A-to-I RNA Editing Blog and Feedback

2008-10-01T12:17:00.000-04:00

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

The use of high-throughput sequencing techniques revealed the dynamic plasticity of the transcriptional landscape as a function of environmental, developmental and genetic factors of transcriptomes under multiple conditions: rapid proliferation, meiotic differentiation, environmental stress, and in RNA processing mutants.

http://www.nature.com/nature/journal/v453/n7199/full/nature07002.html

Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system.

Strong data suggesting extensive connections between the RBP and miRNA post-transcriptional regulatory systems thereby providing perhaps a framework for deciphering the molecular mechanism by which PUF proteins regulate their target mRNAs.

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18776931

2008-02-18T15:09:00.000-05:00

RNA-mediated epigenetic programming of a genome-rearrangement pathway

A demonstration that DNA or RNA templates can orchestrate these genome rearrangements in Oxytricha

http://www.nature.com/nature/journal/v451/n7175/full/nature06452.html

2008-02-18T14:51:00.001-05:00

RNA editing of micro RNAs

More intriguing evidence that miRNAs might be important targets of the A-to-I RNA editing machinery.

This study highlights the notion that for elucidating the function of miRNAs it is important to consider the possibility that the primary miRNA transcript may be modified altering the molecule's target spectrum.

http://www.sciencemag.org/cgi/content/abstract/315/5815/1137

2007-02-15T14:36:00.000-05:00

Splicing and the Evolution of Proteins in Mammals regarding the dual role of exon sequences in encoding protein sequence and regulating splicing. A similar problem that also affects exons of edited genes where the coding sequence might also participate in RNA secondary structures that regulate editing.

http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0050014

Author Summary:
While information for pre-mRNA splicing is largely within the intron sequences of genes, parts of the exons near the intron–exon boundary can, for example, function as splice enhancer elements. In principle, then, these parts of exons have two functions: to specify the amino acids of the resulting protein and to enable the correct removal of introns. What impact might this have on a gene's evolution? The authors show that near intron–exon boundaries, amino acid usage is biased towards nucleotides involved in splice control. Moreover, these parts of genes evolve especially slowly. They estimate that a gene with many exons would evolve at under half the rate of the same gene with no introns, simply owing to the need to specify where to remove introns. Likewise, genes that have lost their introns evolve especially fast near the former intron's location. Thus, human proteins may not be as optimised as they could be, as their sequence is serving two conflicting roles.

2007-02-15T14:31:00.000-05:00

PLoS ONE is launched

A new journal under the open acces model that does things differently. Have a look.

2006-11-29T10:46:00.000-05:00

An intriguing paper on the "Variability and memory of protein levels in human cells".
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17122776&query_hl=1&itool=pubmed_docsum

Might have important implications for 'phenotypic diversity/heterogeneity within populations of cells'.

Interesting new papers!

2006-11-27T14:44:00.000-05:00

Here is a very good review on the state of knowledge regarding
"The complexity of the mammalian transcriptome"
Stefano Gustincich¹, Albin Sandelin², Charles Plessy³, Shintaro Katayama², Roberto Simone¹, Dejan Lazarevic¹, Yoshihide Hayashizaki⁴, and Piero Carninci⁴^*
J. Physiol, in press
http://jp.physoc.org/cgi/content/abstract/jphysiol.2006.115568v1?ck=nck
An analysis of recent data that has been focusing on the mechanisms of brain-specific transcription.

Another interesting paper on the prevalence of pseudo-messenger RNA's, transcribed from pseudogenes, within the mammalian transcriptome.
"Pseudo-Messenger RNA: Phantoms of the Transcriptome"
Martin C. Frith^1,², Laurens G. Wilming³, Alistair Forrest², Hideya Kawaji¹, Sin Lam Tan^4,⁵, Claes Wahlestedt^6,⁷, Vladimir B. Bajic^4,⁵, Chikatoshi Kai¹, Jun Kawai^1,⁸, Piero Carninci^1,⁸, Yoshihide Hayashizaki^1,⁸, Timothy L. Bailey², Lukasz Huminiecki^6,⁹*
PLoS Genetics, in press
http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0020023

2006-11-06T15:13:00.000-05:00

2006 Nobel Prize for Medicine awarded to Andrew Z. Fire and Craig C. Mello for their discovery and work on RNA Interference - gene silencing by double stranded RNA.

http://nobelprize.org/nobel_prizes/medicine/laureates/2006/

New blog forum

2006-10-16T15:22:00.000-04:00

This blog will be a place for research and other news relevant for A-to-I RNA editing questions including an opportunity for feedback and discussion.