Results for 'non-protein coding RNA'

988 found
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  1.  15
    Are non‐protein coding RNAs junk or treasure?Nils G. Walter - 2024 - Bioessays 46 (4):2300201.
    The human genome project's lasting legacies are the emerging insights into human physiology and disease, and the ascendance of biology as the dominant science of the 21st century. Sequencing revealed that >90% of the human genome is not coding for proteins, as originally thought, but rather is overwhelmingly transcribed into non‐protein coding, or non‐coding, RNAs (ncRNAs). This discovery initially led to the hypothesis that most genomic DNA is “junk”, a term still championed by some geneticists and (...)
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  2.  49
    Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms.John S. Mattick - 2003 - Bioessays 25 (10):930-939.
    The central dogma of biology holds that genetic information normally flows from DNA to RNA to protein. As a consequence it has been generally assumed that genes generally code for proteins, and that proteins fulfil not only most structural and catalytic but also most regulatory functions, in all cells, from microbes to mammals. However, the latter may not be the case in complex organisms. A number of startling observations about the extent of non-protein-coding RNA (ncRNA) transcription in (...)
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  3.  75
    The relationship between non‐proteincoding DNA and eukaryotic complexity.Ryan J. Taft, Michael Pheasant & John S. Mattick - 2007 - Bioessays 29 (3):288-299.
    There are two intriguing paradoxes in molecular biology-the inconsistent relationship between organismal complexity and (1) cellular DNA content and (2) the number of protein-coding genes-referred to as the C-value and G-value paradoxes, respectively. The C-value paradox may be largely explained by varying ploidy. The G-value paradox is more problematic, as the extent of protein coding sequence remains relatively static over a wide range of developmental complexity. We show by analysis of sequenced genomes that the relative amount (...)
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  4.  56
    Non‐coding RNAs: Meet thy masters.Fabrício F. Costa - 2010 - Bioessays 32 (7):599-608.
    New DNA sequencing technologies have provided novel insights into eukaryotic genomes, epigenomes, and the transcriptome, including the identification of new non‐coding RNA (ncRNA) classes such as promoter‐associated RNAs and long RNAs. Moreover, it is now clear that up to 90% of eukaryotic genomes are transcribed, generating an extraordinary range of RNAs with no coding capacity. Taken together, these new discoveries are modifying the status quo in genomic science by demonstrating that the eukaryotic gene pool is divided into two (...)
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  5.  13
    Mouse‐centric comparative transcriptomics of protein coding and non‐coding RNAs.Masanori Suzuki & Yoshihide Hayashizaki - 2004 - Bioessays 26 (8):833-843.
    The largest transcriptome reported so far comprises 60,770 mouse full‐length cDNA clones, and is an effective reference data set for comparative transcriptomics. The number of mouse cDNAs identified greatly exceeds the number of genes predicted from the sequenced human and mouse genomes. This is largely because of extensive alternative splicing and the presence of many non‐coding RNAs (ncRNAs), which are difficult to predict from genomic sequences. Notably, ncRNAs are a major component of the transcriptomes of higher organisms, and many (...)
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  6.  38
    Identifying (non‐)coding RNAs and small peptides: Challenges and opportunities.Andrea Pauli, Eivind Valen & Alexander F. Schier - 2015 - Bioessays 37 (1):103-112.
    Over the past decade, high‐throughput studies have identified many novel transcripts. While their existence is undisputed, their coding potential and functionality have remained controversial. Recent computational approaches guided by ribosome profiling have indicated that translation is far more pervasive than anticipated and takes place on many transcripts previously assumed to be non‐coding. Some of these newly discovered translated transcripts encode short, functional proteins that had been missed in prior screens. Other transcripts are translated, but it might be the (...)
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  7.  28
    The H19 locus: Role of an imprinted non‐coding RNA in growth and development.Anne Gabory, Hélène Jammes & Luisa Dandolo - 2010 - Bioessays 32 (6):473-480.
