Genome Biology

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Untranslated regions of mRNAs

Flavio Mignone, Carmela Gissi, Sabino Liuni and Graziano Pesole*

Genome Biology 2002, 3:reviews0004-reviews0004.10 doi:10.1186/gb-2002-3-3-reviews0004

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Research article   Open Access

Exploring the selective constraint on the sizes of insertions and deletions in 5' untranslated regions in mammals

Chun-Hsi Chen, Ben-Yang Liao, Feng-Chi Chen BMC Evolutionary Biology 2011, 11:192 (5 July 2011)

Research article   Open Access

Gene structure, transcripts and calciotropic effects of the PTH family of peptides in Xenopus and chicken

Pedro LC Pinheiro, João CR Cardoso, Ana S Gomes, Juan Fuentes, Deborah M Power, Adelino VM Canário BMC Evolutionary Biology 2010, 10:373 (1 December 2010)

Research   Open Access

Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays

Adnane Sellam, Hervé Hogues, Christopher Askew, Faiza Tebbji, Marco van het Hoog, Hugo Lavoie, Carol A Kumamoto, Malcolm Whiteway, André Nantel Genome Biology 2010, 11:R71 (9 July 2010)

The Candida albicans transcriptional landscape reveals antisense transcription, novel open reading frames and non-coding RNAs, whose expression is correlated with RNA polymerase occupancy.

Research article   Open Access Highly Accessed

Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics

Koh Aoki, Kentaro Yano, Ayako Suzuki, Shingo Kawamura, Nozomu Sakurai, Kunihiro Suda, Atsushi Kurabayashi, Tatsuya Suzuki, Taneaki Tsugane, Manabu Watanabe, Kazuhide Ooga, Maiko Torii, Takanori Narita, Tadasu Shin-i, Yuji Kohara, Naoki Yamamoto, Hideki Takahashi, Yuichiro Watanabe, Mayumi Egusa, Motoichiro Kodama, Yuki Ichinose, Mari Kikuchi, Sumire Fukushima, Akiko Okabe, Tsutomu Arie, Yuko Sato, Katsumi Yazawa, Shinobu Satoh, Toshikazu Omura, Hiroshi Ezura, Daisuke Shibata et al. BMC Genomics 2010, 11:210 (30 March 2010)

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B7-H4 gene polymorphisms are associated with sporadic breast cancer in a Chinese Han population

Jie Zhang, Mingyan Zhang, Wei Jiang, Lihong Wang, Zhenkun Fu, Dalin Li, Da Pang, Dianjun Li BMC Cancer 2009, 9:394 (11 November 2009)

Research article   Open Access

Key role of the 3' untranslated region in the cell cycle regulated expression of the Leishmania infantum histone H2A genes: minor synergistic effect of the 5' untranslated region

Daniel R Abanades, Laura Ramírez, Salvador Iborra, Ketty Soteriadou, Victor M González, Pedro Bonay, Carlos Alonso, Manuel Soto BMC Molecular Biology 2009, 10:48 (21 May 2009)

Research   Open Access

Absence of spermatozoal CD46 protein expression and associated rapid acrosome reaction rate in striped field mice (Apodemus agrarius)

Leanne E Clift, Petra Andrlikova, Michaela Frolikova, Pavel Stopka, Josef Bryja, Brian F Flanagan, Peter M Johnson, Katerina Dvorakova-Hortova Reproductive Biology and Endocrinology 2009, 7:29 (16 April 2009)

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Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast

Craig Lawless, Richard D Pearson, Julian N Selley, Julia B Smirnova, Christopher M Grant, Mark P Ashe, Graham D Pavitt, Simon J Hubbard BMC Genomics 2009, 10:7 (7 January 2009)

Research article   Open Access

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

Mugdha Khaladkar, Jianghui Liu, Dongrong Wen, Jason TL Wang, Bin Tian BMC Genomics 2008, 9:189 (25 April 2008)

Research article   Open Access Highly Accessed

Strategies for measuring evolutionary conservation of RNA secondary structures

Andreas R Gruber, Stephan H Bernhart, Ivo L Hofacker, Stefan Washietl BMC Bioinformatics 2008, 9:122 (26 February 2008)

Simple metrics of folding energy and optimal structures accurately measure evolutionary conservation of RNA secondary structure and should form the basis of tools to predict non-coding RNAs, whereas complex methods fail to improve performance.

