Abstract：
:Ribosome biogenesis is a dynamic multistep process, many features of which are still incompletely documented. Here, we show that changes in this pathway can be captured and annotated by means of a graphic set of pre-rRNA ratios, a technique we call Ratio Analysis of Multiple Precursors (RAMP). We find that knocking down a ribosome synthesis factor produces a characteristic RAMP profile that exhibits consistency across a range of depletion levels. This facilitates the inference of affected steps and simplifies comparative analysis. We applied RAMP to examine how endonucleolytic cleavages of the mouse pre-rRNA transcript in the internal transcribed spacer 1 (ITS1) are affected by depletion of factors required for maturation of the small ribosomal subunit (Rcl1, Fcf1/Utp24, Utp23) and the large subunit (Pes1, Nog1). The data suggest that completion of early maturation in a subunit triggers its release from the common pre-rRNA transcript by stimulating cleavage at the proximal site in ITS1. We also find that splitting of pre-rRNA in the 3' region of ITS1 is prevalent in adult mouse tissues and quiescent cells, as it is in human cells. We propose a model for subunit separation during mammalian ribosome synthesis and discuss its implications for understanding pre-rRNA processing pathways.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Wang M,Anikin L,Pestov DGdoi
10.1093/nar/gku787subject
Has Abstractpub_date
2014-01-01 00:00:00pages
11180-91issue
17eissn
0305-1048issn
1362-4962pii
gku787journal_volume
42pub_type
杂志文章abstract：:Overexpression of the flap endonuclease FEN1 has been observed in a variety of cancer types and is a marker for poor prognosis. To better understand the cellular consequences of FEN1 overexpression we utilized a model of its Saccharomyces cerevisiae homolog, RAD27. In this system, we discovered that flap endonuclease ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky313
更新日期：2018-06-20 00:00:00
abstract：:enod40 is a plant gene that participates in the regulation of symbiotic interaction between leguminous plants and bacteria or fungi. Furthermore, it has been suggested to play a general role in non-symbiotic plant development. Although enod40 seems to have multiple functions, being present in many land plants, the mol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm173
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abstract：:Cell-free extracts employed as chromatin assembly systems contain a myriad of proteins, polyanions and nucleic acids. The roles of ATP, MgCl2 and other cofactors in the catalysis of nucleosome formation by the Xenopus laevis oocyte S-150 have yet to be established unequivocally. In this study we examine the influence ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.4.889
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abstract：:Mollusca represents the second largest animal phylum but remains poorly explored from a genomic perspective. While the recent increase in genomic resources holds great promise for a deep understanding of molluscan biology and evolution, access and utilization of these resources still pose a challenge. Here, we present...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa918
更新日期：2021-01-08 00:00:00
abstract：:We have developed a new bioinformatics approach called ECMFinder (Evolutionary Conserved Motif Finder). This program searches for a given DNA motif within the entire genome of one species and uses the gene association information of a potential transcription factor-binding site (TFBS) to screen the homologous regions ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp077
更新日期：2009-04-01 00:00:00
abstract：:In Pseudomonas aeruginosa the RNA chaperone Hfq and the catabolite repression control protein (Crc) act as post-transcriptional regulators during carbon catabolite repression (CCR). In this regard Crc is required for full-fledged Hfq-mediated translational repression of catabolic genes. RNAseq based transcriptome anal...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1245
更新日期：2018-02-16 00:00:00
abstract：:This article describes recent developments of Europe PMC (http://europepmc.org), the leading database for life science literature. Formerly known as UKPMC, the service was rebranded in November 2012 as Europe PMC to reflect the scope of the funding agencies that support it. Several new developments have enriched Europ...
journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2015-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1117
更新日期：2016-01-04 00:00:00
abstract：:This review takes a second look at a set of mRNAs that purportedly employ an alternative mechanism of initiation when cap-dependent translation is reduced during mitosis or stress conditions. A closer look is necessary because evidence cited in support of the internal initiation hypothesis is often flawed. When putati...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
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更新日期：2005-11-28 00:00:00
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journal_title：Nucleic acids research
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更新日期：2012-06-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2008-02-01 00:00:00
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journal_title：Nucleic acids research
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doi：10.1093/nar/gkz424
更新日期：2019-07-02 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.21.5013
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abstract：:We have isolated a rat cDNA, named FE65, hybridizing to an mRNA of about 2,300 nucleotides present in rat brain, undetectable in rat liver and very poorly represented in other tissues. An mRNA of the same size is present in human neuroblastoma cells and is absent from other human cell lines. The FE65 cDNA contains an ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.19.5269
更新日期：1991-10-11 00:00:00
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journal_title：Nucleic acids research
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更新日期：2002-07-15 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnh172
更新日期：2004-12-07 00:00:00
abstract：:Mitochondrial DNA maintenance and segregation are dependent on the actin cytoskeleton in budding yeast. We found two cytoskeletal proteins among six proteins tightly associated with rat liver mitochondrial DNA: non-muscle myosin heavy chain IIA and β-actin. In human cells, transient gene silencing of MYH9 (encoding no...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr052
更新日期：2011-07-01 00:00:00
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journal_title：Nucleic acids research
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更新日期：2011-07-01 00:00:00
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journal_title：Nucleic acids research
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更新日期：2016-11-02 00:00:00
abstract：:Topoisomerase II is an essential enzyme that is required for virtually every process that requires movement of DNA within the nucleus or the opening of the double helix. This enzyme helps to regulate DNA under- and overwinding and removes knots and tangles from the genetic material. In order to carry out its critical ...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
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更新日期：2009-02-01 00:00:00
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journal_title：Nucleic acids research
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更新日期：2017-07-03 00:00:00
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journal_title：Nucleic acids research
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更新日期：2005-07-01 00:00:00
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journal_title：Nucleic acids research
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更新日期：2015-01-01 00:00:00
abstract：:Alfalfa mosaic virus RNA 4, the subgenomic messenger for viral coat protein, was partially digested with RNase T1 or RNase A and the sequence of a number of fragments was deduced by in vitro labeling with polynucleotide kinase and application of RNA sequencing techniques. From overlapping fragments, the complete prima...
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.21.10283
更新日期：1988-11-11 00:00:00
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pub_type： 杂志文章
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更新日期：2007-01-01 00:00:00
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journal_title：Nucleic acids research
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abstract：:Cellular RNA labeling strategies based on bioorthogonal chemical reactions are much less developed in comparison to glycan, protein and DNA due to its inherent instability and lack of effective methods to introduce bioorthogonal reactive functionalities (e.g. azide) into RNA. Here we report the development of a simple...
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更新日期：2016-01-29 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2004-09-23 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.18.4121
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