    The H19 gene produces a non‐coding RNA, which is abundantly expressed during embryonic development and down‐regulated after birth. Although this gene was discovered over 20 years ago, its function has remained unclear. Only recently a role was identified for the non‐coding RNA and/or its microRNA partner, first as a tumour suppressor gene in mice, then as a trans‐regulator of a group of co‐expressed genes belonging to the imprinted gene network that is likely to control foetal and early postnatal (...)
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  8.  15
    Processing of snoRNAs as a new source of regulatory non‐coding RNAs.Marina Falaleeva & Stefan Stamm - 2013 - Bioessays 35 (1):46-54.
    Recent experimental evidence suggests that most of the genome is transcribed into non‐coding RNAs. The initial transcripts undergo further processing generating shorter, metabolically stable RNAs with diverse functions. Small nucleolar RNAs (snoRNAs) are non‐coding RNAs that modify rRNAs, tRNAs, and snRNAs that were considered stable. We review evidence that snoRNAs undergo further processing. High‐throughput sequencing and RNase protection experiments showed widespread expression of snoRNA fragments, known as snoRNA‐derived RNAs (sdRNAs). Some sdRNAs resemble miRNAs, these can associate with argonaute (...)
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  9.  68
    RNA regulation of epigenetic processes.John S. Mattick, Paulo P. Amaral, Marcel E. Dinger, Tim R. Mercer & Mark F. Mehler - 2009 - Bioessays 31 (1):51-59.
    There is increasing evidence that dynamic changes to chromatin, chromosomes and nuclear architecture are regulated by RNA signalling. Although the precise molecular mechanisms are not well understood, they appear to involve the differential recruitment of a hierarchy of generic chromatin modifying complexes and DNA methyltransferases to specific loci by RNAs during differentiation and development. A significant fraction of the genome-wide transcription of non-protein coding RNAs may be involved in this process, comprising a previously hidden layer of intermediary genetic (...)
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  10.  19
    The long and the short of RNA maps.Jasmina Ponjavic & Chris P. Ponting - 2007 - Bioessays 29 (11):1077-1080.
    The landscapes of mammalian genomes are characterized by complex patterns of intersecting and overlapping sense and antisense transcription, giving rise to large numbers of coding and non‐proteincoding RNAs (ncRNAs). A recent report by Kapranov and colleagues1 describes three potentially novel classes of RNAs located at the very edges of proteincoding genes. The presence of RNAs from one of these classes appears to be correlated with the expression levels of their associated genes. These results suggest that (...)
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  11.  20
    When MicroRNAs Meet RNA Editing in Cancer: A Nucleotide Change Can Make a Difference.Yumeng Wang & Han Liang - 2018 - Bioessays 40 (2):1700188.
    RNA editing is a major post-transcriptional mechanism that changes specific nucleotides at the RNA level. The most common RNA editing type in humans is adenosine to inosine editing, which is mediated by ADAR enzymes. RNA editing events can not only change amino acids in proteins, but also affect the functions of non-coding RNAs such as miRNAs. Recent studies have characterized thousands of miRNA RNA editing events across different cancer types. Importantly, individual cases of miRNA editing have been reported to (...)
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  12.  6
    A Kuhnian revolution in molecular biology: Most genes in complex organisms express regulatory RNAs.John S. Mattick - 2023 - Bioessays 45 (9):2300080.
    Thomas Kuhn described the progress of science as comprising occasional paradigm shifts separated by interludes of ‘normal science’. The paradigm that has held sway since the inception of molecular biology is that genes (mainly) encode proteins. In parallel, theoreticians posited that mutation is random, inferred that most of the genome in complex organisms is non‐functional, and asserted that somatic information is not communicated to the germline. However, many anomalies appeared, particularly in plants and animals: the strange genetic phenomena of paramutation (...)
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  13.  19
    Regulation of Gene Expression and Replication Initiation by Non‐Coding Transcription: A Model Based on Reshaping Nucleosome‐Depleted Regions.Julien Soudet & Françoise Stutz - 2019 - Bioessays 41 (11):1900043.
