Modeling gene expression using chromatin features in various cellular contexts
Xianjun Dong,Melissa C. Greven,Anshul Kundaje,Sarah Djebali,James B. Brown,Chao Cheng,Thomas R. Gingeras,Mark Gerstein,Roderic Guigó,Ewan Birney,Zhiping Weng +10 more
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TLDR
This study builds a novel quantitative model and finds that expression status and expression levels can be predicted by different groups of chromatin features, both with high accuracy, and that expression levels measured by CAGE are better predicted than by RNA-PET or RNA-Seq.Abstract:
Background: Previous work has demonstrated that chromatin feature levels correlate with gene expression. The ENCODE project enables us to further explore this relationship using an unprecedented volume of data. Expression levels from more than 100,000 promoters were measured using a variety of high-throughput techniques applied to RNA extracted by different protocols from different cellular compartments of several human cell lines. ENCODE also generated the genome-wide mapping of eleven histone marks, one histone variant, and DNase I hypersensitivity sites in seven cell lines. Results: We built a novel quantitative model to study the relationship between chromatin features and expression levels. Our study not only confirms that the general relationships found in previous studies hold across various cell lines, but also makes new suggestions about the relationship between chromatin features and gene expression levels. We found that expression status and expression levels can be predicted by different groups of chromatin features, both with high accuracy. We also found that expression levels measured by CAGE are better predicted than by RNA-PET or RNA-Seq, and different categories of chromatin features are the most predictive of expression for different RNA measurement methods. Additionally, PolyA+ RNA is overall more predictable than PolyA- RNA among different cell compartments, and PolyA+ cytosolic RNA measured with RNA-Seq is more predictable than PolyA+ nuclear RNA, while the opposite is true for PolyA- RNA. Conclusions: Our study provides new insights into transcriptional regulation by analyzing chromatin features in different cellular contexts.read more
Citations
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Journal ArticleDOI
An integrated encyclopedia of DNA elements in the human genome
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Journal Article
An integrated encyclopedia of DNA elements in the human genome.
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Journal ArticleDOI
H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency
Bérénice A. Benayoun,Elizabeth A. Pollina,Duygu Ucar,Salah Mahmoudi,Kalpana Karra,Edith D. Wong,Keerthana Devarajan,Aaron Daugherty,Anshul Kundaje,Elena Mancini,Benjamin C. Hitz,Rakhi Gupta,Thomas A. Rando,Thomas A. Rando,Julie C. Baker,Michael Snyder,J. Michael Cherry,Anne Brunet +17 more
TL;DR: It is shown that H3K4me3 domains that spread more broadly over genes in a given cell type preferentially mark genes that are essential for the identity and function of that cell type.
Journal ArticleDOI
Comparison of the transcriptional landscapes between human and mouse tissues
Shin Lin,Yiing Lin,Joseph R. Nery,Mark A. Urich,Alessandra Breschi,Carrie A. Davis,Alexander Dobin,Chris Zaleski,Michael A. Beer,William C. Chapman,Thomas R. Gingeras,Joseph R. Ecker,Michael Snyder +12 more
TL;DR: High-throughput sequencing assays on the transcriptome and epigenome reveal that, in general, differences dominate similarities between the two species, and indicate that there is considerable RNA expression diversity between humans and mice.
Journal ArticleDOI
Comparative analysis of the transcriptome across distant species
Mark Gerstein,Joel Rozowsky,Koon-Kiu Yan,Daifeng Wang,Chao Cheng,James B. Brown,James B. Brown,Carrie A. Davis,LaDeana W. Hillier,Cristina Sisu,Jingyi Jessica Li,Jingyi Jessica Li,Baikang Pei,Arif Harmanci,Michael O. Duff,Sarah Djebali,Roger P. Alexander,Burak H. Alver,Raymond K. Auerbach,Kimberly Bell,Peter J. Bickel,Max E. Boeck,Nathan Boley,Nathan Boley,Benjamin W. Booth,Lucy Cherbas,Peter Cherbas,Chao Di,Alexander Dobin,Jorg Drenkow,Brent Ewing,Gang Fang,Megan Fastuca,Elise A. Feingold,Adam Frankish,Guanjun Gao,Peter J. Good,Roderic Guigó,Ann S. Hammonds,Jen Harrow,Roger A. Hoskins,Cédric Howald,Cédric Howald,Long Hu,Haiyan Huang,Tim Hubbard,Tim Hubbard,Chau Huynh,Sonali Jha,Dionna M. Kasper,Masaomi Kato,Thomas C. Kaufman,Robert R. Kitchen,Erik Ladewig,Julien Lagarde,Eric C. Lai,Jing Leng,Zhi Lu,Michael J. MacCoss,Gemma E. May,Gemma E. May,Rebecca McWhirter,Gennifer E. Merrihew,David M. Miller,Ali Mortazavi,Rabi Murad,Brian Oliver,Sara Olson,Peter J. Park,Michael J. Pazin,Norbert Perrimon,Norbert Perrimon,Dmitri D. Pervouchine,Valerie Reinke,Alexandre Reymond,Garrett Robinson,Anastasia Samsonova,Anastasia Samsonova,Gary Saunders,Gary Saunders,Felix Schlesinger,Anurag Sethi,Frank J. Slack,William C. Spencer,Marcus H. Stoiber,Marcus H. Stoiber,Pnina Strasbourger,Andrea Tanzer,Andrea Tanzer,Owen Thompson,Kenneth H. Wan,Guilin Wang,Huaien Wang,Kathie L. Watkins,Jiayu Wen,Kejia Wen,Chenghai Xue,Li Yang,Li Yang,Kevin Y. Yip,Chris Zaleski,Yan Zhang,Henry Zheng,Steven E. Brenner,Brenton R. Graveley,Susan E. Celniker,Thomas R. Gingeras,Robert H. Waterston +107 more
TL;DR: It is found 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.
References
More filters
Journal ArticleDOI
Random Forests
TL;DR: Internal estimates monitor error, strength, and correlation and these are used to show the response to increasing the number of features used in the forest, and are also applicable to regression.
Journal ArticleDOI
An integrated encyclopedia of DNA elements in the human genome
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Journal ArticleDOI
Mapping and quantifying mammalian transcriptomes by RNA-Seq.
TL;DR: Although >90% of uniquely mapped reads fell within known exons, the remaining data suggest new and revised gene models, including changed or additional promoters, exons and 3′ untranscribed regions, as well as new candidate microRNA precursors.
Journal ArticleDOI
Chromatin Modifications and Their Function
TL;DR: The surface of nucleosomes is studded with a multiplicity of modifications that can dictate the higher-order chromatin structure in which DNA is packaged and can orchestrate the ordered recruitment of enzyme complexes to manipulate DNA.
Journal ArticleDOI
Translating the Histone Code
Thomas Jenuwein,C. David Allis +1 more
TL;DR: It is proposed that this epigenetic marking system represents a fundamental regulatory mechanism that has an impact on most, if not all, chromatin-templated processes, with far-reaching consequences for cell fate decisions and both normal and pathological development.
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