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Comparative analysis of the transcriptome across distant species.

Mark B Gerstein1, Joel Rozowsky2, Koon-Kiu Yan2

  • 11] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [3] Department of Computer Science, Yale University, 51 Prospect Street, New Haven, Connecticut 06511, USA [4] [5].

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Summary

Comparing transcriptomes across species reveals fundamental biological principles. This study identified shared gene expression patterns and a universal model for predicting gene activity from chromatin data in humans, worms, and flies.

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Area of Science:

  • Comparative genomics
  • Transcriptomics
  • Developmental biology

Background:

  • The transcriptome provides a snapshot of genome activity.
  • Cross-species transcriptome comparisons can uncover fundamental biological principles.
  • Previous comparisons were limited within species or phyla.

Purpose of the Study:

  • To identify conserved features in transcriptomes across distant animal species (human, worm, fly).
  • To develop a universal model for predicting gene expression from chromatin data.
  • To compare non-coding transcription levels across species.

Main Methods:

  • RNA-sequencing data generation and uniform processing by ENCODE and modENCODE consortia.
  • Comparative analysis of transcriptomes across human, worm, and fly.
  • Development and application of a predictive model using chromatin features.

Main Results:

  • Discovery of shared co-expression modules, many enriched in developmental genes, across metazoan phyla.
  • Identification of a novel developmental stage alignment between worm pupae and fly embryos.
  • Quantification of similar non-canonical transcription levels per base pair across species.
  • Demonstration that gene expression levels can be predicted from promoter chromatin features using an organism-independent model.

Conclusions:

  • Transcriptome comparisons across diverse species reveal ancient, conserved features.
  • Developmental processes show conserved regulatory principles across animals.
  • A universal model can predict gene expression from chromatin data across species, highlighting conserved regulatory mechanisms.