    RNA polymerase II (RNAP II) non‐coding transcription is now known to cover almost the entire eukaryotic genome, a phenomenon referred to as pervasive transcription. As a consequence, regions previously thought to be non‐transcribed are subject to the passage of RNAP II and its associated proteins for histone modification. This is the case for the nucleosome‐depleted regions (NDRs), which provide key sites of entry into the chromatin for proteins required for the initiation of coding gene transcription and DNA replication. (...)
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  14.  10
    The multifaceted h TR telomerase RNA from a structural perspective.Maya Raghunandan & Anabelle Decottignies - 2021 - Bioessays 43 (10):2100099.
    Human telomerase progressively emerged as a multifaceted ribonucleoprotein complex with additional functions beyond telomeric repeat synthesis. Both the hTERT catalytic subunit and the hTR long non‐coding RNA (lncRNA) subunit are engaged in highly regulated cellular pathways that, together, contribute to cell fitness and protection against apoptosis. We recently described a new role for hTR in regulating the abundance of replication protein A at telomeres, adding to the growing repertoire of hTR’s functions. Here, we focus on the non‐canonical roles (...)
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  15. The development of non-coding RNA ontology.Jingshan Huang, Karen Eilbeck, Barry Smith, Judith Blake, Deijing Dou, Weili Huang, Darren Natale, Alan Ruttenberg, Jun Huan, Michael Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison Strachan, Nisansa de Silva & Mohan Vamsi Kasukurthi - 2016 - International Journal of Data Mining and Bioinformatics 15 (3):214--232.
    Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic (...)
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  16.  20
    The RNA dreamtime.Charles G. Kurland - 2010 - Bioessays 32 (10):866-871.
    Modern cells present no signs of a putative prebiotic RNA world. However, RNA coding is not a sine qua non for the accumulation of catalytic polypeptides. Thus, cellular proteins spontaneously fold into active structures that are resistant to proteolysis. The law of mass action suggests that binding domains are stabilized by specific interactions with their substrates. Random polypeptide synthesis in a prebiotic world has the potential to initially produce only a very small fraction of polypeptides that can fold spontaneously (...)
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  17.  22
    Long non‐coding RNA modifies chromatin.Alka Saxena & Piero Carninci - 2011 - Bioessays 33 (11):830-839.
    Common themes are emerging in the molecular mechanisms of long non‐coding RNA‐mediated gene repression. Long non‐coding RNAs (lncRNAs) participate in targeted gene silencing through chromatin remodelling, nuclear reorganisation, formation of a silencing domain and precise control over the entry of genes into silent compartments. The similarities suggest that these are fundamental processes of transcription regulation governed by lncRNAs. These findings have paved the way for analogous investigations on other lncRNAs and chromatin remodelling enzymes. Here we discuss these common (...)
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  18.  28
    Control of developmental timing by small temporal RNAs: a paradigm for RNA‐mediated regulation of gene expression.Diya Banerjee & Frank Slack - 2002 - Bioessays 24 (2):119-129.
    Heterochronic genes control the timing of developmental programs. In C. elegans, two key genes in the heterochronic pathway, lin-4 and let-7, encode small temporally expressed RNAs (stRNAs) that are not translated into protein. These stRNAs exert negative post-transcriptional regulation by binding to complementary sequences in the 3′ untranslated regions of their target genes. stRNAs are transcribed as longer precursor RNAs that are processed by the RNase Dicer/DCR-1 and members of the RDE-1/AGO1 family of proteins, which are better known for (...)
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  19. The Non-Coding RNA Ontology : a comprehensive resource for the unification of non-coding RNA biology.Huang Jingshan, Eilbeck Karen, Barry Smith, A. Blake Judith, Dou Dejing, Huang Weili, A. Natale Darren, Ruttenberg Alan, Huan Jun & T. Zimmermann Michael - 2016 - Journal of Biomedical Semantics 7 (1).
