# Chromatin Dynamics in Plants: At the Crossroad of Genetics and Epigenetics

Cristel Carles

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## To cite this version:

Cristel Carles. Chromatin Dynamics in Plants: At the Crossroad of Genetics and Epigenetics. Licence. Génétique du développement des plantes - “ Characterization of mutants affected in plant development ”, en distanciel, visio-conférence, Spain. 2024. hal-04933601

HAL Id: hal-04933601

https://hal.science/hal-04933601v1

Submitted on 6 Feb 2025

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Distributed under a Creative Commons Attribution 4.0 International License
# Chromatin Dynamics in Plants:
At the Crossroad of Genetics and Epigenetics

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Christel CARLES

Professor @ Grenoble Alpes University

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Department of Biology & Chemistry
Chromatin Dynamics & Developmental Transitions team
Cell & Plant Physiology Lab

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# My curriculum in brief

1. PhD

ATER

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UPVD

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LABORATOIRE
GENOME
DE DEVELOPMENTS
DES PLANTES

**Plant Genome and Development Laboratory** (1997-2001)

• Embryogenesis and seed maturation

<figure><img src="image_8.png" /></figure>

Bies et al, *J. Exp. Botany* 1998

Delseny et al, *J. Plant Physiology* 2001

Carles et al, *Plant Journal* 2002

2. Post-doc

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USDA

**Plant Gene Expression Center, UC Berkeley, USA** (2001-2008)

• Post-embryonic development ... from genetics to epigenetics ...

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Carles et al, *Genetics* 2004 ; Development 2005

Williams¹, Carles¹ et al, *PNAS* 2005

Carles & Fletcher, *Genes & Development* 2009

Monfared et al, *Mol Plant* 2013

3. Researcher

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**Institute for Research and Development** (2008-2009)

• Viruses, reproductive development and epigenetics

Rodor et al, *Plant J.* 2011

4. Assoc. Professor

CNRS Chair

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cnrs

**Cell and Plant Physiology Laboratory** (2010 - )

• Chromatin dynamics and development

ANR

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Rhône-Alpes

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5. Full Professor

Team Leader

UGA

Université
Grenoble Alpes

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**ChromDev Team** (*Chromatin Dynamics & Developmental Transitions*)

Smaczniak et al, *PNAS* 2012

Mandel et al, *Development* 2014, 2016

Engelhorn et al, *Annals Botany* 2014 *C

O'Maoiléidigh et al, *Plant J* 2015

Moreau et al, *Development* 2016 *C

Engelhorn et al, *Epigenomes* 2017 *C

Vachon et al, *J. Exp. Botany* 2018 *C

Yan et al, *Nature Plants* 2018; *Nature Com* 2019

Thouly et al, *Genes* 2020; Fal et al, *IJMS* 2021 *C

Fal et al, *New Phytol* 2023 *C; Fal & Carles,*

MIMB 2024 *C; Geshkovski et al, *MIMB* 2024 *C

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# My curriculum in brief

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Guiding thread: The molecular basis of development [plant models]

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**OUTLINE**
**for our time together today**

**Introduction to EPIGENETICS**

→ General concepts and definitions

→ The actors

→ Zoom on Polycomb and trithorax complexes: key regulators of developmental genes

**QUIZZ (on what you heard before)**

**Presentation of MY RESEARCH**

*Why it is exciting to study epigenetics & chromatin dynamics in plants*

→ The team

→ The projects

**Presentation of the PLANTA-international Master**
# Understanding how the genes that shape life are regulated

<figure><img src="image_23.png" /></figure>

## Epigenetics

100% identical genes

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<figure><img src="image_25.png" /></figure>

Different individuals

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* epigenetic marks

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A same genome : different features
Some key epigenetic actors

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WRITER

ERASER

READER

REMODELERS

Reader SUs

ATPase SUs
One genome, several epigenomes

<figure><img src="image_30.png" /></figure>

Adapted from Allis *et al*, Epigenetics 2007, CSHL

**Genetic alterations**

- Mutations

- Changes to DNA sequence

- Not reversible

**Epigenetic alterations**

- Heritable and stable

- Changes in gene expression

- Potentially reversible

« The difference between genetics and epigenetics can probably be compared to the difference between writing and reading a book. Epigenetics would allow different interpretations of a fixed template and result in different read-outs, dependent upon the variable conditions under which the template is interrogated. »

Jonathan WEITZMAN, Université Paris Diderot

Another analogy: « if the genome is the **hardware**, then the epigenome is the **software** »

→ Epigenetic regulation contributes to the **selective readout of the genome**
<figure><img src="image_31.png" /></figure>

**Epigenetics** : the study of heritable changes in genome function that occur without a change in DNA sequence.

2004-2009 Epigenome Network of Excellence

PERSPECTIVE

An operational definition of epigenetics

Shelley L. Berger,¹,⁵ Tony Kouzarides,²,⁵ Ramin Shiekhattar,³,⁵ and Ali Shilatifard⁴,⁵

