scholarly journals Long-range RNA interaction of two sequence elements required for endonucleolytic cleavage of human insulin-like growth factor II mRNAs.

1995 ◽  
Vol 15 (1) ◽  
pp. 235-245 ◽  
Author(s):  
W Scheper ◽  
D Meinsma ◽  
P E Holthuizen ◽  
J S Sussenbach
Keyword(s):  
Growth Factor ◽  
Long Range ◽  
Cleavage Site ◽  
Untranslated Region ◽  
Cleavage Product ◽  
Coding Region ◽  
Endonucleolytic Cleavage ◽  
Factor Ii ◽  
Sequence Elements ◽  
Rna Interaction

Human insulin-like growth factor II (IGF-II) mRNAs are subject to site-specific endonucleolytic cleavage in the 3' untranslated region, leading to an unstable 5' cleavage product containing the IGF-II coding region and a very stable 3' cleavage product of 1.8 kb. This endonucleolytic cleavage is most probably the first and rate-limiting step in degradation of IGF-II mRNAs. Two sequence elements within the 3' untranslated region are required for cleavage: element I, located approximately 2 kb upstream of the cleavage site, and element II, encompassing the cleavage site itself. We have identified a stable double-stranded RNA stem structure (delta G = -100 kcal/mol [418.4 kJ/mol]) that can be formed between element I and a region downstream of the cleavage site in element II. This structure is conserved among human, rat, and mouse mRNAs. Detailed analysis of the requirements for cleavage shows that the relative position of the elements is not essential for cleavage. Furthermore, the distance between the coding region and the cleavage site does not affect the cleavage reaction. Mutational analysis of the long-range RNA-RNA interaction shows that not only the double-stranded character but also the sequence of the stable RNA stem is important for cleavage.

scholarly journals Studies of the 5′ Exonuclease and Endonuclease Activities of CPSF-73 in Histone Pre-mRNA Processing

2008 ◽  
Vol 29 (1) ◽  
pp. 31-42 ◽  
Author(s):  
Xiao-cui Yang ◽  
Kelly D. Sullivan ◽  
William F. Marzluff ◽  
Zbigniew Dominski
Keyword(s):  
Cleavage Site ◽  
Complete Removal ◽  
Cleavage Product ◽  
Endonucleolytic Cleavage ◽  
Subsequent Degradation ◽  
U7 Snrnp ◽  
Space Requirements ◽  
Polyadenylation Factor

ABSTRACT Processing of histone pre-mRNA requires a single 3′ endonucleolytic cleavage guided by the U7 snRNP that binds downstream of the cleavage site. Following cleavage, the downstream cleavage product (DCP) is rapidly degraded in vitro by a nuclease that also depends on the U7 snRNP. Our previous studies demonstrated that the endonucleolytic cleavage is catalyzed by the cleavage/polyadenylation factor CPSF-73. Here, by using RNA substrates with different nucleotide modifications, we characterize the activity that degrades the DCP. We show that the degradation is blocked by a 2′-O-methyl nucleotide and occurs in the 5′-to-3′ direction. The U7-dependent 5′ exonuclease activity is processive and continues degrading the DCP substrate even after complete removal of the U7-binding site. Thus, U7 snRNP is required only to initiate the degradation. UV cross-linking studies demonstrate that the DCP and its 5′-truncated version specifically interact with CPSF-73, strongly suggesting that in vitro, the same protein is responsible for the endonucleolytic cleavage of histone pre-mRNA and the subsequent degradation of the DCP. By using various RNA substrates, we define important space requirements upstream and downstream of the cleavage site that dictate whether CPSF-73 functions as an endonuclease or a 5′ exonuclease. RNA interference experiments with HeLa cells indicate that degradation of the DCP does not depend on the Xrn2 5′ exonuclease, suggesting that CPSF-73 degrades the DCP both in vitro and in vivo.

A new 5′-non-coding region for human placental insulin-like growth factor II mRNA expression

FEBS Letters ◽  
1987 ◽  
Vol 222 (1) ◽  
pp. 181-185 ◽  
Author(s):  
Y. Le Bouc ◽  
P. Noguiez ◽  
P. Sondermeijer ◽  
D. Dreyer ◽  
F. Girard ◽  
...  
Keyword(s):  
Growth Factor ◽  
Mrna Expression ◽  
Insulin Like Growth Factor ◽  
Coding Region ◽  
Factor Ii

scholarly journals A guanosine quadruplex and two stable hairpins flank a major cleavage site in insulin-like growth factor II mRNA

1994 ◽  
Vol 22 (25) ◽  
pp. 5709-5716 ◽  
Author(s):  
Jan Christiansen ◽  
Margrethe Kofod ◽  
Finn C. Nielsen
Keyword(s):  
Growth Factor ◽  
Cleavage Site ◽  
Insulin Like Growth Factor ◽  
Factor Ii

scholarly journals Structural and functional analysis of the roles of the HCV 5′ NCR miR122-dependent long-range association and SLVI in genome translation and replication

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5870
Author(s):  
Kirsten Bentley ◽  
Jonathan P. Cook ◽  
Andrew K. Tuplin ◽  
David J. Evans
Keyword(s):  
Long Range ◽  
Conformational Changes ◽  
Core Protein ◽  
Genome Replication ◽  
Translation Efficiency ◽  
Coding Region ◽  
Stem Loop ◽  
Protein Coding ◽  
Virus Rna ◽  
Rna Interaction

The hepatitis C virus RNA genome possesses a variety of conserved structural elements, in both coding and non-coding regions, that are important for viral replication. These elements are known or predicted to modulate key life cycle events, such as translation and genome replication, some involving conformational changes induced by long-range RNA–RNA interactions. One such element is SLVI, a stem-loop (SL) structure located towards the 5′ end of the core protein-coding region. This element forms an alternative RNA–RNA interaction with complementary sequences in the 5′ untranslated regions that are independently involved in the binding of the cellular microRNA 122 (miR122). The switch between ‘open’ and ‘closed’ structures involving SLVI has previously been proposed to modulate translation, with lower translation efficiency associated with the ‘closed’ conformation. In the current study, we have used selective 2′-hydroxyl acylation analysed by primer extension to validate this RNA–RNA interaction in the absence and presence of miR122. We show that the long-range association (LRA) only forms in the absence of miR122, or otherwise requires the blocking of miR122 binding combined with substantial disruption of SLVI. Using site-directed mutations introduced to promote open or closed conformations of the LRA we demonstrate no correlation between the conformation and the translation phenotype. In addition, we observed no influence on virus replication compared to unmodified genomes. The presence of SLVI is well-documented to suppress translation, but these studies demonstrate that this is not due to its contribution to the LRA. We conclude that, although there are roles for SLVI in translation, the LRA is not a riboswitch regulating the translation and replication phenotypes of the virus.

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