    In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary (...)
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  20.  15
    Non‐coding RNAs in Kawasaki disease: Molecular mechanisms and clinical implications.Fuqing Yang, Xiang Ao, Lin Ding, Lin Ye, Xuejuan Zhang, Lanting Yang, Zhonghao Zhao & Jianxun Wang - 2022 - Bioessays 44 (6):2100256.
    Kawasaki disease (KD) is an acute self‐limiting vasculitis with coronary complications, usually occurring in children. The incidence of KD in children is increasing year by year, mainly in East Asian countries, but relatively stably in Europe and America. Although studies on KD have been reported, the pathogenesis of KD is unknown. With the development of high‐throughput sequencing technology, growing number of regulatory noncoding RNAs (ncRNAs) including microRNA (miRNA), long noncoding RNA (lncRNA), and circular RNA (circRNA) have been identified to involved (...)
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  21.  23
    Long non‐coding RNAs in cancer metabolism.Zhen-Dong Xiao, Li Zhuang & Boyi Gan - 2016 - Bioessays 38 (10):991-996.
    Altered cellular metabolism is an emerging hallmark of cancer. Accumulating recent evidence links long non‐coding RNAs (lncRNAs), a still poorly understood class of non‐coding RNAs, to cancer metabolism. Here we review the emerging findings on the functions of lncRNAs in cancer metabolism, with particular emphasis on how lncRNAs regulate glucose and glutamine metabolism in cancer cells, discuss how lncRNAs regulate various aspects of cancer metabolism through their cross‐talk with other macromolecules, explore the mechanistic conceptual framework of lncRNAs in (...)
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  22.  25
    Long non‐coding RNAs in cancer metabolism.Zhen-Dong Xiao, Li Zhuang & Boyi Gan - 2016 - Bioessays 38 (10):991-996.
    Altered cellular metabolism is an emerging hallmark of cancer. Accumulating recent evidence links long non‐coding RNAs (lncRNAs), a still poorly understood class of non‐coding RNAs, to cancer metabolism. Here we review the emerging findings on the functions of lncRNAs in cancer metabolism, with particular emphasis on how lncRNAs regulate glucose and glutamine metabolism in cancer cells, discuss how lncRNAs regulate various aspects of cancer metabolism through their cross‐talk with other macromolecules, explore the mechanistic conceptual framework of lncRNAs in (...)
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  23.  17
    The agotrons: Gene regulators or Argonaute protectors?Lotte V. W. Stagsted, Iben Daugaard & Thomas B. Hansen - 2017 - Bioessays 39 (4):1600239.
    Over the last decades, it has become evident that highly complex networks of regulators govern post‐transcriptional regulation of gene expression. A novel class of Argonaute (Ago)‐associated RNA molecules, the agotrons, was recently shown to function in a Drosha‐ and Dicer‐independent manner, hence bypassing the maturation steps required for canonical microRNA (miRNA) biogenesis. Agotrons are found in most mammals and associate with Ago as ∼100 nucleotide (nt) long RNA species. Here, we speculate on the functional and biological relevance of agotrons: (i) (...)
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  24. A domain ontology for the non-coding RNA field.Jingshan Huang, Karen Eilbeck, Judith A. Blake, Dejing Dou, Darren A. Natale, Alan Ruttenberg, Barry Smith, Michael T. Zimmermann, Guoqian Jiang & Yu Lin - 2015 - In Huang Jingshan, Eilbeck Karen, Blake Judith A., Dou Dejing, Natale Darren A., Ruttenberg Alan, Smith Barry, Zimmermann Michael T., Jiang Guoqian & Lin Yu (eds.), IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2015). pp. 621-624.
    Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.
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  25.  29
    The non‐coding skin: Exploring the roles of long non‐coding RNAs in epidermal homeostasis and disease.Sonja Hombach & Markus Kretz - 2013 - Bioessays 35 (12):1093-1100.