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Genes & Development

2009

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# Chromatin structure

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Nicolas Bouvier ArtWork

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## Nucleus organization

Packaging of DNA

## Nucleosomes

Assembly

Position & Density

## Histones

Modifications

variants

## DNA

methylation

**A nucleosome** = 8 histones
[2x (2A, 2B, 3, 4)] wrapped
with 147 bp of DNA (2 loops)
# The « problems »

## 1- How does all that DNA get into the tiny nucleus?

Nearly 2m of human DNA into a nucleus that averages just 5µ

« Imagine trying to stuff about 10,000 miles of spaghetti inside a basketball. Then, if that was not difficult enough, attempt to find a unique one inch segment of pasta from the middle of this mess, or try to duplicate, untangle and separate individual strings to opposite ends. »

Peterson & Laniel, Curr Biol 2004

## 2- How can transcription factors access DNA that is packaged into the nucleus?

**The solution:** Assembly of eukaryotic genome into **CHROMATIN**

⇒ solves the basic packaging problem

⇒ provides a dynamic platform controlling all DNA-mediated processes within the nucleus

<figure><img src="image_37.png" /></figure>
# Chromatin structure

<figure><img src="image_38.png" /></figure>

Nicolas Bouvier ArtWork

## Nucleus organization

**Nucleosomes**

Assembly

Position & Density

**Histones**

Modifications

variants

**DNA**

methylation

<figure><img src="image_39.png" /></figure>

**A nucleosome** = 8 histones
[2x (2A, 2B, 3, 4)] wrapped
with 147 bp of DNA (2 loops)
Nucleosome assembly model

<figure><img src="image_40.png" /></figure>
Mode of nucleosome assembly

<figure><img src="image_41.png" /></figure>

Essential role of Histone chaperones

- CAF-1 is a **replication-dependent** histone chaperone complex

- HIR histone chaperone complex is **replication-independent**

- ASF1 is actively involved in maintenance of chromatin states during DNA replication
# Chromatin structure

<figure><img src="image_42.png" /></figure>

Nicolas Bouvier ArtWork

## Nucleus organization

**Nucleosomes**

Assembly

Position & Density

**Histones**

Modifications

Variants

**DNA**

methylation

<figure><img src="image_43.png" /></figure>

**A nucleosome** = 8 histones
[2x (2A, 2B, 3, 4)] wrapped
with 147 bp of DNA (2 loops)
Euchromatin and Heterochromatin define two distinct chromatin states in Eukaryotes

<figure><img src="image_44.png" /></figure>

*in blue*: DAPI staining of nuclei from Arabidopsis leaf, mouse fibroblasts and Drosophila salivary glands

*in pink*: DNA fluorescence *in situ* hybridization of repetitive sequences

remains condensed throughout the whole cell cycle, forms at repetitive sequences and transposable elements
Some key epigenetic actors

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WRITER

ERASER

READER

REMODELERS

Reader SUs

ATPase SUs
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Shared characteristics of chromatin remodeling complexes

* bind nucleosomes

* are DNA-dependent ATPases

* recognize histone modifications

* ATPase activity can be regulated

* interact with other proteins
<figure><img src="image_47.png" /><figcaption>Families of chromatin remodeling ATPases</figcaption></figure>

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# Dynamic range of chromatin structure created by ATP-dependent chromatin remodeling

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<figure><img src="image_53.png" /><figcaption>Remodeling activities of ISWI subfamily</figcaption></figure>

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Langst, G. and P.B. Becker, Nucleosome mobilization and positioning by ISWI-containing chromatin-remodeling factors. J Cell Sci, 2001. **114**: p. 2561-8.
# Chromatin structure

<figure><img src="image_55.png" /><figcaption>Nicolas Bouvier ArtWork</figcaption></figure>

## Nucleus organization

### Nucleosomes

- Assembly

- Position & Density

### Histones

- Modifications

- Variants

### DNA

- methylation
# DNA methylation

<figure><img src="image_56.png" /></figure>

DNA can be covalently modified by cytosine methylation

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**SAM**: S-adenosyl-L-methionine

**SAH**: S-Adenosyl-L-homocysteine

WRITERS

ERASERS

SOFT BOX

PLASTIC BOX
4B樓座
The peloric variant of Linaria vulgaris (toadflax):
First recorded example of a spontaneous epimutation

<figure><img src="image_58.png" /></figure>

<figure><img src="image_59.png" /><figcaption>**Cycloida**
controls
floral
symmetry</figcaption></figure>
# DNA methylation

Methylation can affect Cytosines in different positions:

Pattern

mCG

propagated by

DNMT1 (animals) ; MET1 (plants)

Plants also extensively methylate non-CGs:

mCNG

(N = any base)

mCHH

(H = A, T, or C)

CMT3

interacts with histone marks

DRM1/2

preliminary targets repetitive elements

**Asymmetric methylation maintained (and initiated) by information on associated histones, and RNA-directed DNA Methylation**

<figure><img src="image_60.png" /></figure>

Methyltransferase

<figure><img src="image_61.png" /></figure>

CH₃ group exposed in major groove
represses transcription by

⇒ **blocking Transcription Factors** access

⇒ **recruiting proteins** that compact chromatin
# Defects in DNA methylation trigger developmental defects and perturb stable trans-generational inheritance in plants

DNA methylation is **necessary to silence transposons**

**Transposons** are DNA fragments capable of moving autonomously in the genome by a mechanism called transposition. Widely spread in all eukaryotes, they are powerful engines for evolution and diversity.