Research article   Open Access

The 3' untranslated region of human Cyclin-Dependent Kinase 5 Regulatory subunit 1 contains regulatory elements affecting transcript stability

Silvia Moncini, Annamaria Bevilacqua, Marco Venturin, Claudia Fallini, Antonia Ratti, Angelo Nicolin, Paola Riva BMC Molecular Biology 2007, 8:111 (3 December 2007)

Research article   Open Access Highly Accessed

Spatial preferences of microRNA targets in 3' untranslated regions

William H Majoros, Uwe Ohler BMC Genomics 2007, 8:152 (7 June 2007)

Software   Open Access

TISs-ST: a web server to evaluate polymorphic translation initiation sites and their reflections on the secretory targets

Renato Vicentini, Marcelo Menossi BMC Bioinformatics 2007, 8:160 (21 May 2007)

Review   Free

Bench-to-bedside review: Genetics and proteomics: deciphering gene association studies in critical illness

Sachin Yende, Candace M Kammerer, Derek C Angus Critical Care 2006, 10:227 (24 August 2006)

This article is part of a collection on Translational Research

Software   Open Access

Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration

Erdahl T Teber, Edward Crawford, Kent B Bolton, Derek Van Dyk, Peter R Schofield, Vimal Kapoor, W Bret Church BMC Bioinformatics 2006, 7:33 (23 January 2006)

Research article   Open Access Highly Accessed

The variable number of tandem repeats element in DAT1 regulates in vitro dopamine transporter density

Sidney H VanNess, Michael J Owens, Clinton D Kilts BMC Genetics 2005, 6:55 (27 November 2005)

Expression of the human dopamine transporter in stably transfected cells is influenced by the number of tandem repeats present in the 3' untranslated region, suggesting that the naturally occurring polymorphism in tandem repeats is of functional significance.

Research article   Open Access

Evidence for abundant transcription of non-coding regions in the Saccharomyces cerevisiae genome

Moshe Havilio, Erez Y Levanon, Galia Lerman, Martin Kupiec, Eli Eisenberg BMC Genomics 2005, 6:93 (16 June 2005)

Research article   Open Access

Transient expression analysis of allelic variants of a VNTR in the dopamine transporter gene (DAT1)

Jonathan Mill, Philip Asherson, Ian Craig, Ursula M D'Souza BMC Genetics 2005, 6:3 (31 January 2005)

Method   Open Access

Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis

Randolph B Caldwell, Andrzej M Kierzek, Hiroshi Arakawa, Yuri Bezzubov, Jolanta Zaim, Petra Fiedler, Stefan Kutter, Artem Blagodatski, Diyana Kostovska, Marek Koter, Jiri Plachy, Piero Carninci, Yoshihide Hayashizaki, Jean-Marie Buerstedde Genome Biology 2004, 6:R6 (23 December 2004)

This article reports a cDNA collection representing more than 2000 new, full-length transcripts from a high-quality cDNA library.

Opinion   Free

The mammalian transcriptome and the function of non-coding DNA sequences

Svetlana A Shabalina, Nikolay A Spiridonov Genome Biology 2004, 5:105 (25 March 2004)

Many non-coding sequences transcribed from the mammalian genome are proving to have important regulatory roles, but the functions of the majority remain mysterious.

Research   Open Access

Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae

Evan H Hurowitz, Patrick O Brown Genome Biology 2003, 5:R2 (22 December 2003)

A novel 'Virtual Northern' method provides a practical and efficient method for genome-scale analysis of mRNA transcript lengths. A study in Saccharomyces cerevisiae has revealed that approximately 12-15% of the yeast genome is represented in untranslated sequences of mRNAs.

Methodology article   Open Access Highly Accessed

Amplified RNA degradation in T7-amplification methods results in biased microarray hybridizations

Andrej-Nikolai Spiess, Nadine Mueller, Richard Ivell BMC Genomics 2003, 4:44 (10 November 2003)