From transcriptome to epigenome, and back? Mattia Pelizzola Center for Genomic Science Istituto Italiano di Tecnologia (IIT), Milano

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1 From transcriptome to epigenome, and back? Mattia Pelizzola Center for Genomic Science Istituto Italiano di Tecnologia (IIT), Milano m6a epitranscriptome m6a dynamics synthesis processing degradation m5c TFs PII TFs Chromatin DNA 1

2 From transcriptome to epigenome, and back High-throughput quantification of gene expression programs 2

3 From transcriptome to epigenome, and back m5c TFs PII TFs Chromatin DNA High-throughput quantification of gene expression programs.. how these are controlled by chromatin regulation 2

4 From transcriptome to epigenome, and back dynamics synthesis processing degradation m5c TFs PII TFs Chromatin DNA High-throughput quantification of gene expression programs.. how these are controlled by chromatin regulation.. how this interplay entails dynamics 2

5 From transcriptome to epigenome, and back m6a epitranscriptome m6a dynamics synthesis processing degradation m5c TFs PII TFs Chromatin DNA High-throughput quantification of gene expression programs.. how these are controlled by chromatin regulation.. how this interplay entails dynamics.. and how this is mediated by (epi) modifications 2

6 Dynamics of transcriptional regulation time 12

7 Dynamics of transcriptional regulation dynamics synthesis time degradation 12

8 Dynamics of transcriptional regulation PII dynamics dynamics synthesis PII recruitment pause release time degradation 12

9 Dynamics of transcriptional regulation PII dynamics dynamics synthesis PII recruitment pause release time degradation modifications mark bp 12

10 Dynamics of transcriptional regulation PII dynamics dynamics synthesis PII recruitment pause release Chromatin environment nuclear speckles time degradation modifications mark bp chromatin transcription factors chromatin remodeler epigenetic marks 12

11 Lab focus m6a epitranscriptome m6a dynamics synthesis processing degradation m5c TFs PII TFs Chromatin DNA Studying the interplay between epitranscriptome and chromatin and its impacts on dynamics 13

12 dynamics Mathematical modeling of the life-cycle Steady-state synthesis (k 1 ) premature (P) at steady-state (dp = dt = 0): P = k 1 / k 2 M = k 1 / k 3 nucleus gene processing (k 2 ) P M k k k initial value: 10.0 k 5.0 P(0) = (0) = 10 k M(0) = 5 2 (0) = 20 mature k 3 (0) = 2 (M) degradation (k 3 ) dp/dt = k 1 - k 2 P dm/dt = k 2 P - k 3 M ratio to initial value time (a.u.) time (a.u.) de Pretis S.. Pelizzola M, Bioinformatics 2015 Furlan M.. Pelizzola M, biorxiv

13 dynamics P M k 1 k 2 k 3 synthesis (k 1 ) nucleus gene mature (M) dp/dt = k 1 - k 2 P dm/dt = k 2 P - k 3 M premature (P) processing (k 2 ) degradation (k 3 ) ratio to initial value P(0) = 0.5 M(0) = 20 P(0) = 0.5 M(0) = 5 P(0) = 2 M(0) = 5 time (a.u.) k 1 (0) = 10 k 2 (0) = 20 k 3 (0) = 2 k 1 (0) = 10 k 2 (0) = 5 k 3 (0) = 2 k 1 (0) = 10 k 2 (0) = 20 k 3 (0) = 0.5 time (a.u.) Δ synthesis Δ processing Δ degradation P(0) = 0.5 M(0) = 20 P(0) = 0.5 M(0) = 20 P(0) = 0.5 M(0) = k 1 (0) = 10 k 2 (0) = 20 k 3 (0) = 0.5 k 1 (0) = 10 k 2 (0) = 20 k 3 (0) = 0.5 k 1 (0) = 10 k 2 (0) = 20 k 3 (0) = 0.5 Impact of individual kinetic rates synthesis vs degradation Furlan M.. Pelizzola M, biorxiv

14 dynamics 1. Interaction with an object of class INSPEcT 2. Gene-level dynamics 3. Model minimization 4. Model parameters soon available at 16

15 The MYC transcription factor and oncogene Kress TR et al, Nature Rev Cancer

16 MYC impact on dynamics MYC PII mature- vs. MYC synthesis m6a processing m6a PII pre- mature- degradation MYC impacts on: 1. mature 2. dynamics 3. PII dynamics 4. m6a epitranscriptome 18

17 MYC impact on dynamics 4sU 4sU 4sU nascent pre-existing 4sU 4sU synthesis (s) pre- (P) nucleus gene mature (M) processing (p) degradation (d) d(p)/dt = s p P d(m)/dt = p P d M de Pretis S.. Pelizzola M, Genome Res

18 MYC impact on dynamics log2ratio vs 0h following MYC activation Δ synthesis 4.5K degradation rate processing rate synthesis rate pre-m mature m MYC share Δ processing 1.3K Δ degradation 1K de Pretis S.. Pelizzola M, Genome Res 2017 time 20

19 MYC impact on PII dynamics - ChIP-seq reads density PII + p 1 p 2 p 3 p 4 promoter (TSS) gene-body (GB) 3 end (TES) d(tss)/dt = p 1 p 2 TSS d(gb)/dt = p 2 TSS p 3 GB d(tes)/dt = p 3 GB p 4 TES p 3 GB = synthesis rate de Pretis S.. Pelizzola M, Genome Res

20 MYC impact on PII dynamics induced repressed synthesis rate cl1 cl2 cl3 cl4 cl5 cl6 cl7 cl8 cl9 cl10 cl11 cl12 PII flux (p 1 ) Pause release (p 2 ) Elongation (p 3 ) h 4h OHT log 2 ratio vs 0h OHT h 4h OHT h 4h OHT TES release (p 4 ) h 4h OHT explained variance p 1 p 2 p 3 p 4 Explained variance # genes de Pretis S.. Pelizzola M, Genome Res

21 MYC impact on PII dynamics synthesis rate pre-m processing rate PII elongation rate (p 3 ) OHT (min) OHT (hours) log 2 ratio vs 0h OHT h 4h OHT de Pretis S.. Pelizzola M, Genome Res

22 modifications: N6-Methyladenosine (m6a) m6a dynamics m6a profiling MeRIP-seq m6a methyltransferase (writer) miclip m6a demethylase (eraser) m6a binding protein (reader) UV Adapted From Shi, Nat Meth 2016 Adapted from Dominissini at al., Science

23 modifications: N6-Methyladenosine (m6a) m6a profiling m6a dynamics MeRIP-seq m6a methyltransferase (writer) Adapted from Dominissini at al., Science 2014 Molecular determinants? m6a chromatin factors life-cycle Adapted From Shi, Nat Meth 2016? PII?? m6a Interplay with other modifications? Ψ m5c A->I m1a Outstanding questions m6a binding protein (reader) Impact on life-cycle? METTL3,14 FTO, ALKBH5 YTHDF1-3 miclip m6a demethylase (eraser) UV Role as coupling factor? synthesis degradation m6a hm5c 24

24 dynamics from total -seq experiments Furlan M.. Pelizzola M, biorxiv

25 dynamics from total -seq experiments Furlan M.. Pelizzola M, biorxiv

26 dynamics from total -seq experiments Furlan M.. Pelizzola M, biorxiv

27 dynamics from total -seq experiments Furlan M.. Pelizzola M, biorxiv

28 Acknowledgements Epigenomics and transcriptional regulation Funding Stefano de Pretis Eugenia Galeota Mattia Furlan Nunzio del Gaudio Bruno Amatis Lab Bruno Amati Theresia Kress Contacts