    Long non‐coding RNAs (lncRNAs) have recently gained increasing attention because of their crucial roles in gene regulatory processes. Functional studies using mammalian skin as a model system have revealed their role in controlling normal tissue homeostasis as well as the transition to a diseased state. Here, we describe how lncRNAs regulate differentiation to preserve an undifferentiated epidermal progenitor compartment, and to maintain a functional skin permeability barrier. Furthermore, we will reflect on recent work analyzing the impact of lncRNAs on (...)
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  26.  12
    BioEssays in non-coding RNAs: A special collection of recent content.Andrew Moore - 2013 - Bioessays 35 (4):304-304.
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  27. The development of non-coding RNA ontology.Huang Jingshan, Eilbeck Karen, Smith Barry, Blake Judith, A. Dou, Dejing Huang, Weili Natale, A. Darren, Ruttenberg Alan, Huan Jun, Zimmermann Michael & T. Others - 2016 - International Journal of Data Mining and Bioinformatics 15 (3):214--232.
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  28.  12
    AUG as the Translation Start Codon in Circular RNA Molecules: A Connection between ProteinCoding Genes and Transfer RNAs?Paweł Mackiewicz - 2020 - Bioessays 42 (6):2000061.
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  29.  9
    GC‐content biases in proteincoding genes act as an “mRNA identity” feature for nuclear export.Alexander F. Palazzo & Yoon Mo Kang - 2021 - Bioessays 43 (2):2000197.
    It has long been observed that human proteincoding genes have a particular distribution of GC‐content: the 5′ end of these genes has high GC‐content while the 3′ end has low GC‐content. In 2012, it was proposed that this pattern of GC‐content could act as an mRNA identity feature that would lead to it being better recognized by the cellular machinery to promote its nuclear export. In contrast, junk RNA, which largely lacks this feature, would be retained in the (...)
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  30.  21
    The spliceosome: the most complex macromolecular machine in the cell?Timothy W. Nilsen - 2003 - Bioessays 25 (12):1147-1149.
    The primary transcripts, pre‐mRNAs, of almost all proteincoding genes in higher eukaryotes contain multiple non‐coding intervening sequences, introns, which must be precisely removed to yield translatable mRNAs. The process of intron excision, splicing, takes place in a massive ribonucleoprotein complex known as the spliceosome. Extensive studies, both genetic and biochemical, in a variety of systems have revealed that essential components of the spliceosome include five small RNAs–U1, U2, U4, U5 and U6, each of which functions as a (...)
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  31. Are all genes regulatory genes?Rosario Michael Piro - 2011 - Biology and Philosophy 26 (4):595-602.
    Although much has been learned about hereditary mechanisms since Gregor Mendel’s famous experiments, gene concepts have always remained vague, notwithstanding their central role in biology. During over hundred years of genetic research, gene concepts have often and dynamically changed to accommodate novel experimental findings, without ever providing a generally accepted definition of the ‘gene.’ Yet, the distinction between ‘regulatory genes’ and ‘structural genes’ has remained a common theme in modern gene concepts since the definition of the operon-model. This distinction is (...)
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  32.  27
    The interplay between transcription factors and microRNAs in genome‐scale regulatory networks.Natalia J. Martinez & Albertha J. M. Walhout - 2009 - Bioessays 31 (4):435-445.
    Metazoan genomes contain thousands of proteincoding and non‐coding RNA genes, most of which are differentially expressed, i.e., at different locations, at different times during development, or in response to environmental signals. Differential gene expression is achieved through complex regulatory networks that are controlled in part by two types of trans‐regulators: transcription factors (TFs) and microRNAs (miRNAs). TFs bind to cis‐regulatory DNA elements that are often located in or near their target genes, while miRNAs hybridize to cis‐regulatory RNA (...)
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  33.  11
    An embryonic story: Analysis of the gene regulative network controlling Xist expression in mouse embryonic stem cells.Pablo Navarro & Philip Avner - 2010 - Bioessays 32 (7):581-588.
