Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of C. elegans muscle sample

ABSTRACT: We present a global overview of muscle gene expression in C. elegans using a novel technique called mRNA-tagging, and have identified genes involved in contraction, muscle structure, and energy utilization. Furthermore, we found that muscle-expressed genes are clustered in groups of 2-5 along the chromosomes, suggesting that expression from a chromatin domain can extend over several genes. These observations reveal a higher-order organization of the structure of the genome in which the order of genes along the chromosome is correlated with their expression in specific tissues.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Peter Roy

PROVIDER: E-SMDB-1399 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans.

Roy Peter J PJ Stuart Joshua M JM Lund Jim J Kim Stuart K SK

Nature 20020801 6901

Chromosomes are divided into domains of open chromatin, where genes have the potential to be expressed, and domains of closed chromatin, where genes are not expressed. Classic examples of open chromatin domains include 'puffs' on polytene chromosomes in Drosophila and extended loops from lampbrush chromosomes. If multiple genes were typically expressed together from a single open chromatin domain, the position of co-expressed genes along the chromosomes would appear clustered. To investigate whe ...[more]

PMID: 12214599

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Project description:This a model from the article: A mathematical model of fatigue in skeletal muscle force contraction. Shorten PR, O'Callaghan P, Davidson JB, Soboleva TK. J Muscle Res Cell Motil 2007;28(6):293-313 18080210 , Abstract: The ability for muscle to repeatedly generate force is limited by fatigue. The cellular mechanisms behind muscle fatigue are complex and potentially include breakdown at many points along the excitation-contraction pathway. In this paper we construct a mathematical model of the skeletal muscle excitation-contraction pathway based on the cellular biochemical events that link excitation to contraction. The model includes descriptions of membrane voltage, calcium cycling and crossbridge dynamics and was parameterised and validated using the response characteristics of mouse skeletal muscle to a range of electrical stimuli. This model was used to uncover the complexities of skeletal muscle fatigue. We also parameterised our model to describe force kinetics in fast and slow twitch fibre types, which have a number of biochemical and biophysical differences. How these differences interact to generate different force/fatigue responses in fast- and slow- twitch fibres is not well understood and we used our modelling approach to bring new insights to this relationship. This model was taken from the CellML repository and automatically converted to SBML. The original model was: Shorten PR, O'Callaghan P, Davidson JB, Soboleva TK. (2007) - version02 This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Dataset Information

Transcription profiling of C. elegans muscle sample

Publications

Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans.

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