<figure><img src="image_62.png" /><figcaption>**Transposable elements (TEs)** were discovered in *Zea mays* by Barbara McClintock.</figcaption></figure>

McClintock *et al*, Cold Spring Harb Symp. Quant. Biol. 1951

For her discovery, she was awarded the Nobel Prize in Physiology or Medicine in 1983.

<figure><img src="image_63.png" /></figure>
# Defects in DNA methylation trigger developmental defects and perturb stable trans-generational inheritance in plants

Loss of DNA methylation triggers developmental defects due to genome-wide, random deployment of aberrant DNA methylation

<figure><img src="image_64.png" /><figcaption>DDM1 = chromatin remodeling ATPase of the SNF2/SWI2 family
Required for mCG maintenance</figcaption></figure>

6 generations after DNA methylation was reduced by *DDM1* inactivation, **newly inserted transposons were distributed throughout the genome.**

Miura *et al*, Nature 2001
# Chromatin structure

<figure><img src="image_65.png" /><figcaption>Nicolas Bouvier ArtWork</figcaption></figure>

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## Nucleus organization

### Nucleosomes

Assembly

Position & Density

### Histones

Modifications

variants

### DNA

methylation

Histones have accessible Nter tails

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Nucleosome structure

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Groudine, *Nature* 2003

The amino terminal regions of the histone monomers extend beyond the nucleosome and are accessible for modification
# The non-exhaustive list of Histone marks

* Histones can be modified by:

- Acetylation (Ac)

- Ubiquitination (Ub)

- Methylation (Me)

- Phosphorylation (P)

- Sumoylation (Su)

...

<figure><img src="image_69.png" /></figure>

Liu et al, *Annu Rev Plant Biol* 2010

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* Based on their type and position, Histone marks contribute to transcriptional activation or inactivation

## → Histone code hypothesis:

Histone modifications regulate chromatin state and dynamic transitions between condensed heterochromatin and accessible euchromatin.

(Jenuwein & Allis, *Science* 2001)
<figure><img src="image_71.png" /></figure>

# Types of histone modifications and enzymes

<table><thead><tr><th>Residue</th><th>type of modification</th><th>modifying enzyme</th></tr></thead><tbody><tr><td>Lysine</td><td>acetylation<br>deacetylation</td><td>HAT KAT<br>HDAC</td></tr><tr><td>Lysine</td><td><strong>methylation</strong><br><strong>demethylation</strong></td><td><strong>HMT</strong> KMT<br><strong>HDM</strong> KDM</td></tr><tr><td>Lysine</td><td>ubiquitylation<br>deubiquitylation</td><td>Ub ligase<br>Ub protease</td></tr><tr><td>Serine/<br>Threonine</td><td>phosphorylation<br>dephosphorylation</td><td>kinase<br>phosphatase</td></tr><tr><td>Arginine</td><td>methylation<br>demethylation</td><td>PRMT<br>deiminase</td></tr></tbody></table>

* Others: Sumoylation (Lysine), ADP Ribosylation (Glutamate)

* One or up to 3 groups added per residue
Histone Modifications

<figure><img src="image_72.png" /></figure>

Portela & Esteller, *Nature Biotech* 2010
How are histone modifications studied?

* *in situ* immuno-localisation for global view

**chromocenter** : densely staining aggregation of heterochromatic regions in the nucleus of some cells.

Chromocenters are enriched in repressive chromatin marks, vs active chromatin marks

<figure><img src="image_73.png" /></figure>
# How are histone modifications studied?

* *in situ* immuno-localisation for global view

* Chromatin immuno-precipitation (ChIP) followed by PCR (targeted) or by genome-wide approaches (ngs):

* Targeted approach – ChIP-qPCR

* Unbiased approach – ChIP-chip, ChIP-seq, other genome-wide techniques

## Limitations:

- Antibody specificity

- Inherent biases of localization methods
<figure><img src="image_74.png" /></figure>

ChIP-chip
ChIP-seq

« Every few years a new technology comes along that dramatically changes how fundamental questions in biology are addressed. »

Stanley Fields, Science 2007

<figure><img src="image_75.png" /></figure>

Park, Nature Rev 2009
# How are histone modifications studied?

* *in situ* immuno-localisation for global view

* Chromatin immuno-precipitation (ChIP)
  followed by PCR (targeted) or by genome-wide approaches (ngs):

* Targeted approach – ChIP-qPCR

* Unbiased approach – ChIP-chip, ChIP-seq, other genome-wide techniques

## Limitations:

- Antibody specificity

- Inherent biases of localization methods

* **Mass Spectrometry**
  Requires digestion of histones
## Lysine can be acetylated, or mono, di- or tri-methylated

<figure><img src="image_76.png" /><figcaption>Lysine (K)</figcaption></figure>

**Acetylated lysine**
(KAc)

<figure><img src="image_77.png" /></figure>

<figure><img src="image_78.png" /></figure>

### Lysine acetyltransferases: KAT

* Often multi-enzyme complexes

* Can modify *multiple residues*

* Well correlated with transcriptional activation

* Reduces the + charge on the histones (K: + charge)

→ decreases the interaction of their N termini with the negatively charged phosphate groups of DNA

→ Prevents chromatin compaction

**Methylated lysine**

Mono (Kme1)

<figure><img src="image_79.png" /></figure>

Di (Kme2)

<figure><img src="image_80.png" /></figure>

Tri (Kme3)

