determinants of brain tumor growth, infiltration and neovascularisation. Communication with host cells and stroma via microvesicles represents one pathway by which tumors can modify their surroundings to achieve a tumor-permissive environment. ...

journal_title：RNA biology

authors： Li CC,Eaton SA,Young PE,Lee M,Shuttleworth R,Humphreys DT,Grau GE,Combes V,Bebawy M,Gong J,Brammah S,Buckland ME,Suter CM

更新日期：2013-08-01 00:00:00

abstract：:Type II CRISPR-Cas9 systems require a small RNA called the trans-activating CRISPR RNA (tracrRNA) in order to function. The prediction of these non-coding RNAs in prokaryotic genomes is challenging because they have dissimilar structures, having short stems (3-6 bp) and non-canonical base-pairs e.g. G-A. Much of the t...

journal_title：RNA biology

authors： Chyou TY,Brown CM

更新日期：2019-04-01 00:00:00

abstract：:The instructions to make proteins and structural RNAs are laid down in gene sequences. Yet, in certain instances, these primary instructions need to be modified considerably during gene expression, most often at the transcript level. Here we review a case of massive post-transcriptional revisions via trans-splicing an...

journal_title：RNA biology

authors： Valach M,Moreira S,Faktorová D,Lukeš J,Burger G

更新日期：2016-12-01 00:00:00

abstract：:The RIG-I-like receptors (RLRs)--RIG-I, MDA5, and LGP2--detect intracellular pathogenic RNA and elicit an antiviral immune response during viral infection. The protein architecture of the RLR family consists of multiple functional domains, including N-terminal Caspase Activation and Recruitment Domains (CARDs) for sig...

journal_title：RNA biology

authors： Luo D

更新日期：2014-01-01 00:00:00

abstract：:Ribosome biogenesis is an essential process initiated in the nucleolus. In eukaryotes, multiple ribosome biogenesis factors (RBFs) can be found in the nucleolus, the nucleus and in the cytoplasm. They act in processing, folding and modification of the pre-ribosomal (r)RNAs, incorporation of ribosomal proteins (RPs), e...

journal_title：RNA biology

authors： Palm D,Simm S,Darm K,Weis BL,Ruprecht M,Schleiff E,Scharf C

更新日期：2016-01-01 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