    In mice, dosage compensation of X‐linked gene expression is achieved through the inactivation of one of the two X‐chromosomes in XX female cells. The complex epigenetic process leading to X‐inactivation is largely controlled by Xist and Tsix, two non‐coding genes of opposing function. Xist RNA triggers X‐inactivation by coating the inactive X, while Tsix is critical for the designation of the active X‐chromosome through cis‐repression of Xist RNA accumulation. Recently, a plethora of trans‐acting factors and cis‐regulating elements have been (...)
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  34.  11
    Lessons from viruses: Small non‐coding RNA meets transcription factors (comment on DOI 10.1002/bies.201500060).Jérôme Cavaillé - 2015 - Bioessays 37 (9):932-932.
  35.  17
    MicroRNAs at the epicenter of intestinal homeostasis.Antoaneta Belcheva - 2017 - Bioessays 39 (3).
    Maintaining intestinal homeostasis is a key prerequisite for a healthy gut. Recent evidence points out that microRNAs (miRNAs) act at the epicenter of the signaling networks regulating this process. The fine balance in the interaction between gut microbiota, intestinal epithelial cells, and the host immune system is achieved by constant transmission of signals and their precise regulation. Gut microbes extensively communicate with the host immune system and modulate host gene expression. On the other hand, sensing of gut microbiota by the (...)
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  36.  13
    Deciphering the protein‐RNA recognition code: Combining large‐scale quantitative methods with structural biology.Janosch Hennig & Michael Sattler - 2015 - Bioessays 37 (8):899-908.
    RNA binding proteins (RBPs) are key factors for the regulation of gene expression by binding to cis elements, i.e. short sequence motifs in RNAs. Recent studies demonstrate that cooperative binding of multiple RBPs is important for the sequence‐specific recognition of RNA and thereby enables the regulation of diverse biological activities by a limited set of RBPs. Cross‐linking immuno‐precipitation (CLIP) and other recently developed high‐throughput methods provide comprehensive, genome‐wide maps of protein‐RNA interactions in the cell. Structural biology gives detailed insights (...)
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  37.  8
    An emerging role of transcription in chromosome segregation: Ongoing centromeric transcription maintains centromeric cohesion.Yujue Chen, Qian Zhang & Hong Liu - 2022 - Bioessays 44 (1):2100201.
    Non‐coding centromeres, which dictate kinetochore formation for proper chromosome segregation, are extremely divergent in DNA sequences across species but are under active transcription carried out by RNA polymerase (RNAP) II. The RNAP II‐mediated centromeric transcription has been shown to facilitate the deposition of the centromere protein A (CENP‐A) to centromeres, establishing a conserved and critical role of centromeric transcription in centromere maintenance. Our recent work revealed another role of centromeric transcription in chromosome segregation: maintaining centromeric cohesion during mitosis. (...)
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  38.  10
    Alternative polyadenylation in the nervous system: To what lengths will 3′ UTR extensions take us?Pedro Miura, Piero Sanfilippo, Sol Shenker & Eric C. Lai - 2014 - Bioessays 36 (8):766-777.
    Alternative cleavage and polyadenylation (APA) can diversify coding and non‐coding regions, but has particular impact on increasing 3′ UTR diversity. Through the gain or loss of regulatory elements such as RNA binding protein and microRNA sites, APA can influence transcript stability, localization, and translational efficiency. Strikingly, the central nervous systems of invertebrate and vertebrate species express a broad range of transcript isoforms bearing extended 3′ UTRs. The molecular mechanism that permits proximal 3′ end bypass in neurons is (...)
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  39.  27
    Impact of RNA–Protein Interaction Modes on Translation Control: The Versatile Multidomain Protein Gemin5.Rosario Francisco-Velilla, Embarc-Buh Azman & Encarnacion Martinez-Salas - 2019 - Bioessays 41 (4):1800241.
