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One gene – one transcript… mostly
Mar Gonzales Porta, Adam Frankish, Johan Rung,
Jennifer Harrow, Alvis Brazma
European Bi...
Analysis of RNA-seq data across different tissues
and cell lines reveals that the majority of genes have
a single dominant...
aaaaCAP
ATG
ter
polypeptide
transcription
splicing
translation
Figure 1
Central dogma of molecular biolgoy
Gene
Transcript...
The number of genes in human genome
•  Estimates before the Human Genome Project
•  ~100,000 genes
•  After
•  ~21,000 gen...
Central gogma revised – one gene many
transcritps and proteins via alternative
splicing
In human, there are 21,405 protein...
From RNA-seq and other recent experiments
•  Most human genes have more than one splice-form
expressed [Pan et al, Nat Gen...
ENCODE – Nature, September 2012
•  ‘Isoform expression by a gene does not follow a
minimalistic expression strategy, resul...
A fundamental question still remains – are
different isoforms of the same gene
expressed at similar levels?
Expression
lev...
Data and methods
Illumina Body Map	

16 tissues	

PE (80M)	

no replicates	

HiSeq 2000	

ENCODE	

5 cell lines	

PE (40M)...
Most genes express one predominant
transcript
Expression
level
79% of cases 	

 56% of cases 	

2-fold dominance 5-fold do...
Consistent across all studied tissues
What are the RPKM distributions of first,
second, … most abundant isoforms for all
genes?
Most genes express one predominant
transcript
Most genes express one predominant
transcript
We detect a total of 31,902 transcripts expressed above 1 FPKM in at least o...
There is just over one highly expressed
transcript per gene!
85% of transcriptome comes from the
dominant transcripts
Is i...
Major transcripts tend to be recurrent across
tissues
Switch events exist ~ 100 strong switches
that change the protein sequence
Some of the major transcripts are non-
canonical
AES
Do the dominant transcripts of protein coding
genes always code proteins?
•  Only in about 80% cases
•  However much more ...
Conclusions
•  Most genes express one predominant transcript over the
rest
•  ~85% of the mRNA pool comes from major trans...
Mar Gonzales Porta
Funding
•  EMBL member countries
•  European Commission FP7 grants
Mar Gonzales Porta, One gene One transcript, fged_seattle_2013
Mar Gonzales Porta, One gene One transcript, fged_seattle_2013
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Mar Gonzales Porta, One gene One transcript, fged_seattle_2013

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One gene - One transcript... mostly

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Transcript of "Mar Gonzales Porta, One gene One transcript, fged_seattle_2013"

  1. 1. One gene – one transcript… mostly Mar Gonzales Porta, Adam Frankish, Johan Rung, Jennifer Harrow, Alvis Brazma European Bioinformatics Institute European Molecular Biology Laboratory Wellcome Trust Sanger Institute
  2. 2. Analysis of RNA-seq data across different tissues and cell lines reveals that the majority of genes have a single dominant transcript Mar Gonzàlez-Porta Adam Frankish (Sanger) Johan Rung (EBI) Jennifer Harrow (Sanger) Alvis Brazma (EBI) To appear in Genome Biology on July 1, 2013 http://genomebiology.com/
  3. 3. aaaaCAP ATG ter polypeptide transcription splicing translation Figure 1 Central dogma of molecular biolgoy Gene Transcript Spliced transcript
  4. 4. The number of genes in human genome •  Estimates before the Human Genome Project •  ~100,000 genes •  After •  ~21,000 genes •  By comparison •  Yeast ~6,000 genes •  C. Elegance ~17,000
  5. 5. Central gogma revised – one gene many transcritps and proteins via alternative splicing In human, there are 21,405 protein coding genes and 141,031 different isoforms (92,581 of which are protein coding) annotated, 17,413 genes have >1 isoform
  6. 6. From RNA-seq and other recent experiments •  Most human genes have more than one splice-form expressed [Pan et al, Nat Genetics 2008], [Wang et al, Nat Genetics 2008] [Mortazavi, Nat Methods 2008] •  Several isoforms per gene are often expressed to significant levels either in the same cell type or across different [Wang et al, Nat Genetics 2008], [Tang et al, Nat Methods 2009], [Trapnell et al, Nat Biotechy 2010] •  Isoform expression is regulated [Waks et al, Mol Syst Biol 2011] but splicing can be noisy [Melamud, NAR 2009]
  7. 7. ENCODE – Nature, September 2012 •  ‘Isoform expression by a gene does not follow a minimalistic expression strategy, resulting in a tendency for genes to express many isoforms simultaneously’ •  ‘[…] alternative isoforms within a gene are not expressed at similar levels, and one isoform dominates in a given condition)’ •  Which is it then?
  8. 8. A fundamental question still remains – are different isoforms of the same gene expressed at similar levels? Expression level Isoforms 1 2 3 4 5 6 ? Isoforms 1 2 3 4 5 6 We think this is a fundamental question related to the complexity of transcritpome
  9. 9. Data and methods Illumina Body Map 16 tissues PE (80M) no replicates HiSeq 2000 ENCODE 5 cell lines PE (40M) technical replicates GAII •  2 different datasets: 46 samples •  Three different state-of-art tools for transcript quantification (MISO, Cufflinks and mmseq) •  Direct evidence from splice junctions •  Simulated data – can the methods distinuish between the two scenarios? •  All approaches produced very consistent results
  10. 10. Most genes express one predominant transcript Expression level 79% of cases 56% of cases 2-fold dominance 5-fold dominance
  11. 11. Consistent across all studied tissues
  12. 12. What are the RPKM distributions of first, second, … most abundant isoforms for all genes?
  13. 13. Most genes express one predominant transcript
  14. 14. Most genes express one predominant transcript We detect a total of 31,902 transcripts expressed above 1 FPKM in at least one tissue and 26,641 of these are major transcripts (ratio 1.12)
  15. 15. There is just over one highly expressed transcript per gene! 85% of transcriptome comes from the dominant transcripts Is it the same dominant transcript in all tissues or different tissues tend to have different dominant transcripts?
  16. 16. Major transcripts tend to be recurrent across tissues
  17. 17. Switch events exist ~ 100 strong switches that change the protein sequence
  18. 18. Some of the major transcripts are non- canonical AES
  19. 19. Do the dominant transcripts of protein coding genes always code proteins? •  Only in about 80% cases •  However much more often in cytosol than in nucleolus •  In nucleolus the retained intron is predominantly located towards the 3’ end of the transcript •  Is this because we extract mRNA before the splicing is completed or can a retained intron be a form of expression regulation?
  20. 20. Conclusions •  Most genes express one predominant transcript over the rest •  ~85% of the mRNA pool comes from major transcripts •  Major transcripts tend to be recurrent across samples, switch events exist but only a small number of these are likely to express different proteins •  Despite the transcriptome complexity the central dogma of molecular biology may be closer to the truth than recently believed!
  21. 21. Mar Gonzales Porta
  22. 22. Funding •  EMBL member countries •  European Commission FP7 grants
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