scholarly journals Rrp47 functions in RNA surveillance and stable RNA processing when divorced from the exoribonuclease and exosome-binding domains of Rrp6

RNA ◽  
2013 ◽  
Vol 19 (12) ◽  
pp. 1659-1668 ◽  
Author(s):  
W. Garland ◽  
M. Feigenbutz ◽  
M. Turner ◽  
P. Mitchell
Keyword(s):  
Rna Processing ◽  
Rna Surveillance ◽  
Binding Domains

scholarly journals A meiotic gene regulatory cascade driven by alternative fates for newly synthesized transcripts

2011 ◽  
Vol 22 (1) ◽  
pp. 66-77 ◽  
Author(s):  
Nicole Cremona ◽  
Kristine Potter ◽  
Jo Ann Wise
Keyword(s):  
Fission Yeast ◽  
Rna Processing ◽  
Yeast Cells ◽  
Forkhead Transcription Factor ◽  
Rna Surveillance ◽  
Regulatory Cascade ◽  
Show Evidence ◽  
Gene Regulatory ◽  
Rna Accumulation ◽  
Temporal Profiles

To determine the relative importance of transcriptional regulation versus RNA processing and turnover during the transition from proliferation to meiotic differentiation in the fission yeast Schizosaccharomyces pombe, we analyzed temporal profiles and effects of RNA surveillance factor mutants on expression of 32 meiotic genes. A comparison of nascent transcription with steady-state RNA accumulation reveals that the vast majority of these genes show a lag between maximal RNA synthesis and peak RNA accumulation. During meiosis, total RNA levels parallel 3′ processing, which occurs in multiple, temporally distinct waves that peak from 3 to 6 h after meiotic induction. Most early genes and one middle gene, mei4, share a regulatory mechanism in which a specialized RNA surveillance factor targets newly synthesized transcripts for destruction. Mei4p, a member of the forkhead transcription factor family, in turn regulates a host of downstream genes. Remarkably, a spike in transcription is observed for less than one-third of the genes surveyed, and even these show evidence of RNA-level regulation. In aggregate, our findings lead us to propose that a regulatory cascade driven by changes in processing and stability of newly synthesized transcripts operates alongside the well-known transcriptional cascade as fission yeast cells enter meiosis.

Regulated and quality-control mRNA turnover pathways in eukaryotes

2010 ◽  
Vol 38 (6) ◽  
pp. 1506-1510 ◽  
Author(s):  
Boris Reznik ◽  
Jens Lykke-Andersen
Keyword(s):  
Quality Control ◽  
Rna Processing ◽  
Rna Localization ◽  
Rna Degradation ◽  
Eukaryotic Cells ◽  
Mrna Turnover ◽  
Surveillance Systems ◽  
Rna Turnover ◽  
Rna Surveillance ◽  
Multiple Levels

Gene expression can be regulated at multiple levels, including transcription, RNA processing, RNA localization, translation and, finally, RNA turnover. RNA degradation may occur at points along the processing pathway or during translation as it undergoes quality control by RNA surveillance systems. Alternatively, mRNAs may be subject to regulated degradation, often mediated by cis-encoded determinants in the mRNA sequence that, through the recruitment of trans factors, determine the fate of the mRNA. The aim of the present review is to highlight mechanisms of regulated and quality-control RNA degradation in eukaryotic cells, with an emphasis on mammals.

Comparison of the yeast and human nuclear exosome complexes

2012 ◽  
Vol 40 (4) ◽  
pp. 850-855 ◽  
Author(s):  
Katherine E. Sloan ◽  
Claudia Schneider ◽  
Nicholas J. Watkins
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Processing ◽  
Eukaryotic Cells ◽  
Multiprotein Complex ◽  
Yeast Saccharomyces Cerevisiae ◽  
Rna Surveillance ◽  
Mature Transcript ◽  
Nuclear Exosome ◽  
And Function ◽  
Rna Maturation

Most RNAs in eukaryotic cells are produced as precursors that undergo processing at the 3′ and/or 5′ end to generate the mature transcript. In addition, many transcripts are degraded not only as part of normal recycling, but also when recognized as aberrant by the RNA surveillance machinery. The exosome, a conserved multiprotein complex containing two nucleases, is involved in both the 3′ processing and the turnover of many RNAs in the cell. A series of factors, including the TRAMP (Trf4–Air2–Mtr4 polyadenylation) complex, Mpp6 and Rrp47, help to define the targets to be processed and/or degraded and assist in exosome function. The majority of the data on the exosome and RNA maturation/decay have been derived from work performed in the yeast Saccharomyces cerevisiae. In the present paper, we provide an overview of the exosome and its role in RNA processing/degradation and discuss important new insights into exosome composition and function in human cells.

scholarly journals DER containing two consecutive GTP-binding domains plays an essential role in chloroplast ribosomal RNA processing and ribosome biogenesis in higher plants

2013 ◽  
Vol 65 (1) ◽  
pp. 117-130 ◽  
Author(s):  
Young Jeon ◽  
Chang Sook Ahn ◽  
Hyun Ju Jung ◽  
Hunseung Kang ◽  
Guen Tae Park ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Rna Processing ◽  
Ribosome Biogenesis ◽  
Essential Role ◽  
Higher Plants ◽  
Binding Domains ◽  
Gtp Binding ◽  
Ribosomal Rna Processing

scholarly journals U1 snRNP-Dependent Function of TIAR in the Regulation of Alternative RNA Processing of the Human Calcitonin/CGRP Pre-mRNA

2003 ◽  
Vol 23 (17) ◽  
pp. 5959-5971 ◽  
Author(s):  
Hui Zhu ◽  
Robert A. Hasman ◽  
Katherine M. Young ◽  
Nancy L. Kedersha ◽  
Hua Lou
Keyword(s):  
Splice Site ◽  
Rna Processing ◽  
Rna Binding ◽  
Sequence Motif ◽  
Human Calcitonin ◽  
Sequence Motifs ◽  
Multiple Sequence ◽  
Enhancer Element ◽  
Binding Domains ◽  
U6 Snrna

ABSTRACT Alternative RNA processing of human calcitonin/CGRP pre-mRNA is regulated by an intronic enhancer element. Previous studies have demonstrated that multiple sequence motifs within the enhancer and a number of trans-acting factors play critical roles in the regulation. Here, we report the identification of TIAR as a novel player in the regulation of human calcitonin/CGRP alternative RNA processing. TIAR binds to the U tract sequence motif downstream of a pseudo 5′ splice site within the previously characterized intron enhancer element. Binding of TIAR promotes inclusion of the alternative 3′-terminal exon located more than 200 nucleotides upstream from the U tract. In cells that preferentially include this exon, overexpression of a mutant TIAR that lacks the RNA binding domains suppressed inclusion of this exon. In this report, we also demonstrate an unusual novel interaction between U6 snRNA and the pseudo 5′ splice site, which was shown previously to bind U1 snRNA. Interestingly, TIAR binding to the U tract sequence depends on the interaction of not only U1 but also U6 snRNA with the pseudo 5′ splice site. Conversely, TIAR binding promotes U6 snRNA binding to its target. The synergistic relationship between TIAR and U6 snRNA strongly suggests a novel role of U6 snRNP in regulated alternative RNA processing.

scholarly journals Pet127p, a membrane-associated protein involved in stability and processing of Saccharomyces cerevisiae mitochondrial RNAs.

1997 ◽  
Vol 17 (5) ◽  
pp. 2816-2824 ◽  
Author(s):  
G Wiesenberger ◽  
T D Fox
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Processing ◽  
Mitochondrial Gene ◽  
Mitochondrial Gene Expression ◽  
Wild Type ◽  
Rna Surveillance ◽  
Nuclear Mutations ◽  
Membrane Bound ◽  
The Stability ◽  
Untranslated Leaders

Nuclear mutations that inactivate the Saccharomyces cerevisiae gene PET127 dramatically increased the levels of mutant COX3 and COX2 mitochondrial mRNAs that were destabilized by mutations in their 5' untranslated leaders. The stabilizing effect of pet127 delta mutations occurred both in the presence and in the absence of translation. In addition, pet127 delta mutations had pleiotropic effects on the stability and 5' end processing of some wild-type mRNAs and the 15S rRNA but produced only a leaky nonrespiratory phenotype at 37 degrees C. Overexpression of PET127 completely blocked respiratory growth and caused cells to lose wild-type mitochondrial DNA, suggesting that too much Pet127p prevents mitochondrial gene expression. Epitope-tagged Pet127p was specifically located in mitochondria and associated with membranes. These findings suggest that Pet127p plays a role in RNA surveillance and/or RNA processing and that these functions may be membrane bound in yeast mitochondria.

scholarly journals RNA processing machineries in Archaea: the 5’-3’ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3’-5’ exoribonucleolytic RNA exosome machinery

2019 ◽  
Author(s):  
Duy Khanh Phung ◽  
Clarisse Etienne ◽  
Manon Batista ◽  
Petra Langendijk-Genevaux ◽  
Yann Moalic ◽  
...  
Keyword(s):  
Rna Processing ◽  
Cell Extract ◽  
Rna Helicases ◽  
Rna Surveillance ◽  
Protein Protein Interaction ◽  
Rna Exosome ◽  
First Time

ABSTRACTA network of RNA helicases, endoribonucleases, and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focused on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5’-3’ exoribonuclease of the β-CASP family conserved in Euryarchaea, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, and that this occurs in the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses demonstrated that aRNase J interplay with ASH-Ski2 and the Csl4 cap exosome subunit. These in vitro data are strengthened by our phylogenomic studies showing a taxonomic co-distribution of aRNase J and ASH-Ski2 among the archaeal phylogeny. Finally, our T. barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome or polysomes that is stressed in absence of ASH-Ski2. While aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest, for the first time, a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism. Finally, our results position aRNase J at the junction of RNA surveillance and translation processes, thus opening new perspectives and evolutionary scenario on RNA processing players in Archaea.

