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Comparative analysis of the transcriptome across distant species.

Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R - Nature (2014)

Bottom Line: Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings.Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair.Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.

View Article: PubMed Central - PubMed

Affiliation: 1] 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].

ABSTRACT
The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.

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Details on Stage AlignmentThis figure provides further detail beyond Fig. 1b. (A) An alignment of worm and flydevelopmental stages based on all worm-fly orthologs (11,403 pairs,including one-to-one, one-to-many, many-to-many pairs). (B) Alignment ofworm and fly developmental stages based on just worm-fly hourglassorthologs. Note the prominent gap in the aligned stages coincides with theworm and fly phylotypic stages (brown band). This make sense: since theexpression values of genes in all hourglass modules converge at thephylotypic stage, no hourglass genes can be phylotypic-stage specific, andhence, the gap. (C) Key aligned stages from part (A). The correspondencebetween parts (A) and (C) is indicated by the small Greek letters. Worm“early embryo” and “late embryo” stages arematched with fly “early embryo” and “lateembryo” respectively in the “lower diagonal” set ofmatches, and they are also matched with fly “L1” and“prepupa-pupa” stages respectively in the “upperdiagonal” set of matches. (More details on all parts of this figureare in Supplement sectionD.4 and Table S3.)
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Figure 9: Details on Stage AlignmentThis figure provides further detail beyond Fig. 1b. (A) An alignment of worm and flydevelopmental stages based on all worm-fly orthologs (11,403 pairs,including one-to-one, one-to-many, many-to-many pairs). (B) Alignment ofworm and fly developmental stages based on just worm-fly hourglassorthologs. Note the prominent gap in the aligned stages coincides with theworm and fly phylotypic stages (brown band). This make sense: since theexpression values of genes in all hourglass modules converge at thephylotypic stage, no hourglass genes can be phylotypic-stage specific, andhence, the gap. (C) Key aligned stages from part (A). The correspondencebetween parts (A) and (C) is indicated by the small Greek letters. Worm“early embryo” and “late embryo” stages arematched with fly “early embryo” and “lateembryo” respectively in the “lower diagonal” set ofmatches, and they are also matched with fly “L1” and“prepupa-pupa” stages respectively in the “upperdiagonal” set of matches. (More details on all parts of this figureare in Supplement sectionD.4 and Table S3.)

Mentions: Next, we used the expression profiles of orthologous genes to align thedevelopmental stages in worm and fly (Fig. 1b,ED7). For every developmental stage, weidentified stage-associated genes, i.e. genes highly expressed at a particular stage butnot across all stages. We then counted the number of orthologous pairs among thesestage-associated genes for each possible worm-and-fly stage correspondence, aligningstages by the significance of the overlap. Strikingly, worm stages map to two sets offly stages. First, they match in the expected one-to-one fashion to the fly (i.e.embryos-to-embryos, larvae-to-larvae). However, worm late embryonic stages also matchfly pupal stages, suggesting a shared expression program between embryogenesis andmetamorphosis. The ~50 stage-associated genes involved in this dual alignmentare enriched in functions such as ion transport and cation-channel activity (Table S3).


Comparative analysis of the transcriptome across distant species.

Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R - Nature (2014)

Details on Stage AlignmentThis figure provides further detail beyond Fig. 1b. (A) An alignment of worm and flydevelopmental stages based on all worm-fly orthologs (11,403 pairs,including one-to-one, one-to-many, many-to-many pairs). (B) Alignment ofworm and fly developmental stages based on just worm-fly hourglassorthologs. Note the prominent gap in the aligned stages coincides with theworm and fly phylotypic stages (brown band). This make sense: since theexpression values of genes in all hourglass modules converge at thephylotypic stage, no hourglass genes can be phylotypic-stage specific, andhence, the gap. (C) Key aligned stages from part (A). The correspondencebetween parts (A) and (C) is indicated by the small Greek letters. Worm“early embryo” and “late embryo” stages arematched with fly “early embryo” and “lateembryo” respectively in the “lower diagonal” set ofmatches, and they are also matched with fly “L1” and“prepupa-pupa” stages respectively in the “upperdiagonal” set of matches. (More details on all parts of this figureare in Supplement sectionD.4 and Table S3.)
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4155737&req=5

Figure 9: Details on Stage AlignmentThis figure provides further detail beyond Fig. 1b. (A) An alignment of worm and flydevelopmental stages based on all worm-fly orthologs (11,403 pairs,including one-to-one, one-to-many, many-to-many pairs). (B) Alignment ofworm and fly developmental stages based on just worm-fly hourglassorthologs. Note the prominent gap in the aligned stages coincides with theworm and fly phylotypic stages (brown band). This make sense: since theexpression values of genes in all hourglass modules converge at thephylotypic stage, no hourglass genes can be phylotypic-stage specific, andhence, the gap. (C) Key aligned stages from part (A). The correspondencebetween parts (A) and (C) is indicated by the small Greek letters. Worm“early embryo” and “late embryo” stages arematched with fly “early embryo” and “lateembryo” respectively in the “lower diagonal” set ofmatches, and they are also matched with fly “L1” and“prepupa-pupa” stages respectively in the “upperdiagonal” set of matches. (More details on all parts of this figureare in Supplement sectionD.4 and Table S3.)
Mentions: Next, we used the expression profiles of orthologous genes to align thedevelopmental stages in worm and fly (Fig. 1b,ED7). For every developmental stage, weidentified stage-associated genes, i.e. genes highly expressed at a particular stage butnot across all stages. We then counted the number of orthologous pairs among thesestage-associated genes for each possible worm-and-fly stage correspondence, aligningstages by the significance of the overlap. Strikingly, worm stages map to two sets offly stages. First, they match in the expected one-to-one fashion to the fly (i.e.embryos-to-embryos, larvae-to-larvae). However, worm late embryonic stages also matchfly pupal stages, suggesting a shared expression program between embryogenesis andmetamorphosis. The ~50 stage-associated genes involved in this dual alignmentare enriched in functions such as ion transport and cation-channel activity (Table S3).

Bottom Line: Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings.Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair.Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.

View Article: PubMed Central - PubMed

Affiliation: 1] 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].

ABSTRACT
The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.

Show MeSH