Identifying Transcriptional Regulatory Modules Among Different Chromatin States in Mouse Neural Stem Cells
Gene expression regulation is a complex process involving the interplay between transcription factors and chromatin states. Significant progress has been made toward understanding the impact of chromatin states on gene expression. Nevertheless, the mechanism of transcription factors binding combinat...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-01-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2018.00731/full |
| _version_ | 1818158577987092480 |
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| author | Sharmi Banerjee Sharmi Banerjee Hongxiao Zhu Man Tang Wu-chun Feng Xiaowei Wu Hehuang Xie Hehuang Xie Hehuang Xie Hehuang Xie |
| author_facet | Sharmi Banerjee Sharmi Banerjee Hongxiao Zhu Man Tang Wu-chun Feng Xiaowei Wu Hehuang Xie Hehuang Xie Hehuang Xie Hehuang Xie |
| author_sort | Sharmi Banerjee |
| collection | DOAJ |
| description | Gene expression regulation is a complex process involving the interplay between transcription factors and chromatin states. Significant progress has been made toward understanding the impact of chromatin states on gene expression. Nevertheless, the mechanism of transcription factors binding combinatorially in different chromatin states to enable selective regulation of gene expression remains an interesting research area. We introduce a nonparametric Bayesian clustering method for inhomogeneous Poisson processes to detect heterogeneous binding patterns of multiple proteins including transcription factors to form regulatory modules in different chromatin states. We applied this approach on ChIP-seq data for mouse neural stem cells containing 21 proteins and observed different groups or modules of proteins clustered within different chromatin states. These chromatin-state-specific regulatory modules were found to have significant influence on gene expression. We also observed different motif preferences for certain TFs between different chromatin states. Our results reveal a degree of interdependency between chromatin states and combinatorial binding of proteins in the complex transcriptional regulatory process. The software package is available on Github at - https://github.com/BSharmi/DPM-LGCP. |
| first_indexed | 2024-12-11T15:32:18Z |
| format | Article |
| id | doaj.art-6993f517cb6a4b1cb007804d6968115a |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-11T15:32:18Z |
| publishDate | 2019-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-6993f517cb6a4b1cb007804d6968115a2022-12-22T01:00:01ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-01-01910.3389/fgene.2018.00731421281Identifying Transcriptional Regulatory Modules Among Different Chromatin States in Mouse Neural Stem CellsSharmi Banerjee0Sharmi Banerjee1Hongxiao Zhu2Man Tang3Wu-chun Feng4Xiaowei Wu5Hehuang Xie6Hehuang Xie7Hehuang Xie8Hehuang Xie9Bradley Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA, United StatesBiocomplexity Institute of Virginia Tech, Blacksburg, VA, United StatesDepartment of Statistics, Virginia Tech, Blacksburg, VA, United StatesDepartment of Statistics, Virginia Tech, Blacksburg, VA, United StatesDepartment of Computer Science, Virginia Tech, Blacksburg, VA, United StatesDepartment of Statistics, Virginia Tech, Blacksburg, VA, United StatesBiocomplexity Institute of Virginia Tech, Blacksburg, VA, United StatesDepartment of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, United StatesDepartment of Biological Sciences, Virginia Tech, Blacksburg, VA, United StatesSchool of Neuroscience, Virginia Tech, Blacksburg, VA, United StatesGene expression regulation is a complex process involving the interplay between transcription factors and chromatin states. Significant progress has been made toward understanding the impact of chromatin states on gene expression. Nevertheless, the mechanism of transcription factors binding combinatorially in different chromatin states to enable selective regulation of gene expression remains an interesting research area. We introduce a nonparametric Bayesian clustering method for inhomogeneous Poisson processes to detect heterogeneous binding patterns of multiple proteins including transcription factors to form regulatory modules in different chromatin states. We applied this approach on ChIP-seq data for mouse neural stem cells containing 21 proteins and observed different groups or modules of proteins clustered within different chromatin states. These chromatin-state-specific regulatory modules were found to have significant influence on gene expression. We also observed different motif preferences for certain TFs between different chromatin states. Our results reveal a degree of interdependency between chromatin states and combinatorial binding of proteins in the complex transcriptional regulatory process. The software package is available on Github at - https://github.com/BSharmi/DPM-LGCP.https://www.frontiersin.org/article/10.3389/fgene.2018.00731/fulltranscription factorregulatory networkPoisson processchromatin statesneural stem cell |
| spellingShingle | Sharmi Banerjee Sharmi Banerjee Hongxiao Zhu Man Tang Wu-chun Feng Xiaowei Wu Hehuang Xie Hehuang Xie Hehuang Xie Hehuang Xie Identifying Transcriptional Regulatory Modules Among Different Chromatin States in Mouse Neural Stem Cells Frontiers in Genetics transcription factor regulatory network Poisson process chromatin states neural stem cell |
| title | Identifying Transcriptional Regulatory Modules Among Different Chromatin States in Mouse Neural Stem Cells |
| title_full | Identifying Transcriptional Regulatory Modules Among Different Chromatin States in Mouse Neural Stem Cells |
| title_fullStr | Identifying Transcriptional Regulatory Modules Among Different Chromatin States in Mouse Neural Stem Cells |
| title_full_unstemmed | Identifying Transcriptional Regulatory Modules Among Different Chromatin States in Mouse Neural Stem Cells |
| title_short | Identifying Transcriptional Regulatory Modules Among Different Chromatin States in Mouse Neural Stem Cells |
| title_sort | identifying transcriptional regulatory modules among different chromatin states in mouse neural stem cells |
| topic | transcription factor regulatory network Poisson process chromatin states neural stem cell |
| url | https://www.frontiersin.org/article/10.3389/fgene.2018.00731/full |
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