scholarly journals RNA surveillance controls 3D genome structure via stable cohesin-chromosome interaction

2021 ◽  
Author(s):  
Yujin Chun ◽  
Sungwook Han ◽  
Taemook Kim ◽  
Yoonjung Choi ◽  
Daeyoup Lee
Keyword(s):  
Rna Processing ◽  
Genome Structure ◽  
Embryonic Stem ◽  
Rna Surveillance ◽  
Cis Acting ◽  
3D Genome ◽  
Wide Range ◽  
Domain Boundaries ◽  
3D Architecture ◽  
Processing Factors

The 3D architecture that the genome is folded into is regulated by CTCF, which determines domain borders, and cohesin, which generates interactions within domains. However, organisms lacking CTCF have been reported to still have cohesin-mediated 3D structures with strong borders. How this can be achieved and precisely regulated are yet unknown. Using in situ Hi-C, we found that 3'-end RNA processing factors coupled with proper transcription termination are a cis-acting determinant that regulates the localization and dynamics of cohesin on the chromosome arms. Loss of RNA processing factors, including nuclear exosome and Pfs2, destabilizes cohesin from the 3'-ends of convergent genes and results in decreased cohesin-mediated domain boundaries. We observed the co-localization between Rad21 and a wide range of 3'end RNA processing/termination factors. Further, deletion of Rrp6 leads to cohesin redistribution to facultative heterochromatin, resulting in improper domain boundaries. Importantly, we observed that knockdown of Rrp6/Exosc10 caused a defect in cohesin binding and loss of local topologically associating domains (TADs) interactions in mouse embryonic stem cells. Based on these findings, we propose a novel function of the RNA surveillance pathway in 3D genome organization via cohesin complex, which provides the molecular basis underlying the dynamics of cohesin function.

scholarly journals RNA processing machineries in Archaea: the 5′-3′ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3′-5′ exoribonucleolytic RNA exosome machinery

2020 ◽  
Vol 48 (7) ◽  
pp. 3832-3847 ◽  
Author(s):  
Duy Khanh Phung ◽  
Clarisse Etienne ◽  
Manon Batista ◽  
Petra Langendijk-Genevaux ◽  
Yann Moalic ◽  
...  
Keyword(s):  
Rna Processing ◽  
Cell Extract ◽  
Rna Helicases ◽  
Rna Surveillance ◽  
Protein Protein Interaction ◽  
Rna Exosome ◽  
Whole Cell Extract

Abstract A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5′-3′ exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein–protein interaction analyses, strengthened by comprehensive phylogenomic studies demonstrated that aRNase J interplay with ASH-Ski2 and a cap exosome subunit. Finally, Thermococcus barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome that is emphasised in absence of ASH-Ski2. Whilst aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism.

Genomic analysis of C-type lectins

2002 ◽  
Vol 69 ◽  
pp. 59-72 ◽  
Author(s):  
Kurt Drickamer ◽  
Andrew J. Fadden
Keyword(s):  
Biological Effects ◽  
Cell Signalling ◽  
Genomic Analysis ◽  
Binding Activity ◽  
Immunoglobulin Superfamily ◽  
Carbohydrate Binding ◽  
Carbohydrate Recognition ◽  
Calcium Dependent ◽  
Binding Domains ◽  
Carbohydrate Recognition Domains

Many biological effects of complex carbohydrates are mediated by lectins that contain discrete carbohydrate-recognition domains. At least seven structurally distinct families of carbohydrate-recognition domains are found in lectins that are involved in intracellular trafficking, cell adhesion, cell–cell signalling, glycoprotein turnover and innate immunity. Genome-wide analysis of potential carbohydrate-binding domains is now possible. Two classes of intracellular lectins involved in glycoprotein trafficking are present in yeast, model invertebrates and vertebrates, and two other classes are present in vertebrates only. At the cell surface, calcium-dependent (C-type) lectins and galectins are found in model invertebrates and vertebrates, but not in yeast; immunoglobulin superfamily (I-type) lectins are only found in vertebrates. The evolutionary appearance of different classes of sugar-binding protein modules parallels a development towards more complex oligosaccharides that provide increased opportunities for specific recognition phenomena. An overall picture of the lectins present in humans can now be proposed. Based on our knowledge of the structures of several of the C-type carbohydrate-recognition domains, it is possible to suggest ligand-binding activity that may be associated with novel C-type lectin-like domains identified in a systematic screen of the human genome. Further analysis of the sequences of proteins containing these domains can be used as a basis for proposing potential biological functions.

Sign in / Sign up

Export Citation Format

Share Document