Matthew Hindle

University of Edinburgh

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Simone Meddle

Roslin Institute

Andrew Loudon

University of Manchester

David W. Burt

University of Edinburgh

Jacqueline Smith

Roslin Institute

Robert G. Webster

St. Jude Children's Research Hospital

Jérôme Gros

Institut Pasteur

Alain Vignal

Génétique Physiologie et Systèmes d'Elevage

Thierry Jaffredo

Laboratoire de Biologie du Développement

Francis Minvielle

AgroParisTech

Frédérique Pitel

Génétique Physiologie et Systèmes d'Elevage

Cooperative Institutions

University of Edinburgh

Rothamsted Research

Roslin Institute

Centre National de la Recherche Scientifique

University of Manchester

University of New Brunswick

Genomics (United Kingdom)

Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

Institute of Structural and Molecular Biology

Edinburgh College

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Additional file 16 of The quail genome: insights into social behaviour, seasonal biology and infectious disease response

Figshare (2020)

Katrina Morris Matthew Hindle Simon Boitard David W. Burt Angela Danner

Viral read presence in quail samples

10.6084/m9.figshare.11846475

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Data integration for plant genomics--exemplars from the integration of Arabidopsis thaliana databases

Briefings in Bioinformatics (2010)

Artem Lysenko Matthew Hindle Jan Taubert Mansoor Saqi Chris Rawlings

10.1093/bib/bbq005

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Methods in Enzymology

Europe PMC (PubMed Central) (2015)

Johanna Krahmer Matthew Hindle Sarah A. Martin Thierry Le Bihan A. Harvey Millar

Source

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The quail as an avian model system: its genome provides insights into social behaviour, seasonal biology and infectious disease response

bioRxiv (Cold Spring Harbor Laboratory) (2019)

Katrina Morris Matthew Hindle Simon Boitard David W. Burt Angela Danner

ABSTRACT The Japanese quail ( Coturnix japonica ) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research. We have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. In terms of contiguity, assembly statistics, gene content and chromosomal organization, the quail genome shows high similarity to the chicken genome. We demonstrate the utility of this genome through three diverse applications. First, we identify selection signatures and candidate genes associated with social behaviour in the quail genome, an important agricultural and domestication trait. Second, we investigate the effects and interaction of photoperiod and temperature on the transcriptome of the quail medial basal hypothalamus, revealing key mechanisms of photoperiodism. Finally, we investigate the response of quail to H5N1 influenza infection. In quail lung, many critical immune genes and pathways were downregulated, and this may be key to the susceptibility of quail to H5N1. This genome will facilitate further research into diverse research questions using the quail as a model avian species.

Coturnix japonica

Galliformes

10.1101/575332

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A phospho-dawn of protein modification anticipates light onset in the picoeukaryote Ostreococcus tauri

Journal of Experimental Botany (2023)

Zeenat Noordally Matthew Hindle Sarah F. Martin Daniel D. Seaton T. Ian Simpson

Diel regulation of protein levels and protein modification had been less studied than transcript rhythms. Here, we compare transcriptome data under light-dark cycles with partial proteome and phosphoproteome data, assayed using shotgun MS, from the alga Ostreococcus tauri, the smallest free-living eukaryote. A total of 10% of quantified proteins but two-thirds of phosphoproteins were rhythmic. Mathematical modelling showed that light-stimulated protein synthesis can account for the observed clustering of protein peaks in the daytime. Prompted by night-peaking and apparently dark-stable proteins, we also tested cultures under prolonged darkness, where the proteome changed less than under the diel cycle. Among the dark-stable proteins were prasinophyte-specific sequences that were also reported to accumulate when O. tauri formed lipid droplets. In the phosphoproteome, 39% of rhythmic phospho-sites reached peak levels just before dawn. This anticipatory phosphorylation suggests that a clock-regulated phospho-dawn prepares green cells for daytime functions. Acid-directed and proline-directed protein phosphorylation sites were regulated in antiphase, implicating the clock-related casein kinases 1 and 2 in phase-specific regulation, alternating with the CMGC protein kinase family. Understanding the dynamic phosphoprotein network should be facilitated by the minimal kinome and proteome of O. tauri. The data are available from ProteomeXchange, with identifiers PXD001734, PXD001735, and PXD002909.

Posttranslational modification

10.1093/jxb/erad290

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Single Cell RNA Sequencing Defines Cellular Binary Switching Mechanism Driving Circadian Regulation of Mammalian Photoperiodism in Melatonin-Target Calendar Cells.