<figure><img src="image_81.png" /></figure>

<figure><img src="image_82.png" /></figure>

### Lysine methyltransferases: KMT

* *Very specific:* target a certain lysine on a certain histone

* Put on mono, di, or tri me (me, me2, me3)

* Many contain SET domains (me-transferase)

* 'Readout' is *very specific*:

* H3K4me1 vs. H3K4me3 (activating)

* H3K27me2 vs. H3K27me3 (repressive)
# Histone Modifications brought by antagonist Polycomb (PcG) and trithorax (trxG) complexes

## At thousands of developmental genes

above: activation marks

<figure><img src="image_83.png" /></figure>

below: repression marks
PcG and trxG functions first identified in Drosophila

Drosophila *PcG*
and *Trx* mutants

<figure><img src="image_84.png" /></figure>

PcG mutant phenotypes due to mis-expression of Hox genes

trxG mutations rescue
PcG mutant phenotypes

Arabidopsis *PcG*
and *Trx* mutants

<figure><img src="image_85.png" /></figure>

<figure><img src="image_86.png" /></figure>

PcG mutant phenotypes due to mis-expression of MADS-box genes
<figure><img src="image_87.png" /></figure>

Opposing roles of TrxG and PcG

trxG → H3K4me3

PcG PRC2 → H3K27me3
→ PRC1 → H2AK119ub1

<figure><img src="image_88.png" /></figure>
Polycomb group function: PRC2 and PRC1 complexes

<figure><img src="image_89.png" /></figure>
## Opposing roles of TrxG and PcG

<figure><img src="image_90.png" /></figure>

trxG → H3K4me3

PcG PRC2 → H3K27me3
→ PRC1 → H2AK119ub1

<figure><img src="image_91.png" /></figure>

## Reversibility of marks (demethylases)

UTX JMJD3 part of TrxG complex
LSD1 and JARID associate with PcG complex

<figure><img src="image_92.png" /></figure>

<figure><img src="image_93.png" /></figure>

<figure><img src="image_94.png" /></figure>

## Stem cell regulation by polycomb repressors: postponing commitment

Alexandra M Pietersen and Maarten van Lohuizen
# PRC2 core proteins in Drosophila

Drosophila PRC2 has a conserved core of four proteins

<figure><img src="image_95.png" /></figure>

<figure><img src="image_96.png" /><figcaption>E(Z)</figcaption></figure>

<figure><img src="image_97.png" /><figcaption>ESC</figcaption></figure>

<figure><img src="image_98.png" /><figcaption>SU(Z)12</figcaption></figure>

<figure><img src="image_99.png" /><figcaption>NURF55</figcaption></figure>

## Enhancer of zeste (E(Z))

catalytic activity (SET domain methyl transferase)

## Extra sex comb (ESC)

stimulates catalytic activity of E(Z)

## Suppressor of zeste 12 (SU(Z)12)

complex association to nucleosomes

## NURF55

complex association to nucleosomes
# Arabidopsis has multiple forms of three of the core PRC2 proteins

## Drosophila PRC2

<figure><img src="image_100.png" /><figcaption>E(Z)
(methylase)</figcaption></figure>

<figure><img src="image_101.png" /><figcaption>ESC</figcaption></figure>

<figure><img src="image_102.png" /><figcaption>SU(Z)12</figcaption></figure>

<figure><img src="image_103.png" /><figcaption>NURF55</figcaption></figure>

## Arabidopsis PRC2 (plants)

CURLY LEAF (CLF)

MEDEA (MEA)

SWINGER (SWN)

FERTILIZATION
INDEPENDENT
ENDOSPERM
(FIE)

FERTILIZATION-
INDEPENDENT SEED 2
(FIS2)

EMBRYONIC FLOWER 2
(EMF2)

VERNALIZATION 2 (VRN2)

MULTICOPY
SUPPRESSOR
OF IRA1
(MSI1,2,3,4,5)
# Diversification of PRC2 components in plants vs animals

<figure><img src="image_104.png" /><figcaption>*Arabidopsis*
PRC2</figcaption></figure>

