REGULOME – Lecture 1
"Regulome" (4 onderwerpen):
Transcriptome and microarrays
o Microarray data analysis
RNA-seq
o RNA-seq data analysis
Regulatory layers I (chromatin, DNA methylation, ChIP-seq)
o ChIP-seq data analysis I
Regulatory layers II (transcription factors, methods to study chromatin)
o ChIP-seq data analysis II
Developments in DNA sequencing: now more sequences at the same time, sequencing costs per
megabase of DNA has reduced enormously: due to next generation sequencing technologies
More data --> bioinformatics needed to analyse
Transcriptome and microarrays
Microarray data analysis
Transcripts = RNA
Transcriptomics = the study of the complete set of RNAs (transcriptome) encoded by the genome of
a specific cell or organism at a specific time or under a specific set of conditions.
How many genes?
Bacteria - 1,000
Higer eukaryotes - 20,000
Mammals - 22,000
RNA is transcribed from the DNA, but not every part from the gene ends up in the RNA
Transcription - modification of ends - splicing - exons are joined
Different combinations of these processes --> transcript variants
Alternative splicing adds to the size (complexity) of the transcriptome
27 geskipt
Central Dogma of Biology
, DNA --> mRNA --> protein
Active forms of non-coding RNA
"non coding" RNAs (ncRNA)
ncRNA is a RNA that functions without being translated into a protein
Heel veel verschillende functies
Long non-coding RNA (lncRNA)
80% of the transcription is associated with lncRNAs (so more than protein coding gene, larger
variability in noncoding part of transcriptome)
Very long, can be spliced, can contain polyA-tails (many have them) --> behave like protein coding
RNA (so always in transcriptome data sets)
They don't have obvious ORFs --> dont find any long encoded proteins, a lot of stopcodons -->
different from protein coding RNAs
Vast majority of transcriptome is long non coding RNA
Mouse: 20,000 protein coding genes vs. 160,000 lncRNAs
Especially in higher eukaryotes, a bigger part of the transcriptome is long non coding RNA
"Regulome" (4 onderwerpen):
Transcriptome and microarrays
o Microarray data analysis
RNA-seq
o RNA-seq data analysis
Regulatory layers I (chromatin, DNA methylation, ChIP-seq)
o ChIP-seq data analysis I
Regulatory layers II (transcription factors, methods to study chromatin)
o ChIP-seq data analysis II
Developments in DNA sequencing: now more sequences at the same time, sequencing costs per
megabase of DNA has reduced enormously: due to next generation sequencing technologies
More data --> bioinformatics needed to analyse
Transcriptome and microarrays
Microarray data analysis
Transcripts = RNA
Transcriptomics = the study of the complete set of RNAs (transcriptome) encoded by the genome of
a specific cell or organism at a specific time or under a specific set of conditions.
How many genes?
Bacteria - 1,000
Higer eukaryotes - 20,000
Mammals - 22,000
RNA is transcribed from the DNA, but not every part from the gene ends up in the RNA
Transcription - modification of ends - splicing - exons are joined
Different combinations of these processes --> transcript variants
Alternative splicing adds to the size (complexity) of the transcriptome
27 geskipt
Central Dogma of Biology
, DNA --> mRNA --> protein
Active forms of non-coding RNA
"non coding" RNAs (ncRNA)
ncRNA is a RNA that functions without being translated into a protein
Heel veel verschillende functies
Long non-coding RNA (lncRNA)
80% of the transcription is associated with lncRNAs (so more than protein coding gene, larger
variability in noncoding part of transcriptome)
Very long, can be spliced, can contain polyA-tails (many have them) --> behave like protein coding
RNA (so always in transcriptome data sets)
They don't have obvious ORFs --> dont find any long encoded proteins, a lot of stopcodons -->
different from protein coding RNAs
Vast majority of transcriptome is long non coding RNA
Mouse: 20,000 protein coding genes vs. 160,000 lncRNAs
Especially in higher eukaryotes, a bigger part of the transcriptome is long non coding RNA
