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Comparative analysis of the transcriptome across distant species.


Gerstein MBMark B , Rozowsky J Joel , Yan KK Koon-Kiu , Wang D Daifeng , Cheng C Chao , Brown JB James B , Davis CA Carrie A , Hillier L LaDeana , Sisu C Cristina , Li JJ Jingyi Jessica , Pei B Baikang , Harmanci AO Arif O , Duff MO Michael O , Djebali S Sarah , Alexander RP Roger P , Alver BH Burak H , Auerbach R Raymond , Bell K Kimberly , Bickel PJ Peter J , Boeck ME Max E , Boley NP Nathan P , Booth BW Benjamin W , Cherbas L Lucy , Cherbas P Peter , Di C Chao , Dobin A Alex , Drenkow J Jorg , Ewing B Brent , Fang G Gang , Fastuca M Megan , Feingold EA Elise A , Frankish A Adam , Gao G Guanjun , Good PJ Peter J , Guigó R Roderic , Hammonds A Ann , Harrow J Jen , Hoskins RA Roger A , Howald C Cédric , Hu L Long , Huang H Haiyan , Hubbard TJ Tim J P , Huynh C Chau , Jha S Sonali , Kasper D Dionna , Kato M Masaomi , Kaufman TC Thomas C , Kitchen RR Robert R , Ladewig E Erik , Lagarde J Julien , Lai E Eric , Leng J Jing , Lu Z Zhi , MacCoss M Michael , May G Gemma , McWhirter R Rebecca , Merrihew G Gennifer , Miller DM David M , Mortazavi A Ali , Murad R Rabi , Oliver B Brian , Olson S Sara , Park PJ Peter J , Pazin MJ Michael J , Perrimon N Norbert , Pervouchine D Dmitri , Reinke V Valerie , Reymond A Alexandre , Robinson G Garrett , Samsonova A Anastasia , Saunders GI Gary I , Schlesinger F Felix , Sethi A Anurag , Slack FJ Frank J , Spencer WC William C , Stoiber MH Marcus H , Strasbourger P Pnina , Tanzer A Andrea , Thompson OA Owen A , Wan KH Kenneth H , Wang G Guilin , Wang H Huaien , Watkins KL Kathie L , Wen J Jiayu , Wen K Kejia , Xue C Chenghai , Yang L Li , Yip K Kevin , Zaleski C Chris , Zhang Y Yan , Zheng H Henry , Brenner SE Steven E , Graveley BR Brenton R , Celniker SE Susan E , Gingeras TR Thomas R , Waterston R Robert . Nature. 2014 8 ; 512(7515). 445-8


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.