    The fate of cellular RNAs is largely dependent on their structural conformation, which determines the assembly of ribonucleoprotein (RNP) complexes. Consequently, RNA‐binding proteins (RBPs) play a pivotal role in the lifespan of RNAs. The advent of highly sensitive in cellulo approaches for studying RNPs reveals the presence of unprecedented RNA‐binding domains (RBDs). Likewise, the diversity of the RNA targets associated with a given RBP increases the code of RNA–protein interactions. Increasing evidence highlights the biological relevance of RNA conformation for (...)
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  40.  13
    Critical regulatory levels in tumor differentiation: Signaling pathways, epigenetics and non‐coding transcripts.Fatemeh Zolghadr, Babak Bakhshinejad, Sapir Davuchbabny, Babak Sarrafpour & Naisana Seyedasli - 2021 - Bioessays 43 (5):2000190.
    Approaches to induce tumor differentiation often result in manageable and therapy‐naïve cellular states in cancer cells. This transformation is achieved by activating pathways that drive tumor cells away from plasticity, a state that commonly correlates with enhanced aggression, metastasis and resistance to therapy. Here, we discuss signaling pathways, epigenetics and non‐coding RNAs as three main regulatory levels with the potential to drive tumor differentiation and hence as potential targets in differentiation therapy approaches. The success of an effective therapeutic regimen (...)
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  41.  40
    An RNA Phage Lab: MS2 in Walter Fiers’ Laboratory of Molecular Biology in Ghent, from Genetic Code to Gene and Genome, 1963–1976. [REVIEW]Jérôme Pierrel - 2012 - Journal of the History of Biology 45 (1):109 - 138.
    The importance of viruses as model organisms is well-established in molecular biology and Max Delbrück's phage group set standards in the DNA phage field. In this paper, I argue that RNA phages, discovered in the 1960s, were also instrumental in the making of molecular biology. As part of experimental systems, RNA phages stood for messenger RNA (mRNA), genes and genome. RNA was thought to mediate information transfers between DNA and proteins. Furthermore, RNA was more manageable at the bench than DNA (...)
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  42.  10
    An RNA Phage Lab: MS2 in Walter Fiers’ Laboratory of Molecular Biology in Ghent, from Genetic Code to Gene and Genome, 1963–1976. [REVIEW]Jérôme Pierrel - 2012 - Journal of the History of Biology 45 (1):109-138.
    The importance of viruses as model organisms is well-established in molecular biology and Max Delbrück’s phage group set standards in the DNA phage field. In this paper, I argue that RNA phages, discovered in the 1960s, were also instrumental in the making of molecular biology. As part of experimental systems, RNA phages stood for messenger RNA, genes and genome. RNA was thought to mediate information transfers between DNA and proteins. Furthermore, RNA was more manageable at the bench than DNA due (...)
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  43.  21
    Functional interpretation of non‐coding sequence variation: Concepts and challenges.Dirk S. Paul, Nicole Soranzo & Stephan Beck - 2014 - Bioessays 36 (2):191-199.
    Understanding the functional mechanisms underlying genetic signals associated with complex traits and common diseases, such as cancer, diabetes and Alzheimer's disease, is a formidable challenge. Many genetic signals discovered through genome‐wide association studies map to non‐protein coding sequences, where their molecular consequences are difficult to evaluate. This article summarizes concepts for the systematic interpretation of non‐coding genetic signals using genome annotation data sets in different cellular systems. We outline strategies for the global analysis of multiple association intervals (...)
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  44.  11
    RNA at DNA Double‐Strand Breaks: The Challenge of Dealing with DNA:RNA Hybrids.Judit Domingo-Prim, Franziska Bonath & Neus Visa - 2020 - Bioessays 42 (5):1900225.
    RNA polymerase II is recruited to DNA double‐strand breaks (DSBs), transcribes the sequences that flank the break and produces a novel RNA type that has been termed damage‐induced long non‐coding RNA (dilncRNA). DilncRNAs can be processed into short, miRNA‐like molecules or degraded by different ribonucleases. They can also form double‐stranded RNAs or DNA:RNA hybrids. The DNA:RNA hybrids formed at DSBs contribute to the recruitment of repair factors during the early steps of homologous recombination (HR) and, in this way, contribute (...)
