Introducing Indepth

29 April 2018 - By: Geraint Parry

Introducing Indepth


By Geraint Parry, Cardiff University

Impact of Nuclear Domains On Gene Expression and Plant Traits (INDEPTH) is a new collaboration that brings together a pan-European group of researchers interested in how the location of a gene within the plant nucleus can affect its function.

It has long been known that many complex and interacting factors influence how gene expression is controlled. Over the past years evidence has shown that the location of a gene within the nucleus can have a significant effect on its activity.

The complexity and functional significance of these plant nuclear domains is the focus of the newly formed, collaborative INDEPTH project, funded by the COST organisation, which brings together researchers from across Europe to explore the role of domains in the plant nucleus.

COST is the longest-running European framework that supports trans-national cooperation among researchers.Although it does not provide funding for research activities it generously supports meetings, workshops, training schools and short-term scientific missions (STSMs).

The INDEPTH Action is led by SEB member Professor Christophe Tatout, who works in Clermont Ferrand in France. Other SEB members play prominent roles on the INDEPTH Management Committee, including Katja Graumann (Oxford Brookes University), who is leader of the SEB Cell Section Nuclear Dynamics group, David Evans (Oxford Brookes University), who is a regular session organiser at SEB Annual Meetings, and me - a committee member of the SEB Plant Section and INDEPTH SciComm lead.

As is necessary for all COST Actions, INDEPTH includes researchers from across Europe, with a key aim to facilitate research development in less-well supported countries. As such, researchers from 21 countries are taking part in the project, including Bosnia and Herzegovina, Serbia and Hungary.

INDEPTH is split into four workgroups, although the power of consortium lies in the potential cross-fertilisation of ideas between these groupings: 

Workgroup 1: Quantitative imaging and analysis of the plant nucleus in 3D.
– Workgroup 2: Transcriptional regulation through association of chromatin domains with nuclear compartments.
Workgroup 3: Structure of nuclear domains and the functional output for plant traits.
Workgroup 4: Storage, data management and integrative analysis.

A key aim of the project is to provide a database of protocols and expertise in addition to establishing a potential repository for imaging data. This latter aspect of INDEPTH is a major challenge, so the participants will investigate strategies that might be employed for sharing data of this type.

The COST Association provides funding for training opportunities. We are organising six ‘Training Schools’ which will involve up to 20 participants travelling to a partner lab to learn a technique relevant for their research activities. The proposed topics for the training schools are:

Cytogenetics: Cytogenetic analyses of plant nuclear compartments and chromatin domains 
Microscopy: High-resolution and electron microscopy of the plant nucleus 
3D imaging: Advanced development of image analysis software 
Proteomics: Proteomic analysis of nuclear compartments 
Genomics: Profiling of chromatin domains 
Bioinformatics: Bioinformatics for spatial analyses of nuclear dynamics

The second major training activity is the ‘Short Term Scientific Missions (STSM)’ programme. Twenty STSMs will be taking place, and each will consist in one early career researcher (ECR) travelling to a partner lab in a different country for up to six months. The leader for the STSM training programme is Laszlo Kozma-Bognar (, MTA Sezged, Budapest.

Researchers who are not currently INDEPTH partners yet who would like to be involved should write to the Chairman, Christophe Tatout, stating why they would like to join the Action and how their expertise would benefit other members of INDEPTH consortium.

Anyone attending the 2018 SEB Annual Meeting in Florence might be interested to attend an INDEPTH Workgroup I meeting that is associated with the Cell Session entitled ‘Functional organisation of the nuclear periphery’.

The INDEPTH website is currently under development but the basic information about the COST Action can be found here: .



Category: Plant Biology
Geraint Parry

Geraint Parry

Geraint Parry is the national coordinator for the BBSRC-funded GARNet grant, which is a network that supports uptake of new technologies and knowledge dissemination amongst UK and international plant scientists.

He is the science communication manager of the INDEPTH COST Action as well as being the secretary for the Multinational Arabidopsis Steering Committee (MASC). He tweets for GARNet from @GARNetweets

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