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Contents 1 Transcription outside of known gene boundaries. 1.1 Arrays 1.2 RNA-seq 1.3 optional references: 2 Brain transcriptome is one of the most complex. 3 Changes in expression of brain transcripts were suggested to play an essential role in evolutions of the human phenotype 4 Other RNA-seq papers 4.1 human 4.2 mouse 4.3 yeast 5 Indeed, expression of annotated protein-coding genes differs greatly between humans and one of our closest primate relatives, chimpanzees 6 human and chimpanzee brain transcriptomes by tiling arrays 7 Other references 7.1 HITS-CLIP 8 references should be excluded 9 references not so relevant

Transcription outside of known gene boundaries.

Arrays

• Bertone et al. Global identification of human transcribed sequences with genome tiling arrays. Science (2004) vol. 306 (5705) pp. 2242-6.

human liver, tilling array. "A large fraction of them located in intergenic regions".

• Cheng et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science (2005) vol. 308 (5725) pp. 1149-54.

human 8 cell lines, tilling array. They detected polyA+, polyA- and un-annotated transcripts.

RNA-seq

• Sultan et al. A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome. Science (2008) pp.

human embryonic kidney and a B cell line. RNA-seq. 50% of reads mapped to unique genomic location, of which 80% corresponded to known exons. We found that 66% of the polyadenylated transcriptome mapped to known genes and 34% to non-annotated genomic regions.

optional references:

• Chen et al. Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc Natl Acad Sci USA (2002) vol. 99 (19) pp. 12257-62

They used the public SAGE database, showed that most of the unmatched SAGE tags are truly novel SAGE tags that originated from novel transcripts not yet identified in the human genome.

• Kapranov et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science (2002) vol. 296 (5569) pp. 916-9.

Tilling array.

• Origin of phenotypes: Genes and transcripts

another tilling array paper from Thomas Gingeras, this is a perspective in genome research, the ENCODE issue.

Brain transcriptome is one of the most complex.

• Yeo et al. Variation in alternative splicing across human tissues. Genome Biol (2004) vol. 5 (10) pp. R74

brain and testis had the highest levels of exon skipping, alternative 3' splice site while alternative 5' splice site are most frequent in liver and brain

• Pan et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet (2008) vol. 40 (12) pp. 1413-5

brain and liver show relatively high frequencies of alternative splicing compared to other tissues.

Changes in expression of brain transcripts were suggested to play an essential role in evolutions of the human phenotype

• King and Wilson. Evolution at Two Levels Humans and Chimpanze. Science (1975)

Other RNA-seq papers

human

• Sultan et al. A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome. Science (2008) pp.

human embryonic kidney and a B cell line. RNA-seq.

• Pan et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet (2008) vol. 40 (12) pp. 1413-5

brain and liver show relatively high frequencies of alternative splicing compared to other tissues.

mouse

• Mortazavi et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) vol. 5 (7) pp. 621-8

Mouse brain, liver, skeleton muscle tissue. RNA-seq tech. Poly-A selected RNA. 41-52M reads. >90% of uniquely mapped reads fell within know exons, the rest are from previous unknown genes

yeast

• Nagalakshmi et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) vol. 320 (5881) pp. 1344-9

Yeast, RNA-Seq.

Indeed, expression of annotated protein-coding genes differs greatly between humans and one of our closest primate relatives, chimpanzees

Enard et al. Intra- and interspecific variation in primate gene expression patterns. Science (2002) vol. 296 (5566) pp. 340-3

"We identified species-specific gene expression patterns indicating that changes in protein and gene expression have been particularly pronounced in the human brain."

human and chimpanzee brain transcriptomes by tiling arrays

• Khaitovich et al. Functionality of intergenic transcription: an evolutionary comparison. PLoS Genet (2006) vol. 2 (10) pp. e171

Other references

HITS-CLIP

Chi et al. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature (2009) vol. 460 (7254) pp. 479-86

references should be excluded

• Amaral et al. The eukaryotic genome as an RNA machine. Science (2008) vol. 319 (5871) pp. 1787-9

This is a perspective, focus on the diversity of ncRNA control of genome dynamics.

• Nagalakshmi et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) vol. 320 (5881) pp. 1344-9

It's Yeast, RNA-Seq.

• Wilhelm et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature (2008) vol. 453 (7199) pp. 1239-43

Yeast, RNA-seq and tilling array. Sequencing was sensitive enough to detect wide spread transcription in >90% of the genome. This provides information on novel, mostly non-coding transcripts, untranslated regions and gene structures, thus improving the existing genome annotation.

references not so relevant

• Gustincich et al. The complexity of the mammalian transcriptome. J Physiol (Lond) (2006) vol. 575 (Pt 2) pp. 321-32

Here we present a computational analysis of CAGE data from different regions of the central nervous system, suggesting distinctive mechanisms of brain-specific transcription.

• Han et al. Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing. Proc Natl Acad Sci USA (2009) vol. 106 (31) pp. 12741-6