Algoritmo!
-1000
+1000
TSS
Dato ciascun TSS, calcolare quante sequenze mappano tra
-1000 e +1000 bp rispetto al TSS
Contare quante sequenze mappano a -1000, -999, -998...-1,0
+1,+2,...+998,+999,+1000
Sommare per tutti i TSS i conteggi a ciascuna distanza
(-1000, -999, -998,...,-1,0,+1,+2,...+998,+999,+1000)
Attenzione!
-1000
+1000
TSS
+1000
-1000
TSS
Le coordinate rispetto al TSS dipendono dalla direzione della trascrizione!!
Read count (peak height)
Output: histone modifications
at TSS
-1000
0
+1000
Distance from TSS
I risultati!
PolII is found bound to DNA at the TSS of transcribed genes
H3K4me3 is found just before and after the TSS of transcribed genes
H3K4me2 (not me3!) is found just before and after the TSS of transcribed genes,
but farther away than H3K4me3
H3K4me1 is found just before and after the TSS of transcribed genes,
but farther away than H3K4me3 and H3K4me2
H3K27me3 covers the whole locus of “silent” genes - no transcription here
H3K27me1 (not me3!) is vice versa associated before and after loci of
transcribed genes
H3K36me3 is found within the transcribed region - a bit downstream of the TSS as if it “lets” polymerase proceed with transcription
H3K9me1 is similar in profile to H3K4me3
Barski et. al. High-Resolution Profiling of Histone Methylations in the Human Genome, Cell 129(4)
Read count (peak height)
Histone modifications at
transcribed regions
High
Low
Expression level
What you should always
remember
What you should always
remember