<figure><img src="image_105.png" /></figure>

TARGET GENES

<figure><img src="image_106.png" /></figure>

VRN2 complex

<figure><img src="image_107.png" /></figure>

<figure><img src="image_108.png" /></figure>

VEGETATIVE
DEVELOPMENT

FLORAL
TRANSITION

<figure><img src="image_109.png" /></figure>

<figure><img src="image_110.png" /></figure>

EMF2 complex

<figure><img src="image_111.png" /></figure>

<figure><img src="image_112.png" /></figure>

INFLORESCENCE
DEVELOPMENT

FLOWER
ORGANOGENESIS

<figure><img src="image_113.png" /></figure>

FIS complex

<figure><img src="image_114.png" /></figure>

<figure><img src="image_115.png" /></figure>

GAMETOGENESIS

SEED DEVELOPMENT
# Diversification of PRC2 components in plants vs animals

### Drosophila

PRC2

<figure><img src="image_116.png" /></figure>

<figure><img src="image_117.png" /></figure>

### Arabidopsis

PRC2

<figure><img src="image_118.png" /></figure>

<figure><img src="image_119.png" /></figure>

VRN2 complex

<figure><img src="image_120.png" /></figure>

<figure><img src="image_121.png" /></figure>

TARGET GENES

VEGETATIVE DEVELOPMENT

FLORAL TRANSITION

<figure><img src="image_122.png" /></figure>

<figure><img src="image_123.png" /></figure>

EMF2 complex

<figure><img src="image_124.png" /></figure>

<figure><img src="image_125.png" /></figure>

<figure><img src="image_126.png" /></figure>

FIS complex

<figure><img src="image_127.png" /></figure>

<figure><img src="image_128.png" /></figure>

INFLORESCENCE DEVELOPMENT

FLOWER ORGANOGENESIS

GAMETOGENESIS

SEED DEVELOPMENT
# Diversification of PRC2 components in plants vs animals

### Drosophila

PRC2

<figure><img src="image_129.png" /></figure>

<figure><img src="image_130.png" /></figure>

<figure><img src="image_131.png" /></figure>

### Arabidopsis

PRC2

<figure><img src="image_132.png" /></figure>

VRN2 complex

<figure><img src="image_133.png" /></figure>

<figure><img src="image_134.png" /></figure>

<figure><img src="image_135.png" /></figure>

EMF2 complex

<figure><img src="image_136.png" /></figure>

<figure><img src="image_137.png" /></figure>

FIS complex

<figure><img src="image_138.png" /></figure>

<figure><img src="image_139.png" /></figure>

TARGET GENES

VEGETATIVE DEVELOPMENT

FLORAL TRANSITION

INFLORESCENCE DEVELOPMENT

FLOWER ORGANOGENESIS

GAMETOGENESIS

SEED DEVELOPMENT
# Chromatin structure

<figure><img src="image_140.png" /></figure>

Nicolas Bouvier ArtWork

## Nucleus organization

### Nucleosomes

- Assembly

- Position & Density

### Histones

- Modifications

- variants

### DNA

- methylation

## Histone Variants:

- for all, except H4

- **CENH3**: centromeric nucleosomes

- **H3.1**: at repressed *loci*

- **H3.3**: *loci* with active transcription, peak at 3' end of genes

- **H2A.Z**: heterochromatin boundaries and 5' start of active genes

1st Histone Variant EMBO meeting (Oct 2011)

<figure><img src="image_141.png" /></figure>
<figure><img src="image_142.png" /><figcaption>Arabidopsis canonical H3.1 and replacement variant H3.3</figcaption></figure>
Divergences in aa sequences of canonical and variant H3

<figure><img src="image_143.png" /></figure>

<figure><img src="image_144.png" /></figure>

<figure><img src="image_145.png" /></figure>

<figure><img src="image_146.png" /></figure>

<figure><img src="image_147.png" /></figure>
Another, non nucleosomic Histone:
**Histone H1 = linker histone**

- associated with linker DNA between nucleosomes (about one H1 per nucleosome)

• Binds DNA at entry/exit

• stimulates folding 10 nm → 30 nm fiber

• repressive effect on transcription

- H1 binds weaker to acetylated nucleosomes

<figure><img src="image_148.png" /></figure>

- Ordinary nuclear extracts contain high levels of H1

<figure><img src="image_149.png" /></figure>

<figure><img src="image_150.png" /></figure>
The Epigenetic Landscape

<figure><img src="image_151.png" /><figcaption>Conrad Waddington, 1950s</figcaption></figure>

<figure><img src="image_152.png" /></figure>
# Take-Home message

Actors in Chromatin dynamics are:

- Part of large complexes

- Made of several modules
  recognition domain (reader: Bromo, PHD...)
  enzymatic (modifier= writer or eraser: HMT, HAT, HDAC...)

- Involved in cross-talking pathways
e.g. DNA me → Histone PMT → nucleosome remodeling

- Largely conserved between kingdoms, but with some variations
  in function
  in number (more in plants)

- Key to control of gene expression => read-out of the genome
Questions ?
QUIZZ !!
**Question 1:**

"Epigenetics" is the study of heritable changes in genome function that occur without a change in ..." Find the right end for this sentence:

A) Histone sequence

B) DNA sequence

C) RNA sequence

D) Epigenator

Answer: B

**Question 2:**

All the following names correspond to **enzymes that modify epigenetic marks**, but one. Which one isn't such an enzyme?

A) writer

B) eraser

C) DNA methyl transferase

D) ATPase remodeler

Answer: D

**Question 3:**

Which of the following propositions is **false**?

A) A nucleosome is made of 8 histones, each present in two copies (2 H2A, 2 H2B, 2 H3, 2 H4), wrapped with 147 bp of DNA

B) A nucleosome is a tetramer of histones (H2A, H2B, H3, H4), wrapped with 2 loops of DNA

C) Nucleosomes can slide, assemble or disassemble, during DNA replication or transcription

D) Chromatin structure is highly dynamic, contributing to gene expression dynamics

Answer: B
**Question 4:**

Among epigenetic marks that can be deposited at the chromatin (find the **false proposition**):

A) Methylation marks on histones are always activating marks for transcription

B) Acetylation marks are always activating marks for transcription

C) DNA methylation can prevent the binding of transcription factor to target DNA

D) All correspond to covalent modifications

Answer: A

**Question 5:**

The **Polycomb and trithorax chromatin complexes** display **functions** that are, in regard to their effect on gene expression (find the right answer):