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  45.  26
    Nonsense‐mediated RNA decay – a switch and dial for regulating gene expression.Jenna E. Smith & Kristian E. Baker - 2015 - Bioessays 37 (6):612-623.
    Nonsense‐mediated RNA decay (NMD) represents an established quality control checkpoint for gene expression that protects cells from consequences of gene mutations and errors during RNA biogenesis that lead to premature termination during translation. Characterization of NMD‐sensitive transcriptomes has revealed, however, that NMD targets not only aberrant transcripts but also a broad array of mRNA isoforms expressed from many endogenous genes. NMD is thus emerging as a master regulator that drives both fine and coarse adjustments in steady‐state RNA levels in the (...)
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  46.  12
    CLIPing Staufen to secondary RNA structures: Size and location matter!Sandra M. Fernández Moya & Michael A. Kiebler - 2015 - Bioessays 37 (10):1062-1066.
    hiCLIP (RNA hybrid and individual‐nucleotide resolution ultraviolet cross‐linking and immunoprecipitation), is a novel technique developed by Sugimoto et al. (2015). Here, the use of different adaptors permits a controlled ligation of the two strands of a RNA duplex allowing the identification of each arm in the duplex upon sequencing. The authors chose a notoriously difficult to study double‐stranded RNA‐binding protein (dsRBP) termed Staufen1, a mammalian homolog of Drosophila Staufen involved in mRNA localization and translational control. Using hiCLIP, they discovered (...)
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  47. DNA Habitats and Their RNA Inhabitants.Guenther Witzany (ed.) - 2015
    Most molecular biological concepts derive from physical chemical assumptions about the genetic code that are basically more than 40 years old. Additionally, systems biology, another quantitative approach, investigates the sum of interrelations to obtain a more holistic picture of nucleotide sequence order. Recent empirical data on genetic code compositions and rearrangements by mobile genetic elements and non-coding RNAs, together with results of virus research and their role in evolution, does not really fit into these concepts and compel a re-examination. (...)
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  48.  45
    Recombination between RNA viruses and plasmids might have played a central role in the origin and evolution of small DNA viruses.Mart Krupovic - 2012 - Bioessays 34 (10):867-870.
    Graphical AbstractThe finding that viruses with RNA and DNA genomes can recombine to produce chimeric entities provides valuable insights into the origin and evolution of viruses. It also substantiates the hypothesis that certain groups of DNA viruses could have emerged from plasmids via acquisition of capsid protein-coding genes from RNA viruses.
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  49.  7
    Analyses critiques de ľexpression génétique.Par Walter Wahli - 1982 - Dialectica 36 (1):71-81.
    ResumeLa question du filtrage de ľinformation génétique dans la cellule est fondamentale. Comment la cellule sélectionne‐t‐elle, avant de les transformer en RNA puis en protéines, certaines parties bien déterminées de son information génétique? Il ne sera probablement pas possible de donner une explication cohérente du développement embryonnaire, de la différentiation cellulaire et du maintien de ľétat différencie tant que nous n'aurons pas repondu de manière satis‐faisante à cette question.Dans un premier chapitre, quelques notions de base concernant ľexpression génétique sont préséntées. (...)
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  50.  19
    Factors contributing to the outcome of oxidative damage to nucleic acids.Mark D. Evans & Marcus S. Cooke - 2004 - Bioessays 26 (5):533-542.
    Oxidative damage to DNA appears to be a factor in cancer, yet explanations for why highly elevated levels of such lesions do not always result in cancer remain elusive. Much of the genome is non‐coding and lesions in these regions might be expected to have little biological effect, an inference supported by observations that there is preferential repair of coding sequences. RNA has an important coding function in protein synthesis, and yet the consequences of RNA oxidation (...)
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