Yasutaka Mizoro Matthew Hindle Ben Saer Shona H. Wood Andrew Hayes

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Label‐free quantitative analysis of the casein kinase 2‐responsive phosphoproteome of the marine minimal model species Ostreococcus tauri

PROTEOMICS (2015)

Thierry Le Bihan Matthew Hindle Sarah F. Martin Martin E. Barrios‐Llerena Johanna Krahmer

Casein kinase 2 (CK2) is a protein kinase that phosphorylates a plethora of cellular target proteins involved in processes including DNA repair, cell cycle control, and circadian timekeeping. CK2 is functionally conserved across eukaryotes, although the substrate proteins identified in a range of complex tissues are often different. The marine alga Ostreococcus tauri is a unicellular eukaryotic model organism ideally suited to efficiently study generic roles of CK2 in the cellular circadian clock. Overexpression of CK2 leads to a slow circadian rhythm, verifying functional conservation of CK2 in timekeeping. The proteome was analysed in wild‐type and CK2‐overexpressing algae at dawn and dusk, revealing that differential abundance of the global proteome across the day is largely unaffected by overexpression. However, CK2 activity contributed more strongly to timekeeping at dusk than at dawn. The phosphoproteome of a CK2 overexpression line and cells treated with CK2 inhibitor was therefore analysed and compared to control cells at dusk. We report an extensive catalogue of 447 unique CK2‐responsive differential phosphopeptide motifs to inform future studies into CK2 activity in the circadian clock of more complex tissues. All MS data have been deposited in the ProteomeXchange with identifier PXD000975 ( http://proteomecentral.proteomexchange.org/dataset/PXD000975 ).

Casein kinase 2

Proteome

Aurora A kinase

10.1002/pmic.201500086

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Functional Analysis of Casein Kinase 1 in a Minimal Circadian System

PLoS ONE (2013)

Gerben van Ooijen Matthew Hindle Sarah F. Martin Martin E. Barrios‐Llerena Frédéric Sanchez

The Earth's rotation has driven the evolution of cellular circadian clocks to facilitate anticipation of the solar cycle. Some evidence for timekeeping mechanism conserved from early unicellular life through to modern organisms was recently identified, but the components of this oscillator are currently unknown. Although very few clock components appear to be shared across higher species, Casein Kinase 1 (CK1) is known to affect timekeeping across metazoans and fungi, but has not previously been implicated in the circadian clock in the plant kingdom. We now show that modulation of CK1 function lengthens circadian rhythms in Ostreococcus tauri, a unicellular marine algal species at the base of the green lineage, separated from humans by ~1.5 billion years of evolution. CK1 contributes to timekeeping in a phase-dependent manner, indicating clock-mediated gating of CK1 activity. Label-free proteomic analyses upon overexpression as well as inhibition revealed CK1-responsive phosphorylation events on a set of target proteins, including highly conserved potentially clock-relevant cellular regulator proteins. These results have major implications for our understanding of cellular timekeeping and can inform future studies in any circadian organism.

Casein kinase 2

Anticipation (artificial intelligence)

10.1371/journal.pone.0070021

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Citations (42)

Graph-based sequence annotation using a data integration approach

Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics (2008)

Robert Pesch Artem Lysenko Matthew Hindle Keywan Hassani‐Pak Ralf Thiele

Summary The automated annotation of data from high throughput sequencing and genomics experiments is a significant challenge for bioinformatics. Most current approaches rely on sequential pipelines of gene finding and gene function prediction methods that annotate a gene with information from different reference data sources. Each function prediction method contributes evidence supporting a functional assignment. Such approaches generally ignore the links between the information in the reference datasets. These links, however, are valuable for assessing the plausibility of a function assignment and can be used to evaluate the confidence in a prediction. We are working towards a novel annotation system that uses the network of information supporting the function assignment to enrich the annotation process for use by expert curators and predicting the function of previously unannotated genes. In this paper we describe our success in the first stages of this development. We present the data integration steps that are needed to create the core database of integrated reference databases (UniProt, PFAM, PDB, GO and the pathway database Ara- Cyc) which has been established in the ONDEX data integration system. We also present a comparison between different methods for integration of GO terms as part of the function assignment pipeline and discuss the consequences of this analysis for improving the accuracy of gene function annotation. The methods and algorithms presented in this publication are an integral part of the ONDEX system which is freely available from http://ondex.sf.net/.

UniProt

Biological database

Gene Annotation

Protein function prediction

10.1515/jib-2008-94

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qpMerge: Merging different peptide isoforms using a motif centric strategy

bioRxiv (Cold Spring Harbor Laboratory) (2016)

Matthew Hindle Thierry Le Bihan Johanna Krahmer Sarah F. Martin Zeenat Noordally

Abstract Accurate quantification and enumeration of peptide motifs is hampered by redundancy in peptide identification. A single phosphorylation motif may be split across charge states, alternative modifications ( e.g. acetylation and oxidation), and multiple miss-cleavage sites which render the biological interpretation of MS data a challenge. In addition motif redundancy can affect quantitative and statistical analysis and prevent a realistic comparison of peptide numbers between datasets. In this study, we present a merging tool set developed for the Galaxy workflow environment to achieve a non-redundant set of quantifications for phospho-motifs. We present a Galaxy workflow to merge three exemplar dataset, and observe reduced phospho-motif redundancy and decreased replicate variation. The qpMerge tools provide a straightforward and reusable approach to facilitating phospho-motif analysis. The source-code and wiki documentation is publically available at http://sourceforge.net/projects/ppmerge. The galaxy pipeline used in the exemplar analysis can be found at http://www.myexperiment.org/workflows/4186.

Motif (music)

Merge (version control)

Shuffling

10.1101/047100

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Citations (5)