A) Epistatic

B) Bivalent

C) Antagonistic

D) Cooperative

Answer: C
<figure><img src="image_153.png" /></figure>
<figure><img src="image_154.png" /></figure>

## CHROMDEV team

# Exploring molecular regulators of gene expression for developmental transitions

### Permanent

<figure><img src="image_155.png" /><figcaption>Robert Blanvillain
Ass Prof UGA</figcaption></figure>

<figure><img src="image_156.png" /><figcaption>Gilles Vachon
CNRS Scientist</figcaption></figure>

<figure><img src="image_157.png" /><figcaption>Cristel Carles
Prof UGA</figcaption></figure>

<figure><img src="image_158.png" /><figcaption>Marie Le Masson
CNRS Eng.</figcaption></figure>

### Non permanent

<figure><img src="image_159.png" /><figcaption>Vangeli Geshkovski
PhD 3<sup>d</sup> year</figcaption></figure>

<figure><img src="image_160.png" /><figcaption>Salim El Khoury
PhD 1<sup>st</sup> year</figcaption></figure>

<figure><img src="image_161.png" /><figcaption>Laura Turchi
Post-Doc</figcaption></figure>

<figure><img src="image_162.png" /><figcaption>Veronica-Astrid Morlacchi
M2 PLANT-Int</figcaption></figure>

<figure><img src="image_163.png" /><figcaption>Ivan Cubillas
M2 NanoSc</figcaption></figure>

<figure><img src="image_164.png" /><figcaption>Leonard Calistru
M1 PhEDC</figcaption></figure>

Soon ...

TBA
Post-doc

TBA
Engineer

<figure><img src="image_165.png" /></figure>

<figure><img src="image_166.png" /></figure>

<figure><img src="image_167.png" /></figure>

## Two paradigms: **Photo morphogenesis** and **core organogenesis**

* **PAPs**: nucleus – chloroplast communications

Chloroplast biogenesis, photomorphogenesis

* **ULTRAPETALA**: chromatin-TF scaffold

Flowering transition, flower morphogenesis

**REWIRE**: Epigenome editing

▷ to redirect plant development

▷ to depict the genuine function of chromatin marks

**Eco-Devo project**: Epiwarm (alpine meadows)

Coordinators of Dynamics
Plant organogenesis operates post-embryogenesis

<figure><img src="image_168.png" /></figure>
Organs are continuously produced from Meristems

<figure><img src="image_169.png" /></figure>

<figure><img src="image_170.png" /></figure>

<figure><img src="image_171.png" /></figure>

<figure><img src="image_172.png" /></figure>

<figure><img src="image_173.png" /></figure>

<figure><img src="image_174.png" /></figure>

<figure><img src="image_175.png" /></figure>

<figure><img src="image_176.png" /></figure>
Gene

<figure><img src="image_177.png" /></figure>

Gene

<figure><img src="image_178.png" /></figure>

<figure><img src="image_179.png" /></figure>
Gene

<figure><img src="image_180.png" /></figure>

Gene

<figure><img src="image_181.png" /></figure>

H3K27me3

<figure><img src="image_182.png" /></figure>

PcG PRC2

<figure><img src="image_183.png" /></figure>

H3K4/K36me3

<figure><img src="image_184.png" /></figure>

trxG

<figure><img src="image_185.png" /></figure>

<figure><img src="image_186.png" /></figure>

<figure><img src="image_187.png" /></figure>
Gene

<figure><img src="image_188.png" /></figure>

Gene

H3K27me3

<figure><img src="image_189.png" /></figure>

PcG PRC2

<figure><img src="image_190.png" /></figure>

H3K4/K36me3

<figure><img src="image_191.png" /></figure>

trxG

<figure><img src="image_192.png" /></figure>

Ectopic de-repression
of hundreds of developmental genes
**<u>Chromatin dynamics</u>**: the ULTRAPETALA1 (ULT1) dual switch

<figure><img src="image_193.png" /></figure>

Epigenomics

<figure><img src="image_194.png" /><figcaption>ULT1_derep</figcaption></figure>

<figure><img src="image_195.png" /></figure>

in vitro HMT assay

<figure><img src="image_196.png" /></figure>

<figure><img src="image_197.png" /></figure>

TRANSCRIPTION

Interactomics

<figure><img src="image_198.png" /></figure>

ULT1

<figure><img src="image_199.png" /></figure>

CHROMATIN

PRC2

BRM

<figure><img src="image_200.png" /></figure>

RNA BINDING

<figure><img src="image_201.png" /></figure>

<figure><img src="image_202.png" /></figure>

H3 binding
# REWIRE: Editing histone marks to depict their genuine function & redirect plant development

edit

<figure><img src="image_203.png" /></figure>

Active marks

<figure><img src="image_204.png" /></figure>

target
gene

<figure><img src="image_205.png" /></figure>

T

<figure><img src="image_206.png" /></figure>

edit

<figure><img src="image_207.png" /></figure>

Repressive marks

1

<figure><img src="image_208.png" /></figure>

2

<figure><img src="image_209.png" /></figure>

★ **Innovative tools**: Chromatin rewiring [WP1]

**Objective 1. Development** [WP2]

- Morphogenesis and cell fates

- Gene expression

★ **Cutting-edge methods**: *in situ* quantification and visualisation of chromatin & transcription

