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Paper text:
sequencing the mrna in a cell has been used as a high - throughput method for finding genes since the early days of the human genome project . beginning in the early 1990s , the expressed sequence tag ( est )
method was used to capture fragments of thousands of human genes   prior to the sequencing of the genome .
est sequencing relies on the fact that eukaryotic genes are polyadenylated after transcription , and the long poly - a tract can be used to capture the transcripts via reverse transcription pcr ( rt - pcr ) .
the est method was subsequently applied to many other species , and est databases ( notably dbest ) became a vital resource for genome annotation .
recently , a  next - gen version of est sequencing has emerged , allowing researchers to capture and sequence mrna at dramatically lower cost , and higher volume , than was ever possible with the est method .
the new rna - seq methods [ 2 - 5 ] are being applied to a rapidly growing variety of species , cell types , and scientific questions , revealing far more about the transcriptomes of these species than was known just a few years ago .
the field is advancing so rapidly that a brief review can not cover the work of the past 2 years ; this review is just a sampling of a few highlights .
sultan et al .   analyzed approximately 8 million short reads and found that rna - seq could detect 25% more genes as compared to microarrays . about one - third of transcripts in their experiments mapped to genomic regions not annotated as genes . of the 94,241 splice junctions ,
this result has been amplified by subsequent studies that generated even more sequences and showed even larger numbers of novel splicing events .
.   generated approximately 430 million paired - end reads to recover 13,692 known isoforms from mouse myoblast cells , but also detected 12,712 novel isoforms , of which 7395 contained novel splice junctions while the rest represented novel combinations of known exons .
this latter study also demonstrated the power of a new algorithm capable of detecting and quantifying alternative isoforms when aligning rna - seq reads to a genome . in an rna - seq study using liver rna samples from humans , chimpanzees , and rhesus macaques , blekhman et al
.   found that alternative splicing events vary between closely related primates and also between the sexes within species .
wang et al .   generated approximately 600 million short reads from 15 cell types and found that 92 - 94% of human genes are alternatively spliced , and that many alternative splicing events are tissue - specific .
rna - seq is also being used to study genetic variation among individuals ( expression quantitative trait loci , or eqtls ) .
combined rna - seq data and hapmap data from 69 nigerian individuals and 63 caucasian individuals , respectively , and both groups identified variants responsible for alternative splicing as well as variation in expression levels among individuals . in single - celled organisms , rna - seq can reveal novel insights about polycistronic transcripts .
in the first transcriptome analysis of trypanosoma brucei , thousands of splicing and polyadenylation sites were identified and many genes were found to be differentially expressed between the parasite 's two life - cycle stages . in prokaryotes , rna - seq can provide an extremely detailed transcription map , at the single - base level , as has been shown recently in an archaeal species , sulfolobus solfataricus , and in a pathogen bacterium , helicobacter pylori . in s. solfataricus ,
over 1000 transcriptional start sites were detected and 80 novel protein - coding genes were discovered . in h. pylori , hundreds of transcriptional start sites within operons were found , as well as approximately 60 novel small rna genes .
the power of rna - seq stems from its ability to generate deep coverage of the entire transcriptome of a cell with just a single run of a high - throughput sequencer , such as the illumina hiseq , which can produce up to 200 billion bases in a single run . the potential to characterize all genes , to capture alternative isoforms , and to measure differential expression
has already been demonstrated in dozens of studies , but hundreds of species , and countless experimental conditions , are yet to be explored .
several groups have developed methods besides poly - a selection to capture all rnas in a cell , for example , random hexamer priming , which allows them to analyze prokaryotic transcriptomes or to look at noncoding rna in eukaryotes .
it now appears that rna - seq will replace microarray technology in the coming years , as it appears to be not only more comprehensive but also much more accurate than microarrays , particularly for transcripts with low expression levels . as this new method becomes
even more widely adopted , it should greatly expand our understanding of the complex interplay of genes in all phases of cell development .
the latest high - throughput dna sequencing technology can now be applied on a large scale to capture the complete set of mrna transcripts in a cell , using a technique called rna - seq . 
 although rna - seq is only 2 years old , it has rapidly swept through the field of genomics , and it is now being used to analyze the transcriptomes of organisms ranging from bacteria to primates . 
 the depth of sequencing allows researchers to quantify the level of expression of genes , to discover alternative isoforms in eukaryotic species , and even to characterize the operon structure of bacterial genomes .