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Estimating the effects of transcription factors binding and histone modifications on gene expression levels in human cells
- Source :
- Oncotarget
- Publication Year :
- 2016
-
Abstract
- // Lu-Qiang Zhang 1 and Qian-Zhong Li 1 1 Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, China Correspondence to: Qian-Zhong Li, email: // Keywords : transcription factors; histone modifications; DNase-I hypersensitivity; statistical redundancy; regulation mechanism Received : December 15, 2016 Accepted : March 11, 2017 Published : April 09, 2017 Abstract Transcription factors and histone modifications are vital for the regulation of gene expression. Hence, to estimate the effects of transcription factors binding and histone modifications on gene expression, we construct a statistical model for the genome-wide 15 transcription factors binding data, 10 histone modifications profiles and DNase-I hypersensitivity data in three mammalian. Remarkably, our results show POLR2A and H3K36me3 can highly and consistently predict gene expression in three cell lines. And H3K4me3, H3K27me3 and H3K9ac are more reliable predictors than other histone modifications in human embryonic stem cells. Moreover, genome-wide statistical redundancies exist within and between transcription factors and histone modifications, and these phenomena may be caused by the regulation mechanism. In further study, we find that even though transcription factors and histone modifications offer similar effects on expression levels of genome-wide genes, the effects of transcription factors and histone modifications on predictive abilities are different for genes in independent biological processes.
- Subjects :
- 0301 basic medicine
Support Vector Machine
Gene Expression
Biology
Cell Line
regulation mechanism
Histones
03 medical and health sciences
Epigenetics of physical exercise
Cell Line, Tumor
transcription factors
Histone H2A
Histone methylation
Histone code
Animals
Humans
statistical redundancy
Embryonic Stem Cells
Epigenomics
Genetics
histone modifications
Pioneer factor
DNase-I hypersensitivity
DNA-Directed RNA Polymerases
HDAC4
Cell biology
Histone Code
Research Paper: Chromosome
030104 developmental biology
Oncology
H3K4me3
Regression Analysis
K562 Cells
Protein Processing, Post-Translational
Algorithms
Protein Binding
Subjects
Details
- ISSN :
- 19492553
- Volume :
- 8
- Issue :
- 25
- Database :
- OpenAIRE
- Journal :
- Oncotarget
- Accession number :
- edsair.doi.dedup.....14f8246ad9569b2432ac3fcc0b5307df