**Objective 2. Nucleus dynamics** [WP3]

- Chromatin topology & structure

- Transcription

★ **The epigenetic editing tools:**

**HME:** Histone Modifying Enzyme

Genome-wide, Chromatibody-induced

H3 mark editing

Local, dCas9-induced

<figure><img src="image_210.png" /></figure>

<figure><img src="image_211.png" /></figure>
Genome-wide

<figure><img src="image_212.png" /></figure>

CNRS communication

© Christel Carles

<figure><img src="image_213.png" /></figure>

Histone editing, a novel approach
to explore the epigenetic regulation
of plant development

16 février 2023

RÉSULTATS SCIENTIFIQUES BIOLOGIE VÉGÉTALE

H3.3 K27A

@H3K27me3

@H3

WT K27A

<figure><img src="image_214.png" /></figure>

<figure><img src="image_215.png" /></figure>

<figure><img src="image_216.png" /></figure>

<figure><img src="image_217.png" /></figure>

<figure><img src="image_218.png" /></figure>

<figure><img src="image_219.png" /></figure>

Fal et al., New Phytol 2023

Locus specific

Chimeric dCas9 System for Enhanced Targeting

SunTag
("SUperNova")

<figure><img src="image_220.png" /></figure>

H3K27me3/H3
(ChIP-qPCR)

<figure><img src="image_221.png" /></figure>

pCUC3::CFP

<figure><img src="image_222.png" /></figure>

dCas9<sup>CUC3-0</sup> (0)

<figure><img src="image_223.png" /></figure>

dCas9<sup>CUC3-JMJ</sup>

<figure><img src="image_224.png" /></figure>

CUC3 (in rosettes)

Expression
(RT-qPCR)

<figure><img src="image_225.png" /></figure>

Multi-scale impact of epigenetic editing : from chromatin and transcription dynamics to cell fate

PhD Project Salim El Khoury

Co-dir. : J-Philippe Kleman (IBS)

<figure><img src="image_226.png" /></figure>

in cyto
microscopy
EpiWarm

Environmental Epigenetics :

<figure><img src="image_227.png" /></figure>

<figure><img src="image_228.png" /></figure>

**Question:**

How do epigenetics of the transplanted population change ? → Analysis of epigenetics mark dynamics upon warming of the alpine species
ACKNOWLEDGEMENTS

<figure><img src="image_229.png" /><figcaption>Team members</figcaption></figure>

ChromDev, January 2024

<figure><img src="image_230.png" /><figcaption>Colleagues for teaching activities @ UGA & UniMi:</figcaption></figure>

<figure><img src="image_231.png" /></figure>

<figure><img src="image_232.png" /><figcaption>Faycal
Boussouar</figcaption></figure>

<figure><img src="image_233.png" /><figcaption>Florence
Courtois</figcaption></figure>

<figure><img src="image_234.png" /><figcaption>Gabrielle
Tichtinsky</figcaption></figure>

<figure><img src="image_235.png" /><figcaption>Luca
Gianfranceschi</figcaption></figure>

<figure><img src="image_236.png" /><figcaption>Paolo
Pesaresi</figcaption></figure>

<figure><img src="image_237.png" /><figcaption>Camilla
Betti</figcaption></figure>

<figure><img src="image_238.png" /><figcaption>Stephan
Nonchev</figcaption></figure>

<figure><img src="image_239.png" /><figcaption>Sylvie
Canavesio</figcaption></figure>

<figure><img src="image_240.png" /><figcaption>Anahide
Faye</figcaption></figure>
<figure><img src="image_241.png" /></figure>
PLANT-Int

Master's degree in Plant Biology

<figure><img src="image_242.png" /></figure>

<figure><img src="image_243.png" /></figure>

<figure><img src="image_244.png" /></figure>

<figure><img src="image_245.png" /></figure>

UNIVERSITÀ
DEGLI STUDI
DI MILANO

LA STATALE
Manon Sart

<figure><img src="image_246.png" /></figure>

CHEMISTRY
BIOLOGY
HEALTH

Grenoble Graduate School

<figure><img src="image_247.png" /></figure>

Grenoble Alliance for Integrated
Structural & Cell Biology

La Région

Auvergne-Rhône-Alpes

<figure><img src="image_248.png" /></figure>

UNIVERSITÉ
FRANÇO
ITALIENNE

UNIVERSITÀ
ITALO
FRANCESE

<figure><img src="image_249.png" /></figure>

Erasmus+
# Master of Plant Biology

Coord.: Christel CARLES

<figure><img src="image_250.png" /></figure>

M2

PLANTA
International

Plant
Sciences

<figure><img src="image_251.png" /></figure>

**Double**
**Diploma**
UGA / UniMi

<figure><img src="image_252.png" /></figure>

<figure><img src="image_253.png" /></figure>

<figure><img src="image_254.png" /></figure>

M1

# Master of Biology

Coord.: Alain BUISSON

<figure><img src="image_255.png" /></figure>

UGA +
INPG
NNN

Nanoscience
and
Nano
technology

<figure><img src="image_256.png" /></figure>

PhEDC

Physiology
Epigenetics
Development
Differentiation

<figure><img src="image_257.png" /></figure>

NN

Neurosciences
Neurobiology

Integrative
Structural
Biology

<figure><img src="image_258.png" /></figure>

ISB

IMID

Immunology
Microbiology
Infectious Dis.

Pro2Bio

<figure><img src="image_259.png" /></figure>

<figure><img src="image_260.png" /></figure>

LST

Lab
Science
Trading

<figure><img src="image_261.png" /></figure>

BioTechCO

Biologie,
Chimie,
Commerce
(alternance)

<figure><img src="image_262.png" /></figure>

« Professional » M2

Molecular and Cellular
Biology (MCB)

<figure><img src="image_263.png" /></figure>

Bachelor (L3)
# The Master's degree in Plant Biology

PLANTA-International

<figure><img src="image_264.png" /></figure>

UGA
Université
Grenoble Alpes

## CONTACT

Generic email address:
ufrchimiebiologie-master-
plantint@univ-grenoble-alpes.fr

PLANT-Int Academic
Coordinator:
Christel Carles (for course
enquiries)
christel.carles@univ-grenoble-alpes.fr

PLANT-Int Clerical Assistant:

## Objectives

* Training scientists in Plant Sciences

→ careers in the academic/private sector

* Encouraging the development of an international scientific & professional network

<figure><img src="image_265.png" /></figure>

PS - Master Degree in Plant Science

<figure><img src="image_266.png" /></figure>

<figure><img src="image_267.png" /></figure>

A regarder plus tard Partager

UNIVERSITÀ
DEGLI STUDI
DI MILANO

LA STATALE

<figure><img src="image_268.png" /></figure>

PLANT SCIENCE

<figure><img src="image_269.png" /></figure>

## ZOOM

Article "Algal remodeling in a
ubiquitous planktonic
photosymbiosis"

## LINKS TO...

The UNIMI PLANT-Int website

The UGA teaching catalogue

<figure><img src="image_270.png" /></figure>

## Numerous models of study

<figure><img src="image_271.png" /></figure>

<figure><img src="image_272.png" /></figure>

<figure><img src="image_273.png" /></figure>

<figure><img src="image_274.png" /></figure>

<figure><img src="image_275.png" /></figure>

<figure><img src="image_276.png" /></figure>

<figure><img src="image_277.png" /></figure>
<figure><img src="image_278.png" /></figure>

<figure><img src="image_279.png" /></figure>

## International Training, **double diploma (UGA / UniMi)**

* M1: **Semester 1 @ UGA, Semester 2 @ UniMi**

* M2: "à la carte" (UGA or UniMi ou elsewhere ; remote teaching)

## Plant sciences, approached on a **multi-scale basis** :
(community >) organism > cell > molecule (> atome)

## Choice of courses in the disciplines of Developmental biology, Cell biology, molecular genetics, epigenetics, biochemistry, physiology, biostatistics, applied sciences

## 3 internships with mobility strongly recommended

<figure><img src="image_280.png" /><figcaption>### Places of internships</figcaption></figure>

## Innovative teaching methods : Projects, collaborative work, tutorials, internships

<figure><img src="image_281.png" /></figure>
# Strengths of the PLANT-Int Master

* ✓ Attractiveness & Internationalisation
  Groups of around twenty students
  From Europe and beyond (Macedonia, South America, India, ...)

<figure><img src="image_282.png" /></figure>

Annual scientific conference with hosting laboratories

<figure><img src="image_283.png" /></figure>

<figure><img src="image_284.png" /></figure>

<figure><img src="image_285.png" /></figure>

* ✓ Professionalisation and further study

* Jobs in companies or start-ups

* PhD in Plant Sciences

<figure><img src="image_286.png" /></figure>

Financial support for student mobility

Mobility grants, Scholarships

<figure><img src="image_287.png" /></figure>
**MonMaster 2024** : https://candidature.monmaster.gouv.fr/

• Ouverture de campagne : **Du 26 février 2024 au 24 mars 2024**

• Sélection des dossiers et entretiens: avant le 29 mai 2024

• Phase Principale d'admission sur MM : du **4 juin 2024 au 24 juin 2024**

**PEF :**

• Ouverture de campagne sur Portail d'Études en France : **le 1er octobre 2023**

• Sélection des dossiers et entretiens: avant le 29 avril 2024

• Saisie des résultats sur Portail d'Études en France : le **3 mai 2024**
# Coordinators

<figure><img src="image_288.png" /></figure>

UGA Coordinators

## PLANTA International (PLANT-Int)

<figure><img src="image_289.png" /><figcaption>Christel Carles</figcaption></figure>

<figure><img src="image_290.png" /><figcaption>Florence Courtois</figcaption></figure>

<figure><img src="image_291.png" /><figcaption>Gabrielle Tichtinsky</figcaption></figure>

<figure><img src="image_292.png" /><figcaption>Sylvie Canavesio</figcaption></figure>

UGA Clerical
Assistant

<figure><img src="image_293.png" /></figure>

UniMi Coordinators

## Plant Science Master

<figure><img src="image_294.png" /><figcaption>Luca Gianfranceschi</figcaption></figure>

<figure><img src="image_295.png" /><figcaption>Camilla Betti</figcaption></figure>

PLANT-Int email contact:
[ufrchimiebiologie-masterplantint](mailto:ufrchimiebiologie-masterplantint)
[@univ-grenoble-alpes.fr](mailto:@univ-grenoble-alpes.fr)