quantitation of cis-translational control by general mrna...

Quantitationofcis-translationalcontrolbygeneralmRNAfeaturesinfiveeukaryotes

SoCal SysBio Conference, Feb 9, 2019

Joint work with Drs. Guo-Liang Chew (Fred-Hutch) and Mark D. Biggin (LBNL)

Jingyi Jessica Li

University of California, Los Angeles

Translationisoneoffourstepsthatdetermineproteinabundances

transcriptionmRNA

degradationmRNA

translation

protein

proteindegradation

kdr x [mRNA]

kdr x [protein]

Vtxn

ktns x [mRNA]

Gene and condition specifice.g. miRNA

RBPs

Present in a minority of mRNAs, cell types and conditions

General featurese.g. RNA structure

uORFs, codon usage

Present in most or all mRNAs, cell types and conditions

AAAAAUG5’ cap

protein coding sequence

RBP

AAAAAUG5’ cap

protein coding sequence

miRNA

Twoclassesoftranslationalcontrol

AAAAAUG protein coding sequence

AAAAAUG protein coding sequence

efficient codon usage

uORF

inefficient codon usage5’ cap

uORFuORF5’ cap

Therearefivegeneralfeatures

AAAAAAAAAUGAUG

PROTEIN CODING REGION (CDS)

RNAstem loop

poly A tailAPEuORF

1. 5’ UTR RNA secondary structure

2. upstream open reading frames (uORFs)

3. AUG proximal element (APE)

5’ UTR 3’ UTR

5’ cap

4. protein coding sequence (CDS) length

5. CDS codon frequency

protein coding sequence

Amultivariatelinearmodelcombiningallfivefeatures

AAAAAAAAAUGAUG

PROTEIN CODING REGION (CDS)

RNAstem loop

poly A tailAPEuORF

1. 5’ UTR RNA secondary structure

2. upstream open reading frames (uORFs)

3. AUG proximal element (APE)

5’ UTR 3’ UTR

5’ cap

4. protein coding sequence (CDS) length

5. CDS codon frequency

protein coding sequence

Amultivariatelinearmodelcombiningallfivefeatures

S. cerevisiae

GeneralfeaturespredictTRinfiveeukaryotes

general features

0%S. cerevisae mouseArabidopsis

40%

80%

60%

20%

% v

aria

nce

oftra

nsla

tion

rate

100%

humanS. pombe

GeneralfeaturespredictTRinfiveeukaryotes

general features

0%S. cerevisae mouseArabidopsis

40%

80%

60%

20%

% v

aria

nce

oftra

nsla

tion

rate

100%

humanS. pombe

GeneralfeaturespredictTRinfiveeukaryotes

Unexplainedvariancesetsalimitongeneandconditionspecificcontrol

unexplained general features

0%S. cerevisae mouseArabidopsis

40%

80%

60%

20%

% v

aria

nce

oftra

nsla

tion

rate

100%

humanS. pombe

no miRNAs~100 RBPs

>1,800 miRNAs~ 380 RBPs

420 miRNAs559 RBPs

Controloftranslationby5’UTRRNAstructure

1 100755025 125 2001751500.0

-12.0

-8.0

-4.0

RN

A fo

ldin

g en

ergy

Location of 5’ end of 35 nucleotide sliding window

Controloftranslationby5’UTRRNAstructure

5’—C A A C U—3’A

CG

C

G

A

UG

C

U

5’—C A A G C A C C—3’

Themostfoldedregionswithin5’UTRsdeterminetranslationrates

S. cerevisae

H. sapiens

M. musculusArabidopsis

S. pombe

0%

20%

40%

60%

80%

100%

% R

2 f

ea

ture

vs lo

g1

0 T

R

min max90%75%25%10%

1 100755025 125 2001751500.0

-12.0

-8.0

-4.0

RN

A fo

ldin

g en

ergy

Location of 5’ end of 35 nucleotide sliding window

5’—C A A C U—3’A

CG

C

G

A

UG

C

U

5’—C A A G C A C C—3’

Themostfoldedregionswithin5’UTRsdeterminetranslationrates

Contiguousstemsaremosteffective,butothernucleotidepairscontribute

0.00

-0.10

-0.05

-0.25

-0.15

-0.20

S. cerevisae Arabidopsis M. musculus

contig stem max stem all

Pe

ars

on

co

effic

ien

t (r

)

S. pombe H. sapiens

35 25 40 55 60

Mostfoldedregionsaresimilaracrosseukaryotes

0.0

1.0

-1.0

-3.0

-2.0

2.0

-4.0

-5.0

-6.0

-7.0

S. cerevisae

Arabidopsis

M. musculus

low

TR

valu

e -

hig

h T

R v

alu

e

MFE loopTR

contig.

stem

max

stem

all

S. pombe

H. sapiens

Structureatthe5’capcontributeslittle

0%

% o

r TR

exp

lain

ed

mostfolded

leastfolded

90%75%25%10%

10%

8%

6%

4%

2%

16%

14%

12%

5’cap -1 whole allall -whole

sum<10%

0%

% o

r TR

exp

lain

ed

mostfolded

leastfolded

90%75%25%10%

10%

8%

6%

4%

2%

16%

14%

12%

5’cap -1 whole allall -whole

sum<10%

Longdistanceloopsmakelittlecontribution

Translationsequencemotifs

+1-60 +30-30

S. POMBE

01

bits

01

bits

+1-60 +30-30

S. CEREVISAE

ARABIDOPSIS

01

bits

+1-60 +30-30

H. SAPIENS

01

bits

+1-60 +30-30

M. MUSCULUS

01

bits

+1-60 +30-30

5’UTR CDSAUG

SimilarcontrolsequencesacrossEukarya

1.5

2.0

0.0

0.5

1.0

2.5

Yeas

t uA

PE

1.5 2.00.0 1.0 2.5

Arabidopsis uAPE0.5

r=0.88

GGGATG

AACCAA

2.5

1.5

2.0

0.0

0.5

1.0

Mou

se 5

’ of A

PE

1.5 2.00.0 1.0 2.5

Arabidopsis 5’ of APE0.5

r=0.36

GGG

ATG

AACCAA

Generalfeaturesactsimilarlyindifferenttissues,butdifferentlybetweenspecies

uAUG 5’motifscodonfreq.

CDSlength

5’UTRRNAfold

S.cerevisae

S.pombe

kidny

hela

liver

3T3

H. sapiens

M. musculus

Arabidopsis

100%80%60%40%20%0%

% contribution to sum of general feature control

leaf

root

shoot

1

2

R2 all vs TR0.0 0.4 0.8

a b

Gene and condition specifice.g. miRNA

RBPs

Present in a minority of mRNAs, cell types and conditions

General featurese.g. RNA structure

uORFs, codon usage

Present in most or all mRNAs, cell types and conditions

AAAAAUG5’ cap

protein coding sequence

RBP

AAAAAUG5’ cap

protein coding sequence

miRNA

AAAAAUG protein coding sequence

AAAAAUG protein coding sequence

efficient codon usage

uORF

inefficient codon usage5’ cap

uORFuORF5’ cap

Thepercentcontributionssumto>100%

200%80% 160%40% 120%0%

uAUG 5’motifscodonfreq.

CDSlength

5’UTRRNAfold

S.cerevisae

S.pombe

kidny

hela

liver

3T3

H. sapiens

M. musculus

Arabidopsis

% contribution to general feature control

leaf

root

shoot

1

2

Highlycorrelated(collinear)controlbetweenthegeneralfeatures

M. MUSCULUS

S. CEREVISAE

uAUG

RNAfold

CDSlength

RNAfold

CDSlength

codon

80% 27% 78%

47% 77%

51%

92% 40% 59%

89% 100%

59%

uAUG

RNAfold

CDSlength

RNAfold

CDSlength

codon

S.POMBE ARABIDOPSIS

78% 28% 47%

45% 40%

62%

uAUG

RNAfold

CDSlength

RNAfold

CDSlength

codon

H. SAPIENS

59% 37% 55%

45% 39%

52%

uAUG

RNAfold

CDSlength

RNAfold

CDSlength

codon

7% 22% 30%

35% 26%

45%

uAUG

RNAfold

CDSlength

RNAfold

CDSlength

codon

Controlbyseparatestemloopsishighlycorrelated

Controlbyseparatestemloopsishighlycorrelated

Controlbyseparatestemloopsishighlycorrelated

CollinearcontrolbyN- andC- terminalcodonusage

Collinearcontrolbyaminoacidfrequencyandsynonymouscodonpreferences

Correlatedcontrolgivesevenpacking

Uncorrelatedcontrolgivesunevenpacking

Ribosomesarelimitingforcellgrowth

>90% ribosomes bound to mRNA

50% reductions in ribosome copy slows cell growth(in Drosophila)

Correlatedcontrolbygeneralfeaturesaidsefficientuseofthetranslationmachinery

Uncorrelatedcontrolincreasesparticlecollisions,leadingtoRNAdegradation

Thegeneralfeatureshaveseveralroles

AAAAAAAAAUGAUG

PROTEIN CODING REGION (CDS)

RNAstem loop

poly A tailAPEuORF

1. 5’ UTR RNA secondary structure

2. upstream open reading frames (uORFs)

3. AUG proximal element (APE)

5’ UTR 3’ UTR

5’ cap

4. protein coding sequence (CDS) length

5. CDS codon frequency

protein coding sequence

Mark BigginLBNL

Guo-Liang ChewFred Hutchison Center

Quantitationofcis-translationalcontrolbygeneralmRNAfeaturesinfiveeukaryotes