TITLE

Mining small RNA structure elements in untranslated regions of human and mouse mRNAs using structure-based alignment

AUTHOR(S)
Khaladkar, Mugdha; Jianghui Liu; Dongrong Wen; Wang, Jason T. L.; Bin Tian
PUB. DATE
January 2008
SOURCE
BMC Genomics;2008, Vol. 9, Special section p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: UnTranslated Regions (UTRs) of mRNAs contain regulatory elements for various aspects of mRNA metabolism, such as mRNA localization, translation, and mRNA stability. Several RNA stem-loop structures in UTRs have been experimentally identified, including the histone 3' UTR stem-loop structure (HSL3) and iron response element (IRE). These stem-loop structures are conserved among mammalian orthologs, and exist in a group of genes encoding proteins involved in the same biological pathways. It is not known to what extent RNA structures like these exist in all mammalian UTRs. Results: In this paper we took a systematic approach, named GLEAN-UTR, to identify small stem-loop RNA structure elements in UTRs that are conserved between human and mouse orthologs and exist in multiple genes with common Gene Ontology terms. This approach resulted in 90 distinct RNA structure groups containing 748 structures, with HSL3 and IRE among the top hits based on conservation of structure. Conclusion: Our result indicates that there may exist many conserved stem-loop structures in mammalian UTRs that are involved in coordinate post-transcriptional regulation of biological pathways.
ACCESSION #
38122764

 

Related Articles

  • Translating the effects of mTOR on secretory senescence. Tomimatsu, Kosuke; Narita, Masashi // Nature Cell Biology;Oct2015, Vol. 17 Issue 10, p1230 

    Cellular senescence is often accompanied by the production of secreted proteins that mediate the diverse effects of senescence on the tissue microenvironment. The mammalian target of rapamycin (mTOR), a master regulator of protein synthesis, is now shown to control the senescence-associated...

  • A Systems Biology Approach to Transcription Factor Binding Site Prediction. Xiang Zhou; Sumazin, Pavel; Rajbhandari, Presha; Califano, Andrea // PLoS ONE;2010, Vol. 5 Issue 3, p1 

    Abstract Background: The elucidation of mammalian transcriptional regulatory networks holds great promise for both basic and translational research and remains one the greatest challenges to systems biology. Recent reverse engineering methods deduce regulatory interactions from large-scale mRNA...

  • Major role for mRNA stability in shaping the kinetics of gene induction. Elkon, Ran; Zlotorynski, Eitan; Zeller, Karen I.; Agami, Reuven // BMC Genomics;2010, Vol. 11, p259 

    Background: mRNA levels in cells are determined by the relative rates of RNA production and degradation. Yet, to date, most analyses of gene expression profiles were focused on mechanisms which regulate transcription, while the role of mRNA stability in modulating transcriptional networks was to...

  • One for all? A viral protein supplants the mRNA cap-binding complex. von der Haar, Tobias // EMBO Journal;1/14/2009, Vol. 28 Issue 1, p6 

    The article presents a study on the potential of nucleocapsid (N) protein from a species of Hantavirus to replace several host cell translation factors. It shows that recombinantly expressed nucleocapsid or N protein binds to mRNA cap structures and interacts with small ribosomal subunits....

  • From Transcriptome to Noncoding RNAs: Implications in ALS Mechanism. Gagliardi, Stella; Milani, Pamela; Sardone, Valentina; Pansarasa, Orietta; Cereda, Cristina // Neurology Research International;2012, p1 

    In the last years, numerous studies have focused on understanding the metabolism of RNA and its implication in disease processes but abnormal RNA metabolism is still unknown. RNA plays a central role in translating genetic information into proteins and in many other catalytic and regulatory...

  • Transition of a microRNA from Repressing to Activating Translation Depending on the Extent of Base Pairing with the Target. Saraiya, Ashesh A.; Li, Wei; Wang, Ching C. // PLoS ONE;Feb2013, Vol. 8 Issue 2, p1 

    MicroRNAs are major post-transcriptional regulators of gene expression. Here we show in the ancient protozoan Giardia lamblia a snoRNA-derived 26-nucleotide microRNA, miR3, which represses the translation of histone H2A mRNA containing an imperfect target but enhances translation when the target...

  • The Bic-C Family of Developmental Translational Regulators. Gamberi, Chiara; Lasko, Paul // Comparative & Functional Genomics;2012, p1 

    Regulation of mRNA translation is especially important during cellular and developmental processes. Many evolutionarily conserved proteins act in the context of multiprotein complexes and modulate protein translation both at the spatial and the temporal levels. Among these, Bicaudal C...

  • Are the complex distributed genetic networks inherently oscillatory and chaotic? Zhdanov, V. // JETP Letters;Mar2011, Vol. 93 Issue 1, p41 

    Complex mRNA-protein networks with distributed regulation of gene transcription are often mimicked by random Boolean networks. According to this mapping, the gene-expression kinetics are expected to depend strongly on the network connectivity, m. Specifically, the kinetics are predicted to be...

  • Structural model, physiology and regulation of Slr0006 in Synechocystis PCC 6803. Carmel, Dalton; Dahlström, Käthe; Holmström, Maija; Allahverdiyeva, Yagut; Battchikova, Natalia; Aro, Eva-Mari; Salminen, Tiina; Mulo, Paula // Archives of Microbiology;Nov2013, Vol. 195 Issue 10/11, p727 

    The slr0006 gene of Synechocystis sp. PCC 6803 is upregulated at mRNA and protein level under carbon limitation. The T(N)A motif in the upstream region of slr0006 is a binding site for transcriptional regulator NdhR, and accumulation of the Slr0006 protein in ndhR deletion mutant grown in high...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics