Close

Widespread inter-individual gene expression variability in Arabidopsis thaliana

Sandra Cortijo, Zeynep Aydin, Sebastian Ahnert, James Locke

Preprint posted on 31 May 2018 https://www.biorxiv.org/content/early/2018/05/31/335380

Article now published in Molecular Systems Biology at http://dx.doi.org/10.15252/msb.20188591

What is the level of transcriptional noise among genetically identical individuals? In Arabidopsis, more than 1,300 genes are particularly noisy – a trait associated with gene length, transcription factor binding and the chromatin environment.

Selected by Martin Balcerowicz

The broader context: gene expression variability in multicellular organisms – a black box

Differences in gene expression are strong determinants for phenotypic variability and are themselves affected by both the genotype and the local environment of a given organism. But even genetically identical organisms that exist in a homogeneous environment can exhibit variations in gene expression, often referred to as noise in this context1, 2. Such inter-individual differences have mainly been studied in unicellular organisms and cell culture, and this research has particularly taken off with the advance of single cell RNA-seq. However, while phenotypic variability has been widely described in multicellular organisms, plants in particular, data on gene expression noise in these organisms is scarce. Existing studies mostly focus on differences between single cells or tissues within the organism, but global studies of inter-individual variability in gene expression are virtually non-existent. With their preprint, Cortijo et al. have begun filling this gap, studying variability in gene expression among individual Arabidopsis thaliana plants over a 24-h time course.

Key findings: A set of highly variable genes – and factors that may promote their variability

The authors employed RNA-seq to look at the transcriptomes of 14 individual seedlings per time point sampled every 2 hours during a full 24-h day/night cycle (Figure 1). They detected a wide-spread level of inter-individual variability in gene expression and identified more than 1,300 highly variable genes. Different subsets of these genes displayed different variability profiles, with the highest variability of two subsets being specifically observed at day and at night, respectively. This “noisy” set is enriched for genes involved in environmental and stress responses, whereas genes with low variability are mainly related to primary metabolism.

Having established a comprehensive data set of gene expression variability in Arabidopsis, the authors then looked at the factors that may determine the level of variability. Notably, a correlation between expression level and variability was observed for fewer than half of all highly variable genes, implying that additional factors are involved in determining whether a gene exhibits noisy expression. Indeed, several genetic and epigenetic features were correlated with high variability: (1) highly variable genes are significantly shorter than their lowly variable counterparts; (2) their promoters are bound by a higher number of transcription factors; and (3) their chromatin environment is characterised by the presence of repressive epigenetic marks, while lowly variable genes are generally associated with permissive epigenetic marks.

Figure 1: Experimental setup to identify transcriptional variability between seedlings during a 24-h day/night cycle. RNA-seq was performed on individual seedlings (12 time points, 14 seedlings each). Seedlings of different colours represent different transcriptional states, i.e. the inter-individual expression variability the study aimed to detect (reproduced from Cortijo et al., Fig. 1A).

 

What I like about this preprint                                                                                            

I particularly enjoyed that Cortijo et al. ventured into a field of research that is not heavily studied in plants or other multicellular organisms and thus largely lacks predefined concepts and methodology. While their approach itself is rather straightforward, the authors had to take many precautions to ensure their data are meaningful and not the result of either slight variations in experimental setup or technical noise in RNA preparation and sequencing. By doing so they have established ground rules for similar investigations and also provide a valuable resource future research can build upon.

In addition, I like that the authors made their data readily available via an easy-to-use web interface. So if you have a favourite Arabidopsis gene and would like to know about its variability, make sure to check out https://jlgroup.shinyapps.io/AraNoisy.

Future directions: The cause and consequence of noisy gene expression in plants

This article lays important groundwork for further studies on inter-individual variability in plants. Nevertheless, it is only a first step in increasing our understanding of this trait. In particular, there are two lines of research that I expect to be investigated in the near future:

  • A gene’s length, chromatin environment and the number of transcription factors binding it are factors associated with its level of expression variability. However, these observations are just correlations and a causal relationship has yet to be confirmed. How will future research tackle this question? Can we identify a particular genetic background that exhibits perturbations in one of these factors, or can we extrinsically alter any of these factors to study effects on noise?
  • As the authors themselves point out, it has been suggested for unicellular organisms that noisy gene expression is a survival strategy under unpredictable conditions; variability in the expression of stress genes for instance may increase the likelihood of some individuals to survive stress treatment. Intriguingly, many highly variable genes in Arabidopsis are involved in environmental and stress responses. Is there a way to show that noisy expression of these genes indeed benefits the survival of a plant population under certain circumstances?

References/Further reading

  1. Raj, A, and van Oudenaarden, A (2008). Stochastic gene expression and its consequences. Cell 135(2): 216–226.
  2. Raser, JM, and O’Shea, EK (2005). Noise in Gene Expression: Origins, Consequences, and Control. Science 309(5743): 2010–2013.

Tags: arabidopsis, gene expression, noise, transcription

Posted on: 15 June 2018

Read preprint (No Ratings Yet)

Have your say

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Sign up to customise the site to your preferences and to receive alerts

Register here

preLists in the genomics category:

preLights peer support – preprints of interest

This is a preprint repository to organise the preprints and preLights covered through the 'preLights peer support' initiative.

 



List by preLights peer support

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.

 



List by Martin Estermann

Semmelweis Symposium 2022: 40th anniversary of international medical education at Semmelweis University

This preList contains preprints discussed during the 'Semmelweis Symposium 2022' (7-9 November), organised around the 40th anniversary of international medical education at Semmelweis University covering a wide range of topics.

 



List by Nándor Lipták

20th “Genetics Workshops in Hungary”, Szeged (25th, September)

In this annual conference, Hungarian geneticists, biochemists and biotechnologists presented their works. Link: http://group.szbk.u-szeged.hu/minikonf/archive/prg2021.pdf

 



List by Nándor Lipták

EMBL Conference: From functional genomics to systems biology

Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020

 



List by Jesus Victorino

TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20

 



List by Maiko Kitaoka et al.

Zebrafish immunology

A compilation of cutting-edge research that uses the zebrafish as a model system to elucidate novel immunological mechanisms in health and disease.

 



List by Shikha Nayar

Also in the molecular biology category:

‘In preprints’ from Development 2022-2023

A list of the preprints featured in Development's 'In preprints' articles between 2022-2023

 



List by Alex Eve, Katherine Brown

CSHL 87th Symposium: Stem Cells

Preprints mentioned by speakers at the #CSHLsymp23

 



List by Alex Eve

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.

 



List by Martin Estermann

Alumni picks – preLights 5th Birthday

This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.

 



List by Sergio Menchero et al.

CellBio 2022 – An ASCB/EMBO Meeting

This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.

 



List by Nadja Hümpfer et al.

EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)

A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.

 



List by Alex Eve

FENS 2020

A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020

 



List by Ana Dorrego-Rivas

ECFG15 – Fungal biology

Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome

 



List by Hiral Shah

ASCB EMBO Annual Meeting 2019

A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)

 



List by Madhuja Samaddar et al.

Lung Disease and Regeneration

This preprint list compiles highlights from the field of lung biology.

 



List by Rob Hynds

MitoList

This list of preprints is focused on work expanding our knowledge on mitochondria in any organism, tissue or cell type, from the normal biology to the pathology.

 



List by Sandra Franco Iborra
Close