potential

s G

Odds-Ratio

BiQAnalyzer compares the sequences in all aligned Cs and highlightsthe sequence as critical if they are identical in all aligned Cs. All these sequences were excluded in theanalysis.

s

n a

Bonferroni correctionwas conducteddue to multiple comparisonsignificant valuelimitwas set to<0.025.

alpha

Welch’s

Normalised tissue

s 2

different samples

For the analysis,the technical replicates were assumed to be biological replicates

ligation

from

Direct

in a

thus

between methylated und unmethylated CpGs

theirdiscrimination

diverse conversion of cytosines

more

Whereupon

s e

sodium-bisulfite

in a

Protocol

amount

Endogenous

of

defined

threshold

There is only fluorescence if the dye bindsto the PCR product.

The point where the fluorescence becomes measurable is calledthreshold cycleor quantification cycle.

after

Input

SuperScript

e a

appropriate

e a

d t

The ratio 260nm/280nm was used to assess the purity of the DNA.

m g

RNase

RNeasy

in consideration of

in consideration of

Wavy bumps indicatethe activity (read depth, the number of reads).

data

strand

middle top

mentioned

statistical

. c

. E

. Z

. C

yt

mentioned

t t

On

with

RNA-seq data

Genome

UCSC

terminate

across

(activity is defined by the expression levels of the transcripts)

activity

Further requirements were

e a

which means that onlythe intragenicpromoter influencestissue-specific gene transcription

for

to conduct

RNA-seq data

RNA-seq data

s

blue square and the red diamond are overlapping

, which means that the

m,

2c

across

higher CGI promoter activity and

(blue box)

upstream

(red diamond)

terminating

across

(lower left cornerof the figure)

(red diamond in the bottom right cornerindicate transcripts across)

(upper right cornerof the figure)

transcripts

transcripts terminating

RNA-seq data

from a large difference to a non-existing difference in absoluteterms

terminating across than upstream

(red line)

a negative correlation with the data

pattern

in theRNA-seq dataplot

out of 632

single

and forall 30 mouse tissues

RNA-seq data plots were

provided

scalingfora comparable dataset

distinguished

of

Pearson correlation coefficient was calculated to compare the expression level of the intragenic promoter (CGI) or transcriptionalactivity initiating at the intragenic CGI and the ratio upstream/across, which means transcription upstream and splicing across the CGI. For the negative control sample dataset Pearson correlation coefficient was calculated as well with simulated intragenic promoters. The cut-off was set close to the maximum correlation of the negative control dataset and defined at 0.5.

drift

and defined

of

For the negative control sample dataset,Pearson correlation coefficient was calculated alongside simulated intragenic promoters.

compare

Pearson

and splicing

conducting a permutation test for resampling of the dataset

‘Host gene upstream of the intragenic promoter’(Upstream) defined as fragment numbers measured from the TSS until the beginning of the CGI and ‘Gene through the intragenic promoter’(Across), defined as exonic fragmentsoverlapping with the host gene;

fragment

overlapping with the host gene

exonic

sense and antisense orientation

mouse

hybrid cross Mus m. musculus(B6) and Mus m. castaneus(Cast) -BxC or hybrid cross Mus m. castaneus(Cast)and Mus m. musculus(B6)–CxB

list

source

CGIs

with those from

maternal and paternal allele

gene

lab

Work form

has recently

mechanisms

Investigating the utilisation of alternative polyadenylation sites at the H13/Mcts23imprinted locus will shed light on this matter.

However, an allele-specific epigenetic control for mechanisms such as polyadenylation has yet to be proven.

TSS

DNMTs interact with enzymes that regulategene expression andaretypicallyinvolved ingene repression27.

for

nucleosomes

resulting in small fractions called

Notably, CGIs within gene bodies show the highest variationof DNA methylation between different tissues and somatic cells

of

, notwithstanding of gene expression

X

s

CG

a

Dnmt1 copies

paternal

DNA methylation

RNA-binding sites

over

there may be different methylation patterns

ym

and occurs if an intron is retained,which normally would be removed

which

post

it

ExceptforCGI2,where a simultaneousenrichment of H3K4me2 (chromatin mark associated with active transcription) and H3K27me3(silencing chromatin modification) has beendetectedin all somatic tissues, which resultsin bivalent chromatin. In brain,no enrichment of the chromatin marks wasfound.

(1C, 1B1 and 1B2)

s i

the

e

e

juston few

due

-most exon

cause

s a

variances

non-histonic

constituting

cell/tissue-specific combinations

-specific

Each gene generates

hence a specific set

As soon as the stop codon has been transcribed

gi

do not cause

heritable

accepted

p t

these considerations

On the hypothesis

murine

